diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 7db578e..c67dde0 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -9,11 +9,11 @@ jobs: runs-on: ${{ matrix.os}} strategy: matrix: - os: [ubuntu-latest, windows-latest, macos-latest] - python-version: [ '3.8', '3.9', '3.10', '3.11'] + os: [ubuntu-latest, windows-latest] + python-version: [ '3.9', '3.10', '3.11'] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python ${{matrix.python-version}} uses: actions/setup-python@v4 with: diff --git a/.gitignore b/.gitignore index b2b7623..dee853d 100644 --- a/.gitignore +++ b/.gitignore @@ -1,13 +1,8 @@ /venv/ -physiofit/__pycache__/__init__.cpython-310.pyc -physiofit/__pycache__/__main__.cpython-310.pyc -physiofit/__pycache__/logger.cpython-310.pyc -physiofit/base/__pycache__/__init__.cpython-310.pyc -physiofit/base/__pycache__/fitter.cpython-310.pyc -physiofit/base/__pycache__/io.cpython-310.pyc +physiofit/__pycache__/ +physiofit/base/__pycahe__/ physiofit/last_version.txt -physiofit/ui/__pycache__/__init__.cpython-310.pyc -physiofit/ui/__pycache__/cli.cpython-310.pyc +physiofit/ui/__pycache__/ physiofit.egg-info/dependency_links.txt physiofit.egg-info/entry_points.txt physiofit.egg-info/PKG-INFO @@ -16,3 +11,4 @@ physiofit.egg-info/SOURCES.txt physiofit.egg-info/top_level.txt /versions publi/ /physiofit/data/ +/docs/_build/ \ No newline at end of file diff --git a/README.md b/README.md index 936b3a7..93f1d1c 100644 --- a/README.md +++ b/README.md @@ -25,14 +25,16 @@ Detailed documentation can be found online at Read the Docs ## Key features * **calculation of growth rate and extracellular (uptake and production) fluxes**, - * **a set of steady-state and dynamic models** are shipped with PhysioFit, + * a set of **steady-state and dynamic models**, * **tailor-made models** can be constructed by users, - * Monte-Carlo sensitivity analysis to **estimate the precision on the calculated fluxes**, + * Monte-Carlo sensitivity analysis to **estimate the precision of the calculated fluxes**, * **evaluation of the goodness of fit and visual inspection of the fitted curves**, + * calculation of the Akaike information criterion to **guide users to identify the most appropriate model**, * shipped as a **library** with both a **graphical** and a **command line** interface, * **open-source, free and easy to install** everywhere where Python 3 and pip run, * **biologist-friendly**. + ## Quick-start PhysioFit requires Python 3.9 or higher and run on all platforms. Please check [the documentation](https://physiofit.readthedocs.io/en/latest/quickstart.html) for complete diff --git a/docs/_static/usage/example1.JPG b/docs/_static/usage/example1.JPG index 9772338..877b2ac 100644 Binary files a/docs/_static/usage/example1.JPG and b/docs/_static/usage/example1.JPG differ diff --git a/docs/conf.py b/docs/conf.py index abb0df1..a9fc413 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -24,7 +24,6 @@ # The full version, including alpha/beta/rc tags release = __version__ - # -- General configuration --------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be @@ -52,7 +51,6 @@ # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] - # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for @@ -74,11 +72,11 @@ # remove blank pages (between the title page and the TOC, etc.) 'classoptions': ',openany,oneside', - 'babel' : '\\usepackage[english]{babel}', + 'babel': '\\usepackage[english]{babel}', # Additional stuff for the LaTeX preamble. 'preamble': r''' \usepackage{hyperref} \usepackage{upquote} ''' - } \ No newline at end of file +} diff --git a/docs/faq.rst b/docs/faq.rst index dde06fc..8cce97b 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -4,36 +4,45 @@ Frequently asked questions (FAQ) How are fluxes calculated? ------------------------------------------------------------------ -We provide details on the flux calculation approach implemented in PhysioFit in the :doc:`method` section. +We provide details on the flux calculation approach implemented in PhysioFit +in the :doc:`method` section. How many measurements should I use to calculate fluxes? ------------------------------------------------------------------ -As in any model-based fitting procedure, more data usually means more accurate and precise flux estimates. The minimal number of -measurements depend on the model used for flux calculation. For instance, for steady-state built-in models provided with PhysioFit, we recommend using -at least 6 to 8 time points, which should provide reliable and meaningful estimates in most situations. +As in any model-based fitting procedure, more data usually means more +accurate and precise flux estimates. The minimal number of measurements +depend on the model used for flux calculation. For instance, for +steady-state built-in models provided with PhysioFit, we recommend using at +least 6 to 8 time points, which should provide reliable and meaningful +estimates in most situations. -Still, the exact answer to this question strongly depends on the uptake/production/growth rates of your (micro)organism -in the conditions you are investigating, on the sampling time interval, on the questions you are addressing, on the model used for flux calculation, and on -many other parameters! You can make some tests by calculating fluxes from (published or theoretical) datasets similar -to those you have in mind. +Still, the exact answer to this question strongly depends on the +uptake/production/growth rates of your (micro)organism in the conditions you +are investigating, on the sampling time interval, on the questions you are +addressing, on the model used for flux calculation, and on many other +parameters! You can make some tests by calculating fluxes from (published or +theoretical) datasets similar to those you have in mind. Can I calculate fluxes in case of missing values? ------------------------------------------------------------------ -Yes, fluxes can still be calculated if some measurement(s) are missing. In this case, let empty the corresponding field -of the input data file. +Yes, fluxes can still be calculated if some measurement(s) are missing. In +this case, leave empty the corresponding field of the input data file. .. _`conc units`: What units should be used for input data? ----------------------------------------- -Input data (biomass concentration, metabolites concentrations, and time) can be provided to PhysioFit using any unit. -Still, we recommand to use units for which values are as close to unity as possible to ensure numerical stability (e.g. -3 mM instead of 3.10\ :sup:`-3` M). Importantly, units of the estimated fluxes depend on units of time and metabolites and biomass -concentrations. The concentration of different metabolites can be provided using different units, but a single unit -must be used for all measurements of a given metabolite. +Input data (biomass concentration, metabolites concentrations, and time) can +be provided to PhysioFit using any unit. Still, we recommend using units +for which values are as close to unity as possible to ensure numerical +stability (e.g. 3 mM instead of 3.10\ :sup:`-3` M). Importantly, units of +the estimated fluxes depend on units of time and metabolites and biomass +concentrations. The concentration of different metabolites can be provided +using different units, but a single unit must be used for all measurements +of a given metabolite. .. seealso:: :ref:`flux units` @@ -61,49 +70,75 @@ What parameters values should I use? Details on PhysioFit parameters can be found in the :doc:`usage` section. -How can I check if my data have been fitted correctly? +Which model should I use? ------------------------------------------------------------------ -The quality of the fit can be evaluated based on: +The choice of the model depends on the biological question you are addressing, +the data you have, and the assumptions you are willing to make. We provide a +set of models in PhysioFit, each with its own assumptions and requirements. - * the plots of experimental vs simulated data for the best fit, which should be as close as possible, - * the χ² statistical test results given in the log file (see below for help on interpreting the results). +As a starting point, we recommend using the most relevant model based on +the type of experiment you have conducted. Begin with the simplest model that +fits your data and evaluate the quality of the fit based on the χ² test +results and the plots of experimental vs. simulated data. If the fit is +not satisfactory, you may try more complex models. However, keep in mind +that more complex models often require more data, include more assumptions, +and may lead to overfitting. -.. seealso:: :ref:`chi2 test` and :ref:`bad fit` +If different models fit your data, a good practice for comparing them +is to use the AIC (Akaike Information Criterion). For more information, please +refer to the section "Model comparison" from the :doc:`method` page. -.. _`chi2 test`: -What is a χ² test? +How can I check if my data has been fitted correctly? ------------------------------------------------------------------ -A χ² test describes how well a model fits a set of observations. Measures of goodness of fit typically summarize the discrepancy between observed values and the values expected under the model used in PhysioFit (see the :doc:`method` section). It is calculated as the sum of differences between measured and simulated values, each squared and divided by the simulated value. -A good fit corresponds to small differences between measured and simulated values, thereby the χ² value is low. In contrast, a bad fit corresponds to large differences between simulations and measurements, and the χ² value is high. +The quality of the fit can be evaluated based on: + + * the plots of experimental vs simulated data for the best fit, which should be as close as possible, + * the χ² statistical test results given in the stat ouput file (see below + for help on interpreting the results). + +.. seealso:: :ref:`chi2 test` and :ref:`bad fit` -The resulting χ² value can then be compared with a χ² distribution to determine the goodness of fit. The p-value of one-tail χ² test is calculated by PhysioFit from the best fit and is given in the log file (have a look to the :doc:`usage` section). A p-value close to 0 means poor fitting, and a p-value close to 1 means good fitting (keeping in mind that a p-value very close to 1 can be an evidence that standard deviations might be overestimated). A -p-value between 0.95 and 1 means the model fits the data good enough with respect to the standard deviations provided (at a 95% confidence level). PhysioFit provides an explicit meassage stating wether the flux data are satisfactorily fitted or not (at a 95% confidence interval). .. _`bad fit`: My data hasn't been correctly fitted. Why? ------------------------------------------------------------------ -A possible reason to explain a bad fit is that standard deviations on measurements (concentration biomass and metabolites) is under-estimated, thereby making the χ² test too stringent. In this case, plots of measured and fitted data should be in agreement. Reliable estimated of standard deviation on measurements must be provided to PhysioFit (have a look to the :doc:`usage` section to see how to check and adjust this parameter). - -Another possible reason to explain a bad fit is that a key asumption of the flux calculation method is not respected. For instance, -if you use a steady-state model shipped with PhysioFit, cells might not be strictly in metabolic steady-state, i.e. with -constant fluxes during the whole experiment. If this key asumption does not occur (e.g. cells are continuously adapting -to their environment and fluxes change over time), PhysioFit will not be able to fit the data satisfactorily. In this case, -evaluate wether the deviation is significant or not (e.g. based on the detailed χ² statistics or on the plot of fitted vs -measured data), and evaluate the potential biases that would be introduced by interpreting (or not) these flux values. - -In rare situations, it may also be because some parameters have to be tweaked to -help PhysioFit fitting the measurements, which results in obviously aberrant fits (e.g. with flat -time-course profiles for all metabolites). This might happen for instance if some measurements are -provided in units far from unity (e.g. 1.10\ :sup:`-5` M instead of 10 µM). If this situation happens, we suggest modifying the initial values of fluxes, or changing the units of input data, and re-run the flux calculation. For more info on the run parameters and how they may affect the fitting process, +A possible reason to explain a bad fit is that standard deviations on +measurements (concentration biomass and metabolites) is under-estimated, +thereby making the χ² test too stringent. In this case, plots of measured and +fitted data should be in agreement. Reliable estimated of standard deviation +on measurements must be provided to PhysioFit (have a look to the :doc:`usage` +section to see how to check and adjust this parameter). + +Another possible reason to explain a bad fit is that a key asumption of the +flux calculation method is not respected. For instance, if you use a +steady-state model shipped with PhysioFit, cells might not be strictly in +metabolic steady-state, i.e. with constant fluxes during the whole +experiment. If this key asumption does not occur (e.g. cells are continuously +adapting to their environment and fluxes change over time), PhysioFit will +not be able to fit the data satisfactorily. In this case, evaluate wether +the deviation is significant or not (e.g. based on the detailed χ² +statistics or on the plot of fitted vs measured data), and evaluate the +potential biases that would be introduced by interpreting (or not) these +flux values. + +In rare situations, it may also be because some parameters have to be +tweaked to help PhysioFit fit the measurements, which results in +obviously aberrant fits (e.g. with flat time-course profiles for all +metabolites). This might happen for instance if some measurements are +provided in units far from unity (e.g. 1.10\ :sup:`-5` M instead of 10 µM). If +this situation happens, we suggest modifying the initial values of fluxes, +or changing the units of input data, and re-run the flux calculation. For +more info on the run parameters and how they may affect the fitting process, please refer to section :ref:`physiofit parameters`. -If you believe the problem is in PhysioFit, we would greatly appreciate -if you could open a new issue on our `issue tracker `_. +If you think the problem is in PhysioFit, we would greatly appreciate +if you could open a new issue on our `issue tracker `_. I cannot start PhysioFit graphical user interface, can you help me? ------------------------------------------------------------------- @@ -121,8 +156,9 @@ Please follow this simple procedure: * If it is related to your system or your Python installation, you will need to ask some help from your local system administrator or your IT department so they could guide you toward a clean installation. Tell them that you wanted "to use the graphical - user interface of PhysioFit, a Python 3.6 software" and what you did so far (installation), - give them the traceback and a link toward the documentation. They should know what to do. + user interface of PhysioFit, a Python 3.9 software" and what you did so + far (installation), give them the traceback and a link toward the + documentation. They should know what to do. * If you believe the problem is in PhysioFit or that your local system administrator told you so, then you probably have found a bug! We would greatly appreciate if you could open a new issue on our `issue tracker `_. diff --git a/docs/index.rst b/docs/index.rst index 8047163..09b76c0 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -19,10 +19,11 @@ additional tailor-made models can be implemented by users. **PhysioFit includes the following features:** * **calculation of growth rate and extracellular (uptake and production) fluxes**, - * **a set of steady-state and dynamic models** are shipped with PhysioFit, + * a set of **steady-state and dynamic models**, * **tailor-made models** can be constructed by users, * Monte-Carlo sensitivity analysis to **estimate the precision of the calculated fluxes**, * **evaluation of the goodness of fit and visual inspection of the fitted curves**, + * calculation of the Akaike information criterion to **guide users to identify the most appropriate model**, * shipped as a **library** with both a **graphical** and a **command line** interface, * **open-source, free and easy to install** everywhere where Python 3 and pip run, * **biologist-friendly**. diff --git a/docs/method.rst b/docs/method.rst index 2d0b555..5355bd6 100644 --- a/docs/method.rst +++ b/docs/method.rst @@ -10,8 +10,9 @@ metabolite and biomass concentrations, as detailed below. Flux values provided by PhysioFit correspond the best fit. A global sensitivity analysis (Monte-Carlo approach) is available to evaluate the precision of the estimated fluxes (mean, median, standard deviation, 95% confidence -intervals), plots are generated for visual inspection of the fitting quality, and a χ² test is performed to assess the -statistical goodness of fit. +intervals), plots are generated for visual inspection of the fitting quality, a χ² test is performed to assess the +statistical goodness of fit and an AIC (Akaike Information Criterion) is +calculated to compare the different models. .. _method_models: @@ -43,17 +44,93 @@ and the best solution is polished using the L-BFGS-B method (see `scipy.optimize `_ for more information on the optimization process). -Goodness-of-fit evaluation -************************** -PhysioFit performs a χ² test to assess the goodness of fit. Have a look at the :doc:`faq` section for -more details on the interpretation of the khi2 test results. +.. _sensitivity_analysis: Sensitivity analysis ********************* -To determine the precision on the fit and on the estimated parameters (including fluxes), PhysioFit performs a Monte Carlo analysis. Briefly, PhysioFit generates several -datasets by adding noise to the dynamics simulated from the best fit, and calculated fluxes and other growth -parameters for each of these synthetic datasets. This enables PhysioFit to compute statistics (mean, median, standard deviation and 95% confidence interval) for -each parameter (including fluxes). We recommend always running a sensitivity analysis when using PhysioFit. +To determine the precision on the fit and on the estimated parameters, +PhysioFit performs a Monte Carlo analysis. Briefly, +PhysioFit generates several +datasets by adding noise to the dynamics simulated from the best fit, and +calculates fluxes and other growth +parameters for each of these synthetic datasets. This enables PhysioFit to +compute statistics (mean, median, standard deviation and 95 % confidence +interval) for each parameter. We recommend always running +a sensitivity analysis when using PhysioFit. + + +.. _`chi2 test`: + +Goodness-of-fit evaluation +************************** + +PhysioFit performs a χ² test to assess the goodness of fit. A χ² test +describes how well a model fits a set of observations. Measures of +goodness of fit typically summarize the discrepancy between observed values +and the values expected under the model used in PhysioFit (see +:ref:`optimization_process`). It is calculated as the sum of differences +between measured and simulated values, each squared and divided by the +simulated value. +A good fit corresponds to small differences between measured and simulated +values, thereby the χ² value is low. In contrast, a bad fit corresponds to +large differences between simulations and measurements, and the χ² value is +high. + +The resulting χ² value can then be compared with a χ² distribution to +determine the goodness of fit. The p-value of one-tail χ² test is calculated +by PhysioFit from the best fit and is given in the log file (have a look to +the :doc:`usage` section). A p-value close to 1 means poor fitting, and a +p-value close to 0 means good fitting (keeping in mind that a p-value very +close to 0 suggest that standard deviations might be +overestimated). A p-value between 0 and 0.05 means the model fits the data +good enough with respect to the standard deviations provided (at a 95% +confidence level). PhysioFit provides an explicit message stating whether +the flux data are satisfactorily fitted or not (at a 95% confidence interval). + +Model comparison and selection +*********************************** + +PhysioFit calculates the Aikake Information Criterion (both classical and corrected, AIC and AICc) +to help users compare different models and select the most appropriate one for their data. The AIC and AICc values +can be found in the statistical output file or directly in +the graphical user interface. +Briefly, the AIC is a statistical metric that measures the explanatory power of a model with respect to a +given set of data. The model with the lowest AIC value is +thus considered the best model. + +The AIC is calculated as follows: + +.. math:: + + AIC = 2k + n \ln(\frac{residuum}{n}) + +where :math:`k` is the number of parameters in the model (plus 1), :math:`n` is the +number of data points, and :math:`residuum` is the residual sum of squares (see +:ref:`optimization_process`). For +datasets with a low number of measurements (typically less than 40 data points), it is recommended to use +the AICc (corrected AIC), which is +calculated as follows: + +.. math:: + + AICc = AIC + \frac{2k(k+1)}{n-k-1} + +In practice, because the AICc approximates the AIC for large sample sizes, +it's often advised to use AICc as the default. + +To identify the best model, different candidate models that differ in terms +of structure or complexity can be used +to fit the data and then compared based on their AIC. The model +with the lowest AIC value is considered the best-fitting model among +the candidates and should thus used to fit the dataset. However, it is crucial to consider the differences +in AIC values between models, as models with low ΔAIC values (typically < 2) +are considered to have similar support from the data. + +Detailed information on the AIC can be found in the original publication +by `Akaike (1974) `_, and a practical +guide ("what it is, how and when to apply it and what it achieves") has been published by +`Symonds and Moussali (2010) `_. diff --git a/docs/models.rst b/docs/models.rst index 8c2b47b..9e7df6c 100644 --- a/docs/models.rst +++ b/docs/models.rst @@ -192,8 +192,8 @@ method to inherit the logic from the base class: :: def __init__(self, data): super().__init__(data) self.model_name = "Tutorial model" - self.parameters_to_estimate = None - self.fixed_parameters = None + self.parameters = None + self.args = None def get_params(self): pass @@ -235,10 +235,10 @@ If you now run the file, you should have a standard output in your console that 2 2 A 1.2 11.0 3 3 A 1.8 10.2 Experimental matrix: - [['A' 0.5 12.0] - ['A' 0.8 11.6] - ['A' 1.2 11.0] - ['A' 1.8 10.2]] + [[0.5 12.0] + [0.8 11.6] + [1.2 11.0] + [1.8 10.2]] Time vector: [0 1 2 3] Name vector: ['X', 'Glucose'] Biomass & Metabolites: ['Glucose'] @@ -246,15 +246,19 @@ If you now run the file, you should have a standard output in your console that Fixed parameters: None Bounds: None -The next step is to define the parameters (used for simulationsand optimization). PhysioFit supports two types of parameters (**parameters to estimate** and **fixed parameters**) which are detailed below. +The next step is to define the parameters (used for simulations and +optimization). PhysioFit supports two types of parameters (**parameters to +estimate** and **fixed parameters**) which are detailed below. .. _parameters_to_estimate: Free parameters ^^^^^^^^^^^^^^^ -The free parameters are the parameters that will be estimated by PhysioFit, and thus that require defining bounds and initial values -to be initialized. The list of parameters and their initial (default) values must be returned by the :samp:`get_params` method: :: +The free parameters are the parameters that will be estimated by PhysioFit, +and thus that require defining bounds and initial values to be initialized. +The list of parameters and their initial (default) values must be returned +by the :samp:`get_params` method: :: from physiofit.models.base_model import Model @@ -263,8 +267,8 @@ to be initialized. The list of parameters and their initial (default) values mus def __init__(self, data): super().__init__(data) self.model_name = "Tutorial model" - self.parameters_to_estimate = None - self.fixed_parameters = None + self.parameters = None + self.args = None def get_params(self): @@ -272,8 +276,8 @@ to be initialized. The list of parameters and their initial (default) values mus # the parameter name and the value is a number that will # be the initial value for the optimization process - self.parameters_to_estimate = { - "BM_0": 1, + self.parameters = { + "X_0": 1, "growth_rate": 1 } @@ -281,7 +285,7 @@ to be initialized. The list of parameters and their initial (default) values mus # using a for loop: for metabolite in self.metabolites: - self.parameters_to_estimate.update( + self.parameters.update( { f"{metabolite}_flux" : 1, f"{metabolite}_init_value" : 1 @@ -292,7 +296,9 @@ to be initialized. The list of parameters and their initial (default) values mus def simulate(): pass -.. note:: For a given model, the number of metabolites may vary depending on the experiment, hence the metabolite-dependent parameters can be automatically defined in this function (as illustrated here using a for loop). +.. note:: For a given model, the number of metabolites may vary depending on + the experiment, hence the metabolite-dependent parameters can be + automatically defined in this function (as illustrated here using a for loop). The next step is to define the default bounds used for the optimization process (these bounds can be changed in the GUI). The bounds are a class of objects that handle the logic and checks. They are derived from the python :samp:`dict` base class, and as such @@ -305,8 +311,8 @@ implement the same methods (e.g. :samp:`update`). Here is an example of how to i def __init__(self, data): super().__init__(data) self.model_name = "Tutorial model" - self.parameters_to_estimate = None - self.fixed_parameters = None + self.parameters = None + self.args = None def get_params(self): @@ -314,7 +320,7 @@ implement the same methods (e.g. :samp:`update`). Here is an example of how to i # the parameter name and the value is a number that will # be the initial value for the optimization process - self.parameters_to_estimate = { + self.parameters = { "BM_0": 1, "growth_rate": 1 } @@ -332,7 +338,7 @@ implement the same methods (e.g. :samp:`update`). Here is an example of how to i # using a for loop: for metabolite in self.metabolites: - self.parameters_to_estimate.update( + self.parameters.update( { f"{metabolite}_flux" : 1, f"{metabolite}_init_value" : 1 @@ -355,14 +361,17 @@ implement the same methods (e.g. :samp:`update`). Here is an example of how to i .. _fixed_parameters: -Fixed parameters +Extra args ^^^^^^^^^^^^^^^^ -The fixed parameters are parameters that are known and are not estimated by PhysioFit. For example, in the case of -steady-state models that account for non enymatic degradation (see :ref:`default_steady-state_models`.), we need to provide the -degradation constant of all unstable metabolites (these constants must be measured in an independent experiment, e.g. see Peiro et al., 2019): :: +The extra args are parameters that are known, constant and are not estimated +by PhysioFit. For example, in the case of steady-state models that account +for non enymatic degradation (see :ref:`default_steady-state_models`.), we +need to provide the degradation constant of all unstable metabolites (these +constants must be measured in an independent experiment, e.g. see `Peiro et +al., 2019 `_): :: - self.fixed_parameters = {"Degradation": { + self.args = {"Degradation Constants": { metabolite: 2 for metabolite in self.metabolites } } @@ -391,13 +400,17 @@ To do this, first write out the function definition: :: pass As shown above, this function takes four arguments: - * :samp:`params_opti`: list containing the values of each parameter to estimate **in the same order as defined in the :samp:`parameters_to_estimate` dictionary** (see :ref:`parameters_to_estimate`) + * :samp:`params_opti`: list containing the values of each parameter to + estimate **in the same order as defined in the** + :samp:`parameters_to_estimate` **dictionary** (see + :ref:`parameters_to_estimate`) * :samp:`data_matrix`: numpy array containing the experimental data (or data with the same shape) * :samp:`time_vector`: numpy array containing the time points * :samp:`params_non_opti`: dictionary containing the fixed parameters (see :ref:`fixed_parameters`) Now you can start writing the body of the function. For sake of clarity, we recommend unpacking parameters values from the -list of parameters to estimate into internal variables. Th function *simulate* must return a matrix containing the simulation results, with the same shape as +list of parameters to estimate into internal variables. The function +*simulate* must return a matrix containing the simulation results, with the same shape as the matrix containing the experimental data. To initialize the simulated matrix, you can use the :samp:`empty_like` function from the numpy library: :: @@ -412,18 +425,17 @@ use the :samp:`empty_like` function from the numpy library: :: simulated_matrix = np.empty_like(data_matrix) # Get initial params - x_0 = params_opti[0] - mu = params_opti[1] + x_0 = parameters[0] + mu = parameters[1] # Get X_0 values exp_mu_t = np.exp(mu * time_vector) simulated_matrix[:, 0] = x_0 * exp_mu_t - fixed_params = [value for value in params_non_opti["Degradation"].values()] + fixed_params = [value for value in args[("Degradation constants")].values()] - # Get parameter names and run the calculations column by column - for i in range(1, int(len(params_opti) / 2)): - q = params_opti[i * 2] - m_0 = params_opti[i * 2 + 1] + for i in range(1, int(len(parameters) / 2)): + q = parameters[i * 2] + m_0 = parameters[i * 2 + 1] k = fixed_params[i - 1] exp_k_t = np.exp(-k * time_vector) simulated_matrix[:, i] = q * (x_0 / (mu + k)) \ @@ -465,10 +477,10 @@ function. The system of ODEs can be provided directly within the body of the sim def calculate_derivative(t, state, y_BM, y_P, km, qsmax): # get substrate and biomass concentrations - s_t = state[0] - x_t = state[1] + x_t = state[0] + s_t = state[1] - # calculate fluxes + # calculate fluxes at time t qs_t = qsmax * (s_t / (km + s_t)) mu_t = y_BM * qs_t qp_t = y_P * qs_t @@ -503,21 +515,86 @@ behind this implementation can be found :ref:`here `. Test the model -------------- -Once you have completely populated your model file, you can now launch a round of simulations and optimizations in a -programmatic way: :: +**Simulate data from parameters** + +It is possible to simulate synthetic data using the model's default +parameters (or a set of predefined parameters) to asses the functionality of +the model. The number of simulated data points is defined by the length of +the input dataframe (for which the actual data points do not matter): :: + + import pandas as pd + import numpy as np + from physiofit.base.io import IoHandler + + # Generate data to get shape of desired output + data = pd.DataFrame( + { + "time": np.arange(6, step=0.2), + "X": np.arange(6, step=0.2), + "Glucose": np.arange(6, step=0.2), + "Acetate": np.arange(6, step=0.2), + "Glutamate": np.arange(6, step=0.2), + } + ) + + # Initialize model + io = IoHandler() + model = io.select_model( + "Steady-state batch model", + data + ) + + # Get default parameters for the model + model.get_params() + + # Simulate data + sim_data = model.simulate( + list(model.parameters.values()), + model.data.drop("time", axis=1), + model.time_vector, + model.args + ) + # Create a pretty visualisation of the data in a dataframe + df = pd.DataFrame( + data=sim_data, + index=model.time_vector, + columns=model.name_vector + ) + # Give the index the name "time" for clarity + df.index.name = "time" + + # Visualize the simulated data + df.plot() + +The dataframe can then be used as input data for the model, and the model +can be tested as described above. If the parameters to use for the +simulation are not the ones given by default, you can always update the +associated model parameters using the built-in update method: :: + + model.parameters.update( + { + "X_0": 0.02, + "growth_rate": 0.8, + "Glucose_q": -8, + "Glucose_M0": 20, + "Acetate_q": 3, + "Acetate_M0": 0.01, + "Glutamate_q": 2, + "Glutamate_M0": 0.01 + } + ) + +**Parameter estimation** + +Once you have completely populated your model file and generated the +synthetic data,you can now launch the estimation of parameters: :: if __name__ == "__main__": from physiofit.base.io import IoHandler from physiofit.models.base_model import StandardDevs - test_data = pd.DataFrame( - { - "time": [0, 1, 2, 3], - "experiments": ["A", "A", "A", "A"], - "X": [0.5, 0.8, 1.2, 1.8], - "Glucose": [12, 11.6, 11, 10.2] - } - ) + # Use the simulated data from above + test_data = df.reset_index() io = IoHandler() model = ChildModel(data=test_data) @@ -527,7 +604,7 @@ programmatic way: :: model=model, mc=True, iterations=100, - sd=StandardDevs({"X": 1, "Glucose": 1}), + sd=StandardDevs({"X": 0.2, "Glucose": 0.2, "Acetate": 0.2, "Glutamate": 0.2}), debug_mode=True ) fitter.optimize() @@ -536,9 +613,13 @@ programmatic way: :: print(fitter.parameter_stats) This will return the calculated flux values and associated statistics. +comparing the estimated parameters with the initial parameters used to +simulate the data will allow you to assess the quality of the model. This +process can be repeated with different sets of parameters to ensure the +robustness of the model. This code can then be used as unit tests for the +created model. -.. note:: The test data and calculation parameters (e.g. standard deviations) defined in the test function must correspond to those expected for the new model. - +**GUI integration** To test the integration of the model into the GUI, copy the :file:`.py` file in the folder :file:`models` of PhysioFit directory. You can get the path towards this folder by opening a python @@ -556,4 +637,5 @@ have a look to the error message and correct the code. .. note:: We would be happy to broaden the types of models shipped with PhysioFit. If you have developed a new model, it might be usefull and valuable to the fluxomics community! Please, keep in touch with us to discuss on the model and see if we can include your - model in the built-in models shipped with PhysioFit! :) \ No newline at end of file + model in the built-in models shipped with PhysioFit! :) + diff --git a/docs/usage.rst b/docs/usage.rst index ebe349c..8aa99dd 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -37,7 +37,7 @@ name of the condition/experiment, which must be provided even if only one condit .. _yaml_config: Configuration file (:file:`yaml`) ---------------------------- +--------------------------------- The :file:`yaml` configuration file contains all parameters required to calculate fluxes for a given experiment, and is thus key to ensure **reproducibility** of the flux calculation process. A configuration file is generated automatically by @@ -89,8 +89,10 @@ with metabolite degradation model is selected: .. image:: _static/usage/example1.JPG -**Standard deviation** on measurements. As detailed in the methods section, reducing the standard deviation will increase the cost of the corresponding data during the -optimization, thereby forcing an improvement of the fit accuracy for this measurements, but degrading the goodness-of-fit for the +**Standard deviation** on measurements. As detailed in the methods section, +reducing the standard deviation will increase the cost of the corresponding +data during the optimization, thereby forcing an improvement of the fit +accuracy for this measurements, but degrading the goodness-of-fit for the other measurements. Finally, **Verbose logs**: Should debug information be written in log file. Useful in case of trouble (please join it @@ -113,7 +115,9 @@ The following files are generated by PhysioFit in the output directory: * :file:`config_file.yaml` configuration file containing all parameters used for the last run. * :file:`flux_results.tsv` flux calculation results, i.e. fluxes and initial metabolite concentrations for the best fit, with associated precision. - * :file:`stat_results.tsv` results from the χ² statistical test. + * :file:`stat_results.tsv` results from the χ² and AIC statistical tests + (see :doc:`method` for more details on the statistical tests performed by + PhysioFit). * :file:`log.txt` run log file containing information on how the run went. * :file:`plots.pdf` plots of simulated and measured data. * A number of :file:`.svg` files: individual plots of simulated and measured data. diff --git a/physiofit/__init__.py b/physiofit/__init__.py index e56be43..342c17d 100644 --- a/physiofit/__init__.py +++ b/physiofit/__init__.py @@ -1,6 +1,3 @@ import importlib.metadata -import logging __version__ = importlib.metadata.version("physiofit") -logger = logging.getLogger("physiofit") -logger.setLevel(logging.DEBUG) \ No newline at end of file diff --git a/physiofit/__main__.py b/physiofit/__main__.py index 0878863..be21e1c 100644 --- a/physiofit/__main__.py +++ b/physiofit/__main__.py @@ -14,13 +14,14 @@ def get_last_version(): try: pf_path = Path(physiofit.__file__).parent # Get the version from pypi - response = requests.get(f'https://pypi.org/pypi/physiofit/json') + response = requests.get('https://pypi.org/pypi/physiofit/json') latest_version = response.json()['info']['version'] with open(str(Path(pf_path, "last_version.txt")), "w") as f: f.write(latest_version) except Exception: pass + def main(): """The main routine""" @@ -33,5 +34,6 @@ def main(): path_to_app = path_to_app / "ui/gui.py" run(["streamlit", "run", str(path_to_app)]) + if __name__ == "__main__": - sys.exit(main()) \ No newline at end of file + sys.exit(main()) diff --git a/physiofit/__pycache__/__init__.cpython-312.pyc b/physiofit/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 0000000..369ae9a Binary files /dev/null and b/physiofit/__pycache__/__init__.cpython-312.pyc differ diff --git a/physiofit/__pycache__/__main__.cpython-312.pyc b/physiofit/__pycache__/__main__.cpython-312.pyc new file mode 100644 index 0000000..0217fd3 Binary files /dev/null and b/physiofit/__pycache__/__main__.cpython-312.pyc differ diff --git a/physiofit/base/__pycache__/__init__.cpython-312.pyc b/physiofit/base/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 0000000..2ded5a5 Binary files /dev/null and b/physiofit/base/__pycache__/__init__.cpython-312.pyc differ diff --git a/physiofit/base/__pycache__/fitter.cpython-312.pyc b/physiofit/base/__pycache__/fitter.cpython-312.pyc new file mode 100644 index 0000000..b33fe3d Binary files /dev/null and b/physiofit/base/__pycache__/fitter.cpython-312.pyc differ diff --git a/physiofit/base/__pycache__/io.cpython-312.pyc b/physiofit/base/__pycache__/io.cpython-312.pyc new file mode 100644 index 0000000..9b76735 Binary files /dev/null and b/physiofit/base/__pycache__/io.cpython-312.pyc differ diff --git a/physiofit/base/fitter.py b/physiofit/base/fitter.py index 70f0d7c..f461e03 100644 --- a/physiofit/base/fitter.py +++ b/physiofit/base/fitter.py @@ -5,6 +5,7 @@ import logging import numpy as np +import pandas as pd from pandas import DataFrame from scipy.optimize import minimize, differential_evolution from scipy.stats import chi2 @@ -14,17 +15,18 @@ logger = logging.getLogger(f"physiofit.{__name__}") - -# TODO: add estimate deg function (eq 6) with plot of best fit and measured values +# TODO: add estimate deg function (eq 6) with plot of best fit and measured +# values class PhysioFitter: """ - This class is responsible for most of Physiofit's heavy lifting. Features included are: + This class is responsible for most of Physiofit's heavy lifting. + Features included are: - * loading of data from **csv** or **tsv** file - * **equation system initialization** using the following analytical functions (in absence of lag and - degradation: + * loading of data from **csv** or **tsv** file * **equation system + initialization** using the following analytical functions (in + absence of lag and degradation): X(t) = X0 * exp(mu * t) Mi(t) = qMi * (X0 / mu) * (exp(mu * t) - 1) + Mi0 @@ -34,35 +36,39 @@ class PhysioFitter: residuum = sum((sim - meas) / sd)² - * **optimization of the initial parameters** using `scipy.optimize.minimize ('Differential evolution', with polish with 'L-BFGS-B' method) `_ - * **sensitivity analysis, khi2 tests and plotting** + * **optimization of the initial parameters** using + `scipy.optimize.minimize ('Differential evolution', with polish with + 'L-BFGS-B' method) `_ * + **sensitivity analysis, khi2 tests and plotting** :param data: DataFrame containing data and passed by IOstream object - :type data: class: pandas.DataFrame - :param model: Model to initialize parameters and optimize - :type model: physiofit.models.base_model.Model - :param mc: Should Monte-Carlo sensitivity analysis be performed (default=True) - :type mc: Boolean - :param iterations: number of iterations for Monte-Carlo simulation (default=50) - :type iterations: int - :param sd: sd matrix used for residuum calculations. Can be: - - * a matrix with the same dimensions as the measurements matrix (but without the time column) - * a named vector containing sds for all the metabolites provided in the input file - * 0 in which case the matrix is automatically constructed from default values - * a dictionary with the data column headers as keys and the associated value as a scalar or list + :type data: class: pandas.DataFrame :param model: Model to initialize + parameters and optimize :type model: physiofit.models.base_model.Model + :param mc: Should Monte-Carlo sensitivity analysis be performed ( + default=True) :type mc: Boolean :param iterations: number of iterations + for Monte-Carlo simulation (default=50) :type iterations: int :param sd: + sd matrix used for residuum calculations. Can be: + + * a matrix with the same dimensions as the measurements + matrix (but without the time column) * a named vector + containing sds for all the metabolites provided in the input + file * 0 in which case the matrix is automatically + constructed from default values * a dictionary with the data + column headers as keys and the associated value as a scalar + or list :type sd: int, float, list, dict or ndarray """ def __init__( self, - data, - model, - mc=True, - iterations=100, + data: pd.DataFrame, + model: Model, + mc: bool = True, + iterations: int = 100, sd=None, - debug_mode=False + debug_mode: bool = False ): self.data = data @@ -70,18 +76,26 @@ def __init__( self.mc = mc self.iterations = iterations self.sd = sd - self.debug_mode = debug_mode + self.debug_mode = logging.DEBUG if debug_mode else logging.INFO self.experimental_matrix = self.data.drop("time", axis=1).to_numpy() - self.simulated_matrix = None - self.simulated_data = None - self.optimize_results = None + self.simulated_matrix: np.ndarray | None = None + self.simulated_data: pd.DataFrame | None = None + self.large_matrix: np.ndarray | None = None + self.large_simulated_data: pd.DataFrame | None = None + self.large_time_vector: np.ndarray | None = None + self.optimize_results: np.ndarray | None = None self.simulate = None self.parameter_stats = None self.opt_params_sds = None self.matrices_ci = None self.opt_conf_ints = None self.khi2_res = None + self.aic_res = None + self.aic = None + self.aic_c = None + + logger.setLevel(self.debug_mode) def verify_attrs(self): """Check that attributes are valid""" @@ -146,7 +160,6 @@ def initialize_sd_matrix(self): # This function can be optimized, if the input is a matrix we should # detect it directly - logger.info("Initializing sd matrix...\n") # If sd is None, we generate the default matrix if self.sd is None or self.sd == {}: @@ -168,8 +181,8 @@ def initialize_sd_matrix(self): if not isinstance(self.sd, np.ndarray) and not isinstance(self.sd, list): raise TypeError( - f"Cannot coerce SD to array. Please check that a list or array " - f"is given as input.\nCurrent input: \n{self.sd}" + f"Cannot coerce SD to array. Please check that a list or array" + f" is given as input.\nCurrent input: \n{self.sd}" ) else: self.sd = np.array(self.sd) @@ -187,9 +200,6 @@ def initialize_sd_matrix(self): # If the array is not the right shape, we assume it is a vector # that needs to be tiled into a matrix - logger.debug(f"SD matrix: {self.sd}\n") - logger.debug(f"Type of SD matrix: {type(self.sd)}") - if self.sd.shape != self.experimental_matrix.shape: try: self._build_sd_matrix() @@ -197,10 +207,6 @@ def initialize_sd_matrix(self): raise except RuntimeError: raise - else: - logger.debug(f"sd matrix: {self.sd}\n") - return - logger.info(f"sd Matrix:\n{self.sd}\n") def _build_sd_matrix(self): """ @@ -249,33 +255,47 @@ def optimize(self): logger.info("\nRunning optimization...\n") bounds = self.model.bounds() - parameters = [param for param in self.model.parameters_to_estimate.values()] - logger.debug(f"Simulate function = {self.model.simulate}") + parameters = [ + param for param in self.model.parameters.values() + ] self.optimize_results = self._run_optimization( params=parameters, func=self.model.simulate, exp_data_matrix=self.experimental_matrix, time_vector=self.model.time_vector, - non_opt_params=self.model.fixed_parameters, + non_opt_params=self.model.args, sd_matrix=self.sd, bounds=bounds, method="differential_evolution" ) + logger.info(f"SD matrix: {self.sd}") self.parameter_stats = { "optimal": self.optimize_results.x } - logger.info(f"Optimization results: \n{self.optimize_results}\n") + logger.info(f"Optimization results: {self.optimize_results}") for i, param in zip( - self.model.parameters_to_estimate, self.optimize_results.x + self.model.parameters, self.optimize_results.x ): - logger.info(f"\n{i} = {param}\n") + logger.info(f"{i} = {param}") self.simulated_matrix = self.model.simulate( - self.optimize_results.x, - self.experimental_matrix, - self.model.time_vector, - self.model.fixed_parameters + parameters=self.optimize_results.x, + data_matrix=self.experimental_matrix, + time_vector=self.model.time_vector, + args=self.model.args + ) + self.large_time_vector = np.arange( + start=0, + stop=max(self.model.time_vector), + step=(max(self.model.time_vector) / 100) + ) + self.large_matrix = self.model.simulate( + parameters=self.optimize_results.x, + data_matrix=np.ones( + shape=(len(self.large_time_vector), + self.experimental_matrix.shape[1])), + time_vector=self.large_time_vector, + args=self.model.args ) - logger.debug(f"simulated_matrix:\n{self.simulated_matrix}") nan_sim_mat = np.copy(self.simulated_matrix) nan_sim_mat[np.isnan(self.experimental_matrix)] = np.nan self.simulated_data = DataFrame( @@ -283,8 +303,14 @@ def optimize(self): index=self.model.time_vector, columns=self.model.name_vector ) + self.large_simulated_data = DataFrame( + data=self.large_matrix, + index=self.large_time_vector, + columns=self.model.name_vector + ) self.simulated_data.index.name = "Time" - logger.info(f"Final Simulated Data: \n{self.simulated_data}\n") + logger.info(f"Simulated data: \n{self.simulated_data}\n") + logger.debug(f"Large simulated data: \n{self.large_simulated_data}\n") @staticmethod def _calculate_cost( @@ -298,7 +324,16 @@ def _calculate_cost( simulated_matrix = func(params, exp_data_matrix, time_vector, non_opt_params) - cost_val = np.square((simulated_matrix - exp_data_matrix) / sd_matrix) + # print("inside cost function") + # print(f"Params: {params}") + # print(f"Simulated matrix: {simulated_matrix}") + # print(f"Experimental matrix: {exp_data_matrix}") + cost_val = np.square( + np.divide( + np.subtract(simulated_matrix, exp_data_matrix), + sd_matrix + ) + ) residuum = np.nansum(cost_val) return residuum @@ -323,15 +358,25 @@ def _run_optimization( optimize_results = differential_evolution( PhysioFitter._calculate_cost, bounds=bounds, args=( - func, exp_data_matrix, time_vector, non_opt_params, sd_matrix), + func, + exp_data_matrix, + time_vector, + non_opt_params, + sd_matrix + ), polish=True, x0=np.array(params) ) elif method == "L-BFGS-B": optimize_results = minimize( PhysioFitter._calculate_cost, x0=np.array(params), args=( - func, exp_data_matrix, time_vector, non_opt_params, sd_matrix), - method="L-BFGS-B", bounds=bounds, options={'maxcor': 30} + func, + exp_data_matrix, + time_vector, + non_opt_params, + sd_matrix + ), + method="L-BFGS-B", bounds=bounds ) else: raise ValueError(f"{method} is not implemented") @@ -362,26 +407,44 @@ def monte_carlo_analysis(self): opt_params_list = [] matrices = [] - for _ in range(self.iterations): - new_matrix = self._apply_noise() - + for i in range(self.iterations): + noisy_matrix = self._apply_noise() + logger.debug(f"Iteration {i + 1}:\n") + logger.debug(f"New matrix:\n{noisy_matrix}\n") + logger.debug(f"Sd matrix:\n{self.sd}\n") + logger.debug(f"time vector:\n{self.model.time_vector}\n") + sim_mat = self.model.simulate( + opt_res.x, + noisy_matrix, + self.model.time_vector, + self.model.args + ) + logger.debug( + "simulated matrix:" + f"{sim_mat}\n" + ) # We optimise the parameters using the noisy matrix as input - opt_res = PhysioFitter._run_optimization( - opt_res.x, self.model.simulate, new_matrix, self.model.time_vector, - self.model.fixed_parameters, self.sd, self.model.bounds(), + + mc_opt_res = PhysioFitter._run_optimization( + opt_res.x, + self.model.simulate, + noisy_matrix, + self.model.time_vector, + self.model.args, + self.sd, self.model.bounds(), "L-BFGS-B" ) # Store the new simulated matrix in list for later use matrices.append( self.model.simulate( - opt_res.x, new_matrix, self.model.time_vector, - self.model.fixed_parameters + mc_opt_res.x, self.large_matrix, self.large_time_vector, + self.model.args ) ) # Store the new optimised parameters in list for later use - opt_params_list.append(opt_res.x) + opt_params_list.append(mc_opt_res.x) # Build a 3D array from all the simulated matrices to get standard # deviation on each data point @@ -394,22 +457,13 @@ def monte_carlo_analysis(self): # Compute the statistics on the list of parameters: means, sds, # medians and confidence interval self._compute_parameter_stats(opt_params_list) - logger.info(f"Optimized parameters statistics:") + logger.info("Optimized parameters statistics:") for key, value in self.parameter_stats.items(): logger.info(f"{key}: {value}") - # Apply nan mask to be coherent with the experimental matrix - nan_lower_ci = np.copy(self.matrices_ci['lower_ci']) - nan_higher_ci = np.copy(self.matrices_ci['higher_ci']) - nan_lower_ci[np.isnan(self.experimental_matrix)] = np.nan - nan_higher_ci[np.isnan(self.experimental_matrix)] = np.nan - - logger.info( - f"Simulated matrix lower confidence interval:\n{nan_lower_ci}\n" - ) - logger.info( - f"Simulated matrix higher confidence interval:\n{nan_higher_ci}\n" - ) + # # Apply nan mask to be coherent with the experimental matrix + # nan_lower_ci = np.copy(self.matrices_ci['lower_ci']) + # nan_higher_ci = np.copy(self.matrices_ci['higher_ci']) return def _compute_parameter_stats(self, opt_params_list): @@ -441,16 +495,60 @@ def _compute_parameter_stats(self, opt_params_list): # self.parameter_stats_df = DataFrame() + def aic_test(self): + """ + Calculate the Akaike Information Criterion (AIC) for the model + """ + + n = np.count_nonzero(~np.isnan(self.experimental_matrix)) + k = len(self.model.parameters) + 1 # +1 for the cost parameter + logger.debug(f"Number of measurements: {n}") + logger.debug(f"Number of parameters: {k}") + cost = self._calculate_cost( + self.optimize_results.x, + self.model.simulate, + self.experimental_matrix, + self.model.time_vector, + self.model.args, + self.sd + ) + # Calculate AIC + self.aic = 2 * k + n * np.log(cost) + logger.debug(f"AIC: {self.aic}") + # Correct AIC for small sample sizes + if n - k - 1 <= 0: + raise ValueError("Not enough measurements to calculate AIC") + self.aic_c = self.aic + ((2 * k * (k + 1)) / (n - k - 1)) + + self.aic_res = pd.DataFrame.from_dict( + { + "AIC": self.aic, + "AICc": self.aic_c + }, orient="index", columns=["Values"] + ) + def khi2_test(self): + """ + This method performs a chi-squared test to evaluate the goodness of + fit of the model. It calculates the chi-squared statistic and the + p-value and logs the results. + The chi-squared test is a statistical hypothesis test that is valid to + perform when the test statistic is chi-squared distributed under the + null hypothesis. + """ number_measurements = np.count_nonzero( ~np.isnan(self.experimental_matrix) ) - number_params = len(self.model.parameters_to_estimate) + number_params = len(self.model.parameters) dof = number_measurements - number_params cost = self._calculate_cost( - self.optimize_results.x, self.model.simulate, self.experimental_matrix, - self.model.time_vector, self.model.fixed_parameters, self.sd + self.optimize_results.x, + self.model.simulate, + self.experimental_matrix, + self.model.time_vector, + self.model.args, + self.sd ) p_val = chi2.cdf(cost, dof) @@ -466,11 +564,11 @@ def khi2_test(self): ) logger.info(f"khi2 test results:\n" - f"khi2 value: {cost}\n" - f"Number of measurements: {number_measurements}\n" - f"Number of parameters to fit: {number_params}\n" - f"Degrees of freedom: {dof}\n" - f"p-value = {p_val}\n" + f"khi2 value: {cost}\n" + f"Number of measurements: {number_measurements}\n" + f"Number of parameters to fit: {number_params}\n" + f"Degrees of freedom: {dof}\n" + f"p-value = {p_val}\n" ) if p_val < 0.95: @@ -510,8 +608,9 @@ def _apply_noise(self): parameters. SDs are obtained from the sd matrix """ - new_matrix = np.array([ + noisy_matrix = np.array([ PhysioFitter._add_noise(self.simulated_matrix[idx, :], sd) for idx, sd in enumerate(self.sd) ]) - return new_matrix + noisy_matrix[noisy_matrix < 0] = 0 + return noisy_matrix diff --git a/physiofit/base/io.py b/physiofit/base/io.py index 5a8ce38..ba97841 100644 --- a/physiofit/base/io.py +++ b/physiofit/base/io.py @@ -10,14 +10,15 @@ import matplotlib.pyplot as plt import numpy as np - +import pandas as pd from matplotlib.backends.backend_pdf import PdfPages from pandas import DataFrame, read_csv, concat import yaml +import physiofit.models.base_model from physiofit import __file__ from physiofit.base.fitter import PhysioFitter -from physiofit.models.base_model import StandardDevs, Bounds +from physiofit.models.base_model import StandardDevs, Bounds, Model # Switch matplotlib logger to higher level to not get debug logs in root logger logging.getLogger("matplotlib").setLevel(logging.WARNING) @@ -84,44 +85,55 @@ def read_data(data: str) -> DataFrame: elif issubclass(type(data), BytesIO): data = read_csv(data, sep="\t") else: - raise TypeError(f"Input data file is not of right type. Accepted types: file-like (bytes) or string") + raise TypeError("Input data file is not of right type. " + "Accepted types: file-like (bytes) or string") except Exception: logger.exception("There was an error while reading the data") raise IOError( - "Error while reading data. Please ensure you have the right file format (txt, tsv or bytes)" + "Error while reading data. Please ensure you have the right " + "file format (txt, tsv or bytes)" ) IoHandler._verify_data(data) return data - def select_model(self, model_name, data=None): + def select_model( + self, name: str, + data: pd.DataFrame = None + ) -> Model: """ - Select a model from the list of models in the model folder of the package src directory + Select a model from the list of models in the model folder of the + package src directory """ self.get_models(data) - for x in self.models: - if x.model_name == model_name: - model = x - return model + for model in self.models: + if model.name == name: + return model - def read_model(self, model_file): + @staticmethod + def read_model( + model_file: str + ): """ Import and return the model class from .py file containing the model. - .. warning: ONLY USE THIS FUNCTION ON TRUSTED PYTHON FILES. Reading code from untrusted sources can lead to - propagation of viruses and compromised security. + .. warning: ONLY USE THIS FUNCTION ON TRUSTED PYTHON FILES. Reading + code from untrusted sources can lead to propagation of viruses and + compromised security. :param model_file: path to the model.py file to import """ if not Path(model_file).is_file() or Path(model_file).suffix != ".py": raise ValueError( - "The given path is not valid. The path must point to a .py file containing the module " - "from which the model will be loaded." + "The given path is not valid. The path must point to a .py " + "file containing the module from which the model will be " + "loaded." ) - spec = importlib.util.spec_from_file_location("module_to_import", fr"{model_file}") + spec = importlib.util.spec_from_file_location("module_to_import", + fr"{model_file}") module = importlib.util.module_from_spec(spec) sys.modules["module_to_import"] = module spec.loader.exec_module(module) @@ -130,7 +142,9 @@ def read_model(self, model_file): return model_class @staticmethod - def _verify_data(data: DataFrame): + def _verify_data( + data: DataFrame + ): """ Perform checks on DataFrame returned by the _read_data function @@ -153,10 +167,11 @@ def _verify_data(data: DataFrame): raise ValueError("Second column should be 'time'") if len(data.columns) <= 3: - raise ValueError(f"Data does not contain any metabolite columns") + raise ValueError("Data does not contain any metabolite columns") for x in data.columns: - if x != "experiments" and data[x].dtypes != np.int64 and data[x].dtypes != np.float64: + if x != "experiments" and data[x].dtypes != np.int64 and data[ + x].dtypes != np.float64: raise ValueError( f"Column {x} has values that are not of numeric type" ) @@ -166,7 +181,8 @@ def _verify_data(data: DataFrame): ) # To avoid errors when concatenating dataframes for the final summary - data["experiments"] = data["experiments"].str.replace(pat=" ", repl="_") + data["experiments"] = data["experiments"].str.replace(pat=" ", + repl="_") @staticmethod def get_model_list(): @@ -182,12 +198,16 @@ def get_model_list(): ) model_class = getattr(module, "ChildModel") model = model_class(df) - print(model.model_name) + print(model.name) return - def get_models(self, data=None): + def get_models( + self, + data: pd.DataFrame = None + ): """ - Read modules containing the different models and add them to models attribute + Read modules containing the different models and add them to models + attribute :return: list containing the different model objects """ @@ -204,7 +224,8 @@ def get_models(self, data=None): else: self.models.append(model_class(self.data)) - def get_local_model_folder(self) -> str: + @staticmethod + def get_local_model_folder() -> str: """ Return the path towards the actual environment's used models folder """ @@ -212,7 +233,8 @@ def get_local_model_folder(self) -> str: model_dir = Path(__file__).parent / "models" return str(model_dir) - # TODO: Implement this function to add model to model folder and add button to GUI + # TODO: Implement this function to add model to model folder and add + # button to GUI @staticmethod def add_model(model_file): pass @@ -223,22 +245,25 @@ def read_yaml(yaml_file: str | bytes) -> ConfigParser: """ Import yaml configuration file and parse keyword arguments - :param yaml_file: path to the yaml file or json file - :return config_parser: Dictionary containing arguments parsed from yaml file + :param yaml_file: path to the yaml file or json file :return + config_parser: Dictionary containing arguments parsed from yaml file + """ # Load config file try: - if isinstance(yaml_file, str) or issubclass(type(yaml_file), BytesIO): + if isinstance(yaml_file, str) or issubclass(type(yaml_file), + BytesIO): config_parser = ConfigParser.from_file(yaml_file) else: raise TypeError( - f"Trying to read object that is not a file or path to file: {yaml_file}" + f"Trying to read object that is not a file or path to " + f"file: {yaml_file}" ) except Exception as e: raise IOError( - f"Error while reading yaml configuration file {yaml_file}. " - f"\nTraceback:\n\n{e}" + f"Error while reading yaml configuration file. " + f"Traceback:{e}" ) return config_parser @@ -260,7 +285,8 @@ def initialize_fitter(self, data: pd.DataFrame, **kwargs) -> PhysioFitter: mc=kwargs["mc"] if "mc" in kwargs else True, iterations=kwargs["iterations"] if "iterations" in kwargs else 100, sd=kwargs["sd"] if "sd" in kwargs else StandardDevs(), - debug_mode=kwargs["debug_mode"] if "debug_mode" in kwargs else False + debug_mode=kwargs[ + "debug_mode"] if "debug_mode" in kwargs else False ) if "sd" not in kwargs: @@ -274,9 +300,6 @@ def initialize_fitter(self, data: pd.DataFrame, **kwargs) -> PhysioFitter: fitter.initialize_sd_matrix() fitter.verify_attrs() - logger.debug( - f"Fitter attribute dictionary:\n{fitter.__dict__}" - ) return fitter @@ -285,6 +308,7 @@ def output_pdf(self, fitter: PhysioFitter, export_path: str | Path = None): Handle the creation and output of a pdf file containing fit results as a plot + :param fitter: :param export_path: Path to exported pdf. In local mode, it is sent to the _res directory :return: None @@ -323,17 +347,20 @@ def output_recap(self, export_path: str, galaxy=False): ) if not self.multiple_experiments: raise ValueError( - f"It seems that the multiple experiments list is empty: {self.multiple_experiments}" + f"It seems that the multiple experiments list is empty: " + f"{self.multiple_experiments}" ) for idx, element in enumerate(self.multiple_experiments): if not isinstance(element, DataFrame): raise TypeError( - f"All the elements of multiple_experiments must be DataFrames. Wrong element type" + f"All the elements of multiple_experiments must be " + f"DataFrames. Wrong element type" f"detected at indice {idx}" ) final_df = concat(self.multiple_experiments) final_df = final_df.reset_index() - final_df[["experiments", "parameter name"]] = final_df["index"].str.split(" ", expand=True) + final_df[["experiments", "parameter name"]] = final_df[ + "index"].str.split(" ", expand=True) final_df.set_index(["experiments", "parameter name"], inplace=True) final_df.drop("index", axis=1, inplace=True) if galaxy: @@ -341,14 +368,17 @@ def output_recap(self, export_path: str, galaxy=False): else: final_df.to_csv(f"{str(Path(export_path))}/summary.csv") - def output_report(self, fitter, export_path: str | list = None): + @staticmethod + def output_report(fitter, export_path: str | list = None): """ Handle creation and export of the report containing stats from monte carlo analysis of optimization parameters - :param fitter: PhysioFitter object containing results from the optimization of parameters - :param export_path: list of paths to export the stats and fluxes. [0] - is for stats and [1] for fluxes. + :param export_path: Path to export the report + :param fitter: PhysioFitter object containing results from the + optimization of parameters + :param export_path: list of paths to export the stats and fluxes. [ + 0] is for stats and [1] for fluxes. """ if isinstance(export_path, list): @@ -363,20 +393,17 @@ def output_report(self, fitter, export_path: str | list = None): flux_path = fr"{export_path}\flux_results.tsv" stat_path = fr"{export_path}\stat_results.tsv" - logger.debug( - f"Parameter Stats:\n{fitter.parameter_stats}" - ) - # Get optimization results as dataframe opt_data = DataFrame.from_dict(fitter.parameter_stats, orient="columns") # Use IDs to clarify which parameter is described on each line - opt_data.index = [param for param in fitter.model.parameters_to_estimate.keys()] + opt_data.index = [param for param in fitter.model.parameters.keys()] opt_data.to_csv(flux_path, sep="\t") - if isinstance(fitter.khi2_res, DataFrame): - with open(stat_path, "w+") as stat_out: + # Get khi² test results as dataframe and write to file + with open(stat_path, "w+") as stat_out: + if isinstance(fitter.khi2_res, DataFrame): stat_out.write("==================\n" "Khi² test results\n" "==================\n\n") @@ -400,6 +427,28 @@ def output_report(self, fitter, export_path: str | list = None): f"provided measurement SD. Value: " f"{fitter.khi2_res.at['p_val', 'Values']}\n" ) + else: + stat_out.write( + "No khi² test results available. The model has not been " + "tested against the data" + ) + + # Get AIC results as dataframe and write to file + if isinstance(fitter.aic_res, DataFrame): + stat_out.write( + "\n\n==================\n" + "AIC test results\n" + "==================\n\n" + ) + stat_out.write( + fitter.aic_res.to_string( + header=False, justify="center" + ) + ) + else: + stat_out.write( + "\nNo AIC test results available." + ) def _get_plot_data(self, fitter): """ @@ -407,8 +456,8 @@ def _get_plot_data(self, fitter): """ # Initialize vectors and data for plotting - if fitter.model.time_vector is not None: - x = fitter.model.time_vector + if fitter.large_time_vector is not None: + x = fitter.large_time_vector else: raise ValueError( "PhysioFitter model time_vector has not been initialized. " @@ -420,8 +469,8 @@ def _get_plot_data(self, fitter): raise ValueError( "PhysioFitter object does not have experimental data loaded in" ) - if fitter.simulated_matrix is not None: - sim_mat = fitter.simulated_matrix + if fitter.large_matrix is not None: + sim_mat = fitter.large_matrix else: raise ValueError("PhysioFitter simulated data does not exist yet") if fitter.matrices_ci is not None: @@ -444,7 +493,7 @@ def _get_plot_data(self, fitter): self.experimental_data = DataFrame( columns=fitter.model.name_vector, - index=x, + index=fitter.model.time_vector, data=exp_mat ).sort_index(level=0) self.simulated_data = DataFrame( @@ -457,8 +506,9 @@ def plot_data(self, fitter, display: bool = False): """ Plot the data - :param fitter: PhysioFitter object after optimization of parameters has been executed - :param display: should plots be displayed + :param display: Should plots be displayed or not on creation + :param fitter: PhysioFitter object after optimization of parameters + has been executed """ self._get_plot_data(fitter) @@ -535,7 +585,16 @@ def _add_sd_area(self, element: str, ax: plt.Axes): class ConfigParser: - allowed_keys = ["model", "sds", "mc", "iterations"] + """ + The ConfigParser class is used to parse configuration files for the + PhysioFit package. It reads a YAML file and extracts the necessary + parameters for the model fitting process. It also includes methods to + update the model with the parsed parameters and export the run + parameters back to a yaml config file. + """ + + AUTHORIZED_KEYS = ["path_to_data", "model", "sds", "mc", + "iterations"] def __init__( self, @@ -546,52 +605,46 @@ def __init__( path_to_data=None ): - self.path_to_data = path_to_data - self.model = selected_model - self.sds = StandardDevs(sds) - self.mc = mc - self.iterations = iterations + self.path_to_data: str = path_to_data + self.model: physiofit.models.base_model.Model = selected_model + self.sds: physiofit.models.base_model.StandardDevs = StandardDevs(sds) + self.mc: bool = mc + self.iterations: int = iterations if not isinstance(self.mc, bool): raise TypeError( - f"The MonteCarlo option must be given as a boolean (True or False). Detected input: {self.mc}, " + f"The MonteCarlo option must be given as a boolean (True or " + f"False). Detected input: {self.mc}," f"type: {type(self.mc)}" ) if not isinstance(self.iterations, int): raise TypeError( - f"Number of iterations must be an integer: Detected input: {self.mc}, type: {type(self.iterations)}" + f"Number of iterations must be an integer: Detected input: " + f"{self.mc}, type: {type(self.iterations)}" ) + def __repr__(self): + return f"ConfigParser(path_to_data={self.path_to_data}, " \ + f"model={self.model}, sds={self.sds}, mc={self.mc}, " \ + f"iterations={self.iterations})" + @classmethod def from_file(cls, yaml_file): - - if isinstance(yaml_file, str): - with open(yaml_file, 'r') as file: - data = yaml.safe_load(file) - else: - data = yaml.safe_load(yaml_file) - data_keys = [key for key in data.keys()] - for key in cls.allowed_keys: - if key not in data_keys: - raise ValueError( - f"The key {key} is missing from the input config file" - ) - - try: - return ConfigParser( - path_to_data=data["path_to_data"], - selected_model=data["model"], - sds=data["sds"], - mc=data["mc"], - iterations=data["iterations"] - ) - except KeyError: - return ConfigParser( - selected_model=data["model"], - sds=data["sds"], - mc=data["mc"], - iterations=data["iterations"] - ) + data = yaml.safe_load(yaml_file) if not isinstance(yaml_file, str) \ + else yaml.safe_load(open(yaml_file, 'r')) + missing_keys = [key for key in cls.AUTHORIZED_KEYS if + key not in data.keys()] + if missing_keys: + raise ValueError( + f"The keys {missing_keys} are missing from the input config " + f"file") + return cls( + path_to_data=data["path_to_data"], + selected_model=data["model"], + sds=data["sds"], + mc=data["mc"], + iterations=data["iterations"] + ) @classmethod def from_galaxy(cls, galaxy_yaml): @@ -606,10 +659,21 @@ def get_kwargs(self): "sd": self.sds } + def check_data_path(self): + """ + Check if the data path is valid + :return: True if the path is valid, False otherwise, None if no path + """ + path = Path(self.path_to_data) + if self.path_to_data: + return path.is_file() and (path.suffix in ["tsv", "txt"]) + else: + raise ValueError("No data path has been provided") + def update_model(self, model): if self.model["parameters_to_estimate"] is not None: - model.parameters_to_estimate.update(self.model["parameters_to_estimate"]) + model.parameters.update(self.model["parameters_to_estimate"]) if self.model["bounds"] is not None: model.bounds.update(Bounds(self.model["bounds"])) return model @@ -619,9 +683,11 @@ def export_config(self, export_path): with open(fr"{export_path}/config_file.yml", "w") as file: data = { "model": { - "model_name": self.model.model_name, - "parameters_to_estimate": self.model.parameters_to_estimate, - "bounds": {name: f"{bounds[0], bounds[1]}" for name, bounds in self.model.bounds.items()} + "model_name": self.model.name, + "parameters_to_estimate": self.model.parameters, + "bounds": {name: f"{bounds[0], bounds[1]}" for name, bounds + in self.model.bounds.items()}, + "args": self.model.args, }, "sds": dict(self.sds), "mc": self.mc, @@ -632,42 +698,3 @@ def export_config(self, export_path): data, file ) - - -if __name__ == "__main__": - import pandas as pd - - io_handler = IoHandler() - data_file = pd.read_csv( - r"C:\Users\legregam\Documents\Projets\PhysioFit\data\KEIO_test_data" - r"\KEIO_ROBOT6_1\KEIO_ROBOT6_1.tsv", - sep="\t" - ) - io_handler.data = data_file - io_handler.data = io_handler.data.sort_values( - "time", - ignore_index=True - ) - io_handler.get_models() - try: - sd = {"X": 0.} - for col in io_handler.data.columns[2:]: - sd.update({col: 0.5}) - except Exception: - raise - io_handler.names = io_handler.data.columns[1:].to_list() - model = io_handler.models[-1] - model.get_params() - print(model) - keywargs = { - "sd": sd, - "model": model, - "mc": True, - "iterations": 100, - "debug_mode": True, - } - io_handler.res_path = Path( - r"C:\Users\legregam\Documents\Projets\PhysioFit\data\KEIO_test_data" - r"\KEIO_ROBOT6_1") - io_handler.initialize_fitter(kwargs=keywargs) - io_handler.fitter.optimize() diff --git a/physiofit/models/__pycache__/__init__.cpython-312.pyc b/physiofit/models/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 0000000..12a2bb6 Binary files /dev/null and b/physiofit/models/__pycache__/__init__.cpython-312.pyc differ diff --git a/physiofit/models/__pycache__/base_model.cpython-312.pyc b/physiofit/models/__pycache__/base_model.cpython-312.pyc new file mode 100644 index 0000000..e2522ac Binary files /dev/null and b/physiofit/models/__pycache__/base_model.cpython-312.pyc differ diff --git a/physiofit/models/__pycache__/model_1.cpython-312.pyc b/physiofit/models/__pycache__/model_1.cpython-312.pyc new file mode 100644 index 0000000..101fdb9 Binary files /dev/null and b/physiofit/models/__pycache__/model_1.cpython-312.pyc differ diff --git a/physiofit/models/__pycache__/model_2.cpython-312.pyc b/physiofit/models/__pycache__/model_2.cpython-312.pyc new file mode 100644 index 0000000..afed17d Binary files /dev/null and b/physiofit/models/__pycache__/model_2.cpython-312.pyc differ diff --git a/physiofit/models/__pycache__/model_3.cpython-312.pyc b/physiofit/models/__pycache__/model_3.cpython-312.pyc new file mode 100644 index 0000000..66744b3 Binary files /dev/null and b/physiofit/models/__pycache__/model_3.cpython-312.pyc differ diff --git a/physiofit/models/__pycache__/model_4.cpython-312.pyc b/physiofit/models/__pycache__/model_4.cpython-312.pyc new file mode 100644 index 0000000..054772e Binary files /dev/null and b/physiofit/models/__pycache__/model_4.cpython-312.pyc differ diff --git a/physiofit/models/__pycache__/model_5.cpython-312.pyc b/physiofit/models/__pycache__/model_5.cpython-312.pyc new file mode 100644 index 0000000..b1bfa86 Binary files /dev/null and b/physiofit/models/__pycache__/model_5.cpython-312.pyc differ diff --git a/physiofit/models/base_model.py b/physiofit/models/base_model.py index 0f42b12..87f44eb 100644 --- a/physiofit/models/base_model.py +++ b/physiofit/models/base_model.py @@ -23,30 +23,32 @@ def __init__(self, data: pd.DataFrame): self.data = data self.time_vector = self.data.time.to_numpy() if "time" in self.data.columns and "experiments" in self.data.columns: - self.name_vector = self.data.drop(["time", "experiments"], axis=1).columns.to_list() + self.name_vector = self.data.drop(["time", "experiments"], + axis=1).columns.to_list() elif "time" in self.data.columns: - self.name_vector = self.data.drop(["time"], axis=1).columns.to_list() + self.name_vector = self.data.drop(["time"], + axis=1).columns.to_list() else: raise ValueError( - "Couldn't get column names from data. Is data loaded in properly and well formatted?" + "Couldn't get column names from data. Is data loaded in " + "properly and well formatted?" ) self.experimental_matrix = self.data.drop("time", axis=1).to_numpy() self.metabolites = self.name_vector[1:] - self.model_name = None - self.parameters_to_estimate = None - self.fixed_parameters = None + self.name = None + self.parameters = None + self.args = None self.bounds = None - def __repr__(self): - return f"Selected model: {self.model_name}\n" \ + return f"Selected model: {self.name}\n" \ f"Model data: \n{self.data}\n" \ f"Experimental matrix: \n{self.experimental_matrix}\n" \ f"Time vector: {self.time_vector}\n" \ f"Name vector: {self.name_vector}\n" \ f"Biomass & Metabolites: {self.metabolites}\n" \ - f"Parameters to estimate: {self.parameters_to_estimate}\n" \ - f"Fixed parameters: {self.fixed_parameters}\n" \ + f"Parameters to estimate: {self.parameters}\n" \ + f"Fixed parameters: {self.args}\n" \ f"Bounds: {self.bounds}\n" def __setattr__(self, key, value): @@ -54,12 +56,13 @@ def __setattr__(self, key, value): self.__dict__["data"] = value self.time_vector = self.data.time.to_numpy() self.name_vector = self.data.drop("time", axis=1).columns.to_list() - self.experimental_matrix = self.data.drop("time", axis=1).to_numpy() + self.experimental_matrix = self.data.drop("time", + axis=1).to_numpy() self.metabolites = self.name_vector[1:] else: self.__dict__[key] = value - @ abstractmethod + @abstractmethod def get_params(self): """ @@ -74,10 +77,10 @@ def get_params(self): @staticmethod @abstractmethod def simulate( - params_opti: list, - data_matrix: np.ndarray, + parameters: list, + data_matrix: np.ndarray | pd.DataFrame, time_vector: np.ndarray, - params_non_opti: dict | list + args: dict | list ): pass @@ -164,18 +167,21 @@ def _check_sd(key, value): if not isinstance(key, str): raise TypeError( - f"SD name field can only contain strings. Detected type {type(key)} for {key}" + "SD name field can only contain strings. " + f"Detected type {type(key)} for {key}" ) if not isinstance(value, int) and not isinstance(value, float): try: value = float(value) except Exception: raise TypeError( - f"SD value must be a number. Detected type: {type(value)} for {key}" + "SD value must be a number. " + f"Detected type: {type(value)} for {key}" ) if value <= 0: raise ValueError( - f"SD value must be superior to 0. Detected value: {value} for {key}" + "SD value must be superior to 0. " + f"Detected value: {value} for {key}" ) def __setitem__(self, key, value): @@ -191,6 +197,7 @@ def vector(self): self._vector = np.array([value for value in self.values]) return self._vector + class ModelError(Exception): pass diff --git a/physiofit/models/model_1.py b/physiofit/models/model_1.py index 2531e35..e901b5b 100644 --- a/physiofit/models/model_1.py +++ b/physiofit/models/model_1.py @@ -4,38 +4,38 @@ from __future__ import annotations import numpy as np -import pandas as pd from physiofit.models.base_model import Model, Bounds + class ChildModel(Model): def __init__(self, data): super().__init__(data) - self.model_name = "Steady-state batch model with lag phase and " \ - "degradation of metabolites " + self.name = "Steady-state batch model with lag phase and " \ + "degradation of metabolites" self.vini = 1 - self.parameters_to_estimate = None - self.fixed_parameters = None + self.parameters = None + self.args = None def get_params(self): - self.parameters_to_estimate = { - "X_0" : self.vini, - "growth_rate" : self.vini, - "t_lag" : self.vini + self.parameters = { + "X_0": self.vini, + "growth_rate": self.vini, + "t_lag": self.vini } self.bounds = Bounds( X_0=(1e-3, 10), growth_rate=(1e-3, 3), - t_lag = (0, 0.5*self.time_vector.max()) + t_lag=(1e-6, 0.5 * self.time_vector.max()) ) for metabolite in self.metabolites: - self.parameters_to_estimate.update( + self.parameters.update( { - f"{metabolite}_q" : self.vini, - f"{metabolite}_M0" : self.vini + f"{metabolite}_q": self.vini, + f"{metabolite}_M0": self.vini } ) self.bounds.update( @@ -45,61 +45,63 @@ def get_params(self): } ) - self.fixed_parameters = {"Degradation": { + self.args = {"Degradation constants": { met: 0 for met in self.metabolites - } + } } @staticmethod def simulate( - params_opti: list, + parameters: list, data_matrix: np.ndarray, time_vector: np.ndarray, - params_non_opti: dict + args: dict ): # Get end shape simulated_matrix = np.empty_like(data_matrix) + # print("simulated_matrix", simulated_matrix) + # print("simulated_matrix.shape", simulated_matrix.shape) # Get initial params - x_0 = params_opti[0] - mu = params_opti[1] - t_lag = params_opti[2] + x_0, mu, t_lag = parameters[:3] # We get indices in time vector where time < t_lag - idx = np.nonzero(time_vector < t_lag) + mask = (time_vector < t_lag) + # print("mask", mask) + + # Get time vector from length of t_lag to end + time_vector_lag = time_vector[mask] + # print("len(time_vector_lag)", len(time_vector_lag)) + # print("time_vector_lag", time_vector_lag) + time_vector_growth = time_vector[np.logical_not(mask)] + # print("len(time_vector_growth)", len(time_vector_growth)) + # print("time_vector_growth", time_vector_growth) + time_vector_diff = time_vector_growth - t_lag + + # optimize some calculations + exp_mu_t_lag = np.exp(mu * time_vector_diff) # Fill at those indices with x_0 - x_t_lag = np.full((len(idx) - 1,), x_0) + x_t_lag = np.repeat(x_0, len(time_vector_lag)) # The rest of the biomass points are calculated as usual - mult_by_time = x_0 * np.exp(mu * (time_vector[len(idx) - 1:] - t_lag)) - simulated_matrix[:, 0] = np.concatenate((x_t_lag, mult_by_time), - axis=None) - fixed_params = [value for value in params_non_opti["Degradation"].values()] - - for i in range(1, int(len(params_opti) / 2)): - q = params_opti[i * 2 + 1] - m_0 = params_opti[i * 2 + 2] - k = fixed_params[i - 1] - m_t_lag = np.full((len(idx) - 1,), m_0) - mult_by_time = q * (x_0 / (mu + k)) * (np.exp( - mu * (time_vector - t_lag) - ) - np.exp(-k * (time_vector - t_lag))) + (m_0 * np.exp( - -k * time_vector) - ) - simulated_matrix[:, i] = np.concatenate( - (m_t_lag, mult_by_time), - axis=None - ) + mult_by_time = x_0 * exp_mu_t_lag - return simulated_matrix + # Concatenate both vectors and transfer to X_t column of the + # simulated matrix + simulated_matrix[:, 0] = np.concatenate((x_t_lag, mult_by_time)) + # Get extra arguments + arg_values = [value for value in args[("Degradation " + "constants")].values()] -if __name__ == "__main__": - model = ChildModel( - pd.read_csv( - r"C:\Users\legregam\Documents\Projets\PhysioFit\data" - r"\KEIO_test_data\KEIO_ROBOT6_1\KEIO_ROBOT6_1.tsv", - sep='\t') - ) - print(type(model)) + for i in range(1, len(parameters) // 2): + q, m_0 = parameters[i * 2 + 1:i * 2 + 3] + k = arg_values[i - 1] + m_t_lag = m_0 * np.exp(-k * time_vector_lag) + mult_by_time = q * (x_0 / (mu + k)) * (exp_mu_t_lag - np.exp( + -k * time_vector_diff)) + m_0 * np.exp(-k * + time_vector_growth) + simulated_matrix[:, i] = np.concatenate((m_t_lag, mult_by_time)) + + return simulated_matrix diff --git a/physiofit/models/model_2.py b/physiofit/models/model_2.py index a01c717..5ad3bb0 100644 --- a/physiofit/models/model_2.py +++ b/physiofit/models/model_2.py @@ -13,28 +13,28 @@ class ChildModel(Model): def __init__(self, data): super().__init__(data) - self.model_name = "Steady-state batch model with lag phase" + self.name = "Steady-state batch model with lag phase" self.vini = 1 - self.parameters_to_estimate = None - self.fixed_parameters = None + self.parameters = None + self.args = None def get_params(self): - self.parameters_to_estimate = { - "X_0" : self.vini, - "growth_rate" : self.vini, - "t_lag" : self.vini + self.parameters = { + "X_0": self.vini, + "growth_rate": self.vini, + "t_lag": self.vini } self.bounds = Bounds({ "X_0": (1e-3, 10), "growth_rate": (1e-3, 3), - "t_lag": (0, 0.5 * self.time_vector.max()), + "t_lag": (1e-6, 0.5 * self.time_vector.max()), }) for metabolite in self.metabolites: - self.parameters_to_estimate.update( + self.parameters.update( { - f"{metabolite}_q" : 1, - f"{metabolite}_M0" : 1 + f"{metabolite}_q": 1, + f"{metabolite}_M0": 1 } ) self.bounds.update( @@ -46,42 +46,39 @@ def get_params(self): @staticmethod def simulate( - params_opti: list, + parameters: list, data_matrix: np.ndarray, time_vector: np.ndarray, - params_non_opti: dict | list + args: dict | list ): # Get end shape simulated_matrix = np.empty_like(data_matrix) - x_0 = params_opti[0] - mu = params_opti[1] - t_lag = params_opti[2] + x_0, mu, t_lag = parameters[:3] # We get indices in time vector where time < t_lag - idx = np.nonzero(time_vector < t_lag) + idx = np.nonzero(time_vector < t_lag)[0] # Fill at those indices with x_0 - x_t_lag = np.full((len(idx) - 1,), x_0) + x_t_lag = np.full(shape=(len(idx)), fill_value=x_0) + + # Get time vector from length of t_lag to end + time_vector = time_vector[len(idx):] # The rest of the biomass points are calculated as usual - mult_by_time = x_0 * np.exp(mu * (time_vector[len(idx) - 1:] - t_lag)) + mult_by_time = x_0 * np.exp(mu * (time_vector - t_lag)) # Concatenate both vectors and transfer to X_t column of the # simulated matrix - simulated_matrix[:, 0] = np.concatenate( - (x_t_lag, mult_by_time), - axis=None - ) + simulated_matrix[:, 0] = np.concatenate((x_t_lag, mult_by_time)) + + # optimize some calculations exp_mu_t_lag = np.exp(mu * (time_vector - t_lag)) - 1 - for i in range(1, int(len(params_opti) / 2)): - q = params_opti[i * 2 + 1] - m_0 = params_opti[i * 2 + 2] - m_t_lag = np.full((len(idx) - 1,), m_0) + for i in range(1, int(len(parameters) / 2)): + q = parameters[i * 2 + 1] + m_0 = parameters[i * 2 + 2] + m_t_lag = np.full(shape=(len(idx)), fill_value=m_0) mult_by_time = q * (x_0 / mu) * exp_mu_t_lag + m_0 - simulated_matrix[:, i] = np.concatenate( - (m_t_lag, mult_by_time), - axis=None - ) + simulated_matrix[:, i] = np.concatenate((m_t_lag, mult_by_time)) return simulated_matrix diff --git a/physiofit/models/model_3.py b/physiofit/models/model_3.py index 110cf16..7dac3cf 100644 --- a/physiofit/models/model_3.py +++ b/physiofit/models/model_3.py @@ -13,18 +13,19 @@ class ChildModel(Model): def __init__(self, data): super().__init__(data) - self.model_name = "Steady-state batch model with degradation of metabolites" + self.name = ("Steady-state batch model with degradation of " + "metabolites") self.vini = 1 - self.parameters_to_estimate = None - self.fixed_parameters = None + self.parameters = None + self.args = None def get_params(self): - self.parameters_to_estimate = { - "X_0" : self.vini, - "growth_rate" : self.vini + self.parameters = { + "X_0": self.vini, + "growth_rate": self.vini } - self.fixed_parameters = {"Degradation": { + self.args = {"Degradation constant": { met: 0 for met in self.metabolites } } @@ -33,7 +34,7 @@ def get_params(self): "growth_rate": (1e-3, 3), }) for metabolite in self.metabolites: - self.parameters_to_estimate.update( + self.parameters.update( { f"{metabolite}_q": self.vini, f"{metabolite}_M0": self.vini @@ -45,37 +46,38 @@ def get_params(self): f"{metabolite}_M0": (1e-6, 50) } ) - self.fixed_parameters = {"Degradation": { + self.args = {"Degradation constants": { met: 0 for met in self.metabolites - } + } } @staticmethod def simulate( - params_opti: list, + parameters: list, data_matrix: np.ndarray, time_vector: np.ndarray, - params_non_opti: dict | list + args: dict | list ): # Get end shape simulated_matrix = np.empty_like(data_matrix) # Get initial params - x_0 = params_opti[0] - mu = params_opti[1] + x_0 = parameters[0] + mu = parameters[1] # Get X_0 values exp_mu_t = np.exp(mu * time_vector) simulated_matrix[:, 0] = x_0 * exp_mu_t - fixed_params = [value for value in params_non_opti["Degradation"].values()] + fixed_params = [value for value in args[("Degradation " + "constants")].values()] - for i in range(1, int(len(params_opti) / 2)): - q = params_opti[i * 2] - m_0 = params_opti[i * 2 + 1] + for i in range(1, int(len(parameters) / 2)): + q = parameters[i * 2] + m_0 = parameters[i * 2 + 1] k = fixed_params[i - 1] exp_k_t = np.exp(-k * time_vector) - simulated_matrix[:, i] = q * (x_0 / (mu + k)) \ - * (exp_mu_t - exp_k_t) \ - + m_0 * exp_k_t + simulated_matrix[:, i] = (q * (x_0 / (mu + k)) * (exp_mu_t + - exp_k_t) + + m_0 * exp_k_t) return simulated_matrix diff --git a/physiofit/models/model_4.py b/physiofit/models/model_4.py index af82a4d..7faf6d9 100644 --- a/physiofit/models/model_4.py +++ b/physiofit/models/model_4.py @@ -13,16 +13,16 @@ class ChildModel(Model): def __init__(self, data): super().__init__(data) - self.model_name = "Steady-state batch model" + self.name = "Steady-state batch model" self.vini = 1 - self.parameters_to_estimate = None - self.fixed_parameters = None + self.parameters = None + self.args = None def get_params(self): - self.parameters_to_estimate = { - "X_0" : self.vini, - "growth_rate" : self.vini + self.parameters = { + "X_0": self.vini, + "growth_rate": self.vini } self.bounds = Bounds( { @@ -31,10 +31,10 @@ def get_params(self): } ) for metabolite in self.metabolites: - self.parameters_to_estimate.update( + self.parameters.update( { - f"{metabolite}_q" : self.vini, - f"{metabolite}_M0" : self.vini + f"{metabolite}_q": self.vini, + f"{metabolite}_M0": self.vini } ) self.bounds.update( @@ -46,22 +46,22 @@ def get_params(self): @staticmethod def simulate( - params_opti: list, + parameters: list, data_matrix: np.ndarray, time_vector: np.ndarray, - params_non_opti: dict | list + args: dict | list ): # Get end shape simulated_matrix = np.empty_like(data_matrix) - x_0 = params_opti[0] - mu = params_opti[1] + + # Get parameters + x_0, mu = parameters[:2] + + # Build matrix exp_mu_t = np.exp(mu * time_vector) simulated_matrix[:, 0] = x_0 * exp_mu_t - for i in range(1, int(len(params_opti) / 2)): - q = params_opti[i * 2] - m_0 = params_opti[i * 2 + 1] - simulated_matrix[:, i] = q * (x_0 / mu) \ - * (exp_mu_t - 1) \ - + m_0 + for i in range(1, len(parameters) // 2): + q, m_0 = parameters[i * 2:i * 2 + 2] + simulated_matrix[:, i] = q * (x_0 / mu) * (exp_mu_t - 1) + m_0 return simulated_matrix diff --git a/physiofit/models/model_5.py b/physiofit/models/model_5.py index 83f6cfa..7236892 100644 --- a/physiofit/models/model_5.py +++ b/physiofit/models/model_5.py @@ -8,30 +8,31 @@ from physiofit.models.base_model import Model, Bounds + class ChildModel(Model): def __init__(self, data): super().__init__(data) - self.model_name = "Dynamic Monod model (1 substrate, 1 product)" + self.name = "Dynamic Monod model (1 substrate, 1 product)" self.vini = 1 - self.parameters_to_estimate = None + self.parameters = None def get_params(self): - self.parameters_to_estimate = { + self.parameters = { "X_0": self.vini, "y_BM": self.vini } self.bounds = Bounds( - X_0=(1e-3, 10), - y_BM=(1e-3, 3) + X_0=(1e-3, 1), + y_BM=(1e-3, 1) ) for metabolite in self.metabolites: if metabolite.startswith("S_"): - self.parameters_to_estimate.update( + self.parameters.update( { f"{metabolite}_km": self.vini, f"{metabolite}_qsmax": self.vini, @@ -41,15 +42,15 @@ def get_params(self): self.bounds.update( { f"{metabolite}_km": (1e-6, 100), - f"{metabolite}_qsmax": (1e-6, 100), + f"{metabolite}_qsmax": (1e-6, 20), f"{metabolite}_s_0": (1e-6, 100) } ) break - + for metabolite in self.metabolites: if metabolite.startswith("P_"): - self.parameters_to_estimate.update( + self.parameters.update( { f"{metabolite}_y_P": self.vini, f"{metabolite}_p_0": 100 @@ -58,45 +59,36 @@ def get_params(self): ) self.bounds.update( { - f"{metabolite}_y_P": (1e-6, 100), + f"{metabolite}_y_P": (1e-6, 2), f"{metabolite}_p_0": (1e-6, 100) } ) break - if len(self.parameters_to_estimate) != 7: + if len(self.parameters) != 7: raise ValueError( - "This model expects 2 metabolites in the data file (1 substrate with name starting with 'S_' and 1 " - "product with name starting with 'P_')." + "This model expects 2 metabolites in the data file (1 " + "substrate with name starting with 'S_' and 1 product with " + "name starting with 'P_')." ) - @staticmethod def simulate( - params_opti: list, + parameters: list, data_matrix: np.ndarray, time_vector: np.ndarray, - params_non_opti: dict + args: dict ): # Get parameters - x_0 = params_opti[0] - y_BM = params_opti[1] - km = params_opti[2] - qsmax = params_opti[3] - s_0 = params_opti[4] - y_P = params_opti[5] - p_0 = params_opti[6] - params = (y_BM, y_P, km, qsmax) + x_0, y_BM, km, qsmax, s_0, y_P, p_0 = parameters # initialize variables at t=0 state = [x_0, s_0, p_0] - + def calculate_derivative(t, state, y_BM, y_P, km, qsmax): - # get substrate and biomass concentrations - s_t = state[0] - x_t = state[1] + x_t, s_t = state[0], state[1] # calculate fluxes qs_t = qsmax * (s_t / (km + s_t)) @@ -114,25 +106,27 @@ def calculate_derivative(t, state, y_BM, y_P, km, qsmax): sol = solve_ivp( fun=calculate_derivative, t_span=(np.min(time_vector), np.max(time_vector)), - y0 = state, - args=params, + y0=state, + args=(y_BM, y_P, km, qsmax), method="LSODA", - t_eval = list(time_vector) + t_eval=list(time_vector) ) return sol.y.T -if __name__ == "__main__": +if __name__ == "__main__": from physiofit.base.io import IoHandler io = IoHandler() - data = io.read_data(r"C:\Users\legregam\PycharmProjects\PhysioFit\data\KEIO_test_data\ode_test\KEIO_ROBOT6_1.tsv") + data = io.read_data( + r"C:\Users\legregam\PycharmProjects\PhysioFit\data\KEIO_test_data" + r"\ode_test\KEIO_ROBOT6_1.tsv") data = data.sort_values("time") model = ChildModel(data) model.get_params() - params = [param for param in model.parameters_to_estimate.values()] + params = [param for param in model.parameters.values()] sol = ChildModel.simulate( params, model.data, diff --git a/physiofit/tests/conftest.py b/physiofit/tests/conftest.py index b10201e..ce7f702 100644 --- a/physiofit/tests/conftest.py +++ b/physiofit/tests/conftest.py @@ -1,4 +1,3 @@ - """ Configuration variables for the tests @@ -7,48 +6,130 @@ parameter for all test functions. The test's parameter name must be the same as the fixture function's name. """ - -import os - +import numpy as np import pandas as pd import pytest -from numpy import nan -from physiofit.base.io import IoHandler + from physiofit.models.base_model import StandardDevs -@pytest.fixture -def data(): - """Test data to use in tests (taken from Bergès et al., 2021 --> KEIO_ROBOT1_1)""" - return pd.DataFrame.from_dict( +@pytest.fixture +def placeholder_data(): + return pd.DataFrame( { - "time": [0, 1.18, 2.27, 3.13, 3.77, 4.42, 4.82, 0.67, 1.72, 2.8, 3.63, 4.27, 4.88], - "X": [0.03, 0.05, 0.08, 0.13, 0.18, 0.24, 0.34, nan, nan, nan, nan, nan, nan], - "Glucose": [nan, nan, nan, nan, nan, nan, nan, 14, 15.30, 13.68, 12.81, 12.15, 10.93], - "Acetate": [nan, nan, nan, nan, nan, nan, nan, 0.01, 0.33, 0.72, 1.17, 1.63, 2.14] + "time": np.arange(6, step=0.2), + "X": np.arange(6, step=0.2), + "Glucose": np.arange(6, step=0.2), + "Acetate": np.arange(6, step=0.2), + "Glutamate": np.arange(6, step=0.2), } ) -# time X Glc Ace -# 0 0.031752 NA NA -# 1.18888888888889 0.05292 NA NA -# 2.27694444444444 0.084672 NA NA -# 3.12833333333333 0.134568 NA NA -# 3.77138888888889 0.175392 NA NA -# 4.41555555555556 0.244944 NA NA -# 4.82277777777778 0.337176 NA NA -# 0.0666666666666667 NA 14.0042771787617 0.0130592124021829 -# 1.71666666666667 NA 15.3032563161238 0.325073443768164 -# 2.8 NA 13.6751055268759 0.722570137805818 -# 3.63333333333333 NA 12.8110643342243 1.16940283499877 -# 4.26666666666667 NA 12.1520761714542 1.62777664140305 -# 4.88333333333333 NA 10.9297935900362 2.13639255382759 @pytest.fixture -def sds(): +def base_test_data(): + + return pd.DataFrame.from_dict( + {'time': {0: 0.0, 1: 0.2, 2: 0.4, 3: 0.6000000000000001, 4: 0.8, + 5: 1.0, 6: 1.2000000000000002, 7: 1.4000000000000001, 8: 1.6, + 9: 1.8, 10: 2.0, 11: 2.2, 12: 2.4000000000000004, 13: 2.6, + 14: 2.8000000000000003, 15: 3.0, 16: 3.2, + 17: 3.4000000000000004, 18: 3.6, 19: 3.8000000000000003, + 20: 4.0, 21: 4.2, 22: 4.4, 23: 4.6000000000000005, + 24: 4.800000000000001, 25: 5.0, 26: 5.2, 27: 5.4, + 28: 5.6000000000000005, 29: 5.800000000000001}, + 'X': {0: 0.02, 1: 0.023470217419836206, 2: 0.027542555286719145, + 3: 0.03232148804385787, 4: 0.037929617586099036, + 5: 0.044510818569849356, 6: 0.052233929468462365, + 7: 0.06129708406586005, 8: 0.07193279451138565, + 9: 0.08441391633993106, 10: 0.0990606484879023, + 11: 0.1162487478880518, 12: 0.13641916938581505, + 13: 0.16008937828592706, 14: 0.18786662574885568, + 15: 0.2204635276128321, 16: 0.25871634631086166, + 17: 0.3036064448990781, 18: 0.3562854635922441, + 19: 0.4181048647018553, 20: 0.49065060394218707, + 21: 0.5757838175848538, 22: 0.6756885692769915, + 23: 0.7929278814514524, 24: 0.9305094887957849, + 25: 1.0919630006628847, 26: 1.281430451998733, + 27: 1.5037725658404621, 28: 1.7646934535130303, + 29: 2.070886951665622}, + 'Glucose': {0: 20.0, 1: 19.96529782580164, 2: 19.92457444713281, + 3: 19.876785119561422, 4: 19.82070382413901, + 5: 19.754891814301505, 6: 19.677660705315375, + 7: 19.587029159341398, 8: 19.480672054886142, + 9: 19.35586083660069, 10: 19.209393515120976, + 11: 19.03751252111948, 12: 18.83580830614185, + 13: 18.59910621714073, 14: 18.32133374251144, + 15: 17.99536472387168, 16: 17.612836536891383, + 17: 17.163935551009217, 18: 16.63714536407756, + 19: 16.018951352981446, 20: 15.293493960578129, + 21: 14.442161824151462, 22: 13.443114307230086, + 23: 12.270721185485478, 24: 10.894905112042153, + 25: 9.280369993371155, 26: 7.385695480012673, + 27: 5.16227434159538, 28: 2.5530654648697, + 29: -0.5088695166562189}, + 'Acetate': {0: 0.01, 1: 0.02301331532438577, 2: 0.03828458232519679, + 3: 0.05620558016446701, 4: 0.07723606594787137, + 5: 0.10191556963693509, 6: 0.13087723550673386, + 7: 0.1648640652469752, 8: 0.2047479794176962, + 9: 0.25155218627474146, 10: 0.3064774318296336, + 11: 0.37093280458019423, 12: 0.4465718851968064, + 13: 0.5353351685722265, 14: 0.6394998465582088, + 15: 0.7617382285481203, 16: 0.9051862986657312, + 17: 1.0735241683715429, 18: 1.2710704884709152, + 19: 1.5028932426319574, 20: 1.7749397647832015, + 21: 2.094189315943201, 22: 2.4688321347887174, + 23: 2.908479555442946, 24: 3.424410582984193, + 25: 4.0298612524858175, 26: 4.740364194995248, + 27: 5.574147121901733, 28: 6.552600450673863, + 29: 7.700826068746083}, + 'Glutamate': {0: 0.01, 1: 0.018675543549590515, + 2: 0.02885638821679786, 3: 0.04080372010964467, + 4: 0.05482404396524758, 5: 0.07127704642462339, + 6: 0.0905848236711559, 7: 0.11324271016465011, + 8: 0.13983198627846413, 9: 0.17103479084982764, + 10: 0.20765162121975575, 11: 0.25062186972012945, + 12: 0.30104792346453757, 13: 0.3602234457148176, + 14: 0.4296665643721392, 15: 0.5111588190320802, + 16: 0.6067908657771541, 17: 0.7190161122476952, + 18: 0.8507136589806101, 19: 1.0052621617546382, + 20: 1.1866265098554676, 21: 1.3994595439621342, + 22: 1.6492214231924784, 23: 1.9423197036286308, + 24: 2.2862737219894615, 25: 2.689907501657211, + 26: 3.1635761299968315, 27: 3.719431414601155, + 28: 4.371733633782575, 29: 5.1372173791640545}} + ) + + +@pytest.fixture +def parameters(): + return { + "t_lag": 1.4, + "X_0": 0.02, + "growth_rate": 0.8, + "Glucose_q": -8, + "Glucose_M0": 20, + "Acetate_q": 3, + "Acetate_M0": 0.01, + "Glutamate_q": 2, + "Glutamate_M0": 0.01 + } + + +@pytest.fixture +def monod_model_sds(): return StandardDevs( - X = 0.2, - Glucose = 0.5, - Acetate = 0.5 + X=0.2, + S_substrate=0.2, + P_product=0.2 ) + +@pytest.fixture +def sds(): + return StandardDevs( + X=0.2, + Glucose=0.2, + Acetate=0.2, + Glutamate=0.2 + ) diff --git a/physiofit/tests/test_base.py b/physiofit/tests/test_base.py index 97074ee..382f2c4 100644 --- a/physiofit/tests/test_base.py +++ b/physiofit/tests/test_base.py @@ -1,44 +1,49 @@ """ Test the creation and use of the PhysioFitter """ +import logging + import numpy as np import pandas as pd import pytest import physiofit +logging.getLogger("physiofit").setLevel(logging.ERROR) + -def test_physiofitter(data, sds): +def test_physiofitter(base_test_data): """ - Test that the model and PhysioFitter can be safely instanciated from IoHandler + Test that the model and PhysioFitter can be safely instantiated from + IoHandler """ io = physiofit.base.io.IoHandler() - model = io.select_model("Steady-state batch model", data) + model = io.select_model("Steady-state batch model", base_test_data) assert isinstance(model, physiofit.models.base_model.Model) model.get_params() fitter = io.initialize_fitter( model.data, model=model, - sd=sds, - debug_mode=True + sd=0.2, + debug_mode=False ) assert isinstance(fitter, physiofit.base.fitter.PhysioFitter) -def test_simulation(data, sds): +def test_simulation(base_test_data): io = physiofit.base.io.IoHandler() - model = io.select_model("Steady-state batch model", data) + model = io.select_model("Steady-state batch model", base_test_data) model.get_params() sim_mat = model.simulate( - [param for param in model.parameters_to_estimate.values()], + [param for param in model.parameters.values()], model.experimental_matrix, model.time_vector, - model.fixed_parameters + model.args ) assert isinstance(sim_mat, np.ndarray) -def test_wrong_entry_for_model_data(data, sds): +def test_wrong_entry_for_model_data(base_test_data): with pytest.raises(AttributeError): io = physiofit.base.io.IoHandler() model = io.select_model("Steady-state batch model", None) @@ -46,7 +51,7 @@ def test_wrong_entry_for_model_data(data, sds): model = io.select_model( "Steady-state batch model", np.array( - [[0, 1, 2],[0, 1, 2]] + [[0, 1, 2], [0, 1, 2]] ) ) with pytest.raises(AttributeError): @@ -54,57 +59,62 @@ def test_wrong_entry_for_model_data(data, sds): "Steady-state batch model", "Hello world this is an error" ) + return model -def test_optimization_process(data, sds): +def test_optimization_process(base_test_data): io = physiofit.base.io.IoHandler() - model = io.select_model("Steady-state batch model", data) + model = io.select_model("Steady-state batch model", base_test_data) model.get_params() fitter = io.initialize_fitter( model.data, model=model, - sd=sds, - debug_mode=True + sd=0.2, + debug_mode=False ) fitter.optimize() assert isinstance(fitter.simulated_data, pd.DataFrame) for col in ["X", "Glucose", "Acetate"]: assert col in fitter.simulated_data.columns -def test_monte_carlo(data, sds): + +def test_monte_carlo(base_test_data): io = physiofit.base.io.IoHandler() - model = io.select_model("Steady-state batch model", data) + model = io.select_model("Steady-state batch model", base_test_data) model.get_params() fitter = io.initialize_fitter( model.data, model=model, - sd=sds, - debug_mode=True + sd=0.2, + debug_mode=False ) fitter.optimize() fitter.monte_carlo_analysis() assert hasattr(fitter, "matrices_ci") assert isinstance(fitter.matrices_ci["lower_ci"], np.ndarray) assert isinstance(fitter.matrices_ci["higher_ci"], np.ndarray) - assert np.subtract(fitter.matrices_ci["higher_ci"], fitter.matrices_ci["lower_ci"]).all() > 0 + assert np.subtract(fitter.matrices_ci["higher_ci"], + fitter.matrices_ci["lower_ci"]).all() > 0 assert hasattr(fitter, "parameter_stats") assert isinstance(fitter.parameter_stats, dict) -def test_that_simulated_and_experimental_matrices_are_close(data, sds): + +def test_that_simulated_and_experimental_matrices_are_close(base_test_data): io = physiofit.base.io.IoHandler() - model = io.select_model("Steady-state batch model", data) + model = io.select_model("Steady-state batch model", base_test_data) model.get_params() fitter = io.initialize_fitter( model.data, model=model, - sd=sds, - debug_mode=True + sd=0.2, + debug_mode=False ) fitter.optimize() + print(base_test_data) + print(fitter.simulated_data) assert np.allclose( a=fitter.experimental_matrix, - b=fitter.simulated_data, - rtol=1, + b=fitter.simulated_matrix, + rtol=1e-3, equal_nan=True ) - diff --git a/physiofit/tests/test_model_1.py b/physiofit/tests/test_model_1.py new file mode 100644 index 0000000..e6143b1 --- /dev/null +++ b/physiofit/tests/test_model_1.py @@ -0,0 +1,147 @@ +import logging + +import numpy as np +import pandas as pd +import pytest + +import physiofit +import physiofit.base.io + +logging.getLogger("physiofit").setLevel(logging.ERROR) + + +@pytest.fixture +def model_1_data(): + """ Test data to use in tests for the model_1: Steady-state batch model + with lag phase and degradation of metabolites. Data is simulated using + synthetic parameters""" + + return pd.DataFrame( + {'time': {0: 0.0, 1: 0.2, 2: 0.4, 3: 0.6000000000000001, 4: 0.8, + 5: 1.0, 6: 1.2000000000000002, 7: 1.4000000000000001, 8: 1.6, + 9: 1.8, 10: 2.0, 11: 2.2, 12: 2.4000000000000004, 13: 2.6, + 14: 2.8000000000000003, 15: 3.0, 16: 3.2, + 17: 3.4000000000000004, 18: 3.6, 19: 3.8000000000000003, + 20: 4.0, 21: 4.2, 22: 4.4, 23: 4.6000000000000005, + 24: 4.800000000000001, 25: 5.0, 26: 5.2, 27: 5.4, + 28: 5.6000000000000005, 29: 5.800000000000001}, + 'X': {0: 0.02, 1: 0.02, 2: 0.02, 3: 0.02, 4: 0.02, 5: 0.02, 6: 0.02, + 7: 0.020000000000000004, 8: 0.02347021741983621, + 9: 0.027542555286719145, 10: 0.03232148804385787, + 11: 0.037929617586099036, 12: 0.04451081856984937, + 13: 0.052233929468462365, 14: 0.061297084065860055, + 15: 0.07193279451138565, 16: 0.08441391633993109, + 17: 0.09906064848790236, 18: 0.1162487478880518, + 19: 0.13641916938581505, 20: 0.16008937828592706, + 21: 0.18786662574885568, 22: 0.2204635276128321, + 23: 0.25871634631086166, 24: 0.3036064448990781, + 25: 0.3562854635922441, 26: 0.4181048647018553, + 27: 0.49065060394218707, 28: 0.5757838175848543, + 29: 0.6756885692769915}, + 'Glucose': {0: 20.0, 1: 20.0, 2: 20.0, 3: 20.0, 4: 20.0, 5: 20.0, + 6: 20.0, 7: 20.0, 8: 19.96529782580164, + 9: 19.92457444713281, 10: 19.876785119561422, + 11: 19.82070382413901, 12: 19.754891814301505, + 13: 19.677660705315375, 14: 19.587029159341398, + 15: 19.480672054886142, 16: 19.35586083660069, + 17: 19.209393515120976, 18: 19.03751252111948, + 19: 18.83580830614185, 20: 18.59910621714073, + 21: 18.32133374251144, 22: 17.99536472387168, + 23: 17.612836536891383, 24: 17.163935551009217, + 25: 16.63714536407756, 26: 16.018951352981446, + 27: 15.293493960578129, 28: 14.442161824151459, + 29: 13.443114307230086}, + 'Acetate': {0: 0.01, 1: 0.01, 2: 0.01, 3: 0.01, 4: 0.01, 5: 0.01, + 6: 0.01, 7: 0.010000000000000018, 8: 0.02301331532438579, + 9: 0.03828458232519679, 10: 0.05620558016446701, + 11: 0.07723606594787139, 12: 0.10191556963693511, + 13: 0.13087723550673386, 14: 0.16486406524697522, + 15: 0.2047479794176962, 16: 0.2515521862747415, + 17: 0.30647743182963383, 18: 0.37093280458019423, + 19: 0.4465718851968064, 20: 0.5353351685722265, + 21: 0.6394998465582088, 22: 0.7617382285481203, + 23: 0.9051862986657312, 24: 1.0735241683715429, + 25: 1.2710704884709152, 26: 1.5028932426319574, + 27: 1.7749397647832015, 28: 2.0941893159432032, + 29: 2.4688321347887174}, + 'Glutamate': {0: 0.01, 1: 0.008187307530779819, + 2: 0.006703200460356393, 3: 0.005488116360940264, + 4: 0.004493289641172216, 5: 0.0036787944117144234, + 6: 0.0030119421191220205, 7: 0.0024659696394160745, + 8: 0.00990296780025386, 9: 0.017359827066667374, + 10: 0.025070303190118725, 11: 0.03326696303223957, + 12: 0.04218854591780582, 13: 0.05208723048238592, + 14: 0.06323603927850543, 15: 0.07593660862978147, + 16: 0.09052755379033849, 17: 0.10739366916979227, + 18: 0.12697622024758973, 19: 0.14978460807414698, + 20: 0.1764097194129322, 21: 0.20753931631970624, + 22: 0.24397586922733605, 23: 0.28665729861444006, + 24: 0.33668116358145866, 25: 0.39533292296254446, + 26: 0.46411899816057645, 27: 0.5448054893254399, + 28: 0.6394635409132144, 29: 0.7505225227462651}} + ) + + +def test_model_1_estimation( + model_1_data: pd.DataFrame, + sds: physiofit.models.base_model.StandardDevs +): + io = physiofit.base.io.IoHandler() + model = io.select_model( + name="Steady-state batch model with lag phase and " + "degradation of metabolites", + data=model_1_data + ) + model.get_params() + model.args = {"Degradation constants": {"Glucose": 0, "Acetate": 0, + "Glutamine": 1} + } + fitter = io.initialize_fitter( + data=model.data, + model=model, + sd=sds, + debug_mode=False + ) + fitter.optimize() + + assert np.allclose( + a=fitter.parameter_stats["optimal"], + b=[0.02, 0.8, 1.4, -8, 20, 3, 0.01, 2, 0.01], + rtol=1e-3 + ) + + +def test_model_1_simulation( + placeholder_data, + parameters, + model_1_data +): + io = physiofit.base.io.IoHandler() + model = io.select_model( + name="Steady-state batch model with lag phase and degradation of " + "metabolites", + data=placeholder_data + ) + model.get_params() + model.parameters.update(parameters) + model.args = {"Degradation constants": {"Glucose": 0, "Acetate": 0, + "Glutamine": 1} + } + sim_data = model.simulate( + list(model.parameters.values()), + model.data.drop("time", axis=1), + model.time_vector, + model.args + ) + df = pd.DataFrame( + data=sim_data, + index=model.time_vector, + columns=model.name_vector + ) + df.index.name = "time" + + pd.testing.assert_frame_equal( + df.reset_index(), + model_1_data, + atol=1e-6 + ) diff --git a/physiofit/tests/test_model_2.py b/physiofit/tests/test_model_2.py new file mode 100644 index 0000000..fcad221 --- /dev/null +++ b/physiofit/tests/test_model_2.py @@ -0,0 +1,134 @@ +import logging + +import numpy as np +import pandas as pd +import pytest + +import physiofit +import physiofit.base.io + +logging.getLogger("physiofit").setLevel(logging.ERROR) + + +@pytest.fixture +def model_2_data(): + + return pd.DataFrame( + {'time': {0: 0.0, 1: 0.2, 2: 0.4, 3: 0.6000000000000001, 4: 0.8, + 5: 1.0, 6: 1.2000000000000002, 7: 1.4000000000000001, 8: 1.6, + 9: 1.8, 10: 2.0, 11: 2.2, 12: 2.4000000000000004, 13: 2.6, + 14: 2.8000000000000003, 15: 3.0, 16: 3.2, + 17: 3.4000000000000004, 18: 3.6, 19: 3.8000000000000003, + 20: 4.0, 21: 4.2, 22: 4.4, 23: 4.6000000000000005, + 24: 4.800000000000001, 25: 5.0, 26: 5.2, 27: 5.4, + 28: 5.6000000000000005, 29: 5.800000000000001}, + 'X': {0: 0.02, 1: 0.02, 2: 0.02, 3: 0.02, 4: 0.02, 5: 0.02, 6: 0.02, + 7: 0.020000000000000004, 8: 0.02347021741983621, + 9: 0.027542555286719145, 10: 0.03232148804385787, + 11: 0.037929617586099036, 12: 0.04451081856984937, + 13: 0.052233929468462365, 14: 0.061297084065860055, + 15: 0.07193279451138565, 16: 0.08441391633993109, + 17: 0.09906064848790236, 18: 0.1162487478880518, + 19: 0.13641916938581505, 20: 0.16008937828592706, + 21: 0.18786662574885568, 22: 0.2204635276128321, + 23: 0.25871634631086166, 24: 0.3036064448990781, + 25: 0.3562854635922441, 26: 0.4181048647018553, + 27: 0.49065060394218707, 28: 0.5757838175848543, + 29: 0.6756885692769915}, + 'Glucose': {0: 20.0, 1: 20.0, 2: 20.0, 3: 20.0, 4: 20.0, 5: 20.0, + 6: 20.0, 7: 20.0, 8: 19.96529782580164, + 9: 19.92457444713281, 10: 19.876785119561422, + 11: 19.82070382413901, 12: 19.754891814301505, + 13: 19.677660705315375, 14: 19.587029159341398, + 15: 19.480672054886142, 16: 19.35586083660069, + 17: 19.209393515120976, 18: 19.03751252111948, + 19: 18.83580830614185, 20: 18.59910621714073, + 21: 18.32133374251144, 22: 17.99536472387168, + 23: 17.612836536891383, 24: 17.163935551009217, + 25: 16.63714536407756, 26: 16.018951352981446, + 27: 15.293493960578129, 28: 14.442161824151459, + 29: 13.443114307230086}, + 'Acetate': {0: 0.01, 1: 0.01, 2: 0.01, 3: 0.01, 4: 0.01, 5: 0.01, + 6: 0.01, 7: 0.010000000000000018, 8: 0.02301331532438579, + 9: 0.03828458232519679, 10: 0.05620558016446701, + 11: 0.07723606594787139, 12: 0.10191556963693511, + 13: 0.13087723550673386, 14: 0.16486406524697522, + 15: 0.2047479794176962, 16: 0.2515521862747415, + 17: 0.30647743182963383, 18: 0.37093280458019423, + 19: 0.4465718851968064, 20: 0.5353351685722265, + 21: 0.6394998465582088, 22: 0.7617382285481203, + 23: 0.9051862986657312, 24: 1.0735241683715429, + 25: 1.2710704884709152, 26: 1.5028932426319574, + 27: 1.7749397647832015, 28: 2.0941893159432032, + 29: 2.4688321347887174}, + 'Glutamate': {0: 0.01, 1: 0.01, 2: 0.01, 3: 0.01, 4: 0.01, 5: 0.01, + 6: 0.01, 7: 0.01000000000000001, + 8: 0.018675543549590525, 9: 0.02885638821679786, + 10: 0.04080372010964467, 11: 0.05482404396524759, + 12: 0.0712770464246234, 13: 0.0905848236711559, + 14: 0.11324271016465012, 15: 0.13983198627846413, + 16: 0.1710347908498277, 17: 0.20765162121975586, + 18: 0.25062186972012945, 19: 0.30104792346453757, + 20: 0.3602234457148176, 21: 0.4296665643721392, + 22: 0.5111588190320802, 23: 0.6067908657771541, + 24: 0.7190161122476952, 25: 0.8507136589806101, + 26: 1.0052621617546382, 27: 1.1866265098554676, + 28: 1.3994595439621356, 29: 1.6492214231924784}} + ) + + +def test_model_2_estimation( + model_2_data: pd.DataFrame, + sds: physiofit.models.base_model.StandardDevs +): + io = physiofit.base.io.IoHandler() + model = io.select_model( + name="Steady-state batch model with lag phase", + data=model_2_data + ) + model.get_params() + fitter = io.initialize_fitter( + data=model.data, + model=model, + sd=sds, + debug_mode=False + ) + fitter.optimize() + + assert np.allclose( + a=fitter.parameter_stats["optimal"], + b=[0.02, 0.8, 1.4, -8, 20, 3, 0.01, 2, 0.01], + rtol=1e-3 + ) + + +def test_model_2_simulation( + placeholder_data, + parameters, + model_2_data +): + io = physiofit.base.io.IoHandler() + model = io.select_model( + name="Steady-state batch model with lag phase", + data=placeholder_data + ) + model.get_params() + model.parameters.update(parameters) + sim_data = model.simulate( + list(model.parameters.values()), + model.data.drop("time", axis=1), + model.time_vector, + model.args + ) + df = pd.DataFrame( + data=sim_data, + index=model.time_vector, + columns=model.name_vector + ) + df.index.name = "time" + + pd.testing.assert_frame_equal( + df.reset_index(), + model_2_data, + atol=1e-6 + ) diff --git a/physiofit/tests/test_model_3.py b/physiofit/tests/test_model_3.py new file mode 100644 index 0000000..1892873 --- /dev/null +++ b/physiofit/tests/test_model_3.py @@ -0,0 +1,150 @@ +import logging + +import numpy as np +import pandas as pd +import pytest + +import physiofit +import physiofit.base.io + +logging.getLogger("physiofit").setLevel(logging.ERROR) + + +@pytest.fixture +def model_3_data(): + + return pd.DataFrame( + {'time': {0: 0.0, 1: 0.2, 2: 0.4, 3: 0.6000000000000001, 4: 0.8, + 5: 1.0, 6: 1.2000000000000002, 7: 1.4000000000000001, 8: 1.6, + 9: 1.8, 10: 2.0, 11: 2.2, 12: 2.4000000000000004, 13: 2.6, + 14: 2.8000000000000003, 15: 3.0, 16: 3.2, + 17: 3.4000000000000004, 18: 3.6, 19: 3.8000000000000003, + 20: 4.0, 21: 4.2, 22: 4.4, 23: 4.6000000000000005, + 24: 4.800000000000001, 25: 5.0, 26: 5.2, 27: 5.4, + 28: 5.6000000000000005, 29: 5.800000000000001}, + 'X': {0: 0.02, 1: 0.023470217419836206, 2: 0.027542555286719145, + 3: 0.03232148804385787, 4: 0.037929617586099036, + 5: 0.044510818569849356, 6: 0.052233929468462365, + 7: 0.06129708406586005, 8: 0.07193279451138565, + 9: 0.08441391633993106, 10: 0.0990606484879023, + 11: 0.1162487478880518, 12: 0.13641916938581505, + 13: 0.16008937828592706, 14: 0.18786662574885568, + 15: 0.2204635276128321, 16: 0.25871634631086166, + 17: 0.3036064448990781, 18: 0.3562854635922441, + 19: 0.4181048647018553, 20: 0.49065060394218707, + 21: 0.5757838175848538, 22: 0.6756885692769915, + 23: 0.7929278814514524, 24: 0.9305094887957849, + 25: 1.0919630006628847, 26: 1.281430451998733, + 27: 1.5037725658404621, 28: 1.7646934535130303, + 29: 2.070886951665622}, + 'Glucose': {0: 20.0, 1: 19.96529782580164, 2: 19.92457444713281, + 3: 19.876785119561422, 4: 19.82070382413901, + 5: 19.754891814301505, 6: 19.677660705315375, + 7: 19.587029159341398, 8: 19.480672054886142, + 9: 19.35586083660069, 10: 19.209393515120976, + 11: 19.03751252111948, 12: 18.83580830614185, + 13: 18.59910621714073, 14: 18.32133374251144, + 15: 17.99536472387168, 16: 17.612836536891383, + 17: 17.163935551009217, 18: 16.63714536407756, + 19: 16.018951352981446, 20: 15.293493960578129, + 21: 14.442161824151462, 22: 13.443114307230086, + 23: 12.270721185485478, 24: 10.894905112042153, + 25: 9.280369993371155, 26: 7.385695480012673, + 27: 5.16227434159538, 28: 2.5530654648697, + 29: -0.5088695166562189}, + 'Acetate': {0: 0.01, 1: 0.02301331532438577, 2: 0.03828458232519679, + 3: 0.05620558016446701, 4: 0.07723606594787137, + 5: 0.10191556963693509, 6: 0.13087723550673386, + 7: 0.1648640652469752, 8: 0.2047479794176962, + 9: 0.25155218627474146, 10: 0.3064774318296336, + 11: 0.37093280458019423, 12: 0.4465718851968064, + 13: 0.5353351685722265, 14: 0.6394998465582088, + 15: 0.7617382285481203, 16: 0.9051862986657312, + 17: 1.0735241683715429, 18: 1.2710704884709152, + 19: 1.5028932426319574, 20: 1.7749397647832015, + 21: 2.094189315943201, 22: 2.4688321347887174, + 23: 2.908479555442946, 24: 3.424410582984193, + 25: 4.0298612524858175, 26: 4.740364194995248, + 27: 5.574147121901733, 28: 6.552600450673863, + 29: 7.700826068746083}, + 'Glutamate': {0: 0.01, 1: 0.01607131015108712, 2: 0.0224100386448079, + 3: 0.029205066718692864, 4: 0.036652221089788446, + 5: 0.044960160796626104, 6: 0.054356436819364605, + 7: 0.0650939082916693, 8: 0.07745770312604938, + 9: 0.09177292063277068, 10: 0.10841328930255507, + 11: 0.12781101460674013, 12: 0.15046807988847946, + 13: 0.17696929880618822, 14: 0.20799746117775364, + 15: 0.244350966511984, 16: 0.2869644022967774, + 17: 0.3369325988105717, 18: 0.39553878071702653, + 19: 0.4642875402349305, 20: 0.5449434799049011, + 21: 0.6395765180442539, 22: 0.750615020597842, + 23: 0.8809081236202905, 24: 1.0337988461980507, + 25: 1.2132098702732164, 26: 1.4237441886556716, + 27: 1.6708032038334373, 28: 1.9607253077912765, + 29: 2.3009484984038036}} + ) + + +def test_model_3_estimation( + model_3_data: pd.DataFrame, + sds: physiofit.models.base_model.StandardDevs +): + io = physiofit.base.io.IoHandler() + model = io.select_model( + name="Steady-state batch model with degradation of metabolites", + data=model_3_data + ) + model.get_params() + model.args = {"Degradation constants": {"Glucose": 0, "Acetate": 0, + "Glutamine": 1}} + fitter = io.initialize_fitter( + data=model.data, + model=model, + sd=sds, + debug_mode=False + ) + fitter.optimize() + + assert np.allclose( + a=fitter.parameter_stats["optimal"], + b=[0.02, 0.8, -8, 20, 3, 0.01, 2, 0.01], + rtol=1e-3 + ) + + +def test_model_3_simulation( + placeholder_data, + parameters, + model_3_data +): + io = physiofit.base.io.IoHandler() + model = io.select_model( + name="Steady-state batch model with degradation of metabolites", + data=placeholder_data + ) + model.get_params() + model.parameters.update(parameters) + model.args = {"Degradation constants": {"Glucose": 0, "Acetate": 0, + "Glutamine": 1} + } + sim_data = model.simulate( + list(model.parameters.values()), + model.data.drop("time", axis=1), + model.time_vector, + model.args + ) + df = pd.DataFrame( + data=sim_data, + index=model.time_vector, + columns=model.name_vector + ) + df.index.name = "time" + + print(df.reset_index()) + print(model_3_data) + + pd.testing.assert_frame_equal( + df.reset_index(), + model_3_data, + atol=1e-6 + ) diff --git a/physiofit/tests/test_model_4.py b/physiofit/tests/test_model_4.py new file mode 100644 index 0000000..16a22e4 --- /dev/null +++ b/physiofit/tests/test_model_4.py @@ -0,0 +1,142 @@ +import logging + +import numpy as np +import pandas as pd +import pytest + +import physiofit +import physiofit.base.io + +logging.getLogger("physiofit").setLevel(logging.ERROR) + + +@pytest.fixture +def model_4_data(): + + return pd.DataFrame( + {'time': {0: 0.0, 1: 0.2, 2: 0.4, 3: 0.6000000000000001, 4: 0.8, + 5: 1.0, 6: 1.2000000000000002, 7: 1.4000000000000001, 8: 1.6, + 9: 1.8, 10: 2.0, 11: 2.2, 12: 2.4000000000000004, 13: 2.6, + 14: 2.8000000000000003, 15: 3.0, 16: 3.2, + 17: 3.4000000000000004, 18: 3.6, 19: 3.8000000000000003, + 20: 4.0, 21: 4.2, 22: 4.4, 23: 4.6000000000000005, + 24: 4.800000000000001, 25: 5.0, 26: 5.2, 27: 5.4, + 28: 5.6000000000000005, 29: 5.800000000000001}, + 'X': {0: 0.02, 1: 0.023470217419836206, 2: 0.027542555286719145, + 3: 0.03232148804385787, 4: 0.037929617586099036, + 5: 0.044510818569849356, 6: 0.052233929468462365, + 7: 0.06129708406586005, 8: 0.07193279451138565, + 9: 0.08441391633993106, 10: 0.0990606484879023, + 11: 0.1162487478880518, 12: 0.13641916938581505, + 13: 0.16008937828592706, 14: 0.18786662574885568, + 15: 0.2204635276128321, 16: 0.25871634631086166, + 17: 0.3036064448990781, 18: 0.3562854635922441, + 19: 0.4181048647018553, 20: 0.49065060394218707, + 21: 0.5757838175848538, 22: 0.6756885692769915, + 23: 0.7929278814514524, 24: 0.9305094887957849, + 25: 1.0919630006628847, 26: 1.281430451998733, + 27: 1.5037725658404621, 28: 1.7646934535130303, + 29: 2.070886951665622}, + 'Glucose': {0: 20.0, 1: 19.96529782580164, 2: 19.92457444713281, + 3: 19.876785119561422, 4: 19.82070382413901, + 5: 19.754891814301505, 6: 19.677660705315375, + 7: 19.587029159341398, 8: 19.480672054886142, + 9: 19.35586083660069, 10: 19.209393515120976, + 11: 19.03751252111948, 12: 18.83580830614185, + 13: 18.59910621714073, 14: 18.32133374251144, + 15: 17.99536472387168, 16: 17.612836536891383, + 17: 17.163935551009217, 18: 16.63714536407756, + 19: 16.018951352981446, 20: 15.293493960578129, + 21: 14.442161824151462, 22: 13.443114307230086, + 23: 12.270721185485478, 24: 10.894905112042153, + 25: 9.280369993371155, 26: 7.385695480012673, + 27: 5.16227434159538, 28: 2.5530654648697, + 29: -0.5088695166562189}, + 'Acetate': {0: 0.01, 1: 0.02301331532438577, 2: 0.03828458232519679, + 3: 0.05620558016446701, 4: 0.07723606594787137, + 5: 0.10191556963693509, 6: 0.13087723550673386, + 7: 0.1648640652469752, 8: 0.2047479794176962, + 9: 0.25155218627474146, 10: 0.3064774318296336, + 11: 0.37093280458019423, 12: 0.4465718851968064, + 13: 0.5353351685722265, 14: 0.6394998465582088, + 15: 0.7617382285481203, 16: 0.9051862986657312, + 17: 1.0735241683715429, 18: 1.2710704884709152, + 19: 1.5028932426319574, 20: 1.7749397647832015, + 21: 2.094189315943201, 22: 2.4688321347887174, + 23: 2.908479555442946, 24: 3.424410582984193, + 25: 4.0298612524858175, 26: 4.740364194995248, + 27: 5.574147121901733, 28: 6.552600450673863, + 29: 7.700826068746083}, + 'Glutamate': {0: 0.01, 1: 0.018675543549590515, + 2: 0.02885638821679786, 3: 0.04080372010964467, + 4: 0.05482404396524758, 5: 0.07127704642462339, + 6: 0.0905848236711559, 7: 0.11324271016465011, + 8: 0.13983198627846413, 9: 0.17103479084982764, + 10: 0.20765162121975575, 11: 0.25062186972012945, + 12: 0.30104792346453757, 13: 0.3602234457148176, + 14: 0.4296665643721392, 15: 0.5111588190320802, + 16: 0.6067908657771541, 17: 0.7190161122476952, + 18: 0.8507136589806101, 19: 1.0052621617546382, + 20: 1.1866265098554676, 21: 1.3994595439621342, + 22: 1.6492214231924784, 23: 1.9423197036286308, + 24: 2.2862737219894615, 25: 2.689907501657211, + 26: 3.1635761299968315, 27: 3.719431414601155, + 28: 4.371733633782575, 29: 5.1372173791640545}} + ) + + +def test_model_4_estimation( + model_4_data: pd.DataFrame, + sds: physiofit.models.base_model.StandardDevs +): + io = physiofit.base.io.IoHandler() + model = io.select_model( + name="Steady-state batch model", + data=model_4_data + ) + model.get_params() + fitter = io.initialize_fitter( + data=model.data, + model=model, + sd=sds, + debug_mode=False + ) + fitter.optimize() + + assert np.allclose( + a=fitter.parameter_stats["optimal"], + b=[0.02, 0.8, -8, 20, 3, 0.01, 2, 0.01], + rtol=1e-3 + ) + + +def test_model_4_simulation( + placeholder_data, + parameters, + model_4_data +): + io = physiofit.base.io.IoHandler() + model = io.select_model( + name="Steady-state batch model", + data=placeholder_data + ) + model.get_params() + model.parameters.update(parameters) + sim_data = model.simulate( + list(model.parameters.values()), + model.data.drop("time", axis=1), + model.time_vector, + model.args + ) + df = pd.DataFrame( + data=sim_data, + index=model.time_vector, + columns=model.name_vector + ) + df.index.name = "time" + + pd.testing.assert_frame_equal( + df.reset_index(), + model_4_data, + atol=1e-6 + ) diff --git a/physiofit/tests/test_model_5.py b/physiofit/tests/test_model_5.py new file mode 100644 index 0000000..bc9d58f --- /dev/null +++ b/physiofit/tests/test_model_5.py @@ -0,0 +1,311 @@ +""" +This module contains tests for the models module. +""" +import logging + +import numpy as np +import pandas as pd +import pytest +from numpy import array + +import physiofit +import physiofit.base.io + +logging.getLogger("physiofit").setLevel(logging.ERROR) + + +@pytest.fixture +def pyfoomb_simulated_data(): + """ + Test data to use in tests for the Monod model. Data was simulated using + the pyFOOMB package (see the `example 6 notebook `_). + """ + return pd.DataFrame.from_dict( + {'time': array( + [0.00000000e+00, 1.60350555e-06, 1.29272201e-02, 4.73210593e-02, + 8.17148984e-02, 1.16108738e-01, 1.68220493e-01, 2.20332247e-01, + 3.10246576e-01, 4.00160904e-01, 4.90075232e-01, 6.34757887e-01, + 7.79440543e-01, 9.24123199e-01, 1.21353541e+00, 1.50294763e+00, + 1.79235984e+00, 2.08177205e+00, 2.37118427e+00, 2.66059648e+00, + 2.95000869e+00, 3.23942091e+00, 3.52883312e+00, 3.81824533e+00, + 4.10765755e+00, 4.39706976e+00, 4.68648197e+00, 4.97589419e+00, + 5.26530640e+00, 5.55471861e+00, 5.75429441e+00, 5.95387020e+00, + 6.15344600e+00, 6.46543931e+00, 6.69021058e+00, 6.91498185e+00, + 7.13975312e+00, 7.36452439e+00, 7.58929566e+00, 7.81406694e+00, + 8.03883821e+00, 8.26360948e+00, 8.48838075e+00, 8.71315202e+00, + 8.93792329e+00, 9.29231855e+00, 9.64671381e+00, 9.87042767e+00, + 1.00941415e+01, 1.03178554e+01, 1.04707829e+01, 1.06237105e+01, + 1.07766381e+01, 1.08876690e+01, 1.09986998e+01, 1.11097307e+01, + 1.11913085e+01, 1.12728862e+01, 1.13544640e+01, 1.14360417e+01, + 1.14912119e+01, 1.15463820e+01, 1.16015522e+01, 1.16567224e+01, + 1.17118925e+01, 1.17670627e+01, 1.18060238e+01, 1.18344243e+01, + 1.18628249e+01, 1.18912255e+01, 1.19196261e+01, 1.19480267e+01, + 1.19764272e+01, 1.20048278e+01, 1.20247743e+01, 1.20447208e+01, + 1.20646672e+01, 1.20846137e+01, 1.21045602e+01, 1.21245066e+01, + 1.21444531e+01, 1.21685210e+01, 1.21859235e+01, 1.22033260e+01, + 1.22207286e+01, 1.22381311e+01, 1.22555336e+01, 1.22729361e+01, + 1.22903386e+01, 1.23166077e+01, 1.23428768e+01, 1.23691459e+01, + 1.23954150e+01, 1.24216840e+01, 1.24479531e+01, 1.24742222e+01, + 1.25004913e+01, 1.25267604e+01, 1.25530294e+01, 1.25792985e+01, + 1.26055676e+01, 1.26318367e+01, 1.26581058e+01, 1.26843748e+01, + 1.27106439e+01, 1.27369130e+01, 1.27631821e+01, 1.27894512e+01, + 1.28157202e+01, 1.28419893e+01, 1.28682584e+01, 1.28945275e+01, + 1.29207966e+01, 1.29470656e+01, 1.29733347e+01, 1.29996038e+01, + 1.30434980e+01, 1.30873922e+01, 1.31312864e+01, 1.31751806e+01, + 1.32190748e+01, 1.33125773e+01, 1.34060797e+01, 1.34995821e+01, + 1.35930846e+01, 1.36865870e+01, 1.38890130e+01, 1.40914391e+01, + 1.42938651e+01, 1.44962911e+01, 1.48659380e+01, 1.52355849e+01, + 1.72063049e+01, 1.91770248e+01, 2.11477447e+01, + 2.40000000e+01]), 'X': array( + [0.01, 0.01000001, 0.01007442, 0.01027505, 0.01047923, + 0.01068731, 0.01101048, 0.01134339, 0.01194165, 0.01257137, + 0.01323421, 0.01437495, 0.01561403, 0.01695993, 0.02001104, + 0.02361154, 0.02785903, 0.03286946, 0.03878035, 0.04575387, + 0.05398109, 0.06368717, 0.07513765, 0.08864571, 0.10458067, + 0.12337794, 0.14555081, 0.17170425, 0.20255118, 0.23893152, + 0.26775043, 0.30003795, 0.33621059, 0.40167063, 0.45656932, + 0.51894332, 0.58980393, 0.67029632, 0.76171532, 0.86552457, + 0.98337771, 1.1171406, 1.26891467, 1.44106161, 1.63622853, + 1.99798087, 2.43767005, 2.7622085, 3.12812855, 3.53985117, + 3.84993488, 4.18478847, 4.54549087, 4.82397847, 5.11648553, + 5.42271114, 5.65601237, 5.89573243, 6.14096851, 6.39034286, + 6.56033205, 6.73039381, 6.89934182, 7.06561194, 7.22714514, + 7.38125988, 7.48380463, 7.5543561, 7.6207073, 7.68225962, + 7.73844325, 7.78877027, 7.832898, 7.87069075, 7.89349971, + 7.91335326, 7.93042318, 7.94492736, 7.95711585, 7.96725552, + 7.97561473, 7.98369653, 7.98839427, 7.99229022, 7.99550949, + 7.99816155, 8.00034043, 8.00212643, 8.00358754, 8.00530201, + 8.00656218, 8.00748644, 8.00816315, 8.00865792, 8.00901952, + 8.00928373, 8.0094769, 8.009618, 8.00972111, 8.0097963, + 8.00985127, 8.00989131, 8.0099207, 8.00994203, 8.00995777, + 8.00996906, 8.00997753, 8.00998398, 8.00998881, 8.00999209, + 8.0099942, 8.00999568, 8.00999685, 8.00999776, 8.00999839, + 8.0099988, 8.00999914, 8.00999925, 8.00999936, 8.00999958, + 8.00999978, 8.01000023, 8.01000049, 8.01000039, 8.01000014, + 8.00999999, 8.00999983, 8.00999989, 8.00999998, 8.01000001, + 8.01000002, 8.01000001, 8.01000001, 8.01, 8.01, + 8.01]), 'S_substrate': array( + [2.00000000e+01, 2.00000000e+01, 1.99998140e+01, 1.99993124e+01, + 1.99988019e+01, 1.99982817e+01, 1.99974738e+01, 1.99966415e+01, + 1.99951459e+01, 1.99935716e+01, 1.99919145e+01, 1.99890626e+01, + 1.99859649e+01, 1.99826002e+01, 1.99749724e+01, 1.99659711e+01, + 1.99553524e+01, 1.99428263e+01, 1.99280491e+01, 1.99106153e+01, + 1.98900473e+01, 1.98657821e+01, 1.98371559e+01, 1.98033857e+01, + 1.97635483e+01, 1.97165551e+01, 1.96611230e+01, 1.95957394e+01, + 1.95186221e+01, 1.94276712e+01, 1.93556239e+01, 1.92749051e+01, + 1.91844735e+01, 1.90208234e+01, 1.88835767e+01, 1.87276417e+01, + 1.85504902e+01, 1.83492592e+01, 1.81207117e+01, 1.78611886e+01, + 1.75665557e+01, 1.72321485e+01, 1.68527133e+01, 1.64223460e+01, + 1.59344287e+01, 1.50300478e+01, 1.39308249e+01, 1.31194788e+01, + 1.22046786e+01, 1.11753721e+01, 1.04001628e+01, 9.56302883e+00, + 8.66127282e+00, 7.96505382e+00, 7.23378617e+00, 6.46822216e+00, + 5.88496908e+00, 5.28566893e+00, 4.67257871e+00, 4.04914285e+00, + 3.62416986e+00, 3.19901547e+00, 2.77664545e+00, 2.36097015e+00, + 1.95713716e+00, 1.57185031e+00, 1.31548844e+00, 1.13910974e+00, + 9.73231747e-01, 8.19350947e-01, 6.78891873e-01, 5.53074324e-01, + 4.42754998e-01, 3.48273128e-01, 2.91250720e-01, 2.41616847e-01, + 1.98942058e-01, 1.62681603e-01, 1.32210371e-01, 1.06861209e-01, + 8.59631646e-02, 6.57586866e-02, 5.40143186e-02, 4.42744583e-02, + 3.62262631e-02, 2.95961315e-02, 2.41489235e-02, 1.96839254e-02, + 1.60311546e-02, 1.17449793e-02, 8.59454568e-03, 6.28390615e-03, + 4.59212605e-03, 3.35519709e-03, 2.45120231e-03, 1.79067835e-03, + 1.30776192e-03, 9.55007216e-04, 6.97213900e-04, 5.09252537e-04, + 3.71823858e-04, 2.71722143e-04, 1.98247751e-04, 1.44928061e-04, + 1.05565573e-04, 7.73542359e-05, 5.61825443e-05, 4.00431335e-05, + 2.79801017e-05, 1.97696425e-05, 1.44933367e-05, 1.07997649e-05, + 7.87411266e-06, 5.60487745e-06, 4.03634962e-06, 3.00250108e-06, + 2.14584915e-06, 1.88743404e-06, 1.59825382e-06, 1.06207944e-06, + 5.43902318e-07, -5.74527374e-07, -1.22798991e-06, -9.68733873e-07, + -3.40860531e-07, 1.53153067e-08, 4.18994832e-07, 2.87157290e-07, + 5.58479234e-08, -2.89640501e-08, -5.52070633e-08, -1.66479591e-08, + -1.30759119e-08, -7.30389711e-10, 2.00891153e-10, + 5.95679793e-12]), 'P_product': array( + [0.00000000e+00, 2.74886917e-09, 2.23258390e-05, 8.25140254e-05, + 1.43767584e-04, 2.06194151e-04, 3.03143993e-04, 4.03017093e-04, + 5.82495354e-04, 7.71411381e-04, 9.70263731e-04, 1.31248487e-03, + 1.68421018e-03, 2.08797802e-03, 3.00331127e-03, 4.08346290e-03, + 5.35770852e-03, 6.86083829e-03, 8.63410359e-03, 1.07261620e-02, + 1.31943273e-02, 1.61061506e-02, 1.95412948e-02, 2.35937144e-02, + 2.83742018e-02, 3.40133825e-02, 4.06652418e-02, 4.85112736e-02, + 5.77653536e-02, 6.86794565e-02, 7.73251291e-02, 8.70113850e-02, + 9.78631769e-02, 1.17501188e-01, 1.33970795e-01, 1.52682996e-01, + 1.73941180e-01, 1.98088897e-01, 2.25514595e-01, 2.56657370e-01, + 2.92013313e-01, 3.32142179e-01, 3.77674401e-01, 4.29318484e-01, + 4.87868560e-01, 5.96394260e-01, 7.28301016e-01, 8.25662550e-01, + 9.35438564e-01, 1.05895535e+00, 1.15198046e+00, 1.25243654e+00, + 1.36064726e+00, 1.44419354e+00, 1.53194566e+00, 1.62381334e+00, + 1.69380371e+00, 1.76571973e+00, 1.83929055e+00, 1.91410286e+00, + 1.96509962e+00, 2.01611814e+00, 2.06680255e+00, 2.11668358e+00, + 2.16514354e+00, 2.21137796e+00, 2.24214139e+00, 2.26330683e+00, + 2.28321219e+00, 2.30167789e+00, 2.31853298e+00, 2.33363108e+00, + 2.34686940e+00, 2.35820722e+00, 2.36504991e+00, 2.37100598e+00, + 2.37612695e+00, 2.38047821e+00, 2.38413476e+00, 2.38717665e+00, + 2.38968442e+00, 2.39210896e+00, 2.39351828e+00, 2.39468707e+00, + 2.39565285e+00, 2.39644846e+00, 2.39710213e+00, 2.39763793e+00, + 2.39807626e+00, 2.39859060e+00, 2.39896865e+00, 2.39924593e+00, + 2.39944894e+00, 2.39959738e+00, 2.39970586e+00, 2.39978512e+00, + 2.39984307e+00, 2.39988540e+00, 2.39991633e+00, 2.39993889e+00, + 2.39995538e+00, 2.39996739e+00, 2.39997621e+00, 2.39998261e+00, + 2.39998733e+00, 2.39999072e+00, 2.39999326e+00, 2.39999519e+00, + 2.39999664e+00, 2.39999763e+00, 2.39999826e+00, 2.39999870e+00, + 2.39999906e+00, 2.39999933e+00, 2.39999952e+00, 2.39999964e+00, + 2.39999974e+00, 2.39999977e+00, 2.39999981e+00, 2.39999987e+00, + 2.39999993e+00, 2.40000007e+00, 2.40000015e+00, 2.40000012e+00, + 2.40000004e+00, 2.40000000e+00, 2.39999995e+00, 2.39999997e+00, + 2.39999999e+00, 2.40000000e+00, 2.40000001e+00, 2.40000000e+00, + 2.40000000e+00, 2.40000000e+00, 2.40000000e+00, 2.40000000e+00])} + ) + + +@pytest.fixture +def placeholder_data(): + return pd.DataFrame({ + "time": [0.00000000e+00, 1.60350555e-06, 1.29272201e-02, + 4.73210593e-02, + 8.17148984e-02, 1.16108738e-01, 1.68220493e-01, + 2.20332247e-01, + 3.10246576e-01, 4.00160904e-01, 4.90075232e-01, + 6.34757887e-01, + 7.79440543e-01, 9.24123199e-01, 1.21353541e+00, + 1.50294763e+00, + 1.79235984e+00, 2.08177205e+00, 2.37118427e+00, + 2.66059648e+00, + 2.95000869e+00, 3.23942091e+00, 3.52883312e+00, + 3.81824533e+00, + 4.10765755e+00, 4.39706976e+00, 4.68648197e+00, + 4.97589419e+00, + 5.26530640e+00, 5.55471861e+00, 5.75429441e+00, + 5.95387020e+00, + 6.15344600e+00, 6.46543931e+00, 6.69021058e+00, + 6.91498185e+00, + 7.13975312e+00, 7.36452439e+00, 7.58929566e+00, + 7.81406694e+00, + 8.03883821e+00, 8.26360948e+00, 8.48838075e+00, + 8.71315202e+00, + 8.93792329e+00, 9.29231855e+00, 9.64671381e+00, + 9.87042767e+00, + 1.00941415e+01, 1.03178554e+01, 1.04707829e+01, + 1.06237105e+01, + 1.07766381e+01, 1.08876690e+01, 1.09986998e+01, + 1.11097307e+01, + 1.11913085e+01, 1.12728862e+01, 1.13544640e+01, + 1.14360417e+01, + 1.14912119e+01, 1.15463820e+01, 1.16015522e+01, + 1.16567224e+01, + 1.17118925e+01, 1.17670627e+01, 1.18060238e+01, + 1.18344243e+01, + 1.18628249e+01, 1.18912255e+01, 1.19196261e+01, + 1.19480267e+01, + 1.19764272e+01, 1.20048278e+01, 1.20247743e+01, + 1.20447208e+01, + 1.20646672e+01, 1.20846137e+01, 1.21045602e+01, + 1.21245066e+01, + 1.21444531e+01, 1.21685210e+01, 1.21859235e+01, + 1.22033260e+01, + 1.22207286e+01, 1.22381311e+01, 1.22555336e+01, + 1.22729361e+01, + 1.22903386e+01, 1.23166077e+01, 1.23428768e+01, + 1.23691459e+01, + 1.23954150e+01, 1.24216840e+01, 1.24479531e+01, + 1.24742222e+01, + 1.25004913e+01, 1.25267604e+01, 1.25530294e+01, + 1.25792985e+01, + 1.26055676e+01, 1.26318367e+01, 1.26581058e+01, + 1.26843748e+01, + 1.27106439e+01, 1.27369130e+01, 1.27631821e+01, + 1.27894512e+01, + 1.28157202e+01, 1.28419893e+01, 1.28682584e+01, + 1.28945275e+01, + 1.29207966e+01, 1.29470656e+01, 1.29733347e+01, + 1.29996038e+01, + 1.30434980e+01, 1.30873922e+01, 1.31312864e+01, + 1.31751806e+01, + 1.32190748e+01, 1.33125773e+01, 1.34060797e+01, + 1.34995821e+01, + 1.35930846e+01, 1.36865870e+01, 1.38890130e+01, + 1.40914391e+01, + 1.42938651e+01, 1.44962911e+01, 1.48659380e+01, + 1.52355849e+01, + 1.72063049e+01, 1.91770248e+01, 2.11477447e+01, + 2.40000000e+01], + "X": np.arange(136), + "S_substrate": np.arange(136), + "P_product": np.arange(136) + }) + + +@pytest.fixture +def parameters(): + return { + "X_0": 0.01, + "y_BM": 0.4, + "S_substrate_km": 1, + "S_substrate_qsmax": 1.5, + "S_substrate_s_0": 20, + "P_product_y_P": 0.12, + "P_product_p_0": 0 + } + + +def test_monod_model(monod_model_sds, pyfoomb_simulated_data): + """ + Test that the Monod model using pyFOOMB simulated data & parameters given + as input. + """ + + io = physiofit.base.io.IoHandler() + model = io.select_model( + "Dynamic Monod model (1 substrate, 1 product)", + pyfoomb_simulated_data + ) + model.get_params() + fitter = io.initialize_fitter( + data=model.data, + model=model, + sd=monod_model_sds, + debug_mode=True + ) + fitter.optimize() + optimized_params = { + name: param for name, param in zip( + list(fitter.model.parameters.keys()), + fitter.parameter_stats["optimal"] + ) + } + + assert np.allclose( + b=list(optimized_params.values()), + a=[0.01, 0.4, 1, 1.5, 20, 0.12, 0], + rtol=1e-3, + atol=1e-2 + ) + + +def test_physiofit_simulations(parameters, placeholder_data, + pyfoomb_simulated_data): + io = physiofit.base.io.IoHandler() + model = io.select_model("Dynamic Monod model (1 substrate, 1 product)", + placeholder_data) + model.get_params() + model.parameters.update(parameters) + sim_data = model.simulate( + list(model.parameters.values()), + model.data.drop("time", axis=1), + model.time_vector, + model.args + ) + df = pd.DataFrame( + data=sim_data, + index=model.time_vector, + columns=model.name_vector + ) + df.index.name = "time" + df = df.reset_index() + + pd.testing.assert_frame_equal( + df, + pyfoomb_simulated_data, + rtol=1e-3, + atol=1e-2 + ) diff --git a/physiofit/ui/__pycache__/__init__.cpython-312.pyc b/physiofit/ui/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 0000000..6e56dc1 Binary files /dev/null and b/physiofit/ui/__pycache__/__init__.cpython-312.pyc differ diff --git a/physiofit/ui/__pycache__/cli.cpython-312.pyc b/physiofit/ui/__pycache__/cli.cpython-312.pyc new file mode 100644 index 0000000..06f67b4 Binary files /dev/null and b/physiofit/ui/__pycache__/cli.cpython-312.pyc differ diff --git a/physiofit/ui/cli.py b/physiofit/ui/cli.py index 64720ae..5ed1db3 100644 --- a/physiofit/ui/cli.py +++ b/physiofit/ui/cli.py @@ -3,11 +3,12 @@ The Command-Line Interface has two goals: - i) Have a local CLI that can be used to launch jobs in a concise and quick manner, without use of the Graphical - User Interface. This can help when testing many different parameter sets, and also permits easy pipelining of the - tool, as described below. - ii) Have a version compatible with an integration onto the Galaxy W4M platform to be used in automated flux - calculation workflows + i) Have a local CLI that can be used to launch jobs in a concise and quick + manner, without use of the Graphical User Interface. This can help when + testing many different parameter sets, and also permits easy pipelining + of the tool, as described below. + ii) Have a version compatible with an integration onto the Galaxy W4M + platform to be used in automated flux calculation workflows """ import argparse @@ -19,7 +20,9 @@ from physiofit.base.io import IoHandler, StandardDevs, ConfigParser -logger = logging.getLogger(f"physiofit") +logger = logging.getLogger("physiofit") +logger.setLevel(logging.DEBUG) + def args_parse(): """ @@ -43,7 +46,8 @@ def args_parse(): ) parser.add_argument( "-m", "--model", type=str, - help="Which model should be chosen. Useful only if generating related config file" + help="Which model should be chosen. Useful only if generating " + "related config file" ) # Parse developer arguments @@ -88,11 +92,23 @@ def args_parse(): return parser -def run(data, args, logger, experiments): - io = IoHandler() +def run(data, args, experiments): + """ + Run the optimization process + :param data: Dataframe containing the main dataset + :type data: pandas.DataFrame + :param args: Arguments from the user input + :type args: argparse.Namespace + :param experiments: List of experiments to process + :type experiments: list + """ + for exp in experiments: - exp_data = data.loc[exp, :].sort_values("time").copy() + io = IoHandler() + logger.info(f"Processing experiment: {exp}") + exp_data = data.loc[exp, :].sort_values("time") + exp_data = exp_data.reset_index().drop("experiments", axis=1).copy() logger.info(f"Input Data: \n{exp_data}") if args.galaxy: io.wkdir = Path('.') @@ -121,12 +137,19 @@ def run(data, args, logger, experiments): if fitter.mc: fitter.monte_carlo_analysis() fitter.khi2_test() + try: + fitter.aic_test() + except ValueError: + logger.warning( + "Not enough measurements to calculate AIC" + ) + fitter.aic, fitter.aic_c = "NA" df = pd.DataFrame.from_dict( fitter.parameter_stats, orient="columns" ) df.index = [ - f"{exp} {param}" for param in fitter.model.parameters_to_estimate.keys() + f"{exp} {param}" for param in fitter.model.parameters.keys() ] if not io.multiple_experiments: io.multiple_experiments = [] @@ -141,35 +164,23 @@ def run(data, args, logger, experiments): io.output_pdf(fitter, str(res_path)) io.figures = [] if args.output_zip: - # logger.info(io.home_path) - # logger.info(io.home_path / io.home_path.name / "_res") - # logger.info(args.output_zip) - dir = res_path.parents[0] - # for line in dir.rglob("*"): - # print(line) - generate_zips(str(dir), args.output_zip, logger) + output_dir = res_path.parents[0] + generate_zips(str(output_dir), args.output_zip) logger.debug(f"Dataframes to concatenate:\n{io.multiple_experiments}") - # shutil.make_archive( - # args.output_zip, - # format='zip', - # root_dir=str(io.home_path / (io.home_path.name + "_res")) - # ) if args.galaxy: io.output_recap(export_path=args.output_recap, galaxy=args.galaxy) else: io.output_recap(export_path=str(res_path.parent), galaxy=False) -def generate_zips(path_to_data_folder, output_path, logger): - """Generate output zip file containing results - Args: - path_to_data_folder (str): path to folder containing directories & files to zip - output_path (str): path to export archive to - logger (Logging.logger): main logger +def generate_zips(path_to_data_folder, output_path): + """Generate output zip file containing results - Returns: - None: + :param path_to_data_folder: Path to the data folder + :type path_to_data_folder: str + :param output_path: Path to the output zip file + :type output_path: str """ from zipfile import ZipFile directory = Path(path_to_data_folder) @@ -179,17 +190,27 @@ def generate_zips(path_to_data_folder, output_path, logger): archive.write( file_path, arcname=file_path.relative_to(directory) - ) - return 0 - -def generate_config(args, data, logger): - - logger.info("Launching in configuration file generator mode") + ) + return + + +def generate_config(args, data, _logger): + """" + Generate a configuration file for the selected model + :param args: Arguments from the user input + :type args: argparse.Namespace + :param data: Dataframe containing the main dataset + :type data: pandas.DataFrame + :param _logger: Logger object + :type _logger: logging.Logger + """ + _logger.info("Launching in configuration file generator mode") # Run checks if args.model is None: # Must be path to model.py file or name of a model raise ValueError( - f"Please select a model to generate the associated configuration file" + "Please select a model to generate the associated configuration " + "file" ) if args.output_config is None: raise ValueError( @@ -206,7 +227,7 @@ def generate_config(args, data, logger): model = io.select_model(args.model, data) model.get_params() except Exception: - logger.error("There was an error while initialising the model") + _logger.error("There was an error while initialising the model") raise # Build config parser and export configuration file @@ -219,21 +240,39 @@ def generate_config(args, data, logger): iterations=100 ) configparser.export_config(args.output_config) - logger.info(f"Finished exporting the configuration file to {args.output_config}") + _logger.info( + f"Finished exporting the configuration file to {args.output_config}") sys.exit() -def process(args): +def _build_logger(mode): + """ + Build the logger object + :param mode: Debug mode + :type mode: bool + """ + _logger = logging.getLogger("physiofit") cli_handle = logging.StreamHandler() - formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s') + formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - ' + '%(message)s') cli_handle.setFormatter(formatter) - if args.debug_mode: + if mode: cli_handle.setLevel(logging.DEBUG) else: cli_handle.setLevel(logging.INFO) - logger.addHandler(cli_handle) + _logger.addHandler(cli_handle) + return _logger +def process(args): + """ + Process the arguments + :param args: Arguments from the user input + :type args: argparse.Namespace + :return: None + """ + _logger = _build_logger(args.debug_mode) + _logger.info("Starting Physiofit CLI") if args.list: IoHandler.get_model_list() sys.exit() @@ -245,35 +284,41 @@ def process(args): path_to_data = Path(args.data) if not path_to_data.is_file(): raise ValueError( - f"The data path is not correct. Please check and try again. Input data path: \n{args.data}" + f"The data path is not correct. Please check and try again. " + f"Input data path: \n{args.data}" ) # Ensure that the input file is a tsv if we are local if not args.galaxy: - if not path_to_data.suffix in [".tsv", ".txt"]: + if path_to_data.suffix not in [".tsv", ".txt"]: raise TypeError( - f"The input data must be in tsv/txt format. Detected format: {path_to_data.suffix}" + f"The input data must be in tsv/txt format. Detected format:" + f" {path_to_data.suffix}" ) else: if not path_to_data.suffix == ".dat": raise TypeError( - f"The input data must be in dat format (galaxy data format). Detected format: {path_to_data.suffix}" + f"The input data must be in dat format (galaxy data " + f"format). Detected format: {path_to_data.suffix}" ) # Read & check data data = IoHandler.read_data(str(path_to_data)) - # If no configuration file is present we assume the user wants to generate a default one + # If no configuration file is present we assume the user wants to + # generate a default one if args.config is None: - generate_config(args, data, logger) + generate_config(args, data, _logger) # If configuration file is present we launch the optimization experiments = list(data["experiments"].unique()) data = data.set_index("experiments") - run(data, args, logger, experiments) - logger.info("Done!") + run(data, args, experiments) + _logger.info("Done!") sys.exit() + def main(): + """Main routine for the CLI interface""" parser = args_parse() args = parser.parse_args() process(args) diff --git a/physiofit/ui/gui.py b/physiofit/ui/gui.py index 150ac09..1feaeb9 100644 --- a/physiofit/ui/gui.py +++ b/physiofit/ui/gui.py @@ -3,6 +3,7 @@ from tkinter import filedialog from pathlib import Path from copy import copy +import logging import pandas as pd import streamlit as st @@ -11,6 +12,9 @@ from physiofit.base.io import IoHandler, ConfigParser from physiofit.models.base_model import StandardDevs +logger = logging.getLogger("physiofit") +logger.setLevel(logging.DEBUG) + class App: """ @@ -20,9 +24,9 @@ class App: def __init__(self): self.defaults = { - "iterations" : 100, - "sd" : StandardDevs(), - "mc" : True + "iterations": 100, + "sd": StandardDevs(), + "mc": True } self.select_menu = None self.io = None @@ -32,9 +36,13 @@ def __init__(self): def start_app(self): """Launch the application""" - st.set_page_config(page_title=f"PhysioFit (v{physiofit.__version__})") + st.set_page_config(page_title=f"PhysioFit (v{physiofit.__version__})", + layout="wide" + ) st.title(f"Welcome to PhysioFit (v{physiofit.__version__})") - st.write("Documentation available at [https://physiofit.readthedocs.io](https://physiofit.readthedocs.io).") + st.write( + "Documentation available at [https://physiofit.readthedocs.io](" + "https://physiofit.readthedocs.io).") self.update_info = st.empty() self.check_uptodate() self.select_menu = st.selectbox( @@ -65,19 +73,31 @@ def check_uptodate(self): except Exception: pass - def _build_flux_menu(self): - """Build the starting menu with the data upload button""" + @staticmethod + def _get_data_path_config_context(): - self.data_file = st.file_uploader( - "Load a data file or a json configuration file", - key="data_uploader", - accept_multiple_files=False - ) + # Set up tkinter for directory chooser + root = tk.Tk() + root.withdraw() - if self.data_file: - self._initialize_opt_menu() + # Make folder picker dialog appear on top of other windows + root.wm_attributes('-topmost', 1) + + return str(Path( + filedialog.askopenfilename( + master=root, + title="Select the data file", + filetypes=[("Data files", "*.tsv *.txt")] + ) + )) - def _initialize_opt_menu(self): + @staticmethod + def clear_input_from_session_state(): + + if hasattr(st.session_state, "config_parser_data_path"): + del st.session_state["config_parser_data_path"] + + def _run(self): """ Initialize all the options. If a yaml file is given as input, options are parsed from it. If the input is tsv, the defaults are used instead. @@ -86,16 +106,45 @@ def _initialize_opt_menu(self): # Check file extension and initialize defaults file_extension = self.data_file.name.split(".")[1] if file_extension in ["yaml", "yml"]: + # We store the path in session state to + # avoid multiple prompts. try: - # Get parameters from yaml file + # For yaml files, we need to read the configuration file + # before loading the data. self.config_parser = self.io.read_yaml(self.data_file) + # Check if the data path exists, if not open up prompt to + # select file + if not self.config_parser.check_data_path(): + st.info( + "File path in configuration file is incorrect or " + "missing. Loading file from prompt." + ) + input_path = st.session_state.get( + "config_parser_data_path", + None + ) + if not input_path: + input_path = self._get_data_path_config_context() + self.config_parser.path_to_data = input_path + st.session_state["config_parser_data_path"] = input_path + # Load data into io_handler - self.io.data = self.io.read_data(self.config_parser.path_to_data) + self.data_file = Path(self.config_parser.path_to_data) + self.input_datafile_name = Path( + self.config_parser.path_to_data).stem + self.io.data = self.io.read_data( + str(self.config_parser.path_to_data) + ) + st.info(f"Input data: {self.data_file}") except Exception: - st.error("An error has occurred when reading the yaml configuration file.") + st.error( + "An error has occurred when reading the yaml " + "configuration file and/or loading the input data." + ) raise elif file_extension in ["tsv", "txt"]: try: + self.input_datafile_name = self.data_file.name[:-4] self.io.data = self.io.read_data(self.data_file) # Initialize default SDs self.defaults["sd"].update({ @@ -113,6 +162,8 @@ def _initialize_opt_menu(self): f"files or json for configuration files. Detected file: " f"{self.data_file.name}") + # Reset config_parser path to data if it exists to handle new + # data file paths if "experiments" not in self.io.data.columns: raise ValueError( "'experiments' column missing from dataset" @@ -125,30 +176,38 @@ def _initialize_opt_menu(self): # Initialize the list of available models self.io.get_models() except Exception: - st.error(f"An error has occurred when listing models from the models folder: " - f"\n{Path(__file__).parent / 'models'}. Please correct the model or submit an issue at " - f"github.com/MetaSys-LISBP/PhysioFit/issues") + st.error( + f"An error has occurred when listing models from the " + f"models folder: \n{Path(__file__).parent / 'models'}. " + f"Please correct the model or submit an issue at " + f"github.com/MetaSys-LISBP/PhysioFit/issues") raise # Build menu - submitted = self._initialize_opt_menu_widgets( - file_extension - ) + submitted = self._initialize_opt_menu_widgets() if submitted: + _logger = self._build_logger(self.io.res_path) try: self._get_data_from_session_state() except Exception: - st.error("An error has occurred when initializing the model") + st.error( + "An error has occurred when initializing the model") raise if not self.io.wkdir: raise ValueError("No output directory selected") + + _logger.info("=============================================") + _logger.info(f"Physiofit version: {physiofit.__version__}") + _logger.info("Path to results: \n" + str(self.io.res_path)) + _logger.info("=============================================") + self.config_parser = ConfigParser( - path_to_data =self.io.wkdir / self.data_file.name, - selected_model= self.model, - sds = self.sd, - mc = self.mc, - iterations = self.iterations + path_to_data=self.io.wkdir / self.data_file.name, + selected_model=self.model, + sds=self.sd, + mc=self.mc, + iterations=self.iterations ) full_dataframe = self.io.data.copy() @@ -156,18 +215,22 @@ def _initialize_opt_menu(self): experiments = list(self.io.data["experiments"].unique()) self.io.multiple_experiments = [] for experiment in experiments: + _logger.info(f"Running optimization for {experiment}") with st.spinner(f"Running optimization for {experiment}"): # final_table_dict = {} self.model.data = full_dataframe[ full_dataframe["experiments"] == experiment - ].drop("experiments", axis=1).copy() + ].drop("experiments", axis=1).copy() - self.io.res_path = results_path / experiment + self.io.res_path = results_path / str(experiment) if not self.io.res_path.is_dir(): self.io.res_path.mkdir(parents=True) # Initialize the fitter object self.io.names = self.io.data.columns[1:].to_list() kwargs = self._build_fitter_kwargs() + _logger.info("Run options for the fitter:") + for key, value in kwargs.items(): + _logger.info(f"{key} : {value}") fitter = self.io.initialize_fitter( self.model.data, model=kwargs["model"], @@ -181,21 +244,63 @@ def _initialize_opt_menu(self): if self.mc: fitter.monte_carlo_analysis() fitter.khi2_test() + try: + fitter.aic_test() + except ValueError: + st.warning("Not enough measurements to calculate AIC") + logger.warning( + "Not enough measurements to calculate AIC" + ) + fitter.aic, fitter.aic_c = "NA" df = pd.DataFrame.from_dict( fitter.parameter_stats, orient="columns" ) + printed_df = df.copy() df.index = [ - f"{experiment} {param}" for param in fitter.model.parameters_to_estimate.keys() + f"{experiment} {param}" for param in + fitter.model.parameters.keys() + ] + printed_df.index = [ + f"{param}" for param in fitter.model.parameters.keys() ] - st.write(df) + _logger.info(f"Results for {experiment}: \n{df}") self.io.multiple_experiments.append(df) # Export results self.io.output_report(fitter, self.io.res_path) self.io.plot_data(fitter) self.io.output_plots(fitter, self.io.res_path) - with st.expander(f"{experiment} plots"): + with st.expander(f"Experiment {experiment}"): + data_col, stat_col, aic_col = st.columns(3) + with data_col: + st.write("Parameter statistics:") + st.dataframe(printed_df) + with stat_col: + st.write("Khi² test results:") + st.dataframe(fitter.khi2_res) + with aic_col: + st.write("AIC test results:") + st.dataframe( + fitter.aic_res + ) + if fitter.khi2_res.at["p_val", "Values"] < 0.95: + st.write( + f"\n\nAt level of 95% confidence, " + f"the model fits the data good enough " + f"with respect to the provided " + f"measurement SD. Value: " + f"{fitter.khi2_res.at['p_val', 'Values']}" + ) + + else: + st.write( + f"\n\nAt level of 95% confidence, " + f"the model does not fit the data good " + f"enough with respect to the provided " + f"measurement SD. Value: " + f"{fitter.khi2_res.at['p_val', 'Values']}" + ) for fig in self.io.figures: st.pyplot(fig[1]) self.io.output_pdf(fitter, self.io.res_path) @@ -203,33 +308,86 @@ def _initialize_opt_menu(self): self.io.figures = [] self.config_parser.export_config(self.io.res_path) self.io.data = full_dataframe + _logger.info(f"Resulting dataframe: \n{full_dataframe}") self.io.res_path = results_path self.io.output_recap(results_path) + logging.shutdown() + + def _build_flux_menu(self): + """Build the starting menu with the data upload button""" + + self.data_file = st.file_uploader( + "Load a data file or a json configuration file", + key="data_uploader", + accept_multiple_files=False, + on_change=self.clear_input_from_session_state + ) + + if self.data_file: + self._run() def silent_sim(self): self.model.simulate( - [param for param in self.model.parameters_to_estimate.values()], + [param for param in self.model.parameters.values()], self.model.experimental_matrix, self.model.time_vector, - self.model.fixed_parameters + self.model.args ) - def _initialize_opt_menu_widgets(self, file_extension): + def _build_logger(self, output_path): + """ + Sets up a logger for the application. + + This method creates a logging handler that writes to a file and a + stream handler that writes to the console. + The log level is set to INFO by default, but can be set to DEBUG if + the debug_mode attribute is True. + A formatter is also set up to format the log messages. + + :param output_path: The path where the log file will be written. + :type output_path: Path + :return: The configured logger. + :rtype: Logger + """ + try: + handler = logging.FileHandler(output_path / "log.txt", + "w") + except TypeError: + raise TypeError("Please provide a valid output directory") + stream = logging.StreamHandler() + handler.setLevel(logging.INFO) + stream.setLevel(logging.INFO) + if self.debug_mode: + handler.setLevel(logging.DEBUG) + stream.setLevel(logging.DEBUG) + formatter = logging.Formatter('%(asctime)s - %(name)s - %(' + 'levelname)s - %(message)s') + handler.setFormatter(formatter) + if logger.hasHandlers(): + logger.handlers.clear() + logger.addHandler(handler) + logger.addHandler(stream) + return logger + + def _initialize_opt_menu_widgets(self): # Get model names and give as options to user model_options = [ - model.model_name for model in self.io.models + model.name for model in self.io.models ] - if self.config_parser: - if self.config_parser.model: - try: - idx = model_options.index(self.config_parser.model["model_name"]) - except Exception: - st.error("Error while reading model name from configuration file") - raise - else: - idx = None + idx = None + if self.config_parser and self.config_parser.model: + try: + idx = model_options.index( + self.config_parser.model["model_name"]) + except Exception: + st.error( + "Error while reading model name from configuration " + "file" + ) + raise + model_name = st.selectbox( label="Model", options=model_options, @@ -238,7 +396,7 @@ def _initialize_opt_menu_widgets(self, file_extension): index=idx ) - #if model_name == "Dynamic system (only substrates)": + # if model_name == "Dynamic system (only substrates)": # st.error("Not yet implemented...") if model_name: # Initialize selected model @@ -247,7 +405,9 @@ def _initialize_opt_menu_widgets(self, file_extension): self.model.get_params() self.silent_sim() except Exception as e: - st.error(f"The following error occurred with the selected model: {e}") + st.error( + f"The following error occurred with the selected model: " + f"{e}") raise else: st.success("Model successfully initialized") @@ -266,27 +426,28 @@ def _initialize_opt_menu_widgets(self, file_extension): enable_mc = False if self.mc else True self.iterations = st.number_input( "Number of iterations", - value=self.defaults["iterations"] if self.config_parser is None - else self.config_parser.iterations , + value=self.defaults[ + "iterations"] if self.config_parser is None + else self.config_parser.iterations, help="Number of iterations for Monte Carlo analysis.", disabled=enable_mc ) if self.iterations < 0: - st.error("ERROR: Number of Monte-Carlo iterations must be a positive integer") + st.error( + "ERROR: Number of Monte-Carlo iterations must be a " + "positive integer" + ) self.debug_mode = st.checkbox( "Verbose logs", help="Useful in case of trouble. Join it to the " "issue on github." ) - if file_extension in ["tsv", "txt"]: - - self._output_directory_selector() - - else: - self.io.wkdir = Path(self.config_parser.path_to_data).resolve().parent - self.io.res_path = self.io.wkdir / (self.io.wkdir.name + "_res") - + self._output_directory_selector() + if self.io.wkdir: + self.io.res_path = self.io.wkdir / ( + self.input_datafile_name + "_res") + self.io.res_path.mkdir(parents=True, exist_ok=True) # Build the form for advanced parameters form = st.form("Parameter_form") with form: @@ -296,9 +457,9 @@ def _initialize_opt_menu_widgets(self, file_extension): col1, col2, col3, col4 = st.columns(4) with col1: st.write("Parameter Name") - for key in self.model.parameters_to_estimate: + for key in self.model.parameters: st.text_input( - label="label", # Unused + label="label", # Unused label_visibility="collapsed", value=key, key=f"Parameter_name_{key}", @@ -306,12 +467,13 @@ def _initialize_opt_menu_widgets(self, file_extension): ) with col2: st.write("Parameter Value") - for key, value in self.model.parameters_to_estimate.items(): + for key, value in self.model.parameters.items(): st.text_input( - label="label", # Unused - label_visibility = "collapsed", + label="label", # Unused + label_visibility="collapsed", value=value if self.config_parser is None - else self.config_parser.model["parameters_to_estimate"][key], + else self.config_parser.model[ + "parameters_to_estimate"][key], key=f"Parameter_value_{key}" ) with col3: @@ -321,7 +483,9 @@ def _initialize_opt_menu_widgets(self, file_extension): label="label", # Unused label_visibility="collapsed", value=bound[0] if self.config_parser is None - else literal_eval(self.config_parser.model["bounds"][key])[0], + else literal_eval( + self.config_parser.model["bounds"][key])[ + 0], key=f"Parameter_lower_{key}" ) with col4: @@ -331,19 +495,21 @@ def _initialize_opt_menu_widgets(self, file_extension): label="label", # Unused label_visibility="collapsed", value=bound[1] if self.config_parser is None - else literal_eval(self.config_parser.model["bounds"][key])[1], + else literal_eval( + self.config_parser.model["bounds"][key])[ + 1], key=f"Parameter_upper_{key}" ) - if self.model.fixed_parameters is not None: - for param in self.model.fixed_parameters.keys(): + if self.model.args is not None: + for param in self.model.args.keys(): st.subheader(f"Fixed parameters: {param}") col1, col2 = st.columns(2) with col1: st.write("Parameter Name") - for key in self.model.fixed_parameters[param].keys(): + for key in self.model.args[param].keys(): st.text_input( - label="label", # Unused + label="label", # Unused label_visibility="collapsed", value=key, key=f"Fixed_{param}_{key}", @@ -351,12 +517,16 @@ def _initialize_opt_menu_widgets(self, file_extension): ) with col2: st.write("Parameter Value") - for key, value in self.model.fixed_parameters[param].items(): + for key, value in self.model.args[ + param].items(): + st.write(key, value) st.text_input( - label="label", # Unused + label="label", # Unused label_visibility="collapsed", - value=value if self.config_parser is None - else self.config_parser.model["fixed_parameters"][key], + value=value if self.config_parser is + None else + self.config_parser.model["args"][ + param][key], key=f"Fixed_{param}_value_{key}" ) @@ -397,60 +567,75 @@ def _get_data_from_session_state(self): # Start with estimable parameters # Get order of parameter names to build dict - estimable_parameter_name_order = [key for key in self.model.parameters_to_estimate.keys()] + estimable_parameter_name_order = [key for key in + self.model.parameters.keys()] for name in estimable_parameter_name_order: try: # Get values from widgets if st.session_state[f"Parameter_value_{name}"] == "0": - self.model.parameters_to_estimate[name] = 0 + self.model.parameters[name] = 0 else: - self.model.parameters_to_estimate[name] = literal_eval( - st.session_state[f"Parameter_value_{name}"].lstrip("0") # Strip leading zeroes to stop eval errors + self.model.parameters[name] = literal_eval( + st.session_state[f"Parameter_value_{name}"].lstrip("0") + # Strip leading zeroes to stop eval errors ) # Get bounds if st.session_state[f"Parameter_lower_{name}"] == "0": st.warning( - f"WARNING: {name} has a lower bound at 0. Sometimes this might confuse the optimizer. We " - f"strongly recommend to set the lower bound at a non-zero value, 1e-6 for example." + f"WARNING: {name} has a lower bound at 0. Sometimes " + f"this might confuse the optimizer. We strongly " + f"recommend to set the lower bound at a non-zero " + f"value, 1e-6 for example." ) lower_bound = 0 else: - lower_bound = literal_eval(st.session_state[f"Parameter_lower_{name}"].lstrip("0")) + lower_bound = literal_eval( + st.session_state[f"Parameter_lower_{name}"].lstrip( + "0")) if st.session_state[f"Parameter_upper_{name}"] == "0": st.warning( - f"WARNING: {name} has an upper bound at 0. Sometimes this might confuse the optimizer. We " - f"strongly recommend to set the lower bound at a non-zero value, 1e-6 for example." + f"WARNING: {name} has an upper bound at 0. Sometimes " + f"this might confuse the optimizer. We strongly " + f"recommend to set the lower bound at a non-zero " + f"value, 1e-6 for example." ) upper_bound = 0 else: - upper_bound = literal_eval(st.session_state[f"Parameter_upper_{name}"].lstrip("0")) + upper_bound = literal_eval( + st.session_state[f"Parameter_upper_{name}"].lstrip( + "0")) self.model.bounds[name] = ( lower_bound, upper_bound ) except ValueError: st.error( - f"ERROR: An error occurred while parsing the input for {name}. Please check that only numbers " - f"have been entered." + f"ERROR: An error occurred while parsing the input for" + f" {name}. Please check that only numbers have been " + f"entered." ) raise # Do the same for each fixed parameter class - if self.model.fixed_parameters is not None: - fixed_parameter_classes = [param for param in self.model.fixed_parameters] + if self.model.args is not None: + fixed_parameter_classes = [param for param in self.model.args] for param in fixed_parameter_classes: - for key in self.model.fixed_parameters[param].keys(): + for key in self.model.args[param].keys(): try: - if st.session_state[f"Fixed_{param}_value_{key}"] == "0": - self.model.fixed_parameters[param][key] = 0 + if st.session_state[ + f"Fixed_{param}_value_{key}"] == "0": + self.model.args[param][key] = 0 else: - self.model.fixed_parameters[param][key] = literal_eval( - st.session_state[f"Fixed_{param}_value_{key}"].lstrip("0") + self.model.args[param][key] = literal_eval( + st.session_state[ + f"Fixed_{param}_value_{key}"].lstrip("0") ) except ValueError: st.error( - f"ERROR: An error occurred when parsing the input in the fixed parameter class {param} for " - f"{key}. Please check that only numbers have been entered." + f"ERROR: An error occurred when parsing the input " + f"in the fixed parameter class {param} for {key}. " + f"Please check that only numbers have been " + f"entered." ) raise @@ -459,16 +644,18 @@ def _get_data_from_session_state(self): for name in sd_name_order: try: if st.session_state[f"Fixed_{name}_sd_value"] == "0": - self.sd[name] = 0 # will raise Value Error as expected + self.sd[name] = 0 # will raise Value Error as expected else: # Get values from widgets self.sd[name] = literal_eval( - st.session_state[f"Fixed_{name}_sd_value"].lstrip("0") # Strip leading zeroes to stop eval errors + st.session_state[f"Fixed_{name}_sd_value"].lstrip("0") + # Strip leading zeroes to stop eval errors ) except ValueError: st.error( - f"ERROR: An error occurred when parsing the input for {name} (SDs). Please check that only numbers " - f"have been entered and that value is superior to 0." + f"ERROR: An error occurred when parsing the input for " + f"{name} (SDs). Please check that only numbers have been " + f"entered and that value is superior to 0." ) raise @@ -485,19 +672,19 @@ def _build_fitter_kwargs(self): def _output_directory_selector(self): - # Set up tkinter for directory chooser - root = tk.Tk() - root.withdraw() - - # Make folder picker dialog appear on top of other windows - root.wm_attributes('-topmost', 1) - # Initialize folder picker button and add logic clicked = st.button( "Select output data directory", key="clicker" ) if clicked: + # Set up tkinter for directory chooser + root = tk.Tk() + root.withdraw() + + # Make folder picker dialog appear on top of other windows + root.wm_attributes('-topmost', 1) + # Initialize home path from directory selector and add # to session state st.session_state.wkdir = Path(st.text_input( @@ -521,11 +708,9 @@ def _output_directory_selector(self): raise RuntimeError("Please provide a valid output directory") # Initialize the result export directory - self.io.res_path = self.io.wkdir / (self.io.wkdir.name + "_res") - if not clicked: - if not self.io.res_path.is_dir(): - self.io.res_path.mkdir() - + # self.io.res_path = self.io.wkdir / (self.io.wkdir.name + "_res") + # if not clicked and not self.io.res_path.is_dir():: + # self.io.res_path.mkdir() if __name__ == "__main__": diff --git a/poetry.lock b/poetry.lock index 752eb52..36b9310 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,25 +1,25 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. 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pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, - {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, + {file = "zipp-3.18.2-py3-none-any.whl", hash = "sha256:dce197b859eb796242b0622af1b8beb0a722d52aa2f57133ead08edd5bf5374e"}, + {file = "zipp-3.18.2.tar.gz", hash = "sha256:6278d9ddbcfb1f1089a88fde84481528b07b0e10474e09dcfe53dad4069fa059"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" -python-versions = ">=3.8,<3.9.7 || >3.9.7,<3.12" -content-hash = "31de9eeb3d22fe50589b7d15c16ca8f6998d57bd4f50008e50a4903a65665c22" +python-versions = ">=3.9,<3.9.7 || >3.9.7,<4.0.0" +content-hash = "94a897a93e6fea85d5637460b10e074ed25500eebd0074892c0899c58ed671b3" diff --git a/pyproject.toml b/pyproject.toml index bd8af8c..a34a684 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "physiofit" -version = "3.3.6" +version = "3.4.0" description = "Calculate extracellular fluxes from metabolite concentrations and biomass data" authors = ["llegregam "] license = "GNU General Public License (GPL)" @@ -10,7 +10,7 @@ readme = "README.md" physiofit = 'physiofit.__main__:main' [tool.poetry.dependencies] -python = ">=3.8,<3.9.7 || >3.9.7,<3.12" +python = ">=3.9,<3.9.7 || >3.9.7,<4.0.0" pandas = "^2.0.1" numpy = "^1.24.2" scipy = "^1.10.1" @@ -32,6 +32,7 @@ sphinx-rtd-theme = "^1.2.0" [tool.poetry.group.test.dependencies] pytest = "^7.3.1" tox = "^4.5.1" +flake8 = "^7.0.0" [build-system] requires = ["poetry-core"] diff --git a/tox.ini b/tox.ini index 1441a13..17517ed 100644 --- a/tox.ini +++ b/tox.ini @@ -1,19 +1,27 @@ [tox] -minversion = 3.8.0 -envlist = py38, py39, py310, py11, flake8 +minversion = 3.9.0 +envlist = py39, py310, py11, py12, flake8 isolated_build = true [gh-actions] python = - 3.8: py38, flake8 3.9: py39 3.10: py310 - 3.11: py311 + 3.11: py311, flake8 + 3.12: py312 [testenv] +description = Run the tests with pytest setenv = PYTHONPATH = {toxinidir} commands = pytest deps = pytest + +[testenv:flake8] +description = Run flake8 linter +commands = flake8 +deps = flake8 + + diff --git a/validation/Supplementary_information.pdf b/validation/Supplementary_information.pdf new file mode 100644 index 0000000..a8d13a0 Binary files /dev/null and b/validation/Supplementary_information.pdf differ diff --git a/validation/Validation.pdf b/validation/Validation.pdf deleted file mode 100644 index a10633e..0000000 Binary files a/validation/Validation.pdf and /dev/null differ diff --git a/validation/models/Batch exponential steady-state.txt b/validation/models/Batch exponential steady-state.txt deleted file mode 100644 index 740e782..0000000 --- a/validation/models/Batch exponential steady-state.txt +++ /dev/null @@ -1,21 +0,0 @@ -Results (100 mc iterations) - -optimal mean median sd CI_2.5 CI_97.5 -X 0.0314176468392843 0.0317041805675159 0.031270929320175 0.00528845690520736 0.0226061239544647 0.0423756420269034 -Glc 15.8014990383804 15.7888980226922 15.7756658913602 0.203100844373514 15.4018249749975 16.1227376122043 -Ace 0.00173443678157678 0.0542796088063603 0.0382748102620848 0.0594071591250536 9.99999999984737e-07 0.19953969288509 -mu 0.400675418682353 0.400891021329512 0.401033105621402 0.040705290506425 0.326781800308928 0.479864774602962 -qGlc -9.17994696817661 -9.16526423208897 -9.06440188323603 0.9560427332655 -11.0689181726669 -7.33292372954146 -qAce 3.81981335762841 3.69114407167164 3.69597444558068 0.375776229663407 2.97728531031089 4.53980703200308 -res 3.95869762112645 31.7895117978556 31.4589573414922 7.67520055269962 19.2753910175588 50.0381694535088 - - -Goodness of fit (khi2 test) - -khi2 value 3.9586976211267 -data points 19 -fitted parameters 6 -degrees of freedom 13 -khi2 reduced value 0.304515201625131 -p-value, i.e. P(X^2<=value) 0.00837715869207238 -conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/models/Monod_model/physiofit_results/config_file.yml b/validation/models/Monod_model/physiofit_results/config_file.yml deleted file mode 100644 index af50021..0000000 --- a/validation/models/Monod_model/physiofit_results/config_file.yml +++ /dev/null @@ -1,25 +0,0 @@ -iterations: 100 -mc: true -model: - bounds: - P_ethanol_p_0: (0.001, 10) - P_ethanol_y_P: (0.01, 10) - S_GlcEq_km: (1e-06, 100) - S_GlcEq_qsmax: (1e-06, 50) - S_GlcEq_s_0: (1e-06, 150) - X_0: (0.001, 10) - y_BM: (0.001, 3) - model_name: Dynamic Monod model (1 substrate, 1 product) - parameters_to_estimate: - P_ethanol_p_0: 1 - P_ethanol_y_P: 1 - S_GlcEq_km: 1 - S_GlcEq_qsmax: 1 - S_GlcEq_s_0: 100 - X_0: 1 - y_BM: 1 -path_to_data: ".\\validation\\models\\Monod_model\\physiofit_results\\data.tsv" -sds: - P_ethanol: 3 - S_GlcEq: 7 - X: 1 diff --git a/validation/models/Monod_model/physiofit_results/flux_results.tsv b/validation/models/Monod_model/physiofit_results/flux_results.tsv deleted file mode 100644 index 89e88a6..0000000 --- a/validation/models/Monod_model/physiofit_results/flux_results.tsv +++ /dev/null @@ -1,8 +0,0 @@ - optimal mean sd median CI_2.5 CI_97.5 -X_0 0.3585436986928072 0.3563644139730433 0.18354567026418478 0.3371826757523577 0.028841949665995376 0.7505447886146306 -y_BM 0.29006290054186984 0.29314787805130443 0.018586690669371703 0.2905731679231324 0.2614972088615677 0.3309164726568337 -S_GlcEq_km 100.0 87.60609340777533 28.689445024026085 99.9207772554943 10.314027966332667 100.0 -S_GlcEq_qsmax 1.3491467390391916 1.187517402712609 0.37862665221944525 1.2782397225503104 0.20348722006322928 1.6507218796312966 -S_GlcEq_s_0 74.29155413667496 74.40297889614618 3.528083054505281 74.51225340015296 68.34771201392623 81.25473012454886 -P_ethanol_y_P 0.43580679236877207 0.43115405942344603 0.03403669329799693 0.431385147742682 0.3646408223237543 0.48773577000615465 -P_ethanol_p_0 0.0595902941591445 0.5699630153916515 0.8703334932551696 0.007152124586332023 0.001 2.4897156318111104 diff --git a/validation/models/Steady-state_model/data.txt b/validation/models/Steady-state_model/data.txt deleted file mode 100644 index 919e0c1..0000000 --- a/validation/models/Steady-state_model/data.txt +++ /dev/null @@ -1,14 +0,0 @@ -experiments time X Glc Ace -A 0 0.033264 NA NA -A 1.18888889 0.051408 NA NA -A 2.27694444 0.074088 NA NA -A 3.12833333 0.108864 NA NA -A 3.77138889 0.139104 NA NA -A 4.41555556 0.175392 NA NA -A 4.82277778 0.228312 NA NA -A 0.06666667 NA 15.81315 0.009505775 -A 1.71666667 NA 15.6035 0.294995312 -A 2.8 NA 13.76795 0.610747733 -A 3.63333333 NA 13.12348 0.997928907 -A 4.26666667 NA 12.69779 1.377281918 -A 4.88333333 NA 11.58289 1.804833542 diff --git "a/validation/models/Steady-state_model/original_results/BW25113 \342\210\206ymjA.pdf" "b/validation/models/Steady-state_model/original_results/BW25113 \342\210\206ymjA.pdf" deleted file mode 100644 index 6670b03..0000000 Binary files "a/validation/models/Steady-state_model/original_results/BW25113 \342\210\206ymjA.pdf" and /dev/null differ diff --git "a/validation/models/Steady-state_model/original_results/BW25113 \342\210\206ymjA_log.txt" "b/validation/models/Steady-state_model/original_results/BW25113 \342\210\206ymjA_log.txt" deleted file mode 100644 index c360706..0000000 --- "a/validation/models/Steady-state_model/original_results/BW25113 \342\210\206ymjA_log.txt" +++ /dev/null @@ -1,195 +0,0 @@ -$sys -$sys$params - X Glc Ace mu qGlc qAce - 0.6 0.6 0.6 0.6 0.6 0.6 - -$sys$to_est -[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" - -$sys$nconc -[1] "X" "Glc" "Ace" - -$sys$nflux -[1] "mu" "qGlc" "qAce" - -$sys$metab -[1] "Glc" "Ace" - -$sys$weight - col -row X Glc Ace - [1,] 0.02 0.46 0.2 - [2,] 0.02 0.46 0.2 - [3,] 0.02 0.46 0.2 - [4,] 0.02 0.46 0.2 - [5,] 0.02 0.46 0.2 - [6,] 0.02 0.46 0.2 - [7,] 0.02 0.46 0.2 - [8,] 0.02 0.46 0.2 - [9,] 0.02 0.46 0.2 - [10,] 0.02 0.46 0.2 - [11,] 0.02 0.46 0.2 - [12,] 0.02 0.46 0.2 - [13,] 0.02 0.46 0.2 - -$sys$te_upc - X Glc Ace mu qGlc qAce - 50 50 50 50 50 50 - -$sys$te_loc - X Glc Ace mu qGlc qAce - 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 - -$sys$u - X Glc Ace mu qGlc qAce -X <= 50 -1 0 0 0 0 0 -Glc <= 50 0 -1 0 0 0 0 -Ace <= 50 0 0 -1 0 0 0 -mu <= 50 0 0 0 -1 0 0 -qGlc <= 50 0 0 0 0 -1 0 -qAce <= 50 0 0 0 0 0 -1 -X >= 1e-06 1 0 0 0 0 0 -Glc >= 1e-06 0 1 0 0 0 0 -Ace >= 1e-06 0 0 1 0 0 0 -mu >= 0 0 0 0 1 0 0 -qGlc >= -50 0 0 0 0 1 0 -qAce >= -50 0 0 0 0 0 1 - -$sys$co - X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 - -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 - -$sys$times - [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 - -$sys$data_meas - X Glc Ace - [1,] 0.033264 NA NA - [2,] 0.051408 NA NA - [3,] 0.074088 NA NA - [4,] 0.108864 NA NA - [5,] 0.139104 NA NA - [6,] 0.175392 NA NA - [7,] 0.228312 NA NA - [8,] NA 15.81315 0.009505775 - [9,] NA 15.60350 0.294995312 -[10,] NA 13.76795 0.610747733 -[11,] NA 13.12348 0.997928907 -[12,] NA 12.69779 1.377281918 -[13,] NA 11.58289 1.804833542 - -$sys$nb_par -[1] 6 - -$sys$nb_conc -[1] 3 - - -$result -$result$par - X Glc Ace mu qGlc qAce - 0.031417647 15.801499038 0.001734437 0.400675419 -9.179946968 3.819813358 - -$result$lastp - X Glc Ace mu qGlc qAce - 1.996484e-09 1.155996e-07 -1.312254e-08 -1.770526e-08 -3.534122e-07 -1.059004e-08 - -$result$hci - X Glc Ace mu qGlc qAce -0.009221946 0.392940008 0.170394275 0.069145116 1.618652759 0.695841640 - -$result$ci_p -[1] 0.95 - -$result$sd_res -[1] 0.551829 - -$result$laststep - X Glc Ace mu qGlc qAce - 1.996484e-09 1.155996e-07 -1.312254e-08 -1.770526e-08 -3.534122e-07 -1.059004e-08 - -$result$normp -[1] 3.726463e-07 - -$result$res - [1] -0.092317658 -0.040964852 0.207225949 0.058646322 0.163607923 0.445487014 -0.567326227 -0.067685984 -1.117782244 1.180570423 0.676881041 -0.335903100 -0.336080136 0.001685556 0.015391042 0.055928234 -0.057106857 -0.098945348 0.083047373 - -$result$prevres - [1] -0.092317758 -0.040964960 0.207225858 0.058646277 0.163607946 0.445487148 -0.567325990 -0.067686231 -1.117782363 1.180570407 0.676881110 -0.335902969 -0.336079954 0.001685619 0.015391043 0.055928202 -0.057106895 -0.098945369 0.083047400 - -$result$jacobian - [,1] [,2] [,3] [,4] [,5] [,6] - [1,] 50.000000 0.000000 0 0.000000000 0.00000000 0.00000000 - [2,] 80.510014 0.000000 0 3.007217215 0.00000000 0.00000000 - [3,] 124.504108 0.000000 0 8.906554767 0.00000000 0.00000000 - [4,] 175.119628 0.000000 0 17.211609105 0.00000000 0.00000000 - [5,] 226.586301 0.000000 0 26.847793189 0.00000000 0.00000000 - [6,] 293.309291 0.000000 0 40.689729254 0.00000000 0.00000000 - [7,] 345.292401 0.000000 0 52.318814823 0.00000000 0.00000000 - [8,] -1.348355 2.173913 0 -0.001418358 0.00461464 0.00000000 - [9,] -49.278272 2.173913 0 -1.480029542 0.16865101 0.00000000 -[10,] -103.132979 2.173913 0 -5.367198272 0.35296450 0.00000000 -[11,] -163.758074 2.173913 0 -11.538058687 0.56044912 0.00000000 -[12,] -225.449282 2.173913 0 -19.219849204 0.77158242 0.00000000 -[13,] -302.599631 2.173913 0 -30.339856233 1.03562342 0.00000000 -[14,] 1.290429 0.000000 5 0.001357425 0.00000000 0.01061367 -[15,] 47.161248 0.000000 5 1.416446609 0.00000000 0.38789732 -[16,] 98.702326 0.000000 5 5.136620299 0.00000000 0.81181836 -[17,] 156.722931 0.000000 5 11.042376948 0.00000000 1.28903297 -[18,] 215.763849 0.000000 5 18.394153257 0.00000000 1.77463957 -[19,] 289.599774 0.000000 5 29.036438290 0.00000000 2.38193388 - -$result$retres -$result$retres$res - [1] -0.092317758 -0.040964960 0.207225858 0.058646277 0.163607946 0.445487148 -0.567325990 -0.067686231 -1.117782363 1.180570407 0.676881110 -0.335902969 -0.336079954 0.001685619 0.015391043 0.055928202 -0.057106895 -0.098945369 0.083047400 - -$result$retres$sim - col -row X Glc Ace - [1,] 0.03141764 15.80150 0.001734450 - [2,] 0.05058870 15.36227 0.184500472 - [3,] 0.07823252 14.72892 0.448041009 - [4,] 0.11003693 14.00024 0.751246280 - [5,] 0.14237616 13.25931 1.059550270 - [6,] 0.18430174 12.29874 1.459245115 - [7,] 0.21696548 11.55038 1.770642742 - [8,] 0.03226817 15.78201 0.009842899 - [9,] 0.06250183 15.08932 0.298073521 - [10,] 0.09647278 14.31101 0.621933374 - [11,] 0.13471441 13.43485 0.986507528 - [12,] 0.17362854 12.54328 1.357492844 - [13,] 0.22229412 11.42829 1.821443022 - - -$result$it -[1] 8 - -$result$btit -[1] 0 - -$result$history -NULL - -$result$error -[1] 0 - -$result$mes -[1] "" - -$result$resi - X Glc Ace - [1,] 0.0018463552 NA NA - [2,] 0.0008192992 NA NA - [3,] -0.0041445172 NA NA - [4,] -0.0011729255 NA NA - [5,] -0.0032721589 NA NA - [6,] -0.0089097430 NA NA - [7,] 0.0113465198 NA NA - [8,] NA 0.03113567 -0.0003371238 - [9,] NA 0.51417989 -0.0030782086 -[10,] NA -0.54306239 -0.0111856404 -[11,] NA -0.31136531 0.0114213790 -[12,] NA 0.15451537 0.0197890738 -[13,] NA 0.15459678 -0.0166094800 - - diff --git "a/validation/models/Steady-state_model/original_results/BW25113 \342\210\206ymjA_res.txt" "b/validation/models/Steady-state_model/original_results/BW25113 \342\210\206ymjA_res.txt" deleted file mode 100644 index 740e782..0000000 --- "a/validation/models/Steady-state_model/original_results/BW25113 \342\210\206ymjA_res.txt" +++ /dev/null @@ -1,21 +0,0 @@ -Results (100 mc iterations) - -optimal mean median sd CI_2.5 CI_97.5 -X 0.0314176468392843 0.0317041805675159 0.031270929320175 0.00528845690520736 0.0226061239544647 0.0423756420269034 -Glc 15.8014990383804 15.7888980226922 15.7756658913602 0.203100844373514 15.4018249749975 16.1227376122043 -Ace 0.00173443678157678 0.0542796088063603 0.0382748102620848 0.0594071591250536 9.99999999984737e-07 0.19953969288509 -mu 0.400675418682353 0.400891021329512 0.401033105621402 0.040705290506425 0.326781800308928 0.479864774602962 -qGlc -9.17994696817661 -9.16526423208897 -9.06440188323603 0.9560427332655 -11.0689181726669 -7.33292372954146 -qAce 3.81981335762841 3.69114407167164 3.69597444558068 0.375776229663407 2.97728531031089 4.53980703200308 -res 3.95869762112645 31.7895117978556 31.4589573414922 7.67520055269962 19.2753910175588 50.0381694535088 - - -Goodness of fit (khi2 test) - -khi2 value 3.9586976211267 -data points 19 -fitted parameters 6 -degrees of freedom 13 -khi2 reduced value 0.304515201625131 -p-value, i.e. P(X^2<=value) 0.00837715869207238 -conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/models/Steady-state_model/physiofit_results/results/flux_results.tsv b/validation/models/Steady-state_model/physiofit_results/results/flux_results.tsv deleted file mode 100644 index 4c9b073..0000000 --- a/validation/models/Steady-state_model/physiofit_results/results/flux_results.tsv +++ /dev/null @@ -1,7 +0,0 @@ - optimal mean sd median CI_2.5 CI_97.5 -X_0 0.03141744599863818 0.030937509123949266 0.005588743268385279 0.0314435906518126 0.020087699273588378 0.04008291075888095 -growth_rate 0.4006769541201118 0.4073171789727354 0.044919738759394284 0.400399964204328 0.3368041142333426 0.4947137839486294 -Glc_q -9.179962519953397 -9.367213403659251 0.9196598590800444 -9.271153585646687 -11.576339489964397 -7.717390100856105 -Glc_M0 15.80149393328667 15.79757464565157 0.21600160875547877 15.789644754108949 15.362635588087214 16.175750909865833 -Ace_q 3.8198244705175135 3.7812213880313434 0.38968766840313307 3.7092503338702216 3.0207573588314607 4.54932363936233 -Ace_M0 0.0017343519958105242 0.03610681107875325 0.06176707637111388 1e-06 1e-06 0.22185056708169532 diff --git a/validation/models/Steady-state_model/physiofit_results/results/stat_results.tsv b/validation/models/Steady-state_model/physiofit_results/results/stat_results.tsv deleted file mode 100644 index 9642ba1..0000000 --- a/validation/models/Steady-state_model/physiofit_results/results/stat_results.tsv +++ /dev/null @@ -1,11 +0,0 @@ -================== -Khi² test results -================== - -khi2_value 3.958665 -number_of_measurements 19.000000 -number_of_params 6.000000 -Degrees_of_freedom 13.000000 -p_val 0.008377 - -At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.008376820519788792 \ No newline at end of file diff --git a/validation/models/Steady-state_model/physiofit_results/summary.csv b/validation/models/Steady-state_model/physiofit_results/summary.csv deleted file mode 100644 index aaa1cad..0000000 --- a/validation/models/Steady-state_model/physiofit_results/summary.csv +++ /dev/null @@ -1,7 +0,0 @@ -experiments,parameter name,optimal,mean,sd,median,CI_2.5,CI_97.5 -A,X_0,0.03141744599863818,0.030937509123949266,0.005588743268385279,0.0314435906518126,0.020087699273588378,0.04008291075888095 -A,growth_rate,0.4006769541201118,0.4073171789727354,0.044919738759394284,0.400399964204328,0.3368041142333426,0.4947137839486294 -A,Glc_q,-9.179962519953397,-9.367213403659251,0.9196598590800444,-9.271153585646687,-11.576339489964397,-7.717390100856105 -A,Glc_M0,15.80149393328667,15.79757464565157,0.21600160875547877,15.789644754108949,15.362635588087214,16.175750909865833 -A,Ace_q,3.8198244705175135,3.7812213880313434,0.38968766840313307,3.7092503338702216,3.0207573588314607,4.54932363936233 -A,Ace_M0,0.0017343519958105242,0.03610681107875325,0.06176707637111388,1e-06,1e-06,0.22185056708169532 diff --git a/validation/models/Steady-state_model_deg/data.txt b/validation/models/Steady-state_model_deg/data.txt deleted file mode 100644 index d09cd03..0000000 --- a/validation/models/Steady-state_model_deg/data.txt +++ /dev/null @@ -1,7 +0,0 @@ -experiments time X DHA -A 0 0.08 13.091353 -A 7.9825 0.11 12.697156 -A 9.476667 0.15 12.389292 -A 23.892778 0.45 10.069308 -A 26.976111 0.48 10.042876 -A 47.843056 1.09 3.366052 diff --git a/validation/models/Steady-state_model_deg/physiofit_results/results/config_file.yml b/validation/models/Steady-state_model_deg/physiofit_results/results/config_file.yml deleted file mode 100644 index f9f9fa1..0000000 --- a/validation/models/Steady-state_model_deg/physiofit_results/results/config_file.yml +++ /dev/null @@ -1,18 +0,0 @@ -iterations: 100 -mc: true -model: - bounds: - DHA_M0: (1e-06, 50) - DHA_q: (-50, 50) - X_0: (0.001, 10) - growth_rate: (0.001, 3) - model_name: Steady-state batch model with degradation of metabolites - parameters_to_estimate: - DHA_M0: 1 - DHA_q: 1 - X_0: 1 - growth_rate: 1 -path_to_data: C:\Users\millard\Documents\GIT\PhysioFit\data_test\Steady-state_model\DHAklm.txt -sds: - DHA: 0.5 - X: 0.002 diff --git a/validation/models/Steady-state_model_deg/physiofit_results/results/flux_results.tsv b/validation/models/Steady-state_model_deg/physiofit_results/results/flux_results.tsv deleted file mode 100644 index 857a238..0000000 --- a/validation/models/Steady-state_model_deg/physiofit_results/results/flux_results.tsv +++ /dev/null @@ -1,5 +0,0 @@ - optimal mean sd median CI_2.5 CI_97.5 -X_0 0.12631522289113964 0.126381923767271 0.0006929026209877955 0.12641304163547407 0.12490367804211952 0.12756743796858075 -growth_rate 0.045429970890166364 0.04542118138462707 0.00012923139203134898 0.04540237657918154 0.045192698189370176 0.04565776367183036 -DHA_q -0.27367898957210246 -0.2729830494171032 0.03009597207086485 -0.26970653513855086 -0.346680175495912 -0.2268195439073993 -DHA_M0 13.686516281710393 13.661232939453296 0.29303126938982677 13.652247839183685 13.044762488488477 14.217734165517038 diff --git a/validation/models/Steady-state_model_deg/physiofit_results/summary.csv b/validation/models/Steady-state_model_deg/physiofit_results/summary.csv deleted file mode 100644 index b256a73..0000000 --- a/validation/models/Steady-state_model_deg/physiofit_results/summary.csv +++ /dev/null @@ -1,5 +0,0 @@ -experiments,parameter name,optimal,mean,sd,median,CI_2.5,CI_97.5 -A,X_0,0.12631522289113964,0.126381923767271,0.0006929026209877955,0.12641304163547407,0.12490367804211952,0.12756743796858075 -A,growth_rate,0.045429970890166364,0.04542118138462707,0.00012923139203134898,0.04540237657918154,0.045192698189370176,0.04565776367183036 -A,DHA_q,-0.27367898957210246,-0.2729830494171032,0.03009597207086485,-0.26970653513855086,-0.346680175495912,-0.2268195439073993 -A,DHA_M0,13.686516281710393,13.661232939453296,0.29303126938982677,13.652247839183685,13.044762488488477,14.217734165517038 diff --git a/validation/models/summary.xlsx b/validation/models/summary.xlsx deleted file mode 100644 index 5ca83c4..0000000 Binary files a/validation/models/summary.xlsx and /dev/null differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT BW.txt b/validation/validation_results/Berges_2021/Berges_2021/WT BW.txt new file mode 100644 index 0000000..71edb7b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT BW.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.3504000000000005E-2 NA NA +2.2613888888888889 7.5600000000000001E-2 NA NA +2.7741666666666664 9.6768000000000007E-2 NA NA +3.2088888888888891 0.12096 NA NA +3.7063888888888892 0.15875999999999998 NA NA +4.2258333333333331 0.192024 NA NA +4.6355555555555554 0.25704000000000005 NA NA +4.9675000000000002 0.30088800000000004 NA NA +2.8 NA 12.2503876402854 0.68228059479917 +3.73333333333333 NA 11.2647756999073 1.13167881269788 +4.28333333333333 NA 10.762083947783 1.50776307251694 +4.75 NA 9.69020796119422 1.86440782293358 +5.11666666666667 NA 8.80761667454699 2.17848992166165 +5.43333333333333 NA 7.74278266664927 2.44855281309788 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT BW_res/KEIO_ROBOT5_48.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT BW_res/KEIO_ROBOT5_48.pdf new file mode 100644 index 0000000..67bfd78 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT BW_res/KEIO_ROBOT5_48.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT BW_res/KEIO_ROBOT5_48_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT BW_res/KEIO_ROBOT5_48_log.txt new file mode 100644 index 0000000..03a5463 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT BW_res/KEIO_ROBOT5_48_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.063504 NA NA + [2,] 0.075600 NA NA + [3,] 0.096768 NA NA + [4,] 0.120960 NA NA + [5,] 0.158760 NA NA + [6,] 0.192024 NA NA + [7,] 0.257040 NA NA + [8,] 0.300888 NA NA + [9,] NA 12.250388 0.6822806 +[10,] NA 11.264776 1.1316788 +[11,] NA 10.762084 1.5077631 +[12,] NA 9.690208 1.8644078 +[13,] NA 8.807617 2.1784899 +[14,] NA 7.742783 2.4485528 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02335005 13.51226761 0.27305514 0.51319990 -8.13614902 3.23567520 + +$result$lastp + X Glc Ace mu qGlc qAce + 9.446466e-10 9.829259e-09 -3.162282e-08 -9.348430e-09 5.798854e-08 4.275452e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.003478357 0.328665234 0.140894002 0.033727873 0.683316000 0.294797112 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3002075 + +$result$laststep + X Glc Ace mu qGlc qAce + 9.446466e-10 9.829259e-09 -3.162282e-08 -9.348430e-09 5.798854e-08 4.275452e-08 + +$result$normp +[1] 7.984687e-08 + +$result$res + [1] -0.190640110 -0.053716885 0.009612164 0.011747664 -0.115649299 0.610804585 -0.250279497 -0.102233110 0.161665814 0.223628522 -0.466472033 -0.098162970 -0.086709678 0.266050345 0.315191735 -0.028629834 -0.278242622 -0.266976479 -0.092869060 0.351526261 + +$result$prevres + [1] -0.190640180 -0.053716957 0.009612094 0.011747600 -0.115649344 0.610804575 -0.250279461 -0.102233021 0.161665837 0.223628550 -0.466472012 -0.098162967 -0.086709699 0.266050292 0.315191805 -0.028629808 -0.278242623 -0.266976499 -0.092869094 0.351526219 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 127.8182 0.000000 0 5.458428 0.0000000 0.0000000 + [2,] 159.5835 0.000000 0 8.426575 0.0000000 0.0000000 + [3,] 207.6232 0.000000 0 13.449194 0.0000000 0.0000000 + [4,] 259.5176 0.000000 0 19.445057 0.0000000 0.0000000 + [5,] 335.0037 0.000000 0 28.992674 0.0000000 0.0000000 + [6,] 437.3441 0.000000 0 43.154229 0.0000000 0.0000000 + [7,] 539.6872 0.000000 0 58.415976 0.0000000 0.0000000 + [8,] 639.9203 0.000000 0 74.225214 0.0000000 0.0000000 + [9,] -110.5587 2.173913 0 -4.451347 0.3172940 0.0000000 +[10,] -199.6666 2.173913 0 -11.325428 0.5730258 0.0000000 +[11,] -276.0223 2.173913 0 -18.494955 0.7921600 0.0000000 +[12,] -360.0416 2.173913 0 -27.374260 1.0332884 0.0000000 +[13,] -441.7213 2.173913 0 -36.794189 1.2677019 0.0000000 +[14,] -525.7509 2.173913 0 -47.152659 1.5088598 0.0000000 +[15,] 101.1270 0.000000 5 4.071602 0.0000000 0.7297763 +[16,] 182.6330 0.000000 5 10.359254 0.0000000 1.3179594 +[17,] 252.4747 0.000000 5 16.917148 0.0000000 1.8219681 +[18,] 329.3264 0.000000 5 25.038957 0.0000000 2.3765633 +[19,] 404.0380 0.000000 5 33.655270 0.0000000 2.9157144 +[20,] 480.8990 0.000000 5 43.130058 0.0000000 3.4703775 + +$result$retres +$result$retres$res + [1] -0.190640180 -0.053716957 0.009612094 0.011747600 -0.115649344 0.610804575 -0.250279461 -0.102233021 0.161665837 0.223628550 -0.466472012 -0.098162967 -0.086709699 0.266050292 0.315191805 -0.028629808 -0.278242623 -0.266976499 -0.092869094 0.351526219 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05969120 12.936124 0.5021826 + [2,] 0.07452566 12.700942 0.5957124 + [3,] 0.09696024 12.345269 0.7371603 + [4,] 0.12119495 11.961058 0.8899577 + [5,] 0.15644701 11.402180 1.1122185 + [6,] 0.20424009 10.644480 1.4135492 + [7,] 0.25203441 9.886760 1.7148877 + [8,] 0.29884334 9.144663 2.0100134 + [9,] 0.09825427 12.324754 0.7453190 + [10,] 0.15862537 11.367645 1.1259529 + [11,] 0.21035682 10.547507 1.4521145 + [12,] 0.26728046 9.645053 1.8110125 + [13,] 0.32261892 8.767730 2.1599161 + [14,] 0.37954953 7.865166 2.5188581 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0038128036 NA NA + [2,] 0.0010743391 NA NA + [3,] -0.0001922419 NA NA + [4,] -0.0002349520 NA NA + [5,] 0.0023129869 NA NA + [6,] -0.0122160915 NA NA + [7,] 0.0050055892 NA NA + [8,] 0.0020446604 NA NA + [9,] NA -0.07436628 -0.063038361 +[10,] NA -0.10286913 0.005725962 +[11,] NA 0.21457713 0.055648525 +[12,] NA 0.04515497 0.053395300 +[13,] NA 0.03988646 0.018573819 +[14,] NA -0.12238313 -0.070305244 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT BW_res/KEIO_ROBOT5_48_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT BW_res/KEIO_ROBOT5_48_res.txt new file mode 100644 index 0000000..5454f78 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT BW_res/KEIO_ROBOT5_48_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0233500463976034 0.0233441726910459 0.023351319661965 0.00362908921250435 0.0160344942375601 0.0299449517421713 +Glc 13.512267613805 13.5376049592796 13.5336334014308 0.276482780185009 13.0869406408329 14.0917572968177 +Ace 0.27305514458486 0.265592470686017 0.249107770839034 0.120550855423506 0.0386964835261306 0.500848083855111 +mu 0.513199901575259 0.515363976946047 0.512064504436533 0.0351609410189642 0.457078199288941 0.589052272686937 +qGlc -8.13614901931942 -8.23905101972797 -8.25026124320492 0.747754786442238 -9.57754564398731 -6.95608411877359 +qAce 3.23567520384026 3.23971861748944 3.21604616645441 0.307551380629019 2.66018397568496 3.77638432634128 +res 1.26174329343597 36.4751303986936 35.9653657252072 9.04950805849095 22.0217636718015 56.7331272649294 + + +Goodness of fit (khi2 test) + +khi2 value 1.26174329343602 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.0901245209597154 +p-value, i.e. P(X^2<=value) 4.55517155379145e-06 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT1.txt b/validation/validation_results/Berges_2021/Berges_2021/WT1.txt new file mode 100644 index 0000000..46b10fd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT1.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.18888888888889 0.061992 NA NA +2.27694444444444 0.111888 NA NA +3.12833333333333 0.172368 NA NA +3.77138888888889 0.23436 NA NA +4.41555555555556 0.368928 NA NA +4.82277777777778 0.545832 NA NA +0.0666666666666667 NA 15.1537393608889 0.00419622433347224 +1.71666666666667 NA 14.3348460424723 0.348769379662006 +2.8 NA 13.6070637892223 0.760104475519081 +3.63333333333333 NA 12.5887340272941 1.01054974245947 +4.26666666666667 NA 11.3572400036966 1.67458664376349 +4.88333333333333 NA 9.60439982397194 2.02953207344843 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT1_res/KEIO_ROBOT1_46.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT1_res/KEIO_ROBOT1_46.pdf new file mode 100644 index 0000000..7b17e97 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT1_res/KEIO_ROBOT1_46.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT1_res/KEIO_ROBOT1_46_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT1_res/KEIO_ROBOT1_46_log.txt new file mode 100644 index 0000000..7ebaae4 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT1_res/KEIO_ROBOT1_46_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.061992 NA NA + [3,] 0.111888 NA NA + [4,] 0.172368 NA NA + [5,] 0.234360 NA NA + [6,] 0.368928 NA NA + [7,] 0.545832 NA NA + [8,] NA 15.15374 0.004196224 + [9,] NA 14.33485 0.348769380 +[10,] NA 13.60706 0.760104476 +[11,] NA 12.58873 1.010549742 +[12,] NA 11.35724 1.674586644 +[13,] NA 9.60440 2.029532073 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0218755 14.9218147 0.1725214 0.6559618 -6.8647930 2.5534049 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.315531e-08 -2.669417e-07 1.487078e-07 1.380027e-07 -4.675131e-07 1.590385e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.007930074 0.552972026 0.239024164 0.081310714 1.423967391 0.605854979 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.8731482 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.315531e-08 -2.669417e-07 1.487078e-07 1.380027e-07 -4.675131e-07 1.590385e-08 + +$result$normp +[1] 5.756832e-07 + +$result$res + [1] -0.4938251033 -0.7138807330 -0.7237686117 -0.1044823496 1.2634588535 1.3613018842 -1.4187777891 -0.5264308455 0.2391015350 0.2325256841 0.1742981984 0.0726610857 -0.1921556577 0.8606578511 0.0058428045 -0.6916900541 -0.0002305037 -0.9431529378 0.7685728400 + +$result$prevres + [1] -0.4938244456 -0.7138796897 -0.7237672132 -0.1044809052 1.2634599038 1.3613017260 -1.4187794497 -0.5264302769 0.2391017077 0.2325255187 0.1742978419 0.0726607704 -0.1921555615 0.8606571188 0.0058424645 -0.6916900207 -0.0002301865 -0.9431525088 0.7685731327 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.000000000 0.000000000 + [2,] 109.0589518 0.000000 0 2.836356e+00 0.000000000 0.000000000 + [3,] 222.6522968 0.000000 0 1.109016e+01 0.000000000 0.000000000 + [4,] 389.1986368 0.000000 0 2.663438e+01 0.000000000 0.000000000 + [5,] 593.4243022 0.000000 0 4.895813e+01 0.000000000 0.000000000 + [6,] 905.4737805 0.000000 0 8.746201e+01 0.000000000 0.000000000 + [7,] 1182.7298775 0.000000 0 1.247789e+02 0.000000000 0.000000000 + [8,] -1.0169719 2.173913 0 -7.469640e-04 0.003240707 0.000000000 + [9,] -47.4008428 2.173913 0 -1.053631e+00 0.151048653 0.000000000 +[10,] -120.0259584 2.173913 0 -4.742546e+00 0.382477574 0.000000000 +[11,] -223.8858417 2.173913 0 -1.213659e+01 0.713439948 0.000000000 +[12,] -350.9136392 2.173913 0 -2.317360e+01 1.118229748 0.000000000 +[13,] -537.2104733 2.173913 0 -4.190276e+01 1.711887671 0.000000000 +[14,] 0.8700196 0.000000 5 6.390278e-04 0.000000000 0.007453626 +[15,] 40.5514295 0.000000 5 9.013819e-01 0.000000000 0.347411902 +[16,] 102.6822291 0.000000 5 4.057249e+00 0.000000000 0.879698419 +[17,] 191.5343780 0.000000 5 1.038286e+01 0.000000000 1.640911880 +[18,] 300.2066817 0.000000 5 1.982502e+01 0.000000000 2.571928421 +[19,] 459.5836569 0.000000 5 3.584782e+01 0.000000000 3.937341642 + +$result$retres +$result$retres$res + [1] -0.4938244456 -0.7138796897 -0.7237672132 -0.1044809052 1.2634599038 1.3613017260 -1.4187794497 -0.5264302769 0.2391017077 0.2325255187 0.1742978419 0.0726607704 -0.1921555615 0.8606571188 0.0058424645 -0.6916900207 -0.0002301865 -0.9431525088 0.7685731327 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02187551 14.921815 0.1725212 + [2,] 0.04771441 14.651405 0.2731020 + [3,] 0.09741266 14.131301 0.4665581 + [4,] 0.17027838 13.368744 0.7501961 + [5,] 0.25962920 12.433667 1.0980043 + [6,] 0.39615403 11.004903 1.6294426 + [7,] 0.51745641 9.735445 2.1016258 + [8,] 0.02285337 14.911581 0.1763276 + [9,] 0.06745329 14.444833 0.3499379 + [10,] 0.13728520 13.714026 0.6217665 + [11,] 0.23715058 12.668911 1.0105037 + [12,] 0.35929282 11.390664 1.4859561 + [13,] 0.53842457 9.516008 2.1832467 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.009876489 NA NA + [2,] 0.014277594 NA NA + [3,] 0.014475344 NA NA + [4,] 0.002089618 NA NA + [5,] -0.025269198 NA NA + [6,] -0.027226035 NA NA + [7,] 0.028375589 NA NA + [8,] NA 0.24215793 -0.1721314238 + [9,] NA -0.10998679 -0.0011684929 +[10,] NA -0.10696174 0.1383380041 +[11,] NA -0.08017701 0.0000460373 +[12,] NA -0.03342395 0.1886305018 +[13,] NA 0.08839156 -0.1537146265 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT1_res/KEIO_ROBOT1_46_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT1_res/KEIO_ROBOT1_46_res.txt new file mode 100644 index 0000000..3400ff6 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT1_res/KEIO_ROBOT1_46_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0218754979334764 0.0218308878477937 0.0218218581334993 0.00298446051870941 0.0165018717271694 0.0275845528033713 +Glc 14.9218146852764 14.9130649354756 14.8796471000073 0.206324696705192 14.5320648321911 15.3339900161506 +Ace 0.172521371972221 0.176599435515805 0.16639471535849 0.0692828729734934 0.0758794775676803 0.319381710520735 +mu 0.655961835056118 0.659641390407518 0.655287363143681 0.031128934614069 0.602266378687412 0.720040493583203 +qGlc -6.86479298159135 -6.90075082530933 -6.81050823765287 0.51194856376426 -7.80777984783192 -6.02236064595054 +qAce 2.55340490083477 2.54394612781016 2.54047936364483 0.191234151511292 2.2002570403891 2.94783809224524 +res 9.91104140594205 32.092517244434 31.4260225769355 7.39399852439803 20.0019041117924 48.0036492184158 + + +Goodness of fit (khi2 test) + +khi2 value 9.91104140595434 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.762387800458026 +p-value, i.e. P(X^2<=value) 0.298807849234161 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT2.txt b/validation/validation_results/Berges_2021/Berges_2021/WT2.txt new file mode 100644 index 0000000..4765818 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT2.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.111888 NA NA NA +3.34194444444444 0.172368 NA NA NA +3.9975 0.23436 NA NA NA +4.52333333333333 0.368928 NA NA NA +1.95 NA 13.7948497407258 0.388240799163102 0 +3.25 NA 12.6821988761534 0.887038373144795 0 +4.08333333333333 NA 11.3039851865163 1.32910714240064 0 +4.76666666666667 NA 10.0989508508155 1.88442802051972 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT2_res/KEIO_ROBOT2_46.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT2_res/KEIO_ROBOT2_46.pdf new file mode 100644 index 0000000..6440321 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT2_res/KEIO_ROBOT2_46.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT2_res/KEIO_ROBOT2_46_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT2_res/KEIO_ROBOT2_46_log.txt new file mode 100644 index 0000000..773ba70 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT2_res/KEIO_ROBOT2_46_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.111888 NA NA NA +[2,] 0.172368 NA NA NA +[3,] 0.234360 NA NA NA +[4,] 0.368928 NA NA NA +[5,] NA 13.79485 0.3882408 0 +[6,] NA 12.68220 0.8870384 0 +[7,] NA 11.30399 1.3291071 0 +[8,] NA 10.09895 1.8844280 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.175607e-02 1.423913e+01 2.230921e-01 1.000000e-06 6.177683e-01 -6.738506e+00 2.670036e+00 -2.161155e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-6.338184e-09 -2.399736e-07 9.031099e-08 0.000000e+00 7.155641e-08 1.395308e-07 -4.110591e-08 4.962801e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.008874653 0.606211378 0.261132563 0.248840203 0.097812350 1.512414586 0.653046518 0.630398636 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5630465 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-6.338184e-09 -2.399736e-07 9.031099e-08 0.000000e+00 7.155641e-08 1.395308e-07 -4.110591e-08 4.962801e-13 + +$result$normp +[1] 3.034179e-07 + +$result$res + [1] -4.933851e-01 -4.462513e-02 1.136444e+00 -6.582460e-01 -2.390893e-01 5.890855e-02 4.684049e-01 -2.882241e-01 2.723460e-01 -2.888603e-01 -1.419084e-01 1.584227e-01 4.111195e-06 2.546781e-06 6.387617e-07 -1.851742e-06 + +$result$prevres + [1] -4.933845e-01 -4.462468e-02 1.136444e+00 -6.582465e-01 -2.390891e-01 5.890854e-02 4.684047e-01 -2.882242e-01 2.723458e-01 -2.888602e-01 -1.419083e-01 1.584228e-01 4.111194e-06 2.546780e-06 6.387603e-07 -1.851744e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.344639e+02 0.000000 0 0 1.275962e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.940864e+02 0.000000 0 0 2.865308e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.908437e+02 0.000000 0 0 5.138564e+01 0.0000000 0.0000000 0.0000000 + [4,] 8.176176e+02 0.000000 0 0 8.046175e+01 0.0000000 0.0000000 0.0000000 + [5,] -5.538293e+01 2.173913 0 0 -1.405147e+00 0.1788105 0.0000000 0.0000000 + [6,] -1.528641e+02 2.173913 0 0 -7.101811e+00 0.4935402 0.0000000 0.0000000 + [7,] -2.717560e+02 2.173913 0 0 -1.667815e+01 0.8773969 0.0000000 0.0000000 + [8,] -4.269433e+02 2.173913 0 0 -3.169906e+01 1.3784381 0.0000000 0.0000000 + [9,] 5.047278e+01 0.000000 5 0 1.280569e+00 0.0000000 0.4112641 0.0000000 +[10,] 1.393115e+02 0.000000 5 0 6.472178e+00 0.0000000 1.1351426 0.0000000 +[11,] 2.476626e+02 0.000000 5 0 1.519950e+01 0.0000000 2.0180129 0.0000000 +[12,] 3.890914e+02 0.000000 5 0 2.888869e+01 0.0000000 3.1704075 0.0000000 +[13,] -4.085320e-05 0.000000 0 5 -1.036506e-06 0.0000000 0.0000000 0.4112641 +[14,] -1.127602e-04 0.000000 0 5 -5.238649e-06 0.0000000 0.0000000 1.1351426 +[15,] -2.004607e-04 0.000000 0 5 -1.230264e-05 0.0000000 0.0000000 2.0180129 +[16,] -3.149346e-04 0.000000 0 5 -2.338281e-05 0.0000000 0.0000000 3.1704075 + +$result$retres +$result$retres$res + [1] -4.933845e-01 -4.462468e-02 1.136444e+00 -6.582465e-01 -2.390891e-01 5.890854e-02 4.684047e-01 -2.882242e-01 2.723458e-01 -2.888602e-01 -1.419083e-01 1.584228e-01 4.111194e-06 2.546780e-06 6.387603e-07 -1.851744e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10202031 13.363622 0.5699994 7.192095e-07 + [2,] 0.17147551 12.606017 0.8701895 4.762324e-07 + [3,] 0.25708887 11.672162 1.2402163 1.767289e-07 + [4,] 0.35576307 10.595841 1.6666928 -1.684658e-07 + [5,] 0.07256926 13.684869 0.4427100 8.222389e-07 + [6,] 0.16200709 12.709297 0.8292663 5.093561e-07 + [7,] 0.27108894 11.519451 1.3007255 1.277521e-07 + [8,] 0.41347150 9.966368 1.9161126 -3.703487e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.0098676902 NA NA NA +[2,] 0.0008924936 NA NA NA +[3,] -0.0227288744 NA NA NA +[4,] 0.0131649307 NA NA NA +[5,] NA 0.10998098 -0.05446915 -8.222389e-07 +[6,] NA -0.02709793 0.05777205 -5.093561e-07 +[7,] NA -0.21546618 0.02838166 -1.277521e-07 +[8,] NA 0.13258313 -0.03168455 3.703487e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT2_res/KEIO_ROBOT2_46_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT2_res/KEIO_ROBOT2_46_res.txt new file mode 100644 index 0000000..26e803e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT2_res/KEIO_ROBOT2_46_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0217560744110283 0.0224226334896717 0.0221982308074859 0.00466595928425975 0.0150816055449889 0.0334501715815602 +Glc 14.2391296096261 14.2317602089275 14.1878007639613 0.38585547516061 13.5843579968648 14.9719814420028 +Ace 0.22309205021038 0.210362003431633 0.185631746237091 0.137093778917671 9.99999999965959e-07 0.490513235646213 +Lac 1e-06 0.0911992139781477 0.0713415595251186 0.0767314535898862 9.99999999993061e-07 0.250411762232749 +mu 0.617768313350809 0.61507596357349 0.613203324473826 0.0472469719651441 0.519864730959202 0.707021170642829 +qGlc -6.73850604554828 -6.68634017434654 -6.82472918200775 0.986256744584259 -8.36916661691319 -4.84058009201081 +qAce 2.67003622693389 2.71958369176574 2.74185522698645 0.386864463520996 1.916232341112 3.35710684612966 +qLac -2.16115500228865e-06 -0.0290564142692957 -0.035105232793923 0.209573466539953 -0.420875497988719 0.391913744907455 +res 2.53617064887967 20.0165648996058 18.7846409816961 5.9156613527584 11.4504826375608 33.513117330003 + + +Goodness of fit (khi2 test) + +khi2 value 2.53617064888075 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.317021331110094 +p-value, i.e. P(X^2<=value) 0.0399771068372085 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT3.txt b/validation/validation_results/Berges_2021/Berges_2021/WT3.txt new file mode 100644 index 0000000..80acb70 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT3.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.160272 NA NA +3.67805555555556 0.254016 NA NA +4.09222222222222 0.353808 NA NA +4.565 0.482328 NA NA +0.05 NA 14.3578917771037 0.020872091489987 +1.95 NA 13.8846272141345 0.404924565191357 +2.83333333333333 NA 13.6666522742018 0.7986598127634 +3.98333333333333 NA 11.814445529021 1.4360266762163 +4.88333333333333 NA 9.36769778000465 2.06211842173537 +5.16666666666667 NA 8.60212893644277 2.44464598736867 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT3_res/KEIO_ROBOT3_46.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT3_res/KEIO_ROBOT3_46.pdf new file mode 100644 index 0000000..2e9b87d Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT3_res/KEIO_ROBOT3_46.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT3_res/KEIO_ROBOT3_46_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT3_res/KEIO_ROBOT3_46_log.txt new file mode 100644 index 0000000..3c5cc74 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT3_res/KEIO_ROBOT3_46_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.160272 NA NA + [2,] 0.254016 NA NA + [3,] 0.353808 NA NA + [4,] 0.482328 NA NA + [5,] NA 14.357892 0.02087209 + [6,] NA 13.884627 0.40492457 + [7,] NA 13.666652 0.79865981 + [8,] NA 11.814446 1.43602668 + [9,] NA 9.367698 2.06211842 +[10,] NA 8.602129 2.44464599 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02440762 14.50537535 0.21647433 0.65128991 -5.74029199 2.19615092 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.374394e-08 -3.419003e-07 1.824129e-07 2.326241e-07 -4.014780e-07 3.771852e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008568722 0.423153447 0.182065774 0.083021290 0.735508577 0.314548689 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6358412 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.374394e-08 -3.419003e-07 1.824129e-07 2.326241e-07 -4.014780e-07 3.771852e-08 + +$result$normp +[1] 6.061809e-07 + +$result$res + [1] -0.06585852 0.69101071 -0.15211950 -0.25406334 0.30513678 0.15182711 -0.66936181 0.05685430 0.38565723 -0.23011361 0.99163247 0.11159449 -0.71750986 -1.00024045 0.26041971 0.35410364 + +$result$prevres + [1] -0.06585611 0.69101228 -0.15211914 -0.25406547 0.30513751 0.15182710 -0.66936226 0.05685354 0.38565717 -0.23011306 0.99163157 0.11159430 -0.71750961 -1.00023978 0.26042001 0.35410351 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 325.6252618 0.000000 0 2.286522e+01 0.000000000 0.00000000 + [2,] 548.6729867 0.000000 0 4.925583e+01 0.000000000 0.00000000 + [3,] 718.5570363 0.000000 0 7.177054e+01 0.000000000 0.00000000 + [4,] 977.6584441 0.000000 0 1.089316e+02 0.000000000 0.00000000 + [5,] -0.6342151 2.173913 0 -3.890929e-04 0.002696674 0.00000000 + [6,] -49.0676751 2.173913 0 -1.408449e+00 0.208635065 0.00000000 + [7,] -102.1267980 2.173913 0 -4.560316e+00 0.434241710 0.00000000 + [8,] -237.3435052 2.173913 0 -1.604361e+01 1.009181249 0.00000000 + [9,] -441.7964304 2.173913 0 -3.838502e+01 1.878512214 0.00000000 +[10,] -535.2118691 2.173913 0 -4.985221e+01 2.275713347 0.00000000 +[11,] 0.5580751 0.000000 5 3.423806e-04 0.000000000 0.00620235 +[12,] 43.1769079 0.000000 5 1.239360e+00 0.000000000 0.47986065 +[13,] 89.8660747 0.000000 5 4.012832e+00 0.000000000 0.99875593 +[14,] 208.8494849 0.000000 5 1.411751e+01 0.000000000 2.32111687 +[15,] 388.7570331 0.000000 5 3.377675e+01 0.000000000 4.32057809 +[16,] 470.9575814 0.000000 5 4.386725e+01 0.000000000 5.23414070 + +$result$retres +$result$retres$res + [1] -0.06585611 0.69101228 -0.15211914 -0.25406547 0.30513751 0.15182710 -0.66936226 0.05685354 0.38565717 -0.23011306 0.99163157 0.11159430 -0.71750961 -1.00023978 0.26042001 0.35410351 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15895488 13.319513 0.6701679 + [2,] 0.26783625 12.359862 1.0373162 + [3,] 0.35076562 11.628944 1.3169543 + [4,] 0.47724669 10.514174 1.7434489 + [5,] 0.02521554 14.498255 0.2191984 + [6,] 0.08691330 13.954468 0.4272434 + [7,] 0.15450352 13.358746 0.6551579 + [8,] 0.32675153 11.840598 1.2359787 + [9,] 0.58719722 9.545100 2.1142024 + [10,] 0.70619600 8.496277 2.5154667 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.001317122 NA NA + [2,] -0.013820246 NA NA + [3,] 0.003042383 NA NA + [4,] 0.005081309 NA NA + [5,] NA -0.14036325 -0.19832631 + [6,] NA -0.06984047 -0.02231886 + [7,] NA 0.30790664 0.14350192 + [8,] NA -0.02615263 0.20004796 + [9,] NA -0.17740230 -0.05208400 +[10,] NA 0.10585201 -0.07082070 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT3_res/KEIO_ROBOT3_46_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT3_res/KEIO_ROBOT3_46_res.txt new file mode 100644 index 0000000..f8336f8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT3_res/KEIO_ROBOT3_46_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0244076154218182 0.0241210826233665 0.0242454454797088 0.00305436587981422 0.0185822087941339 0.0299736460308275 +Glc 14.5053753487478 14.4821621954881 14.469073059416 0.234542455768876 14.0577346026405 14.9751736359511 +Ace 0.21647432911298 0.221510964640078 0.215136837518264 0.105732182933392 0.0262150873940809 0.41469094594303 +mu 0.651289907203958 0.655339455069455 0.653436295237363 0.0274002101202294 0.605400674889595 0.705097013057007 +qGlc -5.74029198772018 -5.72731302870365 -5.70693605954904 0.422711013191574 -6.53503199872252 -5.02182560012581 +qAce 2.19615091952663 2.20723832191625 2.1908631447366 0.204586763446644 1.877313070061 2.57179498525552 +res 4.04294047882464 23.3160941566864 22.650881175349 6.73366156871433 13.8111896466059 39.5010468201464 + + +Goodness of fit (khi2 test) + +khi2 value 4.04294047884105 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.404294047884105 +p-value, i.e. P(X^2<=value) 0.0546109323904727 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT4.txt b/validation/validation_results/Berges_2021/Berges_2021/WT4.txt new file mode 100644 index 0000000..2495f2f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT4.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.06048 NA NA +1.61361111111111 0.077112 NA NA +2.36138888888889 0.117936 NA NA +3.28638888888889 0.208656 NA NA +3.81944444444444 0.297864 NA NA +4.41083333333333 0.409752 NA NA +0.283333333333333 NA 14.2116830953905 0.0427639227773716 +1.91666666666667 NA 13.5430595208886 0.339709465505823 +2.7 NA 13.0030707860023 0.649267054264322 +3.61666666666667 NA 12.3099913190415 1.09746732275799 +4.05 NA 11.846995811448 1.34586285565091 +4.75 NA 10.2207308621112 1.83260326757302 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT4_res/KEIO_ROBOT4_40.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT4_res/KEIO_ROBOT4_40.pdf new file mode 100644 index 0000000..7e9efc0 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT4_res/KEIO_ROBOT4_40.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT4_res/KEIO_ROBOT4_40_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT4_res/KEIO_ROBOT4_40_log.txt new file mode 100644 index 0000000..15b9378 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT4_res/KEIO_ROBOT4_40_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.060480 NA NA + [3,] 0.077112 NA NA + [4,] 0.117936 NA NA + [5,] 0.208656 NA NA + [6,] 0.297864 NA NA + [7,] 0.409752 NA NA + [8,] NA 14.21168 0.04276392 + [9,] NA 13.54306 0.33970947 +[10,] NA 13.00307 0.64926705 +[11,] NA 12.30999 1.09746732 +[12,] NA 11.84700 1.34586286 +[13,] NA 10.22073 1.83260327 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03103335 14.14588144 0.12107475 0.58553889 -4.80108987 2.25825700 + +$result$lastp + X Glc Ace mu qGlc qAce + 4.670761e-09 7.112782e-08 -2.086803e-07 -4.294613e-08 -4.880016e-08 5.411510e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.004444856 0.239742950 0.104515899 0.036074085 0.568641290 0.248748019 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3602471 + +$result$laststep + X Glc Ace mu qGlc qAce + 4.670761e-09 7.112782e-08 -2.086803e-07 -4.294613e-08 -4.880016e-08 5.411510e-07 + +$result$normp +[1] 5.879614e-07 + +$result$res + [1] -0.18713235 0.09979696 0.13588093 0.28750910 0.19675968 -0.36976534 0.04563357 -0.24287032 0.16440190 0.34937705 -0.05367369 -0.37516671 0.15793177 0.49954647 0.14669739 -0.33124859 -0.50621909 -0.31151335 0.50273717 + +$result$prevres + [1] -0.18713258 0.09979665 0.13588060 0.28750879 0.19675958 -0.36976514 0.04563437 -0.24287046 0.16440188 0.34937708 -0.05367361 -0.37516664 0.15793176 0.49954747 0.14669801 -0.33124828 -0.50621930 -0.31151389 0.50273598 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.0000000 + [2,] 100.659349 0.000000 0 3.73293699 0.00000000 0.0000000 + [3,] 128.619076 0.000000 0 6.44069745 0.00000000 0.0000000 + [4,] 199.279456 0.000000 0 14.60355807 0.00000000 0.0000000 + [5,] 342.520550 0.000000 0 34.93286648 0.00000000 0.0000000 + [6,] 467.994451 0.000000 0 55.47145258 0.00000000 0.0000000 + [7,] 661.650625 0.000000 0 90.56867460 0.00000000 0.0000000 + [8,] -3.216643 2.173913 0 -0.01453247 0.02079178 0.0000000 + [9,] -36.930607 2.173913 0 -1.29957880 0.23871255 0.0000000 +[10,] -68.796757 2.173913 0 -3.61182630 0.44468940 0.0000000 +[11,] -130.335241 2.173913 0 -9.72136678 0.84246267 0.0000000 +[12,] -173.128077 2.173913 0 -14.82420756 1.11906757 0.0000000 +[13,] -269.871108 2.173913 0 -28.10573475 1.74439647 0.0000000 +[14,] 3.479879 0.000000 5 0.01572174 0.00000000 0.0478211 +[15,] 39.952845 0.000000 5 1.40593061 0.00000000 0.5490389 +[16,] 74.426781 0.000000 5 3.90740225 0.00000000 1.0227856 +[17,] 141.001302 0.000000 5 10.51692059 0.00000000 1.9376641 +[18,] 187.296116 0.000000 5 16.03735537 0.00000000 2.5738554 +[19,] 291.956170 0.000000 5 30.40578421 0.00000000 4.0121119 + +$result$retres +$result$retres$res + [1] -0.18713258 0.09979665 0.13588060 0.28750879 0.19675958 -0.36976514 0.04563437 -0.24287046 0.16440188 0.34937708 -0.05367361 -0.37516664 0.15793176 0.49954747 0.14669801 -0.33124828 -0.50621930 -0.31151389 0.50273598 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03103335 14.14588 0.1210750 + [2,] 0.06247593 13.88807 0.2423400 + [3,] 0.07982961 13.74578 0.3092682 + [4,] 0.12368618 13.38618 0.4784105 + [5,] 0.21259119 12.65721 0.8212917 + [6,] 0.29046870 12.01866 1.1216430 + [7,] 0.41066469 11.03312 1.5852046 + [8,] 0.03663357 14.09996 0.1426734 + [9,] 0.09533007 13.61868 0.3690491 + [10,] 0.15080951 13.16378 0.5830174 + [11,] 0.25794891 12.28530 0.9962235 + [12,] 0.33245186 11.67442 1.2835601 + [13,] 0.50088289 10.29338 1.9331505 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0037426516 NA NA + [2,] -0.0019959329 NA NA + [3,] -0.0027176120 NA NA + [4,] -0.0057501758 NA NA + [5,] -0.0039351915 NA NA + [6,] 0.0073953029 NA NA + [7,] -0.0009126874 NA NA + [8,] NA 0.11172041 -0.09990949 + [9,] NA -0.07562486 -0.02933960 +[10,] NA -0.16071346 0.06624966 +[11,] NA 0.02468986 0.10124386 +[12,] NA 0.17257666 0.06230278 +[13,] NA -0.07264861 -0.10054720 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT4_res/KEIO_ROBOT4_40_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT4_res/KEIO_ROBOT4_40_res.txt new file mode 100644 index 0000000..0260d3c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT4_res/KEIO_ROBOT4_40_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0310333530829463 0.0315264910549587 0.0315354397181959 0.00410401569238524 0.0240840336618418 0.0405349162716046 +Glc 14.1458814356202 14.1503550053304 14.1470907615895 0.212168814566187 13.780603468891 14.5592139049331 +Ace 0.121074746711062 0.133392557557418 0.133971630360329 0.0794662234685088 9.99999999998766e-07 0.282279544988252 +mu 0.585538892459058 0.584941458261113 0.583522456094578 0.031192234742122 0.526484740799651 0.643939823377127 +qGlc -4.80108986606804 -4.69700188933503 -4.63759722449243 0.570071430710397 -5.70924055891962 -3.74510773470152 +qAce 2.25825699630613 2.22032012418663 2.19638115370088 0.252009744702445 1.69944258852944 2.7214848859998 +res 1.68711334416446 32.5441695481739 32.2004628567251 7.20051338804515 19.4738330761443 46.5915305247108 + + +Goodness of fit (khi2 test) + +khi2 value 1.68711334416884 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.129777949551449 +p-value, i.e. P(X^2<=value) 8.55657141098212e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1.txt new file mode 100644 index 0000000..86e9d79 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1.txt @@ -0,0 +1,17 @@ +time X Glc Ace +1.69472222222222 6.1992000000000005E-2 NA NA +2.3002777777777799 8.6184000000000011E-2 NA NA +2.6983333333333301 0.11037599999999999 NA NA +3.43611111111111 0.17841599999999999 NA NA +3.8211111111111098 0.20865600000000001 NA NA +4.2011111111111097 0.3024 NA NA +4.5980555555555496 0.378 NA NA +4.9950000000000001 0.54583199999999998 NA NA +5.3752777777777796 0.60933599999999999 NA NA +1.35 NA 13.6276813815462 0.216958848225059 +1.91666666666667 NA 13.5792133323062 0.371914222400848 +2.86666666666667 NA 12.6200457520069 0.707537683463011 +4 NA 11.2499817544224 1.46436775470691 +4.8 NA 9.36560347817446 2.13574936032777 +5.18333333333333 NA 8.20020915137498 2.54657962639804 +5.58333333333333 NA 6.55172432249331 2.88518116059672 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1_res/KEIO_ROBOT6_1.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1_res/KEIO_ROBOT6_1.pdf new file mode 100644 index 0000000..698a167 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1_res/KEIO_ROBOT6_1.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1_res/KEIO_ROBOT6_1_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1_res/KEIO_ROBOT6_1_log.txt new file mode 100644 index 0000000..d96f370 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1_res/KEIO_ROBOT6_1_log.txt @@ -0,0 +1,211 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + [15,] 0.02 0.46 0.2 + [16,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.694722 2.300278 2.698333 3.436111 3.821111 4.201111 4.598056 4.995000 5.375278 1.350000 1.916667 2.866667 4.000000 4.800000 5.183333 5.583333 + +$sys$data_meas + X Glc Ace + [1,] 0.061992 NA NA + [2,] 0.086184 NA NA + [3,] 0.110376 NA NA + [4,] 0.178416 NA NA + [5,] 0.208656 NA NA + [6,] 0.302400 NA NA + [7,] 0.378000 NA NA + [8,] 0.545832 NA NA + [9,] 0.609336 NA NA +[10,] NA 13.627681 0.2169588 +[11,] NA 13.579213 0.3719142 +[12,] NA 12.620046 0.7075377 +[13,] NA 11.249982 1.4643678 +[14,] NA 9.365603 2.1357494 +[15,] NA 8.200209 2.5465796 +[16,] NA 6.551724 2.8851812 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02070843 13.90270361 0.26090354 0.63597381 -6.74767540 2.59298878 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.030079e-08 1.282740e-07 1.254888e-07 -9.974672e-08 7.011575e-07 -6.425619e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.005691808 0.548725697 0.237018693 0.056291237 0.942993947 0.404379410 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.9137875 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.030079e-08 1.282740e-07 1.254888e-07 -9.974672e-08 7.011575e-07 -6.425619e-07 + +$result$normp +[1] 9.730184e-07 + +$result$res + [1] -0.05731851 0.16230572 0.24085807 0.28731773 1.32992196 -0.14165602 0.37968007 -2.47536771 1.13912728 -0.05161219 -0.43528810 0.30885269 0.16442423 0.22827852 -0.03011187 -0.18454328 0.79376656 0.45122453 -0.04165618 -1.06572178 -0.85843352 -0.44502693 1.16584732 + +$result$prevres + [1] -0.05731950 0.16230452 0.24085676 0.28731630 1.32992059 -0.14165719 0.37967932 -2.47536769 1.13912851 -0.05161226 -0.43528806 0.30885293 0.16442461 0.22827871 -0.03011199 -0.18454393 0.79376584 0.45122376 -0.04165695 -1.06572228 -0.85843333 -0.44502612 1.16584908 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 146.91029 0.000000 0 5.1558204 0.00000000 0.0000000 + [2,] 215.92684 0.000000 0 10.2857025 0.00000000 0.0000000 + [3,] 278.13111 0.000000 0 15.5414738 0.00000000 0.0000000 + [4,] 444.65559 0.000000 0 31.6401107 0.00000000 0.0000000 + [5,] 568.01623 0.000000 0 44.9466623 0.00000000 0.0000000 + [6,] 723.29711 0.000000 0 62.9256824 0.00000000 0.0000000 + [7,] 931.00662 0.000000 0 88.6490366 0.00000000 0.0000000 + [8,] 1198.36415 0.000000 0 123.9570804 0.00000000 0.0000000 + [9,] 1526.23538 0.000000 0 169.8906452 0.00000000 0.0000000 +[10,] -31.36339 2.173913 0 -0.5003788 0.09625334 0.0000000 +[11,] -54.97896 2.173913 0 -1.3074506 0.16872883 0.0000000 +[12,] -119.73550 2.173913 0 -4.5784440 0.36746480 0.0000000 +[13,] -270.53541 2.173913 0 -15.5109159 0.83026536 0.0000000 +[14,] -465.26874 2.173913 0 -33.3906401 1.42789636 0.0000000 +[15,] -600.08618 2.173913 0 -47.3483785 1.84164720 0.0000000 +[16,] -780.59701 2.173913 0 -67.5034514 2.39562972 0.0000000 +[17,] 27.72026 0.000000 5 0.4422555 0.00000000 0.2213827 +[18,] 48.59268 0.000000 5 1.1555790 0.00000000 0.3880763 +[19,] 105.82720 0.000000 5 4.0466185 0.00000000 0.8451690 +[20,] 239.11040 0.000000 5 13.7091901 0.00000000 1.9096103 +[21,] 411.22379 0.000000 5 29.5120310 0.00000000 3.2841616 +[22,] 530.38103 0.000000 5 41.8484584 0.00000000 4.2357886 +[23,] 689.92397 0.000000 5 59.6623468 0.00000000 5.5099484 + +$result$retres +$result$retres$res + [1] -0.05731950 0.16230452 0.24085676 0.28731630 1.32992059 -0.14165719 0.37967932 -2.47536769 1.13912851 -0.05161226 -0.43528806 0.30885293 0.16442461 0.22827871 -0.03011199 -0.18454393 0.79376584 0.45122376 -0.04165695 -1.06572228 -0.85843333 -0.44502612 1.16584908 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06084561 13.476848 0.4245505 + [2,] 0.08943009 13.173567 0.5410950 + [3,] 0.11519314 12.900222 0.6461360 + [4,] 0.18416233 12.168459 0.9273368 + [5,] 0.23525441 11.626373 1.1356492 + [6,] 0.29956686 10.944019 1.3978635 + [7,] 0.38559359 10.031276 1.7486112 + [8,] 0.49632465 8.856421 2.2000833 + [9,] 0.63211857 7.415649 2.7537416 + [10,] 0.04886715 13.603940 0.3757120 + [11,] 0.07006971 13.378981 0.4621590 + [12,] 0.12820952 12.762118 0.6992063 + [13,] 0.26360090 11.325617 1.2512233 + [14,] 0.43843665 9.470612 1.9640627 + [15,] 0.55947863 8.186358 2.4575744 + [16,] 0.72154511 6.466834 3.1183510 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.001146390 NA NA + [2,] -0.003246090 NA NA + [3,] -0.004817135 NA NA + [4,] -0.005746326 NA NA + [5,] -0.026598412 NA NA + [6,] 0.002833144 NA NA + [7,] -0.007593586 NA NA + [8,] 0.049507354 NA NA + [9,] -0.022782570 NA NA +[10,] NA 0.02374164 -0.15875317 +[11,] NA 0.20023251 -0.09024475 +[12,] NA -0.14207235 0.00833139 +[13,] NA -0.07563532 0.21314446 +[14,] NA -0.10500821 0.17168667 +[15,] NA 0.01385151 0.08900522 +[16,] NA 0.08489021 -0.23316982 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1_res/KEIO_ROBOT6_1_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1_res/KEIO_ROBOT6_1_res.txt new file mode 100644 index 0000000..df75319 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_1_res/KEIO_ROBOT6_1_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0207084337676758 0.0208976077000703 0.0209356075734266 0.00219256831340121 0.0168484877927683 0.0246485140032572 +Glc 13.9027036100327 13.8993536184307 13.8913215414689 0.204897237029866 13.508785529863 14.2417769957412 +Ace 0.260903544535617 0.272093547195377 0.274905646574454 0.0761138756168814 0.127672831776765 0.425469011902609 +mu 0.635973812785956 0.635126547735 0.633988658630189 0.0208370088956886 0.602287459268798 0.67683144556754 +qGlc -6.74767540047978 -6.71938746799311 -6.74928442189449 0.370928367541282 -7.33013669475001 -6.00854404944626 +qAce 2.59298877697441 2.57625927570946 2.57724406714981 0.150183038358901 2.26019801035397 2.85883149031973 +res 14.1951277011697 41.0447985862981 40.0077470087054 8.07046900932179 28.4020267716968 58.7778655067074 + + +Goodness of fit (khi2 test) + +khi2 value 14.1951277011868 +data points 23 +fitted parameters 6 +degrees of freedom 17 +khi2 reduced value 0.835007511834518 +p-value, i.e. P(X^2<=value) 0.346755341837859 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2.txt new file mode 100644 index 0000000..330c040 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2.txt @@ -0,0 +1,17 @@ +time X Glc Ace +1.69472222222222 9.2231999999999995E-2 NA NA +2.3002777777777799 0.12096 NA NA +2.6983333333333301 0.14666400000000002 NA NA +3.43611111111111 0.22226399999999999 NA NA +3.8211111111111098 0.26611199999999996 NA NA +4.2011111111111097 0.32659199999999999 NA NA +4.5980555555555496 0.41428800000000005 NA NA +4.9950000000000001 0.63050399999999995 NA NA +5.3752777777777796 0.79531200000000002 NA NA +1.35 NA 13.6314464876018 0.198784176667544 +1.91666666666667 NA 13.5227482068367 0.337257134190014 +2.86666666666667 NA 12.5609507702081 0.621968821144039 +4 NA 11.3750632304105 1.30831565908841 +4.8 NA 9.31992576685056 1.97187177862311 +5.18333333333333 NA 7.53324535081232 2.31121478647947 +5.58333333333333 NA 5.96517290124761 2.73382285300386 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2_res/KEIO_ROBOT6_2.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2_res/KEIO_ROBOT6_2.pdf new file mode 100644 index 0000000..a5b6db9 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2_res/KEIO_ROBOT6_2.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2_res/KEIO_ROBOT6_2_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2_res/KEIO_ROBOT6_2_log.txt new file mode 100644 index 0000000..0945090 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2_res/KEIO_ROBOT6_2_log.txt @@ -0,0 +1,211 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + [15,] 0.02 0.46 0.2 + [16,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.694722 2.300278 2.698333 3.436111 3.821111 4.201111 4.598056 4.995000 5.375278 1.350000 1.916667 2.866667 4.000000 4.800000 5.183333 5.583333 + +$sys$data_meas + X Glc Ace + [1,] 0.092232 NA NA + [2,] 0.120960 NA NA + [3,] 0.146664 NA NA + [4,] 0.222264 NA NA + [5,] 0.266112 NA NA + [6,] 0.326592 NA NA + [7,] 0.414288 NA NA + [8,] 0.630504 NA NA + [9,] 0.795312 NA NA +[10,] NA 13.631446 0.1987842 +[11,] NA 13.522748 0.3372571 +[12,] NA 12.560951 0.6219688 +[13,] NA 11.375063 1.3083157 +[14,] NA 9.319926 1.9718718 +[15,] NA 7.533245 2.3112148 +[16,] NA 5.965173 2.7338229 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02110581 13.91028150 0.24438955 0.67174721 -6.17928386 2.04695394 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.754235e-09 6.918794e-08 -4.695705e-08 -2.703232e-08 7.677494e-08 1.887973e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.005711139 0.607981177 0.261655391 0.055129556 0.888473432 0.377652411 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.034694 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.754235e-09 6.918794e-08 -4.695705e-08 -2.703232e-08 7.677494e-08 1.887973e-08 + +$result$normp +[1] 1.182417e-07 + +$result$res + [1] -1.317143632 -1.099812123 -0.868128095 -0.500893687 0.438875722 1.411800485 2.448393043 -1.284352777 -0.723361245 -0.017024896 -0.264931513 0.460135701 -0.265584053 -0.208768319 0.559246606 -0.263073526 0.702833537 0.379386055 -0.003572324 -0.918191178 -0.875328213 -0.197908446 0.912780567 + +$result$prevres + [1] -1.317143911 -1.099812461 -0.868128467 -0.500894086 0.438875348 1.411800184 2.448392900 -1.284352640 -0.723360667 -0.017024986 -0.264931567 0.460135718 -0.265583959 -0.208768234 0.559246638 -0.263073611 0.702833716 0.379386199 -0.003572257 -0.918191224 -0.875328326 -0.197908570 0.912780463 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 156.09238 0.000000 0 5.5831879 0.0000000 0.0000000 + [2,] 234.44670 0.000000 0 11.3822058 0.0000000 0.0000000 + [3,] 306.31714 0.000000 0 17.4449180 0.0000000 0.0000000 + [4,] 502.81442 0.000000 0 36.4650623 0.0000000 0.0000000 + [5,] 651.21761 0.000000 0 52.5191675 0.0000000 0.0000000 + [6,] 840.59317 0.000000 0 74.5335934 0.0000000 0.0000000 + [7,] 1097.46048 0.000000 0 106.5038086 0.0000000 0.0000000 + [8,] 1432.82095 0.000000 0 151.0530326 0.0000000 0.0000000 + [9,] 1849.83369 0.000000 0 209.8628815 0.0000000 0.0000000 +[10,] -29.52684 2.173913 0 -0.4833758 0.1008512 0.0000000 +[11,] -52.46873 2.173913 0 -1.2829304 0.1792109 0.0000000 +[12,] -117.18061 2.173913 0 -4.6179984 0.4002392 0.0000000 +[13,] -273.71268 2.173913 0 -16.1961068 0.9348863 0.0000000 +[14,] -482.70131 2.173913 0 -35.7612251 1.6487027 0.0000000 +[15,] -630.34183 2.173913 0 -51.3412266 2.1529801 0.0000000 +[16,] -830.81617 2.173913 0 -74.1568950 2.8377153 0.0000000 +[17,] 22.49649 0.000000 5 0.3682838 0.0000000 0.2319577 +[18,] 39.97591 0.000000 5 0.9774642 0.0000000 0.4121851 +[19,] 89.27986 0.000000 5 3.5184512 0.0000000 0.9205502 +[20,] 208.54158 0.000000 5 12.3398075 0.0000000 2.1502385 +[21,] 367.76994 0.000000 5 27.2464634 0.0000000 3.7920163 +[22,] 480.25720 0.000000 5 39.1168606 0.0000000 4.9518542 +[23,] 632.99852 0.000000 5 56.5001094 0.0000000 6.5267452 + +$result$retres +$result$retres$res + [1] -1.317143911 -1.099812461 -0.868128467 -0.500894086 0.438875348 1.411800184 2.448392900 -1.284352640 -0.723360667 -0.017024986 -0.264931567 0.460135718 -0.265583959 -0.208768234 0.559246638 -0.263073611 0.702833716 0.379386199 -0.003572257 -0.918191224 -0.875328326 -0.197908570 0.912780463 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06588912 13.498328 0.3808537 + [2,] 0.09896375 13.194080 0.4816390 + [3,] 0.12930143 12.915009 0.5740842 + [4,] 0.21224612 12.152016 0.8268340 + [5,] 0.27488951 11.575770 1.0177214 + [6,] 0.35482800 10.840430 1.2613107 + [7,] 0.46325586 9.843021 1.5917130 + [8,] 0.60481695 8.540826 2.0230792 + [9,] 0.78084479 6.921577 2.5594727 + [10,] 0.05226919 13.623615 0.3393509 + [11,] 0.07648265 13.400880 0.4131344 + [12,] 0.14478122 12.772613 0.6212544 + [13,] 0.30998916 11.252895 1.1246774 + [14,] 0.53056110 9.223892 1.7968061 + [15,] 0.68638469 7.790499 2.2716331 + [16,] 0.89797043 5.844159 2.9163789 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.026342878 NA NA + [2,] 0.021996249 NA NA + [3,] 0.017362569 NA NA + [4,] 0.010017882 NA NA + [5,] -0.008777507 NA NA + [6,] -0.028236004 NA NA + [7,] -0.048967858 NA NA + [8,] 0.025687053 NA NA + [9,] 0.014467213 NA NA +[10,] NA 0.007831493 -0.1405667431 +[11,] NA 0.121868521 -0.0758772397 +[12,] NA -0.211662430 0.0007144514 +[13,] NA 0.122168621 0.1836382449 +[14,] NA 0.096033387 0.1750656652 +[15,] NA -0.257253454 0.0395817139 +[16,] NA 0.121013861 -0.1825560925 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2_res/KEIO_ROBOT6_2_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2_res/KEIO_ROBOT6_2_res.txt new file mode 100644 index 0000000..5ab0a23 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_2_res/KEIO_ROBOT6_2_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0211058132231425 0.0212954541477968 0.0211689846241484 0.00192310141162844 0.0179487930688219 0.025169273141844 +Glc 13.9102815027141 13.8980754647887 13.8984984539419 0.187581249855792 13.5934776657632 14.2605737836008 +Ace 0.244389547448615 0.250289847472858 0.248932190444026 0.0771778813183895 0.128396735279641 0.384765930517539 +mu 0.671747213285856 0.670429410855552 0.669963624474398 0.0174410307709234 0.637854106477387 0.702320768031297 +qGlc -6.17928386172899 -6.17727320160841 -6.11426451083082 0.353415739812146 -6.94321024210717 -5.63542740328909 +qAce 2.04695394245446 2.03446777807302 2.05567378390769 0.14730514995609 1.74101809182244 2.29589828265569 +res 18.2000485999683 40.2577701704235 37.9583833553346 9.94966853046689 23.5903976600824 63.4011381087844 + + +Goodness of fit (khi2 test) + +khi2 value 18.2000485999696 +data points 23 +fitted parameters 6 +degrees of freedom 17 +khi2 reduced value 1.07059109411586 +p-value, i.e. P(X^2<=value) 0.623673190726694 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3.txt new file mode 100644 index 0000000..7be32d7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3.txt @@ -0,0 +1,17 @@ +time X Glc Ace +1.69472222222222 6.8040000000000003E-2 NA NA +2.3002777777777799 0.10584000000000002 NA NA +2.6983333333333301 0.12247200000000001 NA NA +3.43611111111111 0.18143999999999999 NA NA +3.8211111111111098 0.238896 NA NA +4.2011111111111097 0.28123199999999998 NA NA +4.5980555555555496 0.37043999999999999 NA NA +4.9950000000000001 0.60631200000000007 NA NA +5.3752777777777796 0.66376800000000002 NA NA +1.35 NA 13.4255093136864 0.198987511992196 +1.91666666666667 NA 13.5798053445577 0.339570808822952 +2.86666666666667 NA 12.8678920218922 0.637954102999748 +4 NA 11.0688792784027 1.32559135330493 +4.8 NA 9.27686657061253 2.00109343568648 +5.18333333333333 NA 8.04165234247458 2.41251681196779 +5.58333333333333 NA 6.25080870331257 2.76301779935182 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3_res/KEIO_ROBOT6_3.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3_res/KEIO_ROBOT6_3.pdf new file mode 100644 index 0000000..234efdb Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3_res/KEIO_ROBOT6_3.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3_res/KEIO_ROBOT6_3_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3_res/KEIO_ROBOT6_3_log.txt new file mode 100644 index 0000000..de1226d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3_res/KEIO_ROBOT6_3_log.txt @@ -0,0 +1,211 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + [15,] 0.02 0.46 0.2 + [16,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.694722 2.300278 2.698333 3.436111 3.821111 4.201111 4.598056 4.995000 5.375278 1.350000 1.916667 2.866667 4.000000 4.800000 5.183333 5.583333 + +$sys$data_meas + X Glc Ace + [1,] 0.068040 NA NA + [2,] 0.105840 NA NA + [3,] 0.122472 NA NA + [4,] 0.181440 NA NA + [5,] 0.238896 NA NA + [6,] 0.281232 NA NA + [7,] 0.370440 NA NA + [8,] 0.606312 NA NA + [9,] 0.663768 NA NA +[10,] NA 13.425509 0.1989875 +[11,] NA 13.579805 0.3395708 +[12,] NA 12.867892 0.6379541 +[13,] NA 11.068879 1.3255914 +[14,] NA 9.276867 2.0010934 +[15,] NA 8.041652 2.4125168 +[16,] NA 6.250809 2.7630178 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01927487 13.84849206 0.24072009 0.66411102 -6.64780364 2.36937829 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.134540e-08 -3.518228e-07 2.435532e-07 1.229066e-07 -2.498493e-07 -1.561439e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.007062246 0.740448142 0.318991782 0.074723421 1.225900575 0.522407174 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.251179 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.134540e-08 -3.518228e-07 2.435532e-07 1.229066e-07 -2.498493e-07 -1.561439e-07 + +$result$normp +[1] 5.33983e-07 + +$result$res + [1] -0.43202538 -0.85175513 -0.33979016 0.36868897 0.24636739 1.62918965 1.90155874 -3.73174024 1.03299110 0.31086333 -0.49433224 -0.26379321 0.48691072 0.19326156 -0.06832427 -0.16458590 0.70761854 0.38979787 -0.02242046 -0.87002251 -0.81330969 -0.45474464 1.06308089 + +$result$prevres + [1] -0.43202425 -0.85175377 -0.33978868 0.36869054 0.24636884 1.62919078 1.90155922 -3.73174092 1.03298864 0.31086382 -0.49433191 -0.26379321 0.48691033 0.19326115 -0.06832449 -0.16458568 0.70761760 0.38979710 -0.02242084 -0.87002231 -0.81330912 -0.45474396 1.06308153 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 154.08532 0.000000 0 5.0332839 0.00000000 0.0000000 + [2,] 230.36443 0.000000 0 10.2137997 0.00000000 0.0000000 + [3,] 300.06994 0.000000 0 15.6066509 0.00000000 0.0000000 + [4,] 489.79251 0.000000 0 32.4392617 0.00000000 0.0000000 + [5,] 632.49008 0.000000 0 46.5838107 0.00000000 0.0000000 + [6,] 814.05399 0.000000 0 65.9187555 0.00000000 0.0000000 + [7,] 1059.59477 0.000000 0 93.9086599 0.00000000 0.0000000 + [8,] 1379.19731 0.000000 0 132.7863761 0.00000000 0.0000000 + [9,] 1775.44001 0.000000 0 183.9494699 0.00000000 0.0000000 +[10,] -31.57813 2.173913 0 -0.4714327 0.09155876 0.0000000 +[11,] -55.95025 2.173913 0 -1.2470517 0.16222415 0.0000000 +[12,] -124.28267 2.173913 0 -4.4624657 0.36034959 0.0000000 +[13,] -288.23669 2.173913 0 -15.5350121 0.83572371 0.0000000 +[14,] -505.58329 2.173913 0 -34.1157491 1.46590615 0.0000000 +[15,] -658.46799 2.173913 0 -48.8493006 1.90918550 0.0000000 +[16,] -865.44205 2.173913 0 -70.3608520 2.50929343 0.0000000 +[17,] 25.88634 0.000000 5 0.3864593 0.00000000 0.2105852 +[18,] 45.86550 0.000000 5 1.0222769 0.00000000 0.3731155 +[19,] 101.88135 0.000000 5 3.6581289 0.00000000 0.8288040 +[20,] 236.28349 0.000000 5 12.7349047 0.00000000 1.9221645 +[21,] 414.45446 0.000000 5 27.9665578 0.00000000 3.3715842 +[22,] 539.78247 0.000000 5 40.0444611 0.00000000 4.3911267 +[23,] 709.45049 0.000000 5 57.6786641 0.00000000 5.7713749 + +$result$retres +$result$retres$res + [1] -0.43202425 -0.85175377 -0.33978868 0.36869054 0.24636884 1.62919078 1.90155922 -3.73174092 1.03298864 0.31086382 -0.49433191 -0.26379321 0.48691033 0.19326115 -0.06832449 -0.16458568 0.70761760 0.38979710 -0.02242084 -0.87002231 -0.81330912 -0.45474396 1.06308153 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05939951 13.446842 0.3838743 + [2,] 0.08880492 13.152491 0.4887853 + [3,] 0.11567623 12.883507 0.5846553 + [4,] 0.18881381 12.151394 0.8455916 + [5,] 0.24382338 11.600744 1.0418517 + [6,] 0.31381582 10.900114 1.2915669 + [7,] 0.40847118 9.952606 1.6292731 + [8,] 0.53167718 8.719304 2.0688407 + [9,] 0.68442777 7.190259 2.6138159 + [10,] 0.04724526 13.568507 0.3405110 + [11,] 0.06883290 13.352413 0.4175302 + [12,] 0.12935844 12.746547 0.6334699 + [13,] 0.27458096 11.292858 1.1515869 + [14,] 0.46709603 9.365767 1.8384316 + [15,] 0.60251389 8.010223 2.3215680 + [16,] 0.78584147 6.175099 2.9756341 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.008640485 NA NA + [2,] 0.017035075 NA NA + [3,] 0.006795774 NA NA + [4,] -0.007373811 NA NA + [5,] -0.004927377 NA NA + [6,] -0.032583816 NA NA + [7,] -0.038031184 NA NA + [8,] 0.074634818 NA NA + [9,] -0.020659773 NA NA +[10,] NA -0.14299736 -0.141523521 +[11,] NA 0.22739268 -0.077959421 +[12,] NA 0.12134488 0.004484168 +[13,] NA -0.22397875 0.174004463 +[14,] NA -0.08890013 0.162661824 +[15,] NA 0.03142927 0.090948793 +[16,] NA 0.07570941 -0.212616306 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3_res/KEIO_ROBOT6_3_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3_res/KEIO_ROBOT6_3_res.txt new file mode 100644 index 0000000..faa4579 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_3_res/KEIO_ROBOT6_3_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0192748660808494 0.0195146579825119 0.019354796033023 0.00200744341910352 0.0158795931931639 0.023145287972475 +Glc 13.8484920642798 13.8468670179116 13.8631315442893 0.158514283720555 13.4857672771136 14.1069745510498 +Ace 0.240720088600995 0.228032133362436 0.233124518011192 0.0806067892605793 0.059628996182921 0.367194508519684 +mu 0.66411102252026 0.662610760732899 0.662587077441092 0.0200309431316388 0.627605645851042 0.702316284407328 +qGlc -6.64780364196254 -6.606435625221 -6.61820715818219 0.327754838082676 -7.19158321575962 -5.93180957300894 +qAce 2.36937829246753 2.37946239460266 2.38510634249221 0.141298041989887 2.07250870253255 2.64835765659545 +res 26.6126495209184 43.3871724149194 41.7565761959713 10.6400678480773 28.7477167201982 66.9177384851204 + + +Goodness of fit (khi2 test) + +khi2 value 26.6126495209406 +data points 23 +fitted parameters 6 +degrees of freedom 17 +khi2 reduced value 1.56544997182004 +p-value, i.e. P(X^2<=value) 0.936001318953676 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4.txt new file mode 100644 index 0000000..19998ad --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4.txt @@ -0,0 +1,17 @@ +time X Glc Ace +1.69472222222222 7.2576000000000002E-2 NA NA +2.3002777777777799 0.10735199999999999 NA NA +2.6983333333333301 0.145152 NA NA +3.43611111111111 0.2268 NA NA +3.8211111111111098 0.29332800000000003 NA NA +4.2011111111111097 0.35985600000000001 NA NA +4.5980555555555496 0.47779199999999999 NA NA +4.9950000000000001 0.66679200000000005 NA NA +5.3752777777777796 0.80740800000000001 NA NA +1.35 NA 13.6584585436063 0.231295258121677 +1.91666666666667 NA 13.4569126198258 0.381290089942336 +2.86666666666667 NA 12.9817069855121 0.751702154042582 +4 NA 11.0194527088201 1.51250682348908 +4.8 NA 8.90228756407925 2.20037511457438 +5.18333333333333 NA 7.46723781923564 2.62492815792516 +5.58333333333333 NA 5.66355841746783 3.01384977322893 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4_res/KEIO_ROBOT6_4.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4_res/KEIO_ROBOT6_4.pdf new file mode 100644 index 0000000..6b097f7 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4_res/KEIO_ROBOT6_4.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4_res/KEIO_ROBOT6_4_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4_res/KEIO_ROBOT6_4_log.txt new file mode 100644 index 0000000..cd42cb7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4_res/KEIO_ROBOT6_4_log.txt @@ -0,0 +1,211 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + [15,] 0.02 0.46 0.2 + [16,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.694722 2.300278 2.698333 3.436111 3.821111 4.201111 4.598056 4.995000 5.375278 1.350000 1.916667 2.866667 4.000000 4.800000 5.183333 5.583333 + +$sys$data_meas + X Glc Ace + [1,] 0.072576 NA NA + [2,] 0.107352 NA NA + [3,] 0.145152 NA NA + [4,] 0.226800 NA NA + [5,] 0.293328 NA NA + [6,] 0.359856 NA NA + [7,] 0.477792 NA NA + [8,] 0.666792 NA NA + [9,] 0.807408 NA NA +[10,] NA 13.658459 0.2312953 +[11,] NA 13.456913 0.3812901 +[12,] NA 12.981707 0.7517022 +[13,] NA 11.019453 1.5125068 +[14,] NA 8.902288 2.2003751 +[15,] NA 7.467238 2.6249282 +[16,] NA 5.663558 3.0138498 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02414272 14.01493874 0.29069672 0.65476235 -6.10646735 2.12425426 + +$result$lastp + X Glc Ace mu qGlc qAce +-4.607551e-09 -9.659235e-08 1.879625e-08 3.919368e-08 -1.448636e-07 7.576180e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.004233918 0.427164889 0.184098185 0.035818449 0.582374007 0.248424548 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.721544 + +$result$laststep + X Glc Ace mu qGlc qAce +-4.607551e-09 -9.659235e-08 1.879625e-08 3.919368e-08 -1.448636e-07 7.576180e-08 + +$result$normp +[1] 1.948488e-07 + +$result$res + [1] 0.03276575 0.07570184 -0.19355649 0.11111071 0.06778396 0.90376057 0.61557208 -1.56114717 0.39281354 0.07970430 -0.01436904 -0.46251620 0.28443627 0.26268364 0.14669577 -0.29663474 0.85327897 0.52913138 -0.13781845 -1.12643560 -0.86588598 -0.39979851 1.14752819 + +$result$prevres + [1] 0.03276621 0.07570239 -0.19355589 0.11111136 0.06778457 0.90376107 0.61557234 -1.56114733 0.39281273 0.07970441 -0.01436898 -0.46251624 0.28443612 0.26268352 0.14669574 -0.29663457 0.85327895 0.52913139 -0.13781836 -1.12643547 -0.86588592 -0.39979855 1.14752795 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 151.66335 0.000000 0 6.2053376 0.0000000 0.0000000 + [2,] 225.46348 0.000000 0 12.5211075 0.0000000 0.0000000 + [3,] 292.59516 0.000000 0 19.0611457 0.0000000 0.0000000 + [4,] 474.30902 0.000000 0 39.3472910 0.0000000 0.0000000 + [5,] 610.29505 0.000000 0 56.3009564 0.0000000 0.0000000 + [6,] 782.70213 0.000000 0 79.3865527 0.0000000 0.0000000 + [7,] 1015.01276 0.000000 0 112.6761438 0.0000000 0.0000000 + [8,] 1316.27456 0.000000 0 158.7333711 0.0000000 0.0000000 + [9,] 1688.42645 0.000000 0 219.1135915 0.0000000 0.0000000 +[10,] -28.79761 2.173913 0 -0.5375491 0.1138552 0.0000000 +[11,] -50.84221 2.173913 0 -1.4161400 0.2010114 0.0000000 +[12,] -112.19415 2.173913 0 -5.0311574 0.4435744 0.0000000 +[13,] -257.94481 2.173913 0 -17.3568100 1.0198188 0.0000000 +[14,] -449.48433 2.173913 0 -37.8644158 1.7770956 0.0000000 +[15,] -583.50654 2.173913 0 -54.0416733 2.3069700 0.0000000 +[16,] -764.28036 2.173913 0 -77.5746034 3.0216832 0.0000000 +[17,] 23.04097 0.000000 5 0.4300930 0.0000000 0.2618668 +[18,] 40.67886 0.000000 5 1.1330536 0.0000000 0.4623262 +[19,] 89.76655 0.000000 5 4.0254292 0.0000000 1.0202211 +[20,] 206.38165 0.000000 5 13.8871843 0.0000000 2.3455833 +[21,] 359.63243 0.000000 5 30.2953203 0.0000000 4.0873198 +[22,] 466.86360 0.000000 5 43.2387447 0.0000000 5.3060311 +[23,] 611.50074 0.000000 5 62.0674428 0.0000000 6.9498714 + +$result$retres +$result$retres$res + [1] 0.03276621 0.07570239 -0.19355589 0.11111136 0.06778457 0.90376107 0.61557234 -1.56114733 0.39281273 0.07970441 -0.01436898 -0.46251624 0.28443612 0.26268352 0.14669574 -0.29663457 0.85327895 0.52913139 -0.13781836 -1.12643547 -0.86588592 -0.39979855 1.14752795 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.07323132 13.557127 0.4499555 + [2,] 0.10886605 13.224789 0.5655657 + [3,] 0.14128088 12.922481 0.6707296 + [4,] 0.22902223 12.104184 0.9553900 + [5,] 0.29468369 11.491810 1.1684164 + [6,] 0.37793122 10.715424 1.4384975 + [7,] 0.49010345 9.669280 1.8024194 + [8,] 0.63556905 8.312633 2.2743554 + [9,] 0.81526425 6.636753 2.8573430 + [10,] 0.05843483 13.695123 0.4019510 + [11,] 0.08468548 13.450303 0.4871164 + [12,] 0.15774319 12.768950 0.7241385 + [13,] 0.33130263 11.150293 1.2872197 + [14,] 0.55938731 9.023122 2.0271979 + [15,] 0.71898055 7.534718 2.5449684 + [16,] 0.93424548 5.527107 3.2433554 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0006553242 NA NA + [2,] -0.0015140479 NA NA + [3,] 0.0038711178 NA NA + [4,] -0.0022222271 NA NA + [5,] -0.0013556914 NA NA + [6,] -0.0180752213 NA NA + [7,] -0.0123114468 NA NA + [8,] 0.0312229466 NA NA + [9,] -0.0078562546 NA NA +[10,] NA -0.036664030 -0.17065579 +[11,] NA 0.006609731 -0.10582628 +[12,] NA 0.212757472 0.02756367 +[13,] NA -0.130840614 0.22528709 +[14,] NA -0.120834419 0.17317718 +[15,] NA -0.067480041 0.07995971 +[16,] NA 0.136451902 -0.22950559 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4_res/KEIO_ROBOT6_4_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4_res/KEIO_ROBOT6_4_res.txt new file mode 100644 index 0000000..43b6f92 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_BW_6_4_res/KEIO_ROBOT6_4_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0241427187638244 0.0238995646093821 0.0240645702765881 0.00206449629209005 0.0201565892650511 0.0275923688915505 +Glc 14.0149387379447 14.0245076630551 14.040573591562 0.19071677916376 13.6469152271611 14.3544601653459 +Ace 0.290696718286393 0.287025163140172 0.291439271821165 0.0827134335878548 0.139891185272735 0.449646155595672 +mu 0.654762345428378 0.657616797291072 0.655738129809264 0.0171038342182684 0.629976774179519 0.691085030572781 +qGlc -6.10646735123524 -6.11834695978105 -6.15516418707285 0.296893682791537 -6.69239719356834 -5.49840896356456 +qAce 2.12425425827842 2.1480641330888 2.15791092517405 0.129978939386339 1.91620316329499 2.36904952893267 +res 8.85063727575347 43.2333684307271 42.4293188482739 9.89663064840995 28.3196032757244 67.7779874698168 + + +Goodness of fit (khi2 test) + +khi2 value 8.85063727575628 +data points 23 +fitted parameters 6 +degrees of freedom 17 +khi2 reduced value 0.52062572210331 +p-value, i.e. P(X^2<=value) 0.0551686701442287 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1.txt new file mode 100644 index 0000000..e1cb0dc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1.txt @@ -0,0 +1,17 @@ +time X Glc Ace +1.69472222222222 6.9552000000000003E-2 NA NA +2.3002777777777799 0.10130400000000001 NA NA +2.6983333333333301 0.12096 NA NA +3.43611111111111 0.20412000000000002 NA NA +3.8211111111111098 0.238896 NA NA +4.2011111111111097 0.3024 NA NA +4.5980555555555496 0.41731200000000002 NA NA +4.9950000000000001 0.61236000000000002 NA NA +5.3752777777777796 0.74239199999999994 NA NA +1.35 NA 13.691967702492 0.217679548051463 +1.91666666666667 NA 13.4334101547541 0.361661828101966 +2.86666666666667 NA 13.2134196553455 0.708645965795666 +4 NA 11.0297672618978 1.39397786370358 +4.8 NA 9.27619410964019 2.05615745786491 +5.18333333333333 NA 8.01371108153914 2.53164955352933 +5.58333333333333 NA 6.15445854862287 2.8513055571961 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1_res/KEIO_ROBOT6_5.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1_res/KEIO_ROBOT6_5.pdf new file mode 100644 index 0000000..9284353 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1_res/KEIO_ROBOT6_5.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1_res/KEIO_ROBOT6_5_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1_res/KEIO_ROBOT6_5_log.txt new file mode 100644 index 0000000..44f1b67 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1_res/KEIO_ROBOT6_5_log.txt @@ -0,0 +1,211 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + [15,] 0.02 0.46 0.2 + [16,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.694722 2.300278 2.698333 3.436111 3.821111 4.201111 4.598056 4.995000 5.375278 1.350000 1.916667 2.866667 4.000000 4.800000 5.183333 5.583333 + +$sys$data_meas + X Glc Ace + [1,] 0.069552 NA NA + [2,] 0.101304 NA NA + [3,] 0.120960 NA NA + [4,] 0.204120 NA NA + [5,] 0.238896 NA NA + [6,] 0.302400 NA NA + [7,] 0.417312 NA NA + [8,] 0.612360 NA NA + [9,] 0.742392 NA NA +[10,] NA 13.691968 0.2176795 +[11,] NA 13.433410 0.3616618 +[12,] NA 13.213420 0.7086460 +[13,] NA 11.029767 1.3939779 +[14,] NA 9.276194 2.0561575 +[15,] NA 8.013711 2.5316496 +[16,] NA 6.154459 2.8513056 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01821068 13.93073534 0.29767694 0.69091499 -6.46461601 2.28868869 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.554463e-09 -6.937193e-08 5.862033e-08 1.801878e-08 1.032958e-08 -7.154911e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.004686388 0.533319893 0.229899322 0.052283835 0.840501447 0.358410793 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.9138642 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.554463e-09 -6.937193e-08 5.862033e-08 1.801878e-08 1.032958e-08 -7.154911e-08 + +$result$normp +[1] 1.174814e-07 + +$result$res + [1] -0.54119768 -0.60330956 -0.17365190 -0.42602607 0.81550385 1.47143813 0.96126726 -1.90366368 0.22305126 -0.05191387 0.05903120 -0.75468471 0.80293517 0.28012103 -0.07104914 -0.26443968 0.86491756 0.51235599 -0.17055537 -1.00012068 -0.78118789 -0.63789427 1.21248466 + +$result$prevres + [1] -0.54119752 -0.60330936 -0.17365168 -0.42602584 0.81550406 1.47143829 0.96126732 -1.90366382 0.22305083 -0.05191376 0.05903129 -0.75468468 0.80293512 0.28012095 -0.07104921 -0.26443970 0.86491731 0.51235578 -0.17055550 -1.00012068 -0.78118776 -0.63789408 1.21248493 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 161.24613 0.000000 0 4.9763865 0.00000000 0.0000000 + [2,] 245.01498 0.000000 0 10.2635879 0.00000000 0.0000000 + [3,] 322.57701 0.000000 0 15.8509499 0.00000000 0.0000000 + [4,] 537.04593 0.000000 0 33.6050779 0.00000000 0.0000000 + [5,] 700.70424 0.000000 0 48.7585396 0.00000000 0.0000000 + [6,] 911.08261 0.000000 0 69.7024757 0.00000000 0.0000000 + [7,] 1198.57477 0.000000 0 100.3611485 0.00000000 0.0000000 + [8,] 1576.78508 0.000000 0 143.4281092 0.00000000 0.0000000 + [9,] 2050.59014 0.000000 0 200.7271211 0.00000000 0.0000000 +[10,] -31.35379 2.173913 0 -0.4444702 0.08832296 0.0000000 +[11,] -56.12697 2.173913 0 -1.1896461 0.15810847 0.0000000 +[12,] -127.07192 2.173913 0 -4.3462309 0.35795889 0.0000000 +[13,] -302.21364 2.173913 0 -15.5301733 0.85132935 0.0000000 +[14,] -540.25684 2.173913 0 -34.7627935 1.52189195 0.0000000 +[15,] -710.25037 2.173913 0 -50.2416490 2.00076007 0.0000000 +[16,] -942.81953 2.173913 0 -73.0803446 2.65590243 0.0000000 +[17,] 25.53065 0.000000 5 0.3619216 0.00000000 0.2031428 +[18,] 45.70287 0.000000 5 0.9687007 0.00000000 0.3636495 +[19,] 103.47167 0.000000 5 3.5390331 0.00000000 0.8233054 +[20,] 246.08543 0.000000 5 12.6458533 0.00000000 1.9580575 +[21,] 439.91839 0.000000 5 28.3065217 0.00000000 3.5003515 +[22,] 578.34010 0.000000 5 40.9105882 0.00000000 4.6017482 +[23,] 767.71568 0.000000 5 59.5075987 0.00000000 6.1085756 + +$result$retres +$result$retres$res + [1] -0.54119752 -0.60330936 -0.17365168 -0.42602584 0.81550406 1.47143829 0.96126732 -1.90366382 0.22305083 -0.05191376 0.05903129 -0.75468468 0.80293512 0.28012095 -0.07104921 -0.26443970 0.86491731 0.51235578 -0.17055550 -1.00012068 -0.78118776 -0.63789408 1.21248493 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05872805 13.551631 0.4318926 + [2,] 0.08923781 13.266163 0.5329576 + [3,] 0.11748697 13.001847 0.6265343 + [4,] 0.19559948 12.270979 0.8852857 + [5,] 0.25520608 11.713264 1.0827354 + [6,] 0.33182877 10.996336 1.3365517 + [7,] 0.43653735 10.016620 1.6834039 + [8,] 0.57428672 8.727754 2.1397053 + [9,] 0.74685302 7.113120 2.7113393 + [10,] 0.04628156 13.668087 0.3906630 + [11,] 0.06846086 13.460565 0.4641330 + [12,] 0.13197750 12.866265 0.6745349 + [13,] 0.28878094 11.399117 1.1939537 + [14,] 0.50189974 9.405050 1.8999199 + [15,] 0.65409402 7.981028 2.4040707 + [16,] 0.86231195 6.032816 3.0938025 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.010823950 NA NA + [2,] 0.012066187 NA NA + [3,] 0.003473034 NA NA + [4,] 0.008520517 NA NA + [5,] -0.016310081 NA NA + [6,] -0.029428766 NA NA + [7,] -0.019225346 NA NA + [8,] 0.038073276 NA NA + [9,] -0.004461017 NA NA +[10,] NA 0.02388033 -0.1729835 +[11,] NA -0.02715439 -0.1024712 +[12,] NA 0.34715495 0.0341111 +[13,] NA -0.36935015 0.2000241 +[14,] NA -0.12885564 0.1562376 +[15,] NA 0.03268264 0.1275788 +[16,] NA 0.12164226 -0.2424970 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1_res/KEIO_ROBOT6_5_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1_res/KEIO_ROBOT6_5_res.txt new file mode 100644 index 0000000..3e1a64e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_1_res/KEIO_ROBOT6_5_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0182106832833438 0.0182682265987779 0.0182393001817155 0.00172358775324926 0.0150242072908224 0.0219039187838677 +Glc 13.9307353392969 13.9321768817505 13.9226972407902 0.176852316152322 13.5965701947182 14.2665274310905 +Ace 0.297676942476435 0.311832401843659 0.300886227334831 0.0867423047925591 0.160974400117537 0.477855718375345 +mu 0.690914990873694 0.690939567344309 0.690790824730606 0.0184329785924607 0.65566103949386 0.725965085307239 +qGlc -6.46461600658701 -6.45399700327946 -6.41403167498113 0.289903477083837 -6.93355791442434 -5.95047947916729 +qAce 2.28868868774298 2.29005771560736 2.28816301455939 0.147243921178236 2.02008231964877 2.54560071064851 +res 14.1975112336225 40.5999805645397 38.9625549729905 9.51131981729286 26.8346198536872 59.8411195649485 + + +Goodness of fit (khi2 test) + +khi2 value 14.1975112336233 +data points 23 +fitted parameters 6 +degrees of freedom 17 +khi2 reduced value 0.8351477196249 +p-value, i.e. P(X^2<=value) 0.346925126575966 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2.txt new file mode 100644 index 0000000..f984210 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2.txt @@ -0,0 +1,17 @@ +time X Glc Ace +1.69472222222222 6.8040000000000003E-2 NA NA +2.3002777777777799 0.10735199999999999 NA NA +2.6983333333333301 0.12096 NA NA +3.43611111111111 0.20714400000000002 NA NA +3.8211111111111098 0.24796800000000002 NA NA +4.2011111111111097 0.33263999999999999 NA NA +4.5980555555555496 0.41126400000000002 NA NA +4.9950000000000001 0.65469599999999994 NA NA +5.3752777777777796 0.79531200000000002 NA NA +1.35 NA 13.59384334762 0.211549540761834 +1.91666666666667 NA 13.5126898844233 0.364578675109333 +2.86666666666667 NA 12.6400827109594 0.703181908636072 +4 NA 11.2693273658292 1.48906738467552 +4.8 NA 8.98522134798277 2.12877346230347 +5.18333333333333 NA 7.54822371280061 2.53132428480182 +5.58333333333333 NA 5.8625527468519 2.89336820619209 diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2_res/KEIO_ROBOT6_6.pdf b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2_res/KEIO_ROBOT6_6.pdf new file mode 100644 index 0000000..499214a Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2_res/KEIO_ROBOT6_6.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2_res/KEIO_ROBOT6_6_log.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2_res/KEIO_ROBOT6_6_log.txt new file mode 100644 index 0000000..f233f42 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2_res/KEIO_ROBOT6_6_log.txt @@ -0,0 +1,211 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + [15,] 0.02 0.46 0.2 + [16,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.694722 2.300278 2.698333 3.436111 3.821111 4.201111 4.598056 4.995000 5.375278 1.350000 1.916667 2.866667 4.000000 4.800000 5.183333 5.583333 + +$sys$data_meas + X Glc Ace + [1,] 0.068040 NA NA + [2,] 0.107352 NA NA + [3,] 0.120960 NA NA + [4,] 0.207144 NA NA + [5,] 0.247968 NA NA + [6,] 0.332640 NA NA + [7,] 0.411264 NA NA + [8,] 0.654696 NA NA + [9,] 0.795312 NA NA +[10,] NA 13.593843 0.2115495 +[11,] NA 13.512690 0.3645787 +[12,] NA 12.640083 0.7031819 +[13,] NA 11.269327 1.4890674 +[14,] NA 8.985221 2.1287735 +[15,] NA 7.548224 2.5313243 +[16,] NA 5.862553 2.8933682 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01735309 13.79405049 0.33038795 0.71209359 -6.40121483 2.21495008 + +$result$lastp + X Glc Ace mu qGlc qAce +-3.979379e-09 -1.788102e-07 1.523807e-07 4.808386e-08 9.834137e-09 -1.786227e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.005193433 0.631968615 0.272349241 0.060630779 0.961015898 0.409317428 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.093731 + +$result$laststep + X Glc Ace mu qGlc qAce +-3.979379e-09 -1.788102e-07 1.523807e-07 4.808386e-08 9.834137e-09 -1.786227e-07 + +$result$normp +[1] 2.99205e-07 + +$result$res + [1] -0.50162683 -0.90357136 -0.12108139 -0.33431199 0.78590770 0.64926345 2.36309425 -2.31949098 0.10899629 -0.11248977 -0.37690167 0.23626922 -0.02534733 0.44680645 0.32343216 -0.49176906 1.03009530 0.61578466 -0.05552265 -1.40519772 -1.02775520 -0.45617076 1.29876637 + +$result$prevres + [1] -0.50162640 -0.90357083 -0.12108080 -0.33431135 0.78590830 0.64926392 2.36309444 -2.31949131 0.10899513 -0.11248949 -0.37690145 0.23626929 -0.02534746 0.44680624 0.32343198 -0.49176911 1.03009466 0.61578410 -0.05552301 -1.40519772 -1.02775486 -0.45617024 1.29876707 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 167.13866 0.000000 0 4.9153276 0.00000000 0.0000000 + [2,] 257.24681 0.000000 0 10.2685071 0.00000000 0.0000000 + [3,] 341.54818 0.000000 0 15.9928036 0.00000000 0.0000000 + [4,] 577.58496 0.000000 0 34.4397591 0.00000000 0.0000000 + [5,] 759.76681 0.000000 0 50.3787069 0.00000000 0.0000000 + [6,] 995.86042 0.000000 0 72.6005099 0.00000000 0.0000000 + [7,] 1321.16431 0.000000 0 105.4163755 0.00000000 0.0000000 + [8,] 1752.73072 0.000000 0 151.9244669 0.00000000 0.0000000 + [9,] 2297.83720 0.000000 0 214.3370251 0.00000000 0.0000000 +[10,] -31.56340 2.173913 0 -0.4280559 0.08556544 0.0000000 +[11,] -56.96708 2.173913 0 -1.1564598 0.15443246 0.0000000 +[12,] -130.94818 2.173913 0 -4.2951204 0.35498835 0.0000000 +[13,] -317.74593 2.173913 0 -15.6687668 0.86137968 0.0000000 +[14,] -576.67918 2.173913 0 -35.6089929 1.56332365 0.0000000 +[15,] -763.80899 2.173913 0 -51.8466238 2.07061519 0.0000000 +[16,] -1021.95904 2.173913 0 -76.0048348 2.77043598 0.0000000 +[17,] 25.11963 0.000000 5 0.3406669 0.00000000 0.1968005 +[18,] 45.33706 0.000000 5 0.9203647 0.00000000 0.3551946 +[19,] 104.21468 0.000000 5 3.4182573 0.00000000 0.8164732 +[20,] 252.87704 0.000000 5 12.4699360 0.00000000 1.9811733 +[21,] 458.94821 0.000000 5 28.3392988 0.00000000 3.5956444 +[22,] 607.87485 0.000000 5 41.2619635 0.00000000 4.7624149 +[23,] 813.32271 0.000000 5 60.4881955 0.00000000 6.3720027 + +$result$retres +$result$retres$res + [1] -0.50162640 -0.90357083 -0.12108080 -0.33431135 0.78590830 0.64926392 2.36309444 -2.31949131 0.10899513 -0.11248949 -0.37690145 0.23626929 -0.02534746 0.44680624 0.32343198 -0.49176911 1.03009466 0.61578410 -0.05552301 -1.40519772 -1.02775486 -0.45617024 1.29876707 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05800747 13.428597 0.4568423 + [2,] 0.08928058 13.147474 0.5541166 + [3,] 0.11853838 12.884467 0.6451223 + [4,] 0.20045777 12.148070 0.8999306 + [5,] 0.26368617 11.579691 1.0966010 + [6,] 0.34562528 10.843117 1.3514707 + [7,] 0.45852589 9.828221 1.7026454 + [8,] 0.60830617 8.481803 2.1685335 + [9,] 0.79749190 6.781157 2.7569912 + [10,] 0.04538117 13.542098 0.4175685 + [11,] 0.06793946 13.339315 0.4877355 + [12,] 0.13363416 12.748767 0.6920773 + [13,] 0.29950924 11.257668 1.2080278 + [14,] 0.52944013 9.190752 1.9232225 + [15,] 0.69561009 7.697002 2.4400902 + [16,] 0.92484550 5.636339 3.1531216 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.010032528 NA NA + [2,] 0.018071417 NA NA + [3,] 0.002421616 NA NA + [4,] 0.006686227 NA NA + [5,] -0.015718166 NA NA + [6,] -0.012985278 NA NA + [7,] -0.047261889 NA NA + [8,] 0.046389826 NA NA + [9,] -0.002179903 NA NA +[10,] NA 0.05174517 -0.20601893 +[11,] NA 0.17337467 -0.12315682 +[12,] NA -0.10868387 0.01110460 +[13,] NA 0.01165983 0.28103954 +[14,] NA -0.20553087 0.20555097 +[15,] NA -0.14877871 0.09123405 +[16,] NA 0.22621379 -0.25975341 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2_res/KEIO_ROBOT6_6_res.txt b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2_res/KEIO_ROBOT6_6_res.txt new file mode 100644 index 0000000..f35d5ca --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/WT_MG_6_2_res/KEIO_ROBOT6_6_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0173530944873719 0.0176969546597148 0.0175497559219396 0.00163712796335265 0.0147441990780824 0.021231361183361 +Glc 13.7940504858562 13.7722534418636 13.7541148620129 0.193951929380396 13.434659666677 14.1286592584224 +Ace 0.330387951885417 0.33798672355325 0.346094148269184 0.0798680481348011 0.203747207244234 0.487339657224166 +mu 0.712093592432316 0.708970094177806 0.710315108317948 0.0181258816172601 0.671654248862777 0.743227408968407 +qGlc -6.40121483201611 -6.298385802121 -6.32303185881187 0.330780407706951 -6.92669910422484 -5.6976299714541 +qAce 2.21495007650282 2.20015984117314 2.18109561175562 0.132976987364394 1.97167869745329 2.47890472942852 +res 20.3361955511877 40.8588669856541 40.3998630844336 8.82637083360652 25.6206566867706 60.6289387963322 + + +Goodness of fit (khi2 test) + +khi2 value 20.3361955511932 +data points 23 +fitted parameters 6 +degrees of freedom 17 +khi2 reduced value 1.19624679712901 +p-value, i.e. P(X^2<=value) 0.742604411452865 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/artI.txt b/validation/validation_results/Berges_2021/Berges_2021/artI.txt new file mode 100644 index 0000000..9f4409e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/artI.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.184464 NA NA +3.67805555555556 0.297864 NA NA +4.09222222222222 0.361368 NA NA +4.565 0.47628 NA NA +0.05 NA 14.381245810333 0.0160850202994414 +1.95 NA 13.5621449331404 0.439526057291736 +2.83333333333333 NA 13.3766030275724 0.788742133512994 +3.98333333333333 NA 11.6425454396719 1.46200912027406 +4.88333333333333 NA 8.87425168742146 2.00766963832224 +5.16666666666667 NA 8.27929544860947 2.21451931058294 diff --git a/validation/validation_results/Berges_2021/Berges_2021/artI_res/KEIO_ROBOT3_24.pdf b/validation/validation_results/Berges_2021/Berges_2021/artI_res/KEIO_ROBOT3_24.pdf new file mode 100644 index 0000000..c77013f Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/artI_res/KEIO_ROBOT3_24.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/artI_res/KEIO_ROBOT3_24_log.txt b/validation/validation_results/Berges_2021/Berges_2021/artI_res/KEIO_ROBOT3_24_log.txt new file mode 100644 index 0000000..84d5cd0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/artI_res/KEIO_ROBOT3_24_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.184464 NA NA + [2,] 0.297864 NA NA + [3,] 0.361368 NA NA + [4,] 0.476280 NA NA + [5,] NA 14.381246 0.01608502 + [6,] NA 13.562145 0.43952606 + [7,] NA 13.376603 0.78874213 + [8,] NA 11.642545 1.46200912 + [9,] NA 8.874252 2.00766964 +[10,] NA 8.279295 2.21451931 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0400583 14.5425875 0.1842287 0.5409104 -5.5707415 1.8926772 + +$result$lastp + X Glc Ace mu qGlc qAce + 8.628424e-09 6.970587e-08 -6.076661e-08 -5.216992e-08 1.590144e-07 1.829245e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.01281145 0.45144417 0.19239921 0.07645416 0.70511943 0.29682970 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6482606 + +$result$laststep + X Glc Ace mu qGlc qAce + 8.628424e-09 6.970587e-08 -6.076661e-08 -5.216992e-08 1.590144e-07 1.829245e-08 + +$result$normp +[1] 1.922702e-07 + +$result$res + [1] 0.27187014 -0.24815516 0.25408673 -0.15225773 0.32615584 0.45308485 -0.72092952 -0.53378365 0.63332641 -0.15785394 0.85993140 0.03500050 -0.47847478 -1.04529347 0.01706968 0.61176668 + +$result$prevres + [1] 0.27186952 -0.24815551 0.25408670 -0.15225719 0.32615569 0.45308492 -0.72092936 -0.53378347 0.63332637 -0.15785414 0.85993170 0.03500059 -0.47847481 -1.04529363 0.01706955 0.61176661 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 237.0313124 0.000000 0 2.731679e+01 0.000000000 0.00000000 + [2,] 365.5933336 0.000000 0 5.386529e+01 0.000000000 0.00000000 + [3,] 457.3956054 0.000000 0 7.497969e+01 0.000000000 0.00000000 + [4,] 590.6827689 0.000000 0 1.080159e+02 0.000000000 0.00000000 + [5,] -0.6137780 2.173913 0 -6.174429e-04 0.004413577 0.00000000 + [6,] -41.8967378 2.173913 0 -1.918822e+00 0.301272589 0.00000000 + [7,] -81.2735102 2.173913 0 -5.746625e+00 0.584424519 0.00000000 + [8,] -170.7067922 2.173913 0 -1.816933e+01 1.227524622 0.00000000 + [9,] -291.8033198 2.173913 0 -3.985150e+01 2.098309945 0.00000000 +[10,] -343.8415755 2.173913 0 -5.033397e+01 2.472508530 0.00000000 +[11,] 0.4796259 0.000000 5 4.824900e-04 0.000000000 0.01015123 +[12,] 32.7394655 0.000000 5 1.499429e+00 0.000000000 0.69292695 +[13,] 63.5097485 0.000000 5 4.490598e+00 0.000000000 1.34417639 +[14,] 133.3958066 0.000000 5 1.419810e+01 0.000000000 2.82330663 +[15,] 228.0245485 0.000000 5 3.114125e+01 0.000000000 4.82611287 +[16,] 268.6889240 0.000000 5 3.933259e+01 0.000000000 5.68676962 + +$result$retres +$result$retres$res + [1] 0.27186952 -0.24815551 0.25408670 -0.15225719 0.32615569 0.45308492 -0.72092936 -0.53378347 0.63332637 -0.15785414 0.85993170 0.03500059 -0.47847481 -1.04529363 0.01706955 0.61176661 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.18990139 12.999380 0.7085385 + [2,] 0.29290089 11.938606 1.0689398 + [3,] 0.36644973 11.181139 1.3262915 + [4,] 0.47323486 10.081378 1.6999389 + [5,] 0.04115647 14.531277 0.1880714 + [6,] 0.11502057 13.770564 0.4465262 + [7,] 0.18547410 13.044976 0.6930472 + [8,] 0.34548949 11.397005 1.2529504 + [9,] 0.56215725 9.165582 2.0110835 + [10,] 0.65526489 8.206683 2.3368726 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.005437390 NA NA + [2,] 0.004963110 NA NA + [3,] -0.005081734 NA NA + [4,] 0.003045144 NA NA + [5,] NA -0.15003162 -0.171986340 + [6,] NA -0.20841906 -0.007000117 + [7,] NA 0.33162751 0.095694963 + [8,] NA 0.24554040 0.209058726 + [9,] NA -0.29133013 -0.003413910 +[10,] NA 0.07261291 -0.122353322 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/artI_res/KEIO_ROBOT3_24_res.txt b/validation/validation_results/Berges_2021/Berges_2021/artI_res/KEIO_ROBOT3_24_res.txt new file mode 100644 index 0000000..f7a2a46 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/artI_res/KEIO_ROBOT3_24_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0400583005808705 0.040812497757501 0.0406947104029199 0.00469619250141634 0.0321197008229288 0.0504330868062839 +Glc 14.5425874712114 14.5316839580694 14.5071312370624 0.260292120057308 14.0343271085276 15.0149961775423 +Ace 0.184228700083603 0.178139097562502 0.179979909879515 0.113027866524311 9.99999999995709e-07 0.432246923070877 +mu 0.540910374516628 0.538619119318319 0.537990288379013 0.025970037496472 0.490628728765662 0.588538778929052 +qGlc -5.57074147768217 -5.54254161708276 -5.51441290780975 0.435860613635522 -6.44235901654118 -4.67305919026635 +qAce 1.89267724660841 1.88029832094419 1.8727212065108 0.177141300435775 1.54370663757176 2.21701628968164 +res 4.20241836950397 23.0737919036505 21.860583155898 7.88046507843202 11.2746290113276 41.8517611256094 + + +Goodness of fit (khi2 test) + +khi2 value 4.20241836950504 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.420241836950504 +p-value, i.e. P(X^2<=value) 0.0622461694682842 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/hemX.txt b/validation/validation_results/Berges_2021/Berges_2021/hemX.txt new file mode 100644 index 0000000..99e8d3c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/hemX.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.16632 NA NA +3.67805555555556 0.260064 NA NA +4.09222222222222 0.328104 NA NA +4.565 0.44604 NA NA +0.05 NA 14.1334758215365 0.0275345280503521 +1.95 NA 13.9013951003329 0.447037313738487 +2.83333333333333 NA 13.3975521580251 0.857935788195311 +3.98333333333333 NA 11.7518002418634 1.43577373966348 +4.88333333333333 NA 9.18584051118 2.25913839748539 +5.16666666666667 NA 8.36932489281138 2.57909039828179 diff --git a/validation/validation_results/Berges_2021/Berges_2021/hemX_res/KEIO_ROBOT3_18.pdf b/validation/validation_results/Berges_2021/Berges_2021/hemX_res/KEIO_ROBOT3_18.pdf new file mode 100644 index 0000000..c3ad121 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/hemX_res/KEIO_ROBOT3_18.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/hemX_res/KEIO_ROBOT3_18_log.txt b/validation/validation_results/Berges_2021/Berges_2021/hemX_res/KEIO_ROBOT3_18_log.txt new file mode 100644 index 0000000..0e7d224 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/hemX_res/KEIO_ROBOT3_18_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.166320 NA NA + [2,] 0.260064 NA NA + [3,] 0.328104 NA NA + [4,] 0.446040 NA NA + [5,] NA 14.133476 0.02753453 + [6,] NA 13.901395 0.44703731 + [7,] NA 13.397552 0.85793579 + [8,] NA 11.751800 1.43577374 + [9,] NA 9.185841 2.25913840 +[10,] NA 8.369325 2.57909040 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0299979 14.4716496 0.1814192 0.5890563 -5.9989838 2.4300875 + +$result$lastp + X Glc Ace mu qGlc qAce +-9.408047e-10 1.961363e-09 1.409640e-08 7.574887e-09 -4.713594e-08 -1.421831e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.00853389 0.35714258 0.15421300 0.06764924 0.63313739 0.27222422 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5214232 + +$result$laststep + X Glc Ace mu qGlc qAce +-9.408047e-10 1.961363e-09 1.409640e-08 7.574887e-09 -4.713594e-08 -1.421831e-08 + +$result$normp +[1] 5.181483e-08 + +$result$res + [1] -0.149198156 0.088479986 0.303748083 -0.227190676 0.715308982 -0.190830527 -0.525299587 -0.361975437 0.364654344 -0.001857774 0.787919013 0.004707405 -0.717671514 -0.425696798 -0.022379009 0.373120903 + +$result$prevres + [1] -0.149198078 0.088480032 0.303748089 -0.227190747 0.715308977 -0.190830553 -0.525299620 -0.361975460 0.364654372 -0.001857716 0.787918943 0.004707372 -0.717671522 -0.425696770 -0.022378967 0.373120944 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 272.245758 0.000000 0 2.349544e+01 0.000000000 0.000000000 + [2,] 436.419835 0.000000 0 4.815193e+01 0.000000000 0.000000000 + [3,] 557.003865 0.000000 0 6.837673e+01 0.000000000 0.000000000 + [4,] 735.878405 0.000000 0 1.007715e+02 0.000000000 0.000000000 + [5,] -0.661761 2.173913 0 -4.987222e-04 0.003309134 0.000000000 + [6,] -47.687142 2.173913 0 -1.656074e+00 0.238459433 0.000000000 + [7,] -95.349800 2.173913 0 -5.130149e+00 0.476796435 0.000000000 + [8,] -209.171002 2.173913 0 -1.698754e+01 1.045959065 0.000000000 + [9,] -370.900421 2.173913 0 -3.868805e+01 1.854686618 0.000000000 +[10,] -442.290278 2.173913 0 -4.945776e+01 2.211671420 0.000000000 +[11,] 0.616557 0.000000 5 4.646551e-04 0.000000000 0.007611008 +[12,] 44.429698 0.000000 5 1.542950e+00 0.000000000 0.548456697 +[13,] 88.836584 0.000000 5 4.779715e+00 0.000000000 1.096631800 +[14,] 194.882812 0.000000 5 1.582714e+01 0.000000000 2.405705849 +[15,] 345.564713 0.000000 5 3.604532e+01 0.000000000 4.265779222 +[16,] 412.078025 0.000000 5 4.607936e+01 0.000000000 5.086844265 + +$result$retres +$result$retres$res + [1] -0.149198078 0.088480032 0.303748089 -0.227190747 0.715308977 -0.190830553 -0.525299620 -0.361975460 0.364654372 -0.001857716 0.787918943 0.004707372 -0.717671522 -0.425696770 -0.022378967 0.373120944 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.16333604 13.113726 0.7314912 + [2,] 0.26183360 12.110621 1.1378322 + [3,] 0.33417896 11.373852 1.4362851 + [4,] 0.44149619 10.280927 1.8790106 + [5,] 0.03089457 14.462518 0.1851183 + [6,] 0.09461227 13.813613 0.4479788 + [7,] 0.15919347 13.155914 0.7144015 + [8,] 0.31341713 11.585292 1.3506344 + [9,] 0.53255471 9.353582 2.2546626 + [10,] 0.62928541 8.368470 2.6537146 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.002983962 NA NA + [2,] -0.001769601 NA NA + [3,] -0.006074962 NA NA + [4,] 0.004543815 NA NA + [5,] NA -0.3290421295 -0.1575837886 + [6,] NA 0.0877820542 -0.0009414745 + [7,] NA 0.2416378252 0.1435343044 + [8,] NA 0.1665087117 0.0851393541 + [9,] NA -0.1677410110 0.0044757934 +[10,] NA 0.0008545493 -0.0746241887 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/hemX_res/KEIO_ROBOT3_18_res.txt b/validation/validation_results/Berges_2021/Berges_2021/hemX_res/KEIO_ROBOT3_18_res.txt new file mode 100644 index 0000000..b73a864 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/hemX_res/KEIO_ROBOT3_18_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0299979024017838 0.0303261301195554 0.0302203545847507 0.00379505250794635 0.0238119602130571 0.037860084159796 +Glc 14.4716496162677 14.4782113357598 14.4729207167056 0.261728676709937 13.9653293385039 15.0180750915885 +Ace 0.181419247404345 0.18246800853899 0.175753395004706 0.112309332255876 9.99999999999841e-07 0.407828810416279 +mu 0.589056281074826 0.588084006350584 0.587501008298994 0.0271710457416349 0.540765794416159 0.6398560582699 +qGlc -5.99898384969104 -5.97802144516725 -5.96189809505006 0.509080827374942 -6.92190749484408 -5.05778348290984 +qAce 2.43008750636859 2.41350198878156 2.43826819064783 0.20307765663859 2.03485750476992 2.7242909624074 +res 2.71882136877649 22.8974312096937 22.5131150487526 6.78835448711662 12.8369290891765 37.257279983657 + + +Goodness of fit (khi2 test) + +khi2 value 2.71882136877652 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.271882136877652 +p-value, i.e. P(X^2<=value) 0.0127109129710629 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/modF.txt b/validation/validation_results/Berges_2021/Berges_2021/modF.txt new file mode 100644 index 0000000..097111b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/modF.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.148176 NA NA +3.67805555555556 0.24192 NA NA +4.09222222222222 0.322056 NA NA +4.565 0.382536 NA NA +0.05 NA 14.2532679913876 0.0179647286936219 +1.95 NA 14.0904825899408 0.416068258072687 +2.83333333333333 NA 13.5451913151602 0.738217696058503 +3.98333333333333 NA 11.8535655359681 1.41736843460368 +4.88333333333333 NA 9.44599723101056 1.93437059934784 +5.16666666666667 NA 8.90318490242077 2.43945209185069 diff --git a/validation/validation_results/Berges_2021/Berges_2021/modF_res/KEIO_ROBOT3_27.pdf b/validation/validation_results/Berges_2021/Berges_2021/modF_res/KEIO_ROBOT3_27.pdf new file mode 100644 index 0000000..777baad Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/modF_res/KEIO_ROBOT3_27.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/modF_res/KEIO_ROBOT3_27_log.txt b/validation/validation_results/Berges_2021/Berges_2021/modF_res/KEIO_ROBOT3_27_log.txt new file mode 100644 index 0000000..c7ffcb5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/modF_res/KEIO_ROBOT3_27_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.148176 NA NA + [2,] 0.241920 NA NA + [3,] 0.322056 NA NA + [4,] 0.382536 NA NA + [5,] NA 14.253268 0.01796473 + [6,] NA 14.090483 0.41606826 + [7,] NA 13.545191 0.73821770 + [8,] NA 11.853566 1.41736843 + [9,] NA 9.445997 1.93437060 +[10,] NA 8.903185 2.43945209 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03306798 14.63465596 0.13013649 0.54196143 -6.16777154 2.42634308 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.486187e-08 6.200139e-07 2.262689e-08 -1.813357e-07 -3.079925e-07 -5.064172e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01256163 0.46239959 0.19896573 0.09074611 0.87918523 0.37573610 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6595123 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.486187e-08 6.200139e-07 2.262689e-08 -1.813357e-07 -3.079925e-07 -5.064172e-07 + +$result$normp +[1] 8.773527e-07 + +$result$res + [1] 0.45308280 0.04025727 -0.91245849 0.49982608 0.80663208 -0.35278051 -0.61270704 -0.22154213 0.55784454 -0.17744695 0.58119163 -0.04010030 -0.34310421 -0.76543521 0.67993943 -0.11249134 + +$result$prevres + [1] 0.45308099 0.04025624 -0.91245864 0.49982757 0.80663075 -0.35278094 -0.61270695 -0.22154148 0.55784516 -0.17744654 0.58119151 -0.04010088 -0.34310493 -0.76543567 0.67994004 -0.11249008 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 237.7492257 0.000000 0 2.261819e+01 0.000000000 0.000000000 + [2,] 367.0095652 0.000000 0 4.463782e+01 0.000000000 0.000000000 + [3,] 459.3674084 0.000000 0 6.216225e+01 0.000000000 0.000000000 + [4,] 593.5240579 0.000000 0 8.959555e+01 0.000000000 0.000000000 + [5,] -0.6795759 2.173913 0 -5.643417e-04 0.003643486 0.000000000 + [6,] -46.4427006 2.173913 0 -1.756332e+00 0.248998403 0.000000000 + [7,] -90.1509303 2.173913 0 -5.263848e+00 0.483336185 0.000000000 + [8,] -189.5305788 2.173913 0 -1.665962e+01 1.016151321 0.000000000 + [9,] -324.2367418 2.173913 0 -3.657003e+01 1.738366418 0.000000000 +[10,] -382.1574215 2.173913 0 -4.620144e+01 2.048902984 0.000000000 +[11,] 0.6148793 0.000000 5 5.106158e-04 0.000000000 0.008380017 +[12,] 42.0212865 0.000000 5 1.589126e+00 0.000000000 0.572696328 +[13,] 81.5684278 0.000000 5 4.762722e+00 0.000000000 1.111673225 +[14,] 171.4869863 0.000000 5 1.507360e+01 0.000000000 2.337148037 +[15,] 293.3689225 0.000000 5 3.308850e+01 0.000000000 3.998242761 +[16,] 345.7754675 0.000000 5 4.180300e+01 0.000000000 4.712476863 + +$result$retres +$result$retres$res + [1] 0.45308099 0.04025624 -0.91245864 0.49982757 0.80663075 -0.35278094 -0.61270695 -0.22154148 0.55784516 -0.17744654 0.58119151 -0.04010088 -0.34310493 -0.76543567 0.67994004 -0.11249008 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15723762 13.221548 0.6860398 + [2,] 0.24272512 12.248661 1.0687644 + [3,] 0.30380683 11.553523 1.3422251 + [4,] 0.39253255 10.543784 1.7394472 + [5,] 0.03397629 14.624318 0.1342030 + [6,] 0.09514384 13.928203 0.4080481 + [7,] 0.15356480 13.263346 0.6695967 + [8,] 0.28639686 11.751656 1.2642813 + [9,] 0.46644677 9.702606 2.0703586 + [10,] 0.54386426 8.821559 2.4169541 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0090616198 NA NA + [2,] -0.0008051248 NA NA + [3,] 0.0182491728 NA NA + [4,] -0.0099965515 NA NA + [5,] NA -0.37105015 -0.116238301 + [6,] NA 0.16227923 0.008020175 + [7,] NA 0.28184520 0.068620986 + [8,] NA 0.10190908 0.153087133 + [9,] NA -0.25660877 -0.135988009 +[10,] NA 0.08162541 0.022498016 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/modF_res/KEIO_ROBOT3_27_res.txt b/validation/validation_results/Berges_2021/Berges_2021/modF_res/KEIO_ROBOT3_27_res.txt new file mode 100644 index 0000000..1c563f0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/modF_res/KEIO_ROBOT3_27_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0330679811012228 0.0328842107167822 0.0322175418625119 0.00439125601365933 0.0259242391848779 0.0423547179464665 +Glc 14.6346559642446 14.5832222166511 14.5829216406402 0.263631395083863 14.1039455397173 15.0837822086556 +Ace 0.130136492431645 0.144063639884268 0.132019487313911 0.106447220964569 9.99999999992066e-07 0.350645424301129 +mu 0.5419614272975 0.544426542171532 0.547643511304925 0.0278249426526385 0.486467120809161 0.592284486422235 +qGlc -6.16777154422387 -6.15398287067173 -6.13757552821649 0.527542678078952 -7.27488993811706 -5.20630760949523 +qAce 2.42634308313529 2.41296328532004 2.38705926184245 0.210775673492536 1.9818598292832 2.79625226096573 +res 4.34956470786741 24.6268849480881 24.2916479592055 6.93826981999056 11.9526323657938 38.1039334171718 + + +Goodness of fit (khi2 test) + +khi2 value 4.34956470787918 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.434956470787918 +p-value, i.e. P(X^2<=value) 0.0697971683616367 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/nanE.txt b/validation/validation_results/Berges_2021/Berges_2021/nanE.txt new file mode 100644 index 0000000..0bffbc1 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/nanE.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.152712 NA NA +3.67805555555556 0.216216 NA NA +4.09222222222222 0.312984 NA NA +4.565 0.418824 NA NA +0.05 NA 14.4771749259809 0.0189549416820499 +1.95 NA 13.86609892062 0.43593225944473 +2.83333333333333 NA 13.2572108454472 0.809168226761888 +3.98333333333333 NA 12.0009505532612 1.52733310430626 +4.88333333333333 NA 9.31889075322955 2.25252254345599 +5.16666666666667 NA 8.91292399789472 2.68604141592259 diff --git a/validation/validation_results/Berges_2021/Berges_2021/nanE_res/KEIO_ROBOT3_19.pdf b/validation/validation_results/Berges_2021/Berges_2021/nanE_res/KEIO_ROBOT3_19.pdf new file mode 100644 index 0000000..b120160 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/nanE_res/KEIO_ROBOT3_19.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/nanE_res/KEIO_ROBOT3_19_log.txt b/validation/validation_results/Berges_2021/Berges_2021/nanE_res/KEIO_ROBOT3_19_log.txt new file mode 100644 index 0000000..5db7936 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/nanE_res/KEIO_ROBOT3_19_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.152712 NA NA + [2,] 0.216216 NA NA + [3,] 0.312984 NA NA + [4,] 0.418824 NA NA + [5,] NA 14.477175 0.01895494 + [6,] NA 13.866099 0.43593226 + [7,] NA 13.257211 0.80916823 + [8,] NA 12.000951 1.52733310 + [9,] NA 9.318891 2.25252254 +[10,] NA 8.912924 2.68604142 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02541033 14.48354477 0.17587463 0.60977891 -6.20420879 2.74828845 + +$result$lastp + X Glc Ace mu qGlc qAce +-3.131541e-09 -4.983747e-08 8.878846e-08 3.176623e-08 -3.845236e-09 -1.631140e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.009883538 0.447497930 0.194950560 0.092285949 0.872834072 0.380722803 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6580152 + +$result$laststep + X Glc Ace mu qGlc qAce +-3.131541e-09 -4.983747e-08 8.878846e-08 3.176623e-08 -3.845236e-09 -1.631140e-07 + +$result$normp +[1] 1.94954e-07 + +$result$res + [1] -0.292775881 1.157053533 -0.242934460 -0.387022682 -0.003552391 0.058564133 0.064976125 -0.418469072 0.749055067 -0.450573861 0.802326061 0.007599654 -0.516512244 -0.832347559 0.292573031 0.246361057 + +$result$prevres + [1] -0.292775647 1.157053610 -0.242934564 -0.387023130 -0.003552285 0.058564131 0.064976063 -0.418469173 0.749055057 -0.450573794 0.802325620 0.007599401 -0.516512356 -0.832347435 0.292573347 0.246361422 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 288.9700213 0.000000 0 2.112490e+01 0.000000000 0.000000000 + [2,] 470.9837451 0.000000 0 4.401843e+01 0.000000000 0.000000000 + [3,] 606.2992437 0.000000 0 6.304586e+01 0.000000000 0.000000000 + [4,] 808.8905091 0.000000 0 9.382982e+01 0.000000000 0.000000000 + [5,] -0.6847562 2.173913 0 -4.372077e-04 0.002804529 0.000000000 + [6,] -50.5191957 2.173913 0 -1.494005e+00 0.206909472 0.000000000 + [7,] -102.3586509 2.173913 0 -4.696425e+00 0.419226279 0.000000000 + [8,] -228.8601777 2.173913 0 -1.586660e+01 0.937333579 0.000000000 + [9,] -412.3698006 2.173913 0 -3.673038e+01 1.688926685 0.000000000 +[10,] -494.3114780 2.173913 0 -4.720175e+01 2.024531973 0.000000000 +[11,] 0.6976535 0.000000 5 4.454422e-04 0.000000000 0.006450417 +[12,] 51.4707146 0.000000 5 1.522144e+00 0.000000000 0.475891786 +[13,] 104.2865553 0.000000 5 4.784881e+00 0.000000000 0.964220441 +[14,] 233.1707128 0.000000 5 1.616544e+01 0.000000000 2.155867233 +[15,] 420.1367024 0.000000 5 3.742219e+01 0.000000000 3.884531376 +[16,] 503.6217346 0.000000 5 4.809079e+01 0.000000000 4.656423537 + +$result$retres +$result$retres$res + [1] -0.292775647 1.157053610 -0.242934564 -0.387023130 -0.003552285 0.058564131 0.064976063 -0.418469173 0.749055057 -0.450573794 0.802325620 0.007599401 -0.516512356 -0.832347435 0.292573347 0.246361422 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.14685649 13.247888 0.7232354 + [2,] 0.23935707 12.306739 1.1401378 + [3,] 0.30812531 11.607055 1.4500780 + [4,] 0.41108354 10.559504 1.9141133 + [5,] 0.02619700 14.475541 0.1794201 + [6,] 0.08344808 13.893038 0.4374521 + [7,] 0.14300258 13.287100 0.7058658 + [8,] 0.28833079 11.808455 1.3608636 + [9,] 0.49915137 9.663456 2.3110372 + [10,] 0.59328807 8.705660 2.7353137 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.005855513 NA NA + [2,] -0.023141072 NA NA + [3,] 0.004858691 NA NA + [4,] 0.007740463 NA NA + [5,] NA 0.001634051 -0.16046512 + [6,] NA -0.026939500 -0.00151988 + [7,] NA -0.029888989 0.10330247 + [8,] NA 0.192495819 0.16646949 + [9,] NA -0.344565326 -0.05851467 +[10,] NA 0.207263945 -0.04927228 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/nanE_res/KEIO_ROBOT3_19_res.txt b/validation/validation_results/Berges_2021/Berges_2021/nanE_res/KEIO_ROBOT3_19_res.txt new file mode 100644 index 0000000..25afbb8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/nanE_res/KEIO_ROBOT3_19_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.025410329464326 0.0255335150967367 0.025506782819247 0.00297696082319314 0.020155874872756 0.0316600146550032 +Glc 14.4835447714838 14.484977598302 14.4795295378541 0.249244581083165 14.0430032095384 14.8720795295863 +Ace 0.175874633155677 0.17228738115087 0.148434792324253 0.104862221818308 1.00000000000054e-06 0.394889858239569 +mu 0.609778906127111 0.610026607160205 0.609019177079453 0.0254523495968555 0.56151631857958 0.659986824475349 +qGlc -6.2042087943223 -6.19812401435304 -6.18792296583726 0.537085134155794 -7.14303822411358 -5.27914181796082 +qAce 2.74828844877795 2.76455331936844 2.79115007380304 0.215905519197045 2.38673637321181 3.14787013879391 +res 4.32984020782234 23.8384873254891 23.5309821714795 6.65221188323636 11.6738880004981 36.3358352386968 + + +Goodness of fit (khi2 test) + +khi2 value 4.3298402078232 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.43298402078232 +p-value, i.e. P(X^2<=value) 0.0687569370022944 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/wbbJ.txt b/validation/validation_results/Berges_2021/Berges_2021/wbbJ.txt new file mode 100644 index 0000000..43abc6e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/wbbJ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.033264 NA NA +1.195 0.061992 NA NA +1.61361111111111 0.074088 NA NA +2.36138888888889 0.123984 NA NA +3.28638888888889 0.182952 NA NA +3.81944444444444 0.2646 NA NA +4.41083333333333 0.40068 NA NA +0.283333333333333 NA 14.2712504741774 0.0454642313012119 +1.91666666666667 NA 13.735146205263 0.403736854038142 +2.7 NA 13.275729370858 0.704609285752942 +3.61666666666667 NA 12.5045715615216 1.22593760228419 +4.05 NA 11.6233553875376 1.45722163387323 +4.75 NA 10.1257130725276 2.06840275504759 diff --git a/validation/validation_results/Berges_2021/Berges_2021/wbbJ_res/KEIO_ROBOT4_26.pdf b/validation/validation_results/Berges_2021/Berges_2021/wbbJ_res/KEIO_ROBOT4_26.pdf new file mode 100644 index 0000000..a25e394 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/wbbJ_res/KEIO_ROBOT4_26.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/wbbJ_res/KEIO_ROBOT4_26_log.txt b/validation/validation_results/Berges_2021/Berges_2021/wbbJ_res/KEIO_ROBOT4_26_log.txt new file mode 100644 index 0000000..7c8c70d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/wbbJ_res/KEIO_ROBOT4_26_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.033264 NA NA + [2,] 0.061992 NA NA + [3,] 0.074088 NA NA + [4,] 0.123984 NA NA + [5,] 0.182952 NA NA + [6,] 0.264600 NA NA + [7,] 0.400680 NA NA + [8,] NA 14.27125 0.04546423 + [9,] NA 13.73515 0.40373685 +[10,] NA 13.27573 0.70460929 +[11,] NA 12.50457 1.22593760 +[12,] NA 11.62336 1.45722163 +[13,] NA 10.12571 2.06840276 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02815175 14.33755054 0.13834000 0.59566871 -5.54466198 2.68276874 + +$result$lastp + X Glc Ace mu qGlc qAce + 5.909210e-09 4.914170e-08 -8.331540e-08 -5.489004e-08 1.757853e-07 1.037719e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.005438048 0.303694532 0.132684663 0.048528299 0.775289302 0.340799452 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.456174 + +$result$laststep + X Glc Ace mu qGlc qAce + 5.909210e-09 4.914170e-08 -8.331540e-08 -5.489004e-08 1.757853e-07 1.037719e-07 + +$result$normp +[1] 2.325366e-07 + +$result$res + [1] -0.25561238 -0.23135185 -0.02387654 -0.45332151 0.82136109 0.46459039 -0.55625071 0.03939741 0.09500603 0.03287911 -0.35732215 0.11187205 0.07816755 0.58093097 0.02464643 -0.29914031 -0.60593462 -0.15262724 0.45212478 + +$result$prevres + [1] -0.25561268 -0.23135226 -0.02387699 -0.45332197 0.82136080 0.46459039 -0.55625008 0.03939733 0.09500607 0.03287920 -0.35732206 0.11187210 0.07816738 0.58093136 0.02464660 -0.29914029 -0.60593477 -0.15262745 0.45212455 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.0000000 0.00000000 + [2,] 101.885251 0.000000 0 3.42755605 0.0000000 0.00000000 + [3,] 130.738710 0.000000 0 5.93893283 0.0000000 0.00000000 + [4,] 204.103786 0.000000 0 13.56825254 0.0000000 0.00000000 + [5,] 354.115181 0.000000 0 32.76188200 0.0000000 0.00000000 + [6,] 486.456157 0.000000 0 52.30572717 0.0000000 0.00000000 + [7,] 691.884248 0.000000 0 85.91310860 0.0000000 0.00000000 + [8,] -3.720307 2.173913 0 -0.01525435 0.0188890 0.00000000 + [9,] -43.143628 2.173913 0 -1.38077662 0.2190518 0.00000000 +[10,] -80.827226 2.173913 0 -3.86178923 0.4103816 0.00000000 +[11,] -154.237637 2.173913 0 -10.47467480 0.7831061 0.00000000 +[12,] -205.619642 2.173913 0 -16.03303329 1.0439864 0.00000000 +[13,] -322.466705 2.173913 0 -30.58638721 1.6372505 0.00000000 +[14,] 4.140138 0.000000 5 0.01697578 0.0000000 0.04344471 +[15,] 48.012313 0.000000 5 1.53659492 0.0000000 0.50381924 +[16,] 89.948442 0.000000 5 4.29758559 0.0000000 0.94387779 +[17,] 171.643093 0.000000 5 11.65672407 0.0000000 1.80114408 +[18,] 228.823470 0.000000 5 17.84233388 0.0000000 2.40116879 +[19,] 358.856525 0.000000 5 34.03800908 0.0000000 3.76567617 + +$result$retres +$result$retres$res + [1] -0.25561268 -0.23135226 -0.02387699 -0.45332197 0.82136080 0.46459039 -0.55625008 0.03939733 0.09500607 0.03287920 -0.35732206 0.11187210 0.07816738 0.58093136 0.02464660 -0.29914029 -0.60593477 -0.15262745 0.45212455 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02815175 14.33755 0.1383401 + [2,] 0.05736495 14.06563 0.2699103 + [3,] 0.07361046 13.91441 0.3430767 + [4,] 0.11491756 13.52991 0.5291153 + [5,] 0.19937922 12.74371 0.9095131 + [6,] 0.27389181 12.05013 1.2451024 + [7,] 0.38955500 10.97350 1.7660254 + [8,] 0.03332748 14.28937 0.1616505 + [9,] 0.08817362 13.77885 0.4086662 + [10,] 0.14059945 13.29085 0.6447812 + [11,] 0.24272880 12.34020 1.1047506 + [12,] 0.31421200 11.67482 1.4266961 + [13,] 0.47677088 10.16167 2.1588277 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0051122536 NA NA + [2,] 0.0046270452 NA NA + [3,] 0.0004775398 NA NA + [4,] 0.0090664394 NA NA + [5,] -0.0164272160 NA NA + [6,] -0.0092918077 NA NA + [7,] 0.0111250016 NA NA + [8,] NA -0.01812277 -0.116186271 + [9,] NA -0.04370279 -0.004929319 +[10,] NA -0.01512443 0.059828058 +[11,] NA 0.16436815 0.121186953 +[12,] NA -0.05146116 0.030525489 +[13,] NA -0.03595699 -0.090424910 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/wbbJ_res/KEIO_ROBOT4_26_res.txt b/validation/validation_results/Berges_2021/Berges_2021/wbbJ_res/KEIO_ROBOT4_26_res.txt new file mode 100644 index 0000000..f2d2610 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/wbbJ_res/KEIO_ROBOT4_26_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0281517523591484 0.0282005702502064 0.0277517057367555 0.00351592270405845 0.0225108942424459 0.0360331908655369 +Glc 14.3375505392 14.3773306456837 14.3777832036502 0.180161288537838 14.0393378978959 14.712083799045 +Ace 0.138339999085853 0.155748792544396 0.151443093734544 0.0898792156493899 1.00000000000054e-06 0.327005879758154 +mu 0.595668714648596 0.596253916491524 0.596426830125486 0.0304093787932387 0.535204471008549 0.651008793674437 +qGlc -5.54466197649962 -5.65767701398929 -5.56511771538386 0.59188017650838 -6.70565031307767 -4.57578771559776 +qAce 2.68276873989823 2.65798579894943 2.65781840533171 0.253556219958309 2.21003005793342 3.12531117889759 +res 2.7052307672247 32.9169632375837 32.0844382340395 8.18522812662219 18.1671458153862 48.4888821967775 + + +Goodness of fit (khi2 test) + +khi2 value 2.70523076722629 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.208094674402022 +p-value, i.e. P(X^2<=value) 0.001194507519427 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yacC.txt b/validation/validation_results/Berges_2021/Berges_2021/yacC.txt new file mode 100644 index 0000000..1fc9e75 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yacC.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.8040000000000003E-2 NA NA +2.2613888888888889 9.0719999999999995E-2 NA NA +2.7741666666666664 0.12852000000000002 NA NA +3.2088888888888891 0.157248 NA NA +3.7063888888888892 0.235872 NA NA +4.2258333333333331 0.30693600000000004 NA NA +4.6355555555555554 0.39916800000000002 NA NA +4.9675000000000002 0.61236000000000002 NA NA +2.8 NA 12.4666356397146 0.613437693310656 +3.73333333333333 NA 11.6883669752675 1.04999023315843 +4.28333333333333 NA 10.0643404666098 1.3339759251594 +4.75 NA 10.0260087770084 1.71744125206341 +5.11666666666667 NA 9.23878389031604 2.01267427870097 +5.43333333333333 NA 8.47013840794951 2.34198962316039 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yacC_res/KEIO_ROBOT5_1.pdf b/validation/validation_results/Berges_2021/Berges_2021/yacC_res/KEIO_ROBOT5_1.pdf new file mode 100644 index 0000000..af64126 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yacC_res/KEIO_ROBOT5_1.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yacC_res/KEIO_ROBOT5_1_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yacC_res/KEIO_ROBOT5_1_log.txt new file mode 100644 index 0000000..428ce96 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yacC_res/KEIO_ROBOT5_1_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.068040 NA NA + [2,] 0.090720 NA NA + [3,] 0.128520 NA NA + [4,] 0.157248 NA NA + [5,] 0.235872 NA NA + [6,] 0.306936 NA NA + [7,] 0.399168 NA NA + [8,] 0.612360 NA NA + [9,] NA 12.466636 0.6134377 +[10,] NA 11.688367 1.0499902 +[11,] NA 10.064340 1.3339759 +[12,] NA 10.026009 1.7174413 +[13,] NA 9.238784 2.0126743 +[14,] NA 8.470138 2.3419896 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01493126 12.69519335 0.47208911 0.73331625 -4.12420612 1.80929690 + +$result$lastp + X Glc Ace mu qGlc qAce + 3.832716e-09 2.254843e-07 -8.180812e-08 -5.690308e-08 -1.828156e-07 5.041644e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006535277 0.951012226 0.413667448 0.095545211 1.429417247 0.621633050 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.119201 + +$result$laststep + X Glc Ace mu qGlc qAce + 3.832716e-09 2.254843e-07 -8.180812e-08 -5.690308e-08 -1.828156e-07 5.041644e-08 + +$result$normp +[1] 3.110494e-07 + +$result$res + [1] -0.54755154 -0.61621062 -0.71687255 -0.00971844 -0.48368347 1.20669015 2.39666529 -2.10177605 -0.74329901 -0.44942609 1.67975036 0.04022321 -0.08243055 -0.44481792 0.54459988 -0.22754524 -0.23352588 -0.41246528 -0.03808590 0.36702242 + +$result$prevres + [1] -0.547551971 -0.616211124 -0.716873111 -0.009719022 -0.483683985 1.206689879 2.396665444 -2.101775306 -0.743299259 -0.449426178 1.679750370 0.040223295 -0.082430433 -0.444817794 0.544600062 -0.227545189 -0.233525907 -0.412465359 -0.038085981 0.367022374 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 191.17267 0.000000 0 5.220468 0.0000000 0.0000000 + [2,] 262.52239 0.000000 0 8.864167 0.0000000 0.0000000 + [3,] 382.36080 0.000000 0 15.838070 0.0000000 0.0000000 + [4,] 525.92235 0.000000 0 25.198381 0.0000000 0.0000000 + [5,] 757.46584 0.000000 0 41.918947 0.0000000 0.0000000 + [6,] 1108.64687 0.000000 0 69.952289 0.0000000 0.0000000 + [7,] 1497.19930 0.000000 0 103.628148 0.0000000 0.0000000 + [8,] 1909.83434 0.000000 0 141.654346 0.0000000 0.0000000 + [9,] -83.05821 2.173913 0 -2.292433 0.3007035 0.0000000 +[10,] -176.68833 2.173913 0 -6.933129 0.6396816 0.0000000 +[11,] -270.53951 2.173913 0 -12.575905 0.9794599 0.0000000 +[12,] -385.92544 2.173913 0 -20.380359 1.3972026 0.0000000 +[13,] -508.75584 2.173913 0 -29.443202 1.8418972 0.0000000 +[14,] -644.93701 2.173913 0 -40.181603 2.3349269 0.0000000 +[15,] 83.80692 0.000000 5 2.313098 0.0000000 0.6916182 +[16,] 178.28105 0.000000 5 6.995627 0.0000000 1.4712677 +[17,] 272.97823 0.000000 5 12.689268 0.0000000 2.2527579 +[18,] 389.40429 0.000000 5 20.564073 0.0000000 3.2135660 +[19,] 513.34192 0.000000 5 29.708612 0.0000000 4.2363637 +[20,] 650.75066 0.000000 5 40.543812 0.0000000 5.3703319 + +$result$retres +$result$retres$res + [1] -0.547551971 -0.616211124 -0.716873111 -0.009719022 -0.483683985 1.206689879 2.396665444 -2.101775306 -0.743299259 -0.449426178 1.679750370 0.040223295 -0.082430433 -0.444817794 0.544600062 -0.227545189 -0.233525907 -0.412465359 -0.038085981 0.367022374 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05708896 12.458096 0.5761041 + [2,] 0.07839578 12.338266 0.6286740 + [3,] 0.11418254 12.136999 0.7169699 + [4,] 0.15705362 11.895890 0.8227449 + [5,] 0.22619832 11.507017 0.9933443 + [6,] 0.33106980 10.917215 1.2520916 + [7,] 0.44710131 10.264648 1.5383738 + [8,] 0.57032449 9.571635 1.8424000 + [9,] 0.11636623 12.124718 0.7223577 + [10,] 0.23071218 11.481631 1.0044812 + [11,] 0.34532808 10.837026 1.2872707 + [12,] 0.48624334 10.044511 1.6349482 + [13,] 0.63625017 9.200866 2.0050571 + [14,] 0.80256164 8.265522 2.4153941 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0109510394 NA NA + [2,] 0.0123242225 NA NA + [3,] 0.0143374622 NA NA + [4,] 0.0001943804 NA NA + [5,] 0.0096736797 NA NA + [6,] -0.0241337976 NA NA + [7,] -0.0479333089 NA NA + [8,] 0.0420355061 NA NA + [9,] NA 0.34191766 -0.108920012 +[10,] NA 0.20673604 0.045509038 +[11,] NA -0.77268517 0.046705181 +[12,] NA -0.01850272 0.082493072 +[13,] NA 0.03791800 0.007617196 +[14,] NA 0.20461619 -0.073404475 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yacC_res/KEIO_ROBOT5_1_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yacC_res/KEIO_ROBOT5_1_res.txt new file mode 100644 index 0000000..306cd37 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yacC_res/KEIO_ROBOT5_1_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0149312594582037 0.0151325434663916 0.0150756007139449 0.00152642819613739 0.0124847473623253 0.018072120681204 +Glc 12.6951933485984 12.7007362829714 12.6792498504522 0.228063773147337 12.3517280496521 13.2147372436799 +Ace 0.472089112613883 0.487126126322924 0.484657686194374 0.102387478009547 0.251858953383713 0.663723365868439 +mu 0.733316254625636 0.731207994901515 0.731473606699808 0.0204973698309728 0.69157925456723 0.769720187554821 +qGlc -4.12420611775723 -4.17370409250853 -4.17169195429504 0.432570437778494 -4.95500362334854 -3.32960525775913 +qAce 1.80929690268653 1.77486030609753 1.76119613193926 0.184544030846284 1.47128169991195 2.117434851473 +res 17.5365447474385 35.6496282289464 33.6419219213886 8.59734587382932 22.963686947518 54.0148692936888 + + +Goodness of fit (khi2 test) + +khi2 value 17.5365447474409 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 1.25261033910292 +p-value, i.e. P(X^2<=value) 0.771289406834309 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yadG.txt b/validation/validation_results/Berges_2021/Berges_2021/yadG.txt new file mode 100644 index 0000000..9193e9b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yadG.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.14364 NA NA +3.67805555555556 0.210168 NA NA +4.09222222222222 0.305424 NA NA +4.565 0.379512 NA NA +0.05 NA 14.6623106015952 0.0174910824772209 +1.95 NA 13.9354652335065 0.401462077467418 +2.83333333333333 NA 13.6961492022904 0.681097708022526 +3.98333333333333 NA 11.8947709766137 1.34232105330484 +4.88333333333333 NA 9.84409004912274 2.10382966968185 +5.16666666666667 NA 9.1249594635205 2.29211417997483 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yadG_res/KEIO_ROBOT3_15.pdf b/validation/validation_results/Berges_2021/Berges_2021/yadG_res/KEIO_ROBOT3_15.pdf new file mode 100644 index 0000000..cefe3bf Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yadG_res/KEIO_ROBOT3_15.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yadG_res/KEIO_ROBOT3_15_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yadG_res/KEIO_ROBOT3_15_log.txt new file mode 100644 index 0000000..a975f02 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yadG_res/KEIO_ROBOT3_15_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.143640 NA NA + [2,] 0.210168 NA NA + [3,] 0.305424 NA NA + [4,] 0.379512 NA NA + [5,] NA 14.662311 0.01749108 + [6,] NA 13.935465 0.40146208 + [7,] NA 13.696149 0.68109771 + [8,] NA 11.894771 1.34232105 + [9,] NA 9.844090 2.10382967 +[10,] NA 9.124959 2.29211418 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02798571 14.70022019 0.12982758 0.57125708 -6.36246892 2.56271706 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.218863e-09 2.983493e-08 -2.183555e-08 -1.934230e-08 3.884650e-08 9.269752e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.009546667 0.386488266 0.166668293 0.081240075 0.785819069 0.337089644 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5571272 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.218863e-09 2.983493e-08 -2.183555e-08 -1.934230e-08 3.884650e-08 9.269752e-09 + +$result$normp +[1] 5.780087e-08 + +$result$res + [1] 0.05666376 0.93115419 -0.77810028 0.01131970 0.06277894 0.27589187 -0.55868472 0.18143070 0.20639000 -0.16780678 0.57987088 -0.07359608 -0.21664844 -0.58056003 -0.28129191 0.57222557 + +$result$prevres + [1] 0.05666359 0.93115410 -0.77810028 0.01131987 0.06277888 0.27589187 -0.55868468 0.18143076 0.20639000 -0.16780683 0.57987099 -0.07359604 -0.21664845 -0.58056009 -0.28129196 0.57222555 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 258.6557248 0.000000 0 2.082523e+01 0.000000000 0.000000000 + [2,] 408.7641483 0.000000 0 4.207532e+01 0.000000000 0.000000000 + [3,] 517.8750422 0.000000 0 5.930898e+01 0.000000000 0.000000000 + [4,] 678.4505814 0.000000 0 8.667529e+01 0.000000000 0.000000000 + [5,] -0.7015441 2.173913 0 -4.931666e-04 0.003085784 0.000000000 + [6,] -49.5473917 2.173913 0 -1.597913e+00 0.217937226 0.000000000 + [7,] -97.9588451 2.173913 0 -4.888324e+00 0.430877959 0.000000000 + [8,] -211.4426340 2.173913 0 -1.591146e+01 0.930043330 0.000000000 + [9,] -369.8464438 2.173913 0 -3.573480e+01 1.626792155 0.000000000 +[10,] -439.0790746 2.173913 0 -4.547826e+01 1.931316107 0.000000000 +[11,] 0.6499168 0.000000 5 4.568741e-04 0.000000000 0.007097304 +[12,] 45.9011551 0.000000 5 1.480321e+00 0.000000000 0.501255620 +[13,] 90.7499665 0.000000 5 4.528588e+00 0.000000000 0.991019305 +[14,] 195.8823825 0.000000 5 1.474052e+01 0.000000000 2.139099659 +[15,] 342.6291150 0.000000 5 3.310505e+01 0.000000000 3.741621956 +[16,] 406.7668549 0.000000 5 4.213148e+01 0.000000000 4.442027046 + +$result$retres +$result$retres$res + [1] 0.05666359 0.93115410 -0.77810028 0.01131987 0.06277888 0.27589187 -0.55868468 0.18143076 0.20639000 -0.16780683 0.57987099 -0.07359604 -0.21664845 -0.58056009 -0.28129196 0.57222555 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.14477327 13.399480 0.6537484 + [2,] 0.22879108 12.463718 1.0306608 + [3,] 0.28986199 11.783530 1.3046311 + [4,] 0.37973840 10.782517 1.7078257 + [5,] 0.02879659 14.691189 0.1334653 + [6,] 0.08525487 14.062375 0.3867429 + [7,] 0.14121107 13.439154 0.6377680 + [8,] 0.27238088 11.978229 1.2262090 + [9,] 0.45547133 9.939029 2.0475713 + [10,] 0.53549360 9.047768 2.4065593 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0011332718 NA NA + [2,] -0.0186230820 NA NA + [3,] 0.0155620056 NA NA + [4,] -0.0002263974 NA NA + [5,] NA -0.02887828 -0.11597420 + [6,] NA -0.12691026 0.01471921 + [7,] NA 0.25699495 0.04332969 + [8,] NA -0.08345815 0.11611202 + [9,] NA -0.09493940 0.05625839 +[10,] NA 0.07719114 -0.11444511 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yadG_res/KEIO_ROBOT3_15_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yadG_res/KEIO_ROBOT3_15_res.txt new file mode 100644 index 0000000..24c1cb7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yadG_res/KEIO_ROBOT3_15_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0279857102311709 0.0279142648835117 0.0272950709418283 0.00455641832906775 0.0213047025626266 0.0389331460025499 +Glc 14.7002201902878 14.6920311905822 14.6813912610916 0.285076627870653 14.1748294951323 15.2284464365717 +Ace 0.129827582293568 0.149343545908664 0.142720310047699 0.0994508582925671 9.99999999995709e-07 0.36137606481385 +mu 0.571257075100079 0.574145736069901 0.575093071737889 0.0345603484157525 0.498488858677081 0.6332306363534 +qGlc -6.36246891934106 -6.34123813433843 -6.34593837530829 0.555623378708465 -7.37641570417121 -5.37907764673586 +qAce 2.56271705585499 2.53505025803781 2.54281976256069 0.218050094919631 2.15833534757325 3.01296373772576 +res 3.10390664128377 24.205414192046 23.8831955582188 6.90751264135034 12.6041879539954 38.7334125364396 + + +Goodness of fit (khi2 test) + +khi2 value 3.10390664128386 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.310390664128386 +p-value, i.e. P(X^2<=value) 0.0211281371992478 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaeR.txt b/validation/validation_results/Berges_2021/Berges_2021/yaeR.txt new file mode 100644 index 0000000..834f889 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yaeR.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.1134 NA NA NA +3.34194444444444 0.15876 NA NA NA +3.9975 0.21924 NA NA NA +4.52333333333333 0.343224 NA NA NA +1.95 NA 13.5107039141088 0.357959997470828 0 +3.25 NA 12.927053986867 0.98303230304942 0 +4.08333333333333 NA 11.6400359577813 1.41734939532875 0 +4.76666666666667 NA 10.3870251277912 1.99636221676328 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaeR_res/KEIO_ROBOT2_8.pdf b/validation/validation_results/Berges_2021/Berges_2021/yaeR_res/KEIO_ROBOT2_8.pdf new file mode 100644 index 0000000..cc4259e Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yaeR_res/KEIO_ROBOT2_8.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaeR_res/KEIO_ROBOT2_8_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yaeR_res/KEIO_ROBOT2_8_log.txt new file mode 100644 index 0000000..546212c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yaeR_res/KEIO_ROBOT2_8_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.113400 NA NA NA +[2,] 0.158760 NA NA NA +[3,] 0.219240 NA NA NA +[4,] 0.343224 NA NA NA +[5,] NA 13.51070 0.3579600 0 +[6,] NA 12.92705 0.9830323 0 +[7,] NA 11.64004 1.4173494 0 +[8,] NA 10.38703 1.9963622 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.193189e-02 1.411303e+01 2.002845e-01 1.000000e-06 5.994293e-01 -6.200146e+00 3.068956e+00 -2.279991e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 9.504713e-09 1.495541e-07 -1.581743e-07 2.117582e-22 -1.058810e-07 3.476969e-07 8.916974e-08 -5.489135e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.01024215 0.66380094 0.29265994 0.27448615 0.11223184 1.74161099 0.76500376 0.73032777 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6135628 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 9.504713e-09 1.495541e-07 -1.581743e-07 2.117582e-22 -1.058810e-07 3.476969e-07 8.916974e-08 -5.489135e-13 + +$result$normp +[1] 4.330486e-07 + +$result$res + [1] -7.583236e-01 1.912522e-01 1.080332e+00 -6.567829e-01 2.153908e-01 -3.884344e-01 1.676977e-01 5.345872e-03 4.571125e-01 -5.363415e-01 -1.558107e-01 2.350396e-01 4.074700e-06 2.490861e-06 5.948413e-07 -1.846333e-06 + +$result$prevres + [1] -7.583244e-01 1.912515e-01 1.080332e+00 -6.567821e-01 2.153908e-01 -3.884343e-01 1.676978e-01 5.345697e-03 4.571129e-01 -5.363415e-01 -1.558109e-01 2.350394e-01 4.074700e-06 2.490862e-06 5.948430e-07 -1.846330e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.239514e+02 0.000000 0 0 1.228601e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.706591e+02 0.000000 0 0 2.716751e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.490788e+02 0.000000 0 0 4.813922e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.525309e+02 0.000000 0 0 7.465498e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.988245e+01 2.173913 0 0 -1.269885e+00 0.1764500 0.0000000 0.0000000 + [6,] -1.352663e+02 2.173913 0 0 -6.295230e+00 0.4784799 0.0000000 0.0000000 + [7,] -2.374798e+02 2.173913 0 0 -1.459236e+01 0.8400412 0.0000000 0.0000000 + [8,] -3.690822e+02 2.173913 0 0 -2.743132e+01 1.3055607 0.0000000 0.0000000 + [9,] 5.678901e+01 0.000000 5 0 1.445708e+00 0.0000000 0.4058351 0.0000000 +[10,] 1.539949e+02 0.000000 5 0 7.166846e+00 0.0000000 1.1005038 0.0000000 +[11,] 2.703604e+02 0.000000 5 0 1.661277e+01 0.0000000 1.9320949 0.0000000 +[12,] 4.201841e+02 0.000000 5 0 3.122937e+01 0.0000000 3.0027896 0.0000000 +[13,] -4.218972e-05 0.000000 0 5 -1.074046e-06 0.0000000 0.0000000 0.4058351 +[14,] -1.144059e-04 0.000000 0 5 -5.324397e-06 0.0000000 0.0000000 1.1005038 +[15,] -2.008563e-04 0.000000 0 5 -1.234197e-05 0.0000000 0.0000000 1.9320949 +[16,] -3.121634e-04 0.000000 0 5 -2.320094e-05 0.0000000 0.0000000 3.0027896 + +$result$retres +$result$retres$res + [1] -7.583244e-01 1.912515e-01 1.080332e+00 -6.567821e-01 2.153908e-01 -3.884343e-01 1.676978e-01 5.345697e-03 4.571129e-01 -5.363415e-01 -1.558109e-01 2.350394e-01 4.074700e-06 2.490862e-06 5.948430e-07 -1.846330e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09823351 13.32381 0.5909333 7.097791e-07 + [2,] 0.16258503 12.65820 0.9203998 4.650116e-07 + [3,] 0.24084665 11.84871 1.3210832 1.673357e-07 + [4,] 0.33008836 10.92564 1.7779825 -1.721042e-07 + [5,] 0.07058578 13.60978 0.4493826 8.149400e-07 + [6,] 0.15386674 12.74837 0.8757640 4.981725e-07 + [7,] 0.25356278 11.71718 1.3861872 1.189686e-07 + [8,] 0.38192396 10.38948 2.0433701 -3.692661e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.01516649 NA NA NA +[2,] -0.00382503 NA NA NA +[3,] -0.02160665 NA NA NA +[4,] 0.01313564 NA NA NA +[5,] NA -0.099079767 -0.09142258 -8.149400e-07 +[6,] NA 0.178679760 0.10726829 -4.981725e-07 +[7,] NA -0.077140972 0.03116217 -1.189686e-07 +[8,] NA -0.002459021 -0.04700789 3.692661e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaeR_res/KEIO_ROBOT2_8_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yaeR_res/KEIO_ROBOT2_8_res.txt new file mode 100644 index 0000000..304d877 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yaeR_res/KEIO_ROBOT2_8_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0219318910390378 0.0227597476831781 0.0224665683296566 0.00435774777164813 0.0149332520482741 0.0311684984514086 +Glc 14.1130312164877 14.1438959020434 14.1222200971268 0.36734736483327 13.3672713630615 14.9127036114129 +Ace 0.200284454432145 0.192513001738239 0.179960017563088 0.12897365373252 9.99999999979837e-07 0.447479209087677 +Lac 1e-06 0.0945739677332041 0.0668010729356037 0.089950273613638 9.99999999991066e-07 0.303109474348127 +mu 0.599429299918394 0.595873804275454 0.593471959818216 0.0459645713992243 0.516107842012692 0.687784114896493 +qGlc -6.20014590062461 -6.30388519492873 -6.30352801834894 0.970672857304069 -7.90209855175058 -4.19264759611313 +qAce 3.06895553846714 3.03426668959843 3.02529279267435 0.408731944450241 2.16504842470442 3.83480703799369 +qLac -2.27999059143303e-06 -0.0179063871089237 -0.00486621545488 0.249981892267559 -0.495472300632213 0.385078295833399 +res 3.01167413518766 20.8953821374491 19.6870871306959 6.87502284395614 11.3195043565087 36.0756111326464 + + +Goodness of fit (khi2 test) + +khi2 value 3.01167413518974 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.376459266898717 +p-value, i.e. P(X^2<=value) 0.0663772056723945 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yafJ.txt b/validation/validation_results/Berges_2021/Berges_2021/yafJ.txt new file mode 100644 index 0000000..765655e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yafJ.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.111888 NA NA NA +3.34194444444444 0.17388 NA NA NA +3.9975 0.252504 NA NA NA +4.52333333333333 0.359856 NA NA NA +1.95 NA 13.4691540474642 0.320140259065198 0 +3.25 NA 12.5718581148689 0.996182209325596 0 +4.08333333333333 NA 11.9953770530925 1.25551097896958 0 +4.76666666666667 NA 11.1595708900597 1.71802568265367 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yafJ_res/KEIO_ROBOT2_17.pdf b/validation/validation_results/Berges_2021/Berges_2021/yafJ_res/KEIO_ROBOT2_17.pdf new file mode 100644 index 0000000..9a355ee Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yafJ_res/KEIO_ROBOT2_17.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yafJ_res/KEIO_ROBOT2_17_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yafJ_res/KEIO_ROBOT2_17_log.txt new file mode 100644 index 0000000..ede664d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yafJ_res/KEIO_ROBOT2_17_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.111888 NA NA NA +[2,] 0.173880 NA NA NA +[3,] 0.252504 NA NA NA +[4,] 0.359856 NA NA NA +[5,] NA 13.46915 0.3201403 0 +[6,] NA 12.57186 0.9961822 0 +[7,] NA 11.99538 1.2555110 0 +[8,] NA 11.15957 1.7180257 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.508668e-02 1.370547e+01 2.441916e-01 1.000000e-06 5.849991e-01 -3.977954e+00 2.342603e+00 -2.091387e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 2.963037e-09 7.618631e-08 -6.315297e-08 2.117582e-22 -2.933974e-08 -7.645802e-08 9.674555e-08 -2.655984e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.008624795 0.516703917 0.228709690 0.219695510 0.082798605 1.248019167 0.549445988 0.534319461 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4863019 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 2.963037e-09 7.618631e-08 -6.315297e-08 2.117582e-22 -2.933974e-08 -7.645802e-08 9.674555e-08 -2.655984e-13 + +$result$normp +[1] 1.608346e-07 + +$result$res + [1] -1.753802e-01 1.668187e-01 3.772599e-01 -3.072030e-01 -2.758270e-01 3.527140e-01 4.632330e-02 -1.232103e-01 6.896923e-01 -8.997801e-01 -8.399105e-02 2.940789e-01 4.045249e-06 2.446546e-06 5.606464e-07 -1.841458e-06 + +$result$prevres + [1] -1.753805e-01 1.668186e-01 3.772599e-01 -3.072027e-01 -2.758270e-01 3.527139e-01 4.632334e-02 -1.232103e-01 6.896924e-01 -8.997800e-01 -8.399112e-02 2.940787e-01 4.045249e-06 2.446547e-06 5.606471e-07 -1.841457e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.160119e+02 0.000000 0 0 1.355508e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.532081e+02 0.000000 0 0 2.961236e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.183014e+02 0.000000 0 0 5.197733e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.049797e+02 0.000000 0 0 7.999785e+01 0.0000000 0.0000000 0.0000000 + [5,] -3.147347e+01 2.173913 0 0 -9.131093e-01 0.1984851 0.0000000 0.0000000 + [6,] -8.417484e+01 2.173913 0 0 -4.458464e+00 0.5308425 0.0000000 0.0000000 + [7,] -1.463437e+02 2.173913 0 0 -1.022963e+01 0.9229059 0.0000000 0.0000000 + [8,] -2.255293e+02 2.173913 0 0 -1.906500e+01 1.4222841 0.0000000 0.0000000 + [9,] 4.262961e+01 0.000000 5 0 1.236772e+00 0.0000000 0.4565158 0.0000000 +[10,] 1.140116e+02 0.000000 5 0 6.038820e+00 0.0000000 1.2209378 0.0000000 +[11,] 1.982170e+02 0.000000 5 0 1.385564e+01 0.0000000 2.1226836 0.0000000 +[12,] 3.054709e+02 0.000000 5 0 2.582282e+01 0.0000000 3.2712535 0.0000000 +[13,] -3.805810e-05 0.000000 0 5 -1.104143e-06 0.0000000 0.0000000 0.4565158 +[14,] -1.017852e-04 0.000000 0 5 -5.391229e-06 0.0000000 0.0000000 1.2209378 +[15,] -1.769606e-04 0.000000 0 5 -1.236979e-05 0.0000000 0.0000000 2.1226836 +[16,] -2.727128e-04 0.000000 0 5 -2.305363e-05 0.0000000 0.0000000 3.2712535 + +$result$retres +$result$retres$res + [1] -1.753805e-01 1.668186e-01 3.772599e-01 -3.072027e-01 -2.758270e-01 3.527139e-01 4.632334e-02 -1.232103e-01 6.896924e-01 -8.997800e-01 -8.399112e-02 2.940787e-01 4.045249e-06 2.446547e-06 5.606471e-07 -1.841457e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10838039 13.13908 0.5777377 7.022228e-07 + [2,] 0.17721637 12.67100 0.8533883 4.561324e-07 + [3,] 0.26004920 12.10774 1.1850887 1.600029e-07 + [4,] 0.35371195 11.47084 1.5601571 -1.748438e-07 + [5,] 0.07849894 13.34227 0.4580787 8.090498e-07 + [6,] 0.16793618 12.73411 0.8162262 4.893093e-07 + [7,] 0.27344028 12.01669 1.2387128 1.121294e-07 + [8,] 0.40782275 11.10289 1.7768414 -3.682914e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.003507610 NA NA NA +[2,] -0.003336371 NA NA NA +[3,] -0.007545198 NA NA NA +[4,] 0.006144055 NA NA NA +[5,] NA 0.12688044 -0.13793849 -8.090498e-07 +[6,] NA -0.16224841 0.17995601 -4.893093e-07 +[7,] NA -0.02130874 0.01679822 -1.121294e-07 +[8,] NA 0.05667672 -0.05881574 3.682914e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yafJ_res/KEIO_ROBOT2_17_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yafJ_res/KEIO_ROBOT2_17_res.txt new file mode 100644 index 0000000..a6cccf2 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yafJ_res/KEIO_ROBOT2_17_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.025086679779663 0.0257528925919203 0.0254863794103163 0.00471649375278555 0.0174445620300158 0.0349820754664873 +Glc 13.7054734549666 13.699877184611 13.7224484944981 0.298297197809713 13.152311124261 14.3591828175589 +Ace 0.244191619657268 0.201918870500307 0.187582924199014 0.136372337472832 9.99999999987122e-07 0.460627250894721 +Lac 1e-06 0.0675133302567826 0.0488236655348782 0.0651137371669487 9.99999999992887e-07 0.205259725815291 +mu 0.58499907901067 0.58251779638997 0.582040753151522 0.0431387982391577 0.506775394485388 0.671045946043866 +qGlc -3.97795410056887 -3.89712896799884 -3.94501206602975 0.784687005086656 -5.48159091869165 -2.39563750350705 +qAce 2.34260323125667 2.43723148761652 2.45690114582234 0.352959293850076 1.76742583457219 3.01188186834109 +qLac -2.09138721448791e-06 0.021473035238973 0.00900850222839176 0.189318356608278 -0.340703179509717 0.400239132222298 +res 1.89191616266955 19.5516192099069 18.8512416112436 6.11622904742312 10.7194721058358 32.0328459034608 + + +Goodness of fit (khi2 test) + +khi2 value 1.89191616266979 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.236489520333724 +p-value, i.e. P(X^2<=value) 0.0158520386091432 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yahJ.txt b/validation/validation_results/Berges_2021/Berges_2021/yahJ.txt new file mode 100644 index 0000000..fcf8ba6 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yahJ.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.161784 NA NA +3.67805555555556 0.258552 NA NA +4.09222222222222 0.378 NA NA +4.565 0.585144 NA NA +0.05 NA 14.2181504166793 0.015991232229232 +1.95 NA 13.786019452882 0.422845019076729 +2.83333333333333 NA 13.4673227039794 0.792222292200696 +3.98333333333333 NA 11.8180172020272 1.45667330104467 +4.88333333333333 NA 9.24583068057176 2.28596594075861 +5.16666666666667 NA 8.48188793002252 2.50471695994088 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yahJ_res/KEIO_ROBOT3_31.pdf b/validation/validation_results/Berges_2021/Berges_2021/yahJ_res/KEIO_ROBOT3_31.pdf new file mode 100644 index 0000000..09eca60 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yahJ_res/KEIO_ROBOT3_31.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yahJ_res/KEIO_ROBOT3_31_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yahJ_res/KEIO_ROBOT3_31_log.txt new file mode 100644 index 0000000..46d7112 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yahJ_res/KEIO_ROBOT3_31_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.161784 NA NA + [2,] 0.258552 NA NA + [3,] 0.378000 NA NA + [4,] 0.585144 NA NA + [5,] NA 14.218150 0.01599123 + [6,] NA 13.786019 0.42284502 + [7,] NA 13.467323 0.79222229 + [8,] NA 11.818017 1.45667330 + [9,] NA 9.245831 2.28596594 +[10,] NA 8.481888 2.50471696 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01510086 14.18294867 0.29760316 0.79491385 -5.21003133 2.10643947 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.206500e-09 -3.902305e-08 4.632332e-08 1.969139e-08 3.279463e-08 -8.106620e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.007724334 0.581965995 0.251914501 0.119560974 0.955679170 0.412586891 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.927465 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.206500e-09 -3.902305e-08 4.632332e-08 1.969139e-08 3.279463e-08 -8.106620e-08 + +$result$normp +[1] 1.0819e-07 + +$result$res + [1] -0.65610597 1.12428453 0.63061704 -0.81707659 -0.08524949 0.06424196 -0.27513350 0.25224162 0.50993550 -0.46603609 1.41617206 0.11645356 -0.77059464 -1.24914732 -0.43550638 0.92262272 + +$result$prevres + [1] -0.65610579 1.12428464 0.63061702 -0.81707688 -0.08524941 0.06424199 -0.27513350 0.25224156 0.50993545 -0.46603610 1.41617183 0.11645340 -0.77059473 -1.24914727 -0.43550618 0.92262296 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 492.2299303 0.000000 0 2.138460e+01 0.000000000 0.000000000 + [2,] 930.5355220 0.000000 0 5.168361e+01 0.000000000 0.000000000 + [3,] 1293.3448695 0.000000 0 7.992362e+01 0.000000000 0.000000000 + [4,] 1883.3448675 0.000000 0 1.298292e+02 0.000000000 0.000000000 + [5,] -0.5777125 2.173913 0 -2.195437e-04 0.001674453 0.000000000 + [6,] -52.8875709 2.173913 0 -9.722303e-01 0.153290381 0.000000000 + [7,] -121.2409402 2.173913 0 -3.493814e+00 0.351407137 0.000000000 + [8,] -323.7507389 2.173913 0 -1.418099e+01 0.938365538 0.000000000 + [9,] -676.9767604 2.173913 0 -3.811225e+01 1.962162818 0.000000000 +[10,] -851.5838381 2.173913 0 -5.137576e+01 2.468247422 0.000000000 +[11,] 0.5372152 0.000000 5 2.041537e-04 0.000000000 0.003851243 +[12,] 49.1801807 0.000000 5 9.040774e-01 0.000000000 0.352567875 +[13,] 112.7420156 0.000000 5 3.248900e+00 0.000000000 0.808236414 +[14,] 301.0559863 0.000000 5 1.318691e+01 0.000000000 2.158240738 +[15,] 629.5210538 0.000000 5 3.544060e+01 0.000000000 4.512974482 +[16,] 791.8882693 0.000000 5 4.777435e+01 0.000000000 5.676969071 + +$result$retres +$result$retres$res + [1] -0.65610579 1.12428464 0.63061702 -0.81707688 -0.08524941 0.06424199 -0.27513350 0.25224156 0.50993545 -0.46603610 1.41617183 0.11645340 -0.77059473 -1.24914727 -0.43550618 0.92262296 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.14866188 13.307562 0.6515260 + [2,] 0.28103769 12.439943 1.0023083 + [3,] 0.39061234 11.721768 1.2926698 + [4,] 0.56880246 10.553873 1.7648552 + [5,] 0.01571314 14.178936 0.2992256 + [6,] 0.07115307 13.815571 0.4461357 + [7,] 0.14359652 13.340761 0.6381033 + [8,] 0.35822394 11.934048 1.2068438 + [9,] 0.73258603 9.480401 2.1988647 + [10,] 0.91764111 8.267511 2.6892416 + + +$result$it +[1] 10 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.01312212 NA NA + [2,] -0.02248569 NA NA + [3,] -0.01261234 NA NA + [4,] 0.01634154 NA NA + [5,] NA 0.03921473 -0.28323437 + [6,] NA -0.02955132 -0.02329068 + [7,] NA 0.12656141 0.15411895 + [8,] NA -0.11603112 0.24982945 + [9,] NA -0.23457031 0.08710124 +[10,] NA 0.21437661 -0.18452459 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yahJ_res/KEIO_ROBOT3_31_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yahJ_res/KEIO_ROBOT3_31_res.txt new file mode 100644 index 0000000..0b8658b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yahJ_res/KEIO_ROBOT3_31_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0151008566406257 0.015402095286252 0.0154804331263144 0.00192726195532725 0.0118729555989705 0.0193255614241483 +Glc 14.1829486686973 14.1599459507844 14.1564671633646 0.233115495753844 13.7585781367586 14.6235223522028 +Ace 0.297603161853604 0.294833258122243 0.287583893571709 0.10739005184916 0.0863459755973094 0.518733739088075 +mu 0.794913854170709 0.792681311232777 0.792012308477462 0.0267986836498316 0.743489723148003 0.84362726276875 +qGlc -5.21003133110475 -5.11968363411517 -5.09225508262423 0.425337386631193 -5.98855545155261 -4.39208918406209 +qAce 2.10643947050864 2.10798543168045 2.09514627658087 0.189388731672828 1.77691619948693 2.45808558397739 +res 8.60191372782534 23.7988728700312 23.6518278714707 6.05327815035969 13.7314249805056 36.6880776259407 + + +Goodness of fit (khi2 test) + +khi2 value 8.60191372782569 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.860191372782569 +p-value, i.e. P(X^2<=value) 0.429746833083044 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yahO.txt b/validation/validation_results/Berges_2021/Berges_2021/yahO.txt new file mode 100644 index 0000000..1f60c36 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yahO.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.18888888888889 0.057456 NA NA +2.27694444444444 0.099792 NA NA +3.12833333333333 0.1512 NA NA +3.77138888888889 0.216216 NA NA +4.41555555555556 0.300888 NA NA +4.82277777777778 0.397656 NA NA +0.0666666666666667 NA 14.6214296800077 0.00801209303512972 +1.71666666666667 NA 14.796643473525 0.34393831838864 +2.8 NA 13.3684971401723 0.744427522087894 +3.63333333333333 NA 13.0618154867972 1.23164211503433 +4.26666666666667 NA 12.3017208355208 1.77085778008479 +4.88333333333333 NA 10.443630544426 2.19326809749828 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yahO_res/KEIO_ROBOT1_42.pdf b/validation/validation_results/Berges_2021/Berges_2021/yahO_res/KEIO_ROBOT1_42.pdf new file mode 100644 index 0000000..86a45c7 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yahO_res/KEIO_ROBOT1_42.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yahO_res/KEIO_ROBOT1_42_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yahO_res/KEIO_ROBOT1_42_log.txt new file mode 100644 index 0000000..2bbc4a1 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yahO_res/KEIO_ROBOT1_42_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.057456 NA NA + [3,] 0.099792 NA NA + [4,] 0.151200 NA NA + [5,] 0.216216 NA NA + [6,] 0.300888 NA NA + [7,] 0.397656 NA NA + [8,] NA 14.62143 0.008012093 + [9,] NA 14.79664 0.343938318 +[10,] NA 13.36850 0.744427522 +[11,] NA 13.06182 1.231642115 +[12,] NA 12.30172 1.770857780 +[13,] NA 10.44363 2.193268097 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02859629 14.89178128 0.09809659 0.54044826 -6.11104447 3.24020714 + +$result$lastp + X Glc Ace mu qGlc qAce + 7.559748e-10 -2.151930e-09 -1.130921e-08 -6.227155e-09 6.291146e-08 9.087022e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.007401222 0.394182338 0.172796061 0.059120901 1.108494412 0.497680053 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5973918 + +$result$laststep + X Glc Ace mu qGlc qAce + 7.559748e-10 -2.151930e-09 -1.130921e-08 -6.227155e-09 6.291146e-08 9.087022e-09 + +$result$normp +[1] 6.490227e-08 + +$result$res + [1] -0.30898557 -0.15430723 -0.09508432 0.19429571 0.16601402 0.50347520 -0.50735528 0.56193254 -0.86786452 0.82206158 -0.32736538 -0.71924847 0.53048424 0.48187158 0.08138087 -0.19577655 -0.41706646 -0.62014704 0.66973761 + +$result$prevres + [1] -0.30898561 -0.15430728 -0.09508438 0.19429565 0.16601398 0.50347522 -0.50735521 0.56193255 -0.86786450 0.82206160 -0.32736537 -0.71924847 0.53048420 0.48187163 0.08138089 -0.19577655 -0.41706648 -0.62014707 0.66973757 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.000000000 0.000000000 + [2,] 95.0645320 0.000000 0 3.231986e+00 0.000000000 0.000000000 + [3,] 171.1591260 0.000000 0 1.114454e+01 0.000000000 0.000000000 + [4,] 271.1644153 0.000000 0 2.425802e+01 0.000000000 0.000000000 + [5,] 383.8545083 0.000000 0 4.139783e+01 0.000000000 0.000000000 + [6,] 543.7025722 0.000000 0 6.865251e+01 0.000000000 0.000000000 + [7,] 677.5510493 0.000000 0 9.344346e+01 0.000000000 0.000000000 + [8,] -0.9018071 2.173913 0 -8.647729e-04 0.004219955 0.000000000 + [9,] -37.5813057 2.173913 0 -1.063069e+00 0.175859598 0.000000000 +[10,] -87.0541553 2.173913 0 -4.332377e+00 0.407365004 0.000000000 +[11,] -150.5633153 2.173913 0 -1.023086e+01 0.704552531 0.000000000 +[12,] -222.0503137 2.173913 0 -1.834256e+01 1.039071903 0.000000000 +[13,] -319.6012290 2.173913 0 -3.115264e+01 1.495555902 0.000000000 +[14,] 1.0997622 0.000000 5 1.054599e-03 0.000000000 0.009705897 +[15,] 45.8307566 0.000000 5 1.296422e+00 0.000000000 0.404477075 +[16,] 106.1633629 0.000000 5 5.283374e+00 0.000000000 0.936939508 +[17,] 183.6133822 0.000000 5 1.247663e+01 0.000000000 1.620470821 +[18,] 270.7924506 0.000000 5 2.236892e+01 0.000000000 2.389865378 +[19,] 389.7567112 0.000000 5 3.799093e+01 0.000000000 3.439778575 + +$result$retres +$result$retres$res + [1] -0.30898561 -0.15430728 -0.09508438 0.19429565 0.16601398 0.50347522 -0.50735521 0.56193255 -0.86786450 0.82206160 -0.32736537 -0.71924847 0.53048420 0.48187163 0.08138089 -0.19577655 -0.41706648 -0.62014707 0.66973757 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02859629 14.89178 0.0980966 + [2,] 0.05436985 14.60035 0.2526196 + [3,] 0.09789031 14.10825 0.5135425 + [4,] 0.15508591 13.46152 0.8564533 + [5,] 0.21953628 12.73275 1.2428595 + [6,] 0.31095750 11.69902 1.7909669 + [7,] 0.38750890 10.83343 2.2499236 + [8,] 0.02964539 14.87992 0.1043864 + [9,] 0.07231607 14.39743 0.3602145 + [10,] 0.12986975 13.74665 0.7052722 + [11,] 0.20375242 12.91123 1.1482288 + [12,] 0.28691601 11.97087 1.6468284 + [13,] 0.40040076 10.68765 2.3272156 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.006179712 NA NA + [2,] 0.003086146 NA NA + [3,] 0.001901688 NA NA + [4,] -0.003885913 NA NA + [5,] -0.003320280 NA NA + [6,] -0.010069504 NA NA + [7,] 0.010147104 NA NA + [8,] NA -0.2584890 -0.09637433 + [9,] NA 0.3992177 -0.01627618 +[10,] NA -0.3781483 0.03915531 +[11,] NA 0.1505881 0.08341330 +[12,] NA 0.3308543 0.12402941 +[13,] NA -0.2440227 -0.13394751 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yahO_res/KEIO_ROBOT1_42_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yahO_res/KEIO_ROBOT1_42_res.txt new file mode 100644 index 0000000..4816fb5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yahO_res/KEIO_ROBOT1_42_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0285962885346934 0.0284616406906902 0.0282629773471167 0.00452858768110459 0.0200809552230361 0.037374010667912 +Glc 14.8917812844245 14.8963281608141 14.896836215041 0.212146065786688 14.4953605064081 15.2618477520676 +Ace 0.098096585083065 0.12861956064579 0.122855589204063 0.0860404111038642 9.99999999990418e-07 0.318752994400873 +mu 0.540448261165012 0.543609843264663 0.543303909655064 0.0369438262335551 0.48056328651624 0.619733799760845 +qGlc -6.11104446851624 -6.12491152838225 -6.19509239037358 0.589674041328652 -7.27553303798882 -4.99959979224406 +qAce 3.24020714288057 3.20626885553222 3.20116993264235 0.297776877429322 2.60130078505043 3.74852983915958 +res 4.63940095948319 31.8935412362617 30.6491568047722 7.72904596289374 18.9588517682738 48.1885203068471 + + +Goodness of fit (khi2 test) + +khi2 value 4.63940095948322 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.356876996883325 +p-value, i.e. P(X^2<=value) 0.0177021709225804 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaiA.txt b/validation/validation_results/Berges_2021/Berges_2021/yaiA.txt new file mode 100644 index 0000000..20afe40 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yaiA.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.18888888888889 0.069552 NA NA +2.27694444444444 0.110376 NA NA +3.12833333333333 0.161784 NA NA +3.77138888888889 0.217728 NA NA +4.41555555555556 0.337176 NA NA +4.82277777777778 0.443016 NA NA +0.0666666666666667 NA 15.8709754542477 0.00975994940138714 +1.71666666666667 NA 15.2773787108012 0.356493538890212 +2.8 NA 13.1884963277773 0.707464102619191 +3.63333333333333 NA 12.658574644048 1.15277135482524 +4.26666666666667 NA 11.7714167817144 1.63608002897089 +4.88333333333333 NA 10.1336156409488 2.07903294817693 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaiA_res/KEIO_ROBOT1_43.pdf b/validation/validation_results/Berges_2021/Berges_2021/yaiA_res/KEIO_ROBOT1_43.pdf new file mode 100644 index 0000000..fff6b78 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yaiA_res/KEIO_ROBOT1_43.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaiA_res/KEIO_ROBOT1_43_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yaiA_res/KEIO_ROBOT1_43_log.txt new file mode 100644 index 0000000..a52ba05 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yaiA_res/KEIO_ROBOT1_43_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.069552 NA NA + [3,] 0.110376 NA NA + [4,] 0.161784 NA NA + [5,] 0.217728 NA NA + [6,] 0.337176 NA NA + [7,] 0.443016 NA NA + [8,] NA 15.87098 0.009759949 + [9,] NA 15.27738 0.356493539 +[10,] NA 13.18850 0.707464103 +[11,] NA 12.65857 1.152771355 +[12,] NA 11.77142 1.636080029 +[13,] NA 10.13362 2.079032948 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03138964 15.54347834 0.10301033 0.54050955 -7.43091751 2.75471100 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.205894e-08 3.831700e-07 -1.150700e-07 -9.259361e-08 -2.511613e-07 9.376369e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.01006697 0.54122819 0.23372748 0.07325509 1.41915574 0.60091597 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.8137286 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.205894e-08 3.831700e-07 -1.150700e-07 -9.259361e-08 -2.511613e-07 9.376369e-09 + +$result$normp +[1] 4.816111e-07 + +$result$res + [1] -0.24491816 -0.49334145 -0.14542748 0.42418446 1.16543868 0.21244504 -0.87643193 -0.74637160 -0.85605863 1.79638253 0.52380858 -0.27685392 -0.44090695 0.49560062 -0.04428522 -0.18885154 -0.34811624 -0.43760063 0.52325301 + +$result$prevres + [1] -0.24491877 -0.49334227 -0.14542841 0.42418365 1.16543826 0.21244546 -0.87643060 -0.74637242 -0.85605899 1.79638255 0.52380888 -0.27685348 -0.44090654 0.49560119 -0.04428501 -0.18885161 -0.34811649 -0.43760092 0.52325283 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.000000000 0.00000000 + [2,] 95.0714690 0.000000 0 3.547951e+00 0.000000000 0.00000000 + [3,] 171.1830468 0.000000 0 1.223487e+01 0.000000000 0.00000000 + [4,] 271.2164844 0.000000 0 2.663270e+01 0.000000000 0.00000000 + [5,] 383.9433692 0.000000 0 4.545217e+01 0.000000000 0.00000000 + [6,] 543.8499385 0.000000 0 7.537903e+01 0.000000000 0.00000000 + [7,] 677.7516333 0.000000 0 1.026016e+02 0.000000000 0.00000000 + [8,] -1.0965830 2.173913 0 -1.154268e-03 0.004632178 0.00000000 + [9,] -45.7009480 2.173913 0 -1.419049e+00 0.193049600 0.00000000 +[10,] -105.8675520 2.173913 0 -5.783424e+00 0.447204916 0.00000000 +[11,] -183.1089128 2.173913 0 -1.365807e+01 0.773487290 0.00000000 +[12,] -270.0569549 2.173913 0 -2.448788e+01 1.140772555 0.00000000 +[13,] -388.7105023 2.173913 0 -4.159110e+01 1.641987976 0.00000000 +[14,] 0.9349814 0.000000 5 9.841657e-04 0.000000000 0.01065401 +[15,] 38.9660750 0.000000 5 1.209926e+00 0.000000000 0.44401408 +[16,] 90.2660262 0.000000 5 4.931130e+00 0.000000000 1.02857131 +[17,] 156.1244556 0.000000 5 1.164530e+01 0.000000000 1.77902077 +[18,] 230.2591087 0.000000 5 2.087914e+01 0.000000000 2.62377688 +[19,] 331.4268794 0.000000 5 3.546189e+01 0.000000000 3.77657234 + +$result$retres +$result$retres$res + [1] -0.24491877 -0.49334227 -0.14542841 0.42418365 1.16543826 0.21244546 -0.87643060 -0.74637242 -0.85605899 1.79638255 0.52380888 -0.27685348 -0.44090654 0.49560119 -0.04428501 -0.18885161 -0.34811649 -0.43760092 0.52325283 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03138962 15.543478 0.1030104 + [2,] 0.05968515 15.154471 0.2472188 + [3,] 0.10746743 14.497562 0.4907415 + [4,] 0.17026767 13.634185 0.8108033 + [5,] 0.24103677 12.661253 1.1714785 + [6,] 0.34142491 11.281118 1.6831073 + [7,] 0.42548739 10.125429 2.1115323 + [8,] 0.03254134 15.527644 0.1088802 + [9,] 0.07938840 14.883592 0.3476365 + [10,] 0.14258017 14.014832 0.6696938 + [11,] 0.22370520 12.899527 1.0831481 + [12,] 0.31502496 11.644064 1.5485598 + [13,] 0.43964438 9.930799 2.1836835 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.004898375 NA NA + [2,] 0.009866845 NA NA + [3,] 0.002908568 NA NA + [4,] -0.008483673 NA NA + [5,] -0.023308765 NA NA + [6,] -0.004248909 NA NA + [7,] 0.017528612 NA NA + [8,] NA 0.3433313 -0.099120238 + [9,] NA 0.3937871 0.008857001 +[10,] NA -0.8263360 0.037770322 +[11,] NA -0.2409521 0.069623298 +[12,] NA 0.1273526 0.087520184 +[13,] NA 0.2028170 -0.104650567 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaiA_res/KEIO_ROBOT1_43_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yaiA_res/KEIO_ROBOT1_43_res.txt new file mode 100644 index 0000000..d6aa1de --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yaiA_res/KEIO_ROBOT1_43_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0313896367495382 0.0320245445307375 0.0314917450912312 0.00417557778078478 0.0250932192702204 0.040548479730696 +Glc 15.5434783358918 15.5230375781723 15.5385850970755 0.209075509155331 15.1199976808832 15.907214628708 +Ace 0.103010328924012 0.129844836798412 0.125121409749352 0.0735368135406507 1.00000000000219e-06 0.281947907381757 +mu 0.540509549962255 0.537397961643393 0.539689105929648 0.0287930964905528 0.483378590812737 0.591785468276953 +qGlc -7.43091750569651 -7.37920031833386 -7.3594864830016 0.631161612278904 -8.36283234214532 -6.19043957504172 +qAce 2.75471100316149 2.70457546897816 2.71764479996678 0.224181308044788 2.31979522654242 3.16907183906239 +res 8.60800402178097 32.7739507059649 31.3599995051396 9.90663266078334 19.1229697710635 56.2413401518916 + + +Goodness of fit (khi2 test) + +khi2 value 8.60800402178796 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.662154155522151 +p-value, i.e. P(X^2<=value) 0.198137070020915 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaiL.txt b/validation/validation_results/Berges_2021/Berges_2021/yaiL.txt new file mode 100644 index 0000000..61f251e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yaiL.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.065016 NA NA +1.61361111111111 0.080136 NA NA +2.36138888888889 0.111888 NA NA +3.28638888888889 0.190512 NA NA +3.81944444444444 0.29484 NA NA +4.41083333333333 0.418824 NA NA +0.283333333333333 NA 14.3873428882465 0.0395895259152495 +1.91666666666667 NA 14.1321813735476 0.419289197674054 +2.7 NA 13.1621006638913 0.631246058186351 +3.61666666666667 NA 12.3106505317186 1.10241934304351 +4.05 NA 11.9161138049268 1.34894298363053 +4.75 NA 10.3530047360213 1.97140838376132 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaiL_res/KEIO_ROBOT4_22.pdf b/validation/validation_results/Berges_2021/Berges_2021/yaiL_res/KEIO_ROBOT4_22.pdf new file mode 100644 index 0000000..ceae891 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yaiL_res/KEIO_ROBOT4_22.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaiL_res/KEIO_ROBOT4_22_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yaiL_res/KEIO_ROBOT4_22_log.txt new file mode 100644 index 0000000..5111dc2 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yaiL_res/KEIO_ROBOT4_22_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.065016 NA NA + [3,] 0.080136 NA NA + [4,] 0.111888 NA NA + [5,] 0.190512 NA NA + [6,] 0.294840 NA NA + [7,] 0.418824 NA NA + [8,] NA 14.38734 0.03958953 + [9,] NA 14.13218 0.41928920 +[10,] NA 13.16210 0.63124606 +[11,] NA 12.31065 1.10241934 +[12,] NA 11.91611 1.34894298 +[13,] NA 10.35300 1.97140838 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02809684 14.41279761 0.13034975 0.61005902 -5.20076071 2.40849728 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.617128e-08 -2.435282e-07 1.437462e-07 1.487478e-07 -1.177610e-07 -4.007403e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.005354867 0.304453045 0.132700355 0.047751933 0.742848729 0.324768074 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4611681 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.617128e-08 -2.435282e-07 1.437462e-07 1.487478e-07 -1.177610e-07 -4.007403e-08 + +$result$normp +[1] 3.432637e-07 + +$result$res + [1] -0.33395823 -0.33849400 -0.24716195 0.33848893 0.90575171 -0.30186897 -0.22754111 -0.04291500 -0.54576708 0.53598759 0.36111432 -0.21231681 -0.09610301 0.55845269 -0.21360465 -0.17936507 -0.37741356 -0.08568746 0.29761806 + +$result$prevres + [1] -0.33395742 -0.33849284 -0.24716069 0.33849026 0.90575261 -0.30186886 -0.22754278 -0.04291452 -0.54576700 0.53598746 0.36111404 -0.21231706 -0.09610292 0.55845203 -0.21360485 -0.17936500 -0.37741324 -0.08568711 0.29761818 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.0000000 + [2,] 103.652437 0.000000 0 3.48020705 0.00000000 0.0000000 + [3,] 133.809986 0.000000 0 6.06659577 0.00000000 0.0000000 + [4,] 211.158543 0.000000 0 14.00986115 0.00000000 0.0000000 + [5,] 371.264110 0.000000 0 34.28148132 0.00000000 0.0000000 + [6,] 513.941253 0.000000 0 55.15327865 0.00000000 0.0000000 + [7,] 737.223425 0.000000 0 91.36448972 0.00000000 0.0000000 + [8,] -3.496883 2.173913 0 -0.01431973 0.01889174 0.0000000 + [9,] -41.136382 2.173913 0 -1.31873812 0.22223727 0.0000000 +[10,] -77.692672 2.173913 0 -3.72158524 0.41973081 0.0000000 +[11,] -149.795126 2.173913 0 -10.20599415 0.80926076 0.0000000 +[12,] -200.730358 2.173913 0 -15.70559877 1.08443582 0.0000000 +[13,] -317.535226 2.173913 0 -30.22724044 1.71546834 0.0000000 +[14,] 3.724674 0.000000 5 0.01525253 0.00000000 0.0434510 +[15,] 43.816051 0.000000 5 1.40464216 0.00000000 0.5111457 +[16,] 82.753658 0.000000 5 3.96401337 0.00000000 0.9653809 +[17,] 159.552945 0.000000 5 10.87082378 0.00000000 1.8612997 +[18,] 213.806153 0.000000 5 16.72867866 0.00000000 2.4942024 +[19,] 338.219818 0.000000 5 32.19627595 0.00000000 3.9455772 + +$result$retres +$result$retres$res + [1] -0.33395742 -0.33849284 -0.24716069 0.33849026 0.90575261 -0.30186886 -0.22754278 -0.04291452 -0.54576700 0.53598746 0.36111404 -0.21231706 -0.09610292 0.55845203 -0.21360485 -0.17936500 -0.37741324 -0.08568711 0.29761818 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02809685 14.41280 0.1303496 + [2,] 0.05824614 14.15577 0.2493783 + [3,] 0.07519279 14.01130 0.3162832 + [4,] 0.11865781 13.64076 0.4878820 + [5,] 0.20862705 12.87378 0.8430784 + [6,] 0.28880262 12.19028 1.1596095 + [7,] 0.41427314 11.12064 1.6549641 + [8,] 0.03339838 14.36760 0.1512799 + [9,] 0.09046265 13.88113 0.3765682 + [10,] 0.14588468 13.40865 0.5953731 + [11,] 0.25519733 12.47676 1.0269367 + [12,] 0.33241891 11.81845 1.3318056 + [13,] 0.50950372 10.30880 2.0309320 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.006679148 NA NA + [2,] 0.006769857 NA NA + [3,] 0.004943214 NA NA + [4,] -0.006769805 NA NA + [5,] -0.018115052 NA NA + [6,] 0.006037377 NA NA + [7,] 0.004550856 NA NA + [8,] NA 0.01974068 -0.11169041 + [9,] NA 0.25105282 0.04272097 +[10,] NA -0.24655423 0.03587300 +[11,] NA -0.16611246 0.07548265 +[12,] NA 0.09766585 0.01713742 +[13,] NA 0.04420734 -0.05952364 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yaiL_res/KEIO_ROBOT4_22_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yaiL_res/KEIO_ROBOT4_22_res.txt new file mode 100644 index 0000000..135f78a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yaiL_res/KEIO_ROBOT4_22_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0280968354873362 0.0280301860909688 0.027956119394614 0.0039497890765185 0.0211161892133745 0.0366031985116634 +Glc 14.4127976118337 14.4281656473053 14.4099175150017 0.178883854074117 14.0852348532238 14.7630165887453 +Ace 0.130349753370702 0.123054485253773 0.123102284941996 0.0735928518434984 0.000781238089281573 0.265527785059301 +mu 0.610059018014423 0.612648955631553 0.61011731203898 0.0343608117298973 0.546383717179914 0.681148995244498 +qGlc -5.20076070800957 -5.32488205729423 -5.3118654178553 0.579876125922503 -6.42792743682515 -4.19698368545594 +qAce 2.40849727527431 2.39306752245021 2.38064912609363 0.211140479514392 2.01626864364111 2.7835887168545 +res 2.76478795339491 31.4079624157449 29.9954412598781 7.68477098859129 19.7719262726343 47.5591095577864 + + +Goodness of fit (khi2 test) + +khi2 value 2.76478795340543 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.212675996415802 +p-value, i.e. P(X^2<=value) 0.00134190594021847 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajD.txt b/validation/validation_results/Berges_2021/Berges_2021/yajD.txt new file mode 100644 index 0000000..7411700 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yajD.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.033264 NA NA +1.18888888888889 0.065016 NA NA +2.27694444444444 0.116424 NA NA +3.12833333333333 0.182952 NA NA +3.77138888888889 0.261576 NA NA +4.41555555555556 0.409752 NA NA +4.82277777777778 0.577584 NA NA +0.0666666666666667 NA 15.6566618526162 0.0122465082756402 +1.71666666666667 NA 15.5441605753139 0.377292507322046 +2.8 NA 13.4906825774061 0.834703868075398 +3.63333333333333 NA 12.6014776820772 1.36998975661077 +4.26666666666667 NA 11.6135826720544 1.9474453207621 +4.88333333333333 NA 9.75544126279989 2.42512764218372 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajD_res/KEIO_ROBOT1_37.pdf b/validation/validation_results/Berges_2021/Berges_2021/yajD_res/KEIO_ROBOT1_37.pdf new file mode 100644 index 0000000..63cd86c Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yajD_res/KEIO_ROBOT1_37.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajD_res/KEIO_ROBOT1_37_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yajD_res/KEIO_ROBOT1_37_log.txt new file mode 100644 index 0000000..aed2c84 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yajD_res/KEIO_ROBOT1_37_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.033264 NA NA + [2,] 0.065016 NA NA + [3,] 0.116424 NA NA + [4,] 0.182952 NA NA + [5,] 0.261576 NA NA + [6,] 0.409752 NA NA + [7,] 0.577584 NA NA + [8,] NA 15.656662 0.01224651 + [9,] NA 15.544161 0.37729251 +[10,] NA 13.490683 0.83470387 +[11,] NA 12.601478 1.36998976 +[12,] NA 11.613583 1.94744532 +[13,] NA 9.755441 2.42512764 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02587617 15.51500058 0.18495348 0.63504324 -6.91180279 2.80586522 + +$result$lastp + X Glc Ace mu qGlc qAce +-5.179622e-09 -1.575888e-07 7.705069e-08 4.686116e-08 1.905230e-08 -4.532197e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.009089977 0.604363382 0.262030554 0.079016722 1.409788645 0.606593338 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.9465539 + +$result$laststep + X Glc Ace mu qGlc qAce +-5.179622e-09 -1.575888e-07 7.705069e-08 4.686116e-08 1.905230e-08 -4.532197e-08 + +$result$normp +[1] 1.881779e-07 + +$result$res + [1] -0.3693913 -0.4980891 -0.3277937 0.2854291 1.1118791 0.8753696 -1.2115808 -0.3344362 -1.2724316 1.3891916 0.7943952 -0.1036740 -0.4730450 0.8882561 0.1671753 -0.4369410 -0.7531384 -0.7967034 0.9313514 + +$result$prevres + [1] -0.3693910 -0.4980887 -0.3277932 0.2854296 1.1118794 0.8753695 -1.2115815 -0.3344359 -1.2724315 1.3891916 0.7943951 -0.1036742 -0.4730452 0.8882558 0.1671751 -0.4369410 -0.7531383 -0.7967032 0.9313516 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.000000000 0.00000000 + [2,] 106.3801284 0.000000 0 3.272668e+00 0.000000000 0.00000000 + [3,] 212.2959020 0.000000 0 1.250818e+01 0.000000000 0.00000000 + [4,] 364.5449197 0.000000 0 2.950966e+01 0.000000000 0.00000000 + [5,] 548.4070651 0.000000 0 5.351857e+01 0.000000000 0.00000000 + [6,] 825.5843880 0.000000 0 9.432938e+01 0.000000000 0.00000000 + [7,] 1069.2312199 0.000000 0 1.334348e+02 0.000000000 0.00000000 + [8,] -1.0232173 2.173913 0 -8.887922e-04 0.003830687 0.00000000 + [9,] -46.7240752 2.173913 0 -1.222681e+00 0.174924050 0.00000000 +[10,] -116.3811708 2.173913 0 -5.404309e+00 0.435703984 0.00000000 +[11,] -214.0714303 2.173913 0 -1.362803e+01 0.801433551 0.00000000 +[12,] -331.7730085 2.173913 0 -2.572289e+01 1.242080832 0.00000000 +[13,] -502.1539931 2.173913 0 -4.598169e+01 1.879947536 0.00000000 +[14,] 0.9553691 0.000000 5 8.298577e-04 0.000000000 0.00881058 +[15,] 43.6258623 0.000000 5 1.141607e+00 0.000000000 0.40232531 +[16,] 108.6640862 0.000000 5 5.045956e+00 0.000000000 1.00211916 +[17,] 199.8766312 0.000000 5 1.272437e+01 0.000000000 1.84329717 +[18,] 309.7735703 0.000000 5 2.401724e+01 0.000000000 2.85678591 +[19,] 468.8568125 0.000000 5 4.293270e+01 0.000000000 4.32387933 + +$result$retres +$result$retres$res + [1] -0.3693910 -0.4980887 -0.3277932 0.2854296 1.1118794 0.8753695 -1.2115815 -0.3344359 -1.2724315 1.3891916 0.7943951 -0.1036742 -0.4730452 0.8882558 0.1671751 -0.4369410 -0.7531383 -0.7967032 0.9313516 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02587618 15.515001 0.1849534 + [2,] 0.05505423 15.197427 0.3138732 + [3,] 0.10986814 14.600833 0.5560622 + [4,] 0.18866059 13.743257 0.9041976 + [5,] 0.28381359 12.707613 1.3246202 + [6,] 0.42725939 11.146350 1.9584189 + [7,] 0.55335237 9.773956 2.5155463 + [8,] 0.02699520 15.502821 0.1898977 + [9,] 0.07697497 14.958842 0.4107275 + [10,] 0.15315397 14.129711 0.7473157 + [11,] 0.25999084 12.966899 1.2193621 + [12,] 0.38871267 11.565893 1.7881047 + [13,] 0.57504620 9.537840 2.6113980 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.007387821 NA NA + [2,] 0.009961775 NA NA + [3,] 0.006555864 NA NA + [4,] -0.005708593 NA NA + [5,] -0.022237589 NA NA + [6,] -0.017507390 NA NA + [7,] 0.024231629 NA NA + [8,] NA 0.15384051 -0.17765115 + [9,] NA 0.58531848 -0.03343502 +[10,] NA -0.63902815 0.08738820 +[11,] NA -0.36542175 0.15062766 +[12,] NA 0.04769012 0.15934064 +[13,] NA 0.21760079 -0.18627033 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajD_res/KEIO_ROBOT1_37_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yajD_res/KEIO_ROBOT1_37_res.txt new file mode 100644 index 0000000..5ac2f2d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yajD_res/KEIO_ROBOT1_37_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0258761739098494 0.0259741296628243 0.0258149806686988 0.00269916805965352 0.0217081446740415 0.0303503148743752 +Glc 15.5150005802499 15.5153454871347 15.4773357467519 0.199081431095896 15.1494522066606 15.854165979679 +Ace 0.184953477092617 0.184312382838627 0.17956087396711 0.0780871865288827 0.0502712640765389 0.342620419292339 +mu 0.635043235421176 0.635377729153189 0.634175087994824 0.0230541916199617 0.598583557571946 0.676148620207254 +qGlc -6.91180278892531 -6.91560120328563 -6.97406083317756 0.517552687858669 -7.78321215627917 -5.92390384056857 +qAce 2.80586522443663 2.81024152280803 2.83107962972695 0.195377013882443 2.45418649404795 3.15189050919048 +res 11.6475365709476 32.0486793442351 31.5958768989267 7.42097348543 19.31066318462 45.5628318195332 + + +Goodness of fit (khi2 test) + +khi2 value 11.6475365709497 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.895964351611515 +p-value, i.e. P(X^2<=value) 0.443264199057056 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajG.txt b/validation/validation_results/Berges_2021/Berges_2021/yajG.txt new file mode 100644 index 0000000..251650a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yajG.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.119448 NA NA NA +3.34194444444444 0.189 NA NA NA +3.9975 0.276696 NA NA NA +4.52333333333333 0.412776 NA NA NA +1.95 NA 13.5490264644724 0.352071366657538 0 +3.25 NA 12.7981633331333 0.885312795453896 0 +4.08333333333333 NA 11.8165902868022 1.28446765468799 0 +4.76666666666667 NA 10.6465012985279 1.71691760299109 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajG_res/KEIO_ROBOT2_22.pdf b/validation/validation_results/Berges_2021/Berges_2021/yajG_res/KEIO_ROBOT2_22.pdf new file mode 100644 index 0000000..466d223 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yajG_res/KEIO_ROBOT2_22.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajG_res/KEIO_ROBOT2_22_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yajG_res/KEIO_ROBOT2_22_log.txt new file mode 100644 index 0000000..854a599 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yajG_res/KEIO_ROBOT2_22_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.119448 NA NA NA +[2,] 0.189000 NA NA NA +[3,] 0.276696 NA NA NA +[4,] 0.412776 NA NA NA +[5,] NA 13.54903 0.3520714 0 +[6,] NA 12.79816 0.8853128 0 +[7,] NA 11.81659 1.2844677 0 +[8,] NA 10.64650 1.7169176 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.275370e-02 1.395222e+01 2.609959e-01 1.000000e-06 6.363794e-01 -4.707303e+00 2.148831e+00 -1.940109e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-3.187643e-09 -6.110955e-08 6.273406e-08 2.117582e-22 3.422537e-08 -2.623844e-08 -8.175499e-08 3.156441e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.006320028 0.434886097 0.189622368 0.183706269 0.066466713 0.985855036 0.429535521 0.419708029 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4207027 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-3.187643e-09 -6.110955e-08 6.273406e-08 2.117582e-22 3.422537e-08 -2.623844e-08 -8.175499e-08 3.156441e-13 + +$result$normp +[1] 1.273727e-07 + +$result$res + [1] -3.832457e-01 9.235447e-02 6.474292e-01 -4.010061e-01 -2.316101e-02 -1.978020e-02 8.946460e-02 -4.652339e-02 4.892109e-01 -4.667424e-01 -3.368295e-01 3.143610e-01 4.147163e-06 2.603031e-06 6.838187e-07 -1.856343e-06 + +$result$prevres + [1] -3.832454e-01 9.235472e-02 6.474293e-01 -4.010064e-01 -2.316096e-02 -1.978022e-02 8.946456e-02 -4.652338e-02 4.892107e-01 -4.667424e-01 -3.368294e-01 3.143612e-01 4.147162e-06 2.603031e-06 6.838178e-07 -1.856344e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.456371e+02 0.000000 0 0 1.398065e+01 0.0000000 0.0000000 0.0000000 + [2,] 4.193759e+02 0.000000 0 0 3.189002e+01 0.0000000 0.0000000 0.0000000 + [3,] 6.364779e+02 0.000000 0 0 5.789271e+01 0.0000000 0.0000000 0.0000000 + [4,] 8.894285e+02 0.000000 0 0 9.154229e+01 0.0000000 0.0000000 0.0000000 + [5,] -3.953962e+01 2.173913 0 0 -1.054111e+00 0.1911228 0.0000000 0.0000000 + [6,] -1.111293e+02 2.173913 0 0 -5.433681e+00 0.5371660 0.0000000 0.0000000 + [7,] -2.001086e+02 2.173913 0 0 -1.293146e+01 0.9672658 0.0000000 0.0000000 + [8,] -3.178767e+02 2.173913 0 0 -2.485511e+01 1.5365216 0.0000000 0.0000000 + [9,] 4.151361e+01 0.000000 5 0 1.106736e+00 0.0000000 0.4395824 0.0000000 +[10,] 1.166774e+02 0.000000 5 0 5.704955e+00 0.0000000 1.2354819 0.0000000 +[11,] 2.100990e+02 0.000000 5 0 1.357706e+01 0.0000000 2.2247113 0.0000000 +[12,] 3.337465e+02 0.000000 5 0 2.609598e+01 0.0000000 3.5339997 0.0000000 +[13,] -3.748127e-05 0.000000 0 5 -9.992358e-07 0.0000000 0.0000000 0.4395824 +[14,] -1.053441e-04 0.000000 0 5 -5.150815e-06 0.0000000 0.0000000 1.2354819 +[15,] -1.896914e-04 0.000000 0 5 -1.225828e-05 0.0000000 0.0000000 2.2247113 +[16,] -3.013287e-04 0.000000 0 5 -2.356120e-05 0.0000000 0.0000000 3.5339997 + +$result$retres +$result$retres$res + [1] -3.832454e-01 9.235472e-02 6.474293e-01 -4.010064e-01 -2.316096e-02 -1.978022e-02 8.946456e-02 -4.652338e-02 4.892107e-01 -4.667424e-01 -3.368294e-01 3.143612e-01 4.147162e-06 2.603031e-06 6.838178e-07 -1.856344e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.11178309 13.29367 0.5616170 7.285790e-07 + [2,] 0.19084709 12.70883 0.8285886 4.875392e-07 + [3,] 0.28964459 11.97803 1.1621934 1.863385e-07 + [4,] 0.40475587 11.12655 1.5508841 -1.645975e-07 + [5,] 0.07870194 13.53837 0.4499135 8.294325e-07 + [6,] 0.18000075 12.78906 0.7919643 5.206061e-07 + [7,] 0.30590579 11.85774 1.2171018 1.367636e-07 + [8,] 0.47254663 10.62510 1.7797898 -3.712689e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.007664908 NA NA NA +[2,] -0.001847094 NA NA NA +[3,] -0.012948585 NA NA NA +[4,] 0.008020127 NA NA NA +[5,] NA 0.010654042 -0.09784215 -8.294325e-07 +[6,] NA 0.009098902 0.09334849 -5.206061e-07 +[7,] NA -0.041153699 0.06736589 -1.367636e-07 +[8,] NA 0.021400756 -0.06287223 3.712689e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajG_res/KEIO_ROBOT2_22_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yajG_res/KEIO_ROBOT2_22_res.txt new file mode 100644 index 0000000..4d90a7b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yajG_res/KEIO_ROBOT2_22_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0227537013300903 0.0235097040603341 0.0239743677346592 0.00451467963642033 0.0151135342730753 0.0321365529505838 +Glc 13.9522218374668 13.9418955260667 13.9196633161688 0.39153856391864 13.2010388737543 14.6550149428604 +Ace 0.260995878583757 0.286803176782473 0.288382426397598 0.141310355467626 9.99999999995709e-07 0.537789209056774 +Lac 1e-06 0.0707500738441419 0.0532342972035173 0.0701895423016905 9.99999999997354e-07 0.274120885754308 +mu 0.636379430067916 0.632462263191761 0.627121792854827 0.0463585611045007 0.558434355109882 0.728095242274543 +qGlc -4.70730282429701 -4.66227564459371 -4.62173548734797 0.847770039505886 -6.39518805204724 -3.15906147933122 +qAce 2.14883146541117 2.08673608501811 2.0807522458446 0.354441528606435 1.45553202050132 2.66072911086173 +qLac -1.94010863254893e-06 0.0203877628140947 0.0425619382057281 0.185677026911221 -0.348374588277809 0.377767676613681 +res 1.41592585505544 19.6584248757283 18.6034110744607 5.59118309994982 11.0270881018555 31.5138872278503 + + +Goodness of fit (khi2 test) + +khi2 value 1.41592585505576 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.17699073188197 +p-value, i.e. P(X^2<=value) 0.00598247852519262 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajO.txt b/validation/validation_results/Berges_2021/Berges_2021/yajO.txt new file mode 100644 index 0000000..b8286e2 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yajO.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 5.8968E-2 NA NA +2.2613888888888889 7.2576000000000002E-2 NA NA +2.7741666666666664 9.6768000000000007E-2 NA NA +3.2088888888888891 0.111888 NA NA +3.7063888888888892 0.16783200000000001 NA NA +4.2258333333333331 0.20412000000000002 NA NA +4.6355555555555554 0.29030400000000001 NA NA +4.9675000000000002 0.334152 NA NA +2.8 NA 12.3137192766246 0.621801065046665 +3.73333333333333 NA 11.7566393214133 1.07634678352239 +4.28333333333333 NA 11.0555390236118 1.40381688184894 +4.75 NA 10.4071886475874 1.79274589751825 +5.11666666666667 NA 9.45577446308081 2.08506798005448 +5.43333333333333 NA 8.62526786083256 2.40438796152585 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajO_res/KEIO_ROBOT5_15.pdf b/validation/validation_results/Berges_2021/Berges_2021/yajO_res/KEIO_ROBOT5_15.pdf new file mode 100644 index 0000000..68c533f Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yajO_res/KEIO_ROBOT5_15.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajO_res/KEIO_ROBOT5_15_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yajO_res/KEIO_ROBOT5_15_log.txt new file mode 100644 index 0000000..fe6ea62 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yajO_res/KEIO_ROBOT5_15_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.058968 NA NA + [2,] 0.072576 NA NA + [3,] 0.096768 NA NA + [4,] 0.111888 NA NA + [5,] 0.167832 NA NA + [6,] 0.204120 NA NA + [7,] 0.290304 NA NA + [8,] 0.334152 NA NA + [9,] NA 12.313719 0.6218011 +[10,] NA 11.756639 1.0763468 +[11,] NA 11.055539 1.4038169 +[12,] NA 10.407189 1.7927459 +[13,] NA 9.455774 2.0850680 +[14,] NA 8.625268 2.4043880 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01885743 13.26837532 0.30305347 0.58010847 -6.27965454 2.97015073 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.443230e-09 7.646119e-09 -9.177185e-08 -2.956774e-08 1.690428e-07 1.276780e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.003563968 0.373575758 0.164039923 0.042232284 0.772801065 0.337798920 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3765425 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.443230e-09 7.646119e-09 -9.177185e-08 -2.956774e-08 1.690428e-07 1.276780e-07 + +$result$normp +[1] 2.328903e-07 + +$result$res + [1] -0.2243254050 -0.1278803669 -0.1246092274 0.4714729426 -0.2963098639 0.7360870444 -0.6372689685 0.1173628447 0.2670556364 -0.1399298552 -0.0703024769 -0.3162803287 0.0975981569 0.1618588675 0.3734104041 -0.1391391678 -0.1942021317 -0.3379755802 0.0001738817 0.2977325939 + +$result$prevres + [1] -0.22432561 -0.12788059 -0.12460945 0.47147273 -0.29631003 0.73608699 -0.63726886 0.11736314 0.26705571 -0.13992977 -0.07030242 -0.31628032 0.09759809 0.16185871 0.37341063 -0.13913908 -0.19420213 -0.33797564 0.00017377 0.29773245 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 144.45629 0.000000 0 4.982029 0.0000000 0.0000000 + [2,] 185.65199 0.000000 0 7.916940 0.0000000 0.0000000 + [3,] 249.96994 0.000000 0 13.076841 0.0000000 0.0000000 + [4,] 321.67018 0.000000 0 19.464712 0.0000000 0.0000000 + [5,] 429.28915 0.000000 0 30.004293 0.0000000 0.0000000 + [6,] 580.25337 0.000000 0 46.239436 0.0000000 0.0000000 + [7,] 735.93970 0.000000 0 64.331921 0.0000000 0.0000000 + [8,] 892.21933 0.000000 0 83.578004 0.0000000 0.0000000 + [9,] -95.89236 2.173913 0 -3.188583 0.2879591 0.0000000 +[10,] -181.69562 2.173913 0 -8.541952 0.5456211 0.0000000 +[11,] -258.82722 2.173913 0 -14.393321 0.7772428 0.0000000 +[12,] -346.61412 2.173913 0 -21.887778 1.0408616 0.0000000 +[13,] -434.34682 2.173913 0 -30.060294 1.3043177 0.0000000 +[14,] -526.68117 2.173913 0 -39.253500 1.5815922 0.0000000 +[15,] 104.31688 0.000000 5 3.468713 0.0000000 0.6623059 +[16,] 197.65828 0.000000 5 9.292395 0.0000000 1.2549286 +[17,] 281.56618 0.000000 5 15.657830 0.0000000 1.7876583 +[18,] 377.06550 0.000000 5 23.810703 0.0000000 2.3939816 +[19,] 472.50585 0.000000 5 32.701206 0.0000000 2.9999307 +[20,] 572.95213 0.000000 5 42.702070 0.0000000 3.6376622 + +$result$retres +$result$retres$res + [1] -0.22432561 -0.12788059 -0.12460945 0.47147273 -0.29631003 0.73608699 -0.63726886 0.11736314 0.26705571 -0.13992977 -0.07030242 -0.31628032 0.09759809 0.16185871 0.37341063 -0.13913908 -0.19420213 -0.33797564 0.00017377 0.29773245 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05448149 12.882746 0.4854484 + [2,] 0.07001839 12.714560 0.5649972 + [3,] 0.09427581 12.451974 0.6891950 + [4,] 0.12131745 12.159249 0.8276480 + [5,] 0.16190580 11.719882 1.0354600 + [6,] 0.21884174 11.103552 1.3269715 + [7,] 0.27755862 10.467944 1.6276015 + [8,] 0.33649926 9.829913 1.9293771 + [9,] 0.09569928 12.436565 0.6964832 + [10,] 0.16445638 11.692272 1.0485190 + [11,] 0.22626459 11.023200 1.3649765 + [12,] 0.29661125 10.261700 1.7251508 + [13,] 0.36691448 9.500670 2.0851027 + [14,] 0.44090518 8.699723 2.4639345 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.004486512 NA NA + [2,] 0.002557612 NA NA + [3,] 0.002492189 NA NA + [4,] -0.009429455 NA NA + [5,] 0.005926201 NA NA + [6,] -0.014721740 NA NA + [7,] 0.012745377 NA NA + [8,] -0.002347263 NA NA + [9,] NA -0.12284563 -7.468213e-02 +[10,] NA 0.06436770 2.782782e-02 +[11,] NA 0.03233911 3.884043e-02 +[12,] NA 0.14548895 6.759513e-02 +[13,] NA -0.04489512 -3.475399e-05 +[14,] NA -0.07445501 -5.954649e-02 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yajO_res/KEIO_ROBOT5_15_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yajO_res/KEIO_ROBOT5_15_res.txt new file mode 100644 index 0000000..037d075 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yajO_res/KEIO_ROBOT5_15_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0188574320160127 0.0186173430881478 0.018262342938242 0.00304612388667033 0.0137807098009295 0.0243405819400393 +Glc 13.2683753236111 13.2633363863807 13.2534112723524 0.239178559426049 12.8330467467121 13.7104349013411 +Ace 0.303053473155435 0.31223946885707 0.321438392358374 0.106047163738442 0.114402339066 0.497162064806604 +mu 0.580108471696076 0.585143405458807 0.587330832621665 0.0335259227330613 0.528661120687825 0.643921510150374 +qGlc -6.27965453582652 -6.28701846251798 -6.33050085041134 0.652976206326567 -7.52833192139996 -5.09414733331951 +qAce 2.97015073116658 2.94902750601874 2.93080843603747 0.299295591453284 2.35116078148309 3.49584068589798 +res 1.98497910019256 36.261422319808 35.5421437912507 7.9050223783808 25.2379826822407 51.4640712444794 + + +Goodness of fit (khi2 test) + +khi2 value 1.98497910019301 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.141784221442358 +p-value, i.e. P(X^2<=value) 7.94751020147127e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybaQ.txt b/validation/validation_results/Berges_2021/Berges_2021/ybaQ.txt new file mode 100644 index 0000000..c19d764 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybaQ.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.1134 NA NA NA +3.34194444444444 0.178416 NA NA NA +3.9975 0.240408 NA NA NA +4.52333333333333 0.403704 NA NA NA +1.95 NA 13.8068075193119 0.380478810608258 0 +3.25 NA 12.6742315612711 0.923825238728801 0 +4.08333333333333 NA 11.8049154901105 1.32014536512 0 +4.76666666666667 NA 10.6997698421708 1.84232097364151 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybaQ_res/KEIO_ROBOT2_6.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybaQ_res/KEIO_ROBOT2_6.pdf new file mode 100644 index 0000000..11d1079 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybaQ_res/KEIO_ROBOT2_6.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybaQ_res/KEIO_ROBOT2_6_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybaQ_res/KEIO_ROBOT2_6_log.txt new file mode 100644 index 0000000..868839c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybaQ_res/KEIO_ROBOT2_6_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.113400 NA NA NA +[2,] 0.178416 NA NA NA +[3,] 0.240408 NA NA NA +[4,] 0.403704 NA NA NA +[5,] NA 13.80681 0.3804788 0 +[6,] NA 12.67423 0.9238252 0 +[7,] NA 11.80492 1.3201454 0 +[8,] NA 10.69977 1.8423210 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 1.860791e-02 1.401035e+01 2.892913e-01 1.000000e-06 6.707675e-01 -5.245933e+00 2.460713e+00 -2.108298e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-7.176805e-09 -2.373421e-07 1.125439e-07 -2.117582e-22 9.369393e-08 1.371338e-07 -6.793687e-08 4.146613e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.01025212 0.77896726 0.34048310 0.32747724 0.13131011 1.93493250 0.84471009 0.82001073 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.766195 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-7.176805e-09 -2.373421e-07 1.125439e-07 -2.117582e-22 9.369393e-08 1.371338e-07 -6.793687e-08 4.146613e-13 + +$result$normp +[1] 3.181958e-07 + +$result$res + [1] -6.886299e-01 -1.666990e-01 1.568423e+00 -8.493769e-01 -4.113185e-01 4.223063e-01 2.162767e-01 -2.272646e-01 4.651910e-01 -4.946169e-01 -2.150866e-01 2.445124e-01 4.210792e-06 2.705489e-06 7.681891e-07 -1.862545e-06 + +$result$prevres + [1] -6.886292e-01 -1.666983e-01 1.568423e+00 -8.493776e-01 -4.113182e-01 4.223063e-01 2.162766e-01 -2.272647e-01 4.651907e-01 -4.946169e-01 -2.150865e-01 2.445126e-01 4.210792e-06 2.705488e-06 7.681877e-07 -1.862547e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.677016e+02 0.000000 0 0 1.246035e+01 0.0000000 0.0000000 0.0000000 + [2,] 4.704503e+02 0.000000 0 0 2.925572e+01 0.0000000 0.0000000 0.0000000 + [3,] 7.302709e+02 0.000000 0 0 5.432132e+01 0.0000000 0.0000000 0.0000000 + [4,] 1.039118e+03 0.000000 0 0 8.746237e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.588350e+01 2.173913 0 0 -1.008953e+00 0.1627540 0.0000000 0.0000000 + [6,] -1.333998e+02 2.173913 0 0 -5.394969e+00 0.4731844 0.0000000 0.0000000 + [7,] -2.460318e+02 2.173913 0 0 -1.316068e+01 0.8727028 0.0000000 0.0000000 + [8,] -3.989792e+02 2.173913 0 0 -2.582839e+01 1.4152244 0.0000000 0.0000000 + [9,] 4.950199e+01 0.000000 5 0 1.088522e+00 0.0000000 0.3743342 0.0000000 +[10,] 1.439201e+02 0.000000 5 0 5.820430e+00 0.0000000 1.0883240 0.0000000 +[11,] 2.654345e+02 0.000000 5 0 1.419856e+01 0.0000000 2.0072165 0.0000000 +[12,] 4.304437e+02 0.000000 5 0 2.786529e+01 0.0000000 3.2550160 0.0000000 +[13,] -4.241249e-05 0.000000 0 5 -9.326275e-07 0.0000000 0.0000000 0.3743342 +[14,] -1.233084e-04 0.000000 0 5 -4.986849e-06 0.0000000 0.0000000 1.0883240 +[15,] -2.274199e-04 0.000000 0 5 -1.216509e-05 0.0000000 0.0000000 2.0072165 +[16,] -3.687971e-04 0.000000 0 5 -2.387452e-05 0.0000000 0.0000000 3.2550160 + +$result$retres +$result$retres$res + [1] -6.886292e-01 -1.666983e-01 1.568423e+00 -8.493776e-01 -4.113182e-01 4.223063e-01 2.162766e-01 -2.272647e-01 4.651907e-01 -4.946169e-01 -2.150865e-01 2.445126e-01 4.210792e-06 2.705488e-06 7.681877e-07 -1.862547e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09962742 13.37671 0.5865116 7.453464e-07 + [2,] 0.17508203 12.78660 0.8633172 5.081839e-07 + [3,] 0.27177646 12.03037 1.2180412 2.042622e-07 + [4,] 0.38671645 11.13145 1.6396991 -1.570074e-07 + [5,] 0.06882615 13.61760 0.4735170 8.421583e-07 + [6,] 0.16461037 12.86849 0.8249019 5.410975e-07 + [7,] 0.28788298 11.90440 1.2771281 1.536375e-07 + [8,] 0.45527962 10.59523 1.8912235 -3.725093e-07 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.013772583 NA NA NA +[2,] 0.003333967 NA NA NA +[3,] -0.031368461 NA NA NA +[4,] 0.016987553 NA NA NA +[5,] NA 0.18920638 -0.09303815 -8.421583e-07 +[6,] NA -0.19426089 0.09892337 -5.410975e-07 +[7,] NA -0.09948724 0.04301729 -1.536375e-07 +[8,] NA 0.10454176 -0.04890252 3.725093e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybaQ_res/KEIO_ROBOT2_6_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybaQ_res/KEIO_ROBOT2_6_res.txt new file mode 100644 index 0000000..8f41288 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybaQ_res/KEIO_ROBOT2_6_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0186079143627295 0.0190927095489351 0.0189132916204924 0.00382492196487479 0.0124100222743805 0.026580745577917 +Glc 14.010347308507 14.0292177208431 14.0537637319206 0.352811985580267 13.420008222273 14.824059046921 +Ace 0.289291254488966 0.300822942303377 0.315673742158695 0.135875419228238 0.0170009172813879 0.579349824113568 +Lac 1e-06 0.0747699656215601 0.05358259899498 0.0762079533930315 9.99999999993061e-07 0.281070070513671 +mu 0.670767452097636 0.669378902128928 0.670086215325447 0.0486670981248022 0.575814700670856 0.756879541651935 +qGlc -5.24593324240979 -5.28172406203061 -5.303524606066 0.959854473581606 -7.1394169050967 -3.53561022396652 +qAce 2.46071338003436 2.43408809346767 2.44940627766308 0.374688248243239 1.79641442613153 3.23859055103316 +qLac -2.10829843996391e-06 0.0261647396247216 0.0170427264733876 0.210343266303512 -0.369083730913924 0.454950928881069 +res 4.696438641005 20.6436992666836 19.3993579634117 6.69118475732809 10.4669457638297 34.2231433101545 + + +Goodness of fit (khi2 test) + +khi2 value 4.69643864100691 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.587054830125864 +p-value, i.e. P(X^2<=value) 0.210526465687028 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybaY.txt b/validation/validation_results/Berges_2021/Berges_2021/ybaY.txt new file mode 100644 index 0000000..fd0856b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybaY.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.12852 NA NA NA +3.34194444444444 0.198072 NA NA NA +3.9975 0.267624 NA NA NA +4.52333333333333 0.38556 NA NA NA +1.95 NA 13.8707825739758 0.393298289033487 0 +3.25 NA 12.773738532054 0.906010506939849 0 +4.08333333333333 NA 11.5763505631218 1.43575758428676 0 +4.76666666666667 NA 10.4281325704501 1.98091492950703 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybaY_res/KEIO_ROBOT2_24.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybaY_res/KEIO_ROBOT2_24.pdf new file mode 100644 index 0000000..01d8701 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybaY_res/KEIO_ROBOT2_24.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybaY_res/KEIO_ROBOT2_24_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybaY_res/KEIO_ROBOT2_24_log.txt new file mode 100644 index 0000000..f98e105 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybaY_res/KEIO_ROBOT2_24_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.128520 NA NA NA +[2,] 0.198072 NA NA NA +[3,] 0.267624 NA NA NA +[4,] 0.385560 NA NA NA +[5,] NA 13.87078 0.3932983 0 +[6,] NA 12.77374 0.9060105 0 +[7,] NA 11.57635 1.4357576 0 +[8,] NA 10.42813 1.9809149 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 3.127602e-02 1.439959e+01 1.511253e-01 1.000000e-06 5.502747e-01 -5.595526e+00 2.570679e+00 -1.880355e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 4.876486e-09 1.554263e-07 -6.952296e-08 -2.117582e-22 -3.882550e-08 -1.207682e-07 5.077325e-08 -4.659946e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.007270732 0.411299939 0.179714652 0.171010761 0.056239654 0.879192586 0.383564893 0.370849918 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3694214 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 4.876486e-09 1.554263e-07 -6.952296e-08 -2.117582e-22 -3.882550e-08 -1.207682e-07 5.077325e-08 -4.659946e-13 + +$result$normp +[1] 2.183687e-07 + +$result$res + [1] -2.320653e-01 -6.703082e-02 7.282195e-01 -4.339841e-01 -1.808020e-01 9.151052e-02 2.891877e-01 -1.998963e-01 1.948903e-01 -1.364095e-01 -2.435212e-01 1.850404e-01 3.971743e-06 2.338928e-06 4.798256e-07 -1.827462e-06 + +$result$prevres + [1] -2.320657e-01 -6.703108e-02 7.282195e-01 -4.339838e-01 -1.808021e-01 9.151051e-02 2.891878e-01 -1.998962e-01 1.948904e-01 -1.364095e-01 -2.435212e-01 1.850404e-01 3.971743e-06 2.338929e-06 4.798269e-07 -1.827460e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 1.980410e+02 0.000000 0 0 1.549344e+01 0.0000000 0.000000 0.000000 + [2,] 3.145083e+02 0.000000 0 0 3.287327e+01 0.0000000 0.000000 0.000000 + [3,] 4.511258e+02 0.000000 0 0 5.640240e+01 0.0000000 0.000000 0.000000 + [4,] 6.025069e+02 0.000000 0 0 8.523777e+01 0.0000000 0.000000 0.000000 + [5,] -4.253667e+01 2.173913 0 0 -1.524761e+00 0.2377574 0.000000 0.000000 + [6,] -1.100825e+02 2.173913 0 0 -7.179770e+00 0.6153029 0.000000 0.000000 + [7,] -1.869894e+02 2.173913 0 0 -1.607568e+01 1.0451714 0.000000 0.000000 + [8,] -2.824366e+02 2.173913 0 0 -2.934900e+01 1.5786708 0.000000 0.000000 + [9,] 4.494674e+01 0.000000 5 0 1.611152e+00 0.0000000 0.546842 0.000000 +[10,] 1.163197e+02 0.000000 5 0 7.586567e+00 0.0000000 1.415197 0.000000 +[11,] 1.975840e+02 0.000000 5 0 1.698651e+01 0.0000000 2.403894 0.000000 +[12,] 2.984391e+02 0.000000 5 0 3.101188e+01 0.0000000 3.630943 0.000000 +[13,] -3.287684e-05 0.000000 0 5 -1.178497e-06 0.0000000 0.000000 0.546842 +[14,] -8.508344e-05 0.000000 0 5 -5.549287e-06 0.0000000 0.000000 1.415197 +[15,] -1.445252e-04 0.000000 0 5 -1.242499e-05 0.0000000 0.000000 2.403894 +[16,] -2.182970e-04 0.000000 0 5 -2.268402e-05 0.0000000 0.000000 3.630943 + +$result$retres +$result$retres$res + [1] -2.320657e-01 -6.703108e-02 7.282195e-01 -4.339838e-01 -1.808021e-01 9.151051e-02 2.891878e-01 -1.998962e-01 1.948904e-01 -1.364095e-01 -2.435212e-01 1.850404e-01 3.971743e-06 2.338929e-06 4.798269e-07 -1.827460e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.12387869 13.45795 0.5837306 6.835656e-07 + [2,] 0.19673138 12.71714 0.9240712 4.346193e-07 + [3,] 0.28218839 11.84816 1.3232946 1.426025e-07 + [4,] 0.37688032 10.88527 1.7656601 -1.809712e-07 + [5,] 0.09145869 13.78761 0.4322764 7.943486e-07 + [6,] 0.18702542 12.81583 0.8787286 4.677857e-07 + [7,] 0.29583646 11.70938 1.3870533 9.596538e-08 + [8,] 0.43087925 10.33618 2.0179230 -3.654919e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.004641314 NA NA NA +[2,] 0.001340622 NA NA NA +[3,] -0.014564390 NA NA NA +[4,] 0.008679675 NA NA NA +[5,] NA 0.08316897 -0.03897809 -7.943486e-07 +[6,] NA -0.04209484 0.02728191 -4.677857e-07 +[7,] NA -0.13302637 0.04870425 -9.596538e-08 +[8,] NA 0.09195223 -0.03700807 3.654919e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybaY_res/KEIO_ROBOT2_24_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybaY_res/KEIO_ROBOT2_24_res.txt new file mode 100644 index 0000000..aebafe5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybaY_res/KEIO_ROBOT2_24_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0312760239519037 0.0317321805324896 0.0318080785039935 0.00524468250807631 0.0216909304852643 0.0409168529240371 +Glc 14.3995874877449 14.3705435482057 14.3493500252607 0.393020749923634 13.5869231078393 15.2124465320913 +Ace 0.151125259589873 0.154119519570818 0.139700907577559 0.134286493471436 9.99999999990418e-07 0.432884130855986 +Lac 1e-06 0.0832733448128766 0.0587299390539323 0.0802441449294252 9.9999999998777e-07 0.256297212826328 +mu 0.550274697246852 0.549107815939425 0.544962415896071 0.039956597934589 0.48211080399717 0.633890976198743 +qGlc -5.5955260181304 -5.50431020284543 -5.47866773369319 0.773680576362292 -6.89100104747632 -4.21307902153159 +qAce 2.57067897180742 2.57739147478605 2.5911770593937 0.317170729283194 1.86558469547598 3.08054297237619 +qLac -1.88035492721817e-06 0.000155306863549422 -0.0120759687000778 0.192638799237632 -0.368343573219133 0.373274482147302 +res 1.0917771856284 20.9585593710987 19.7689070460608 7.27534607333073 9.74930840785726 35.7426112387501 + + +Goodness of fit (khi2 test) + +khi2 value 1.09177718562882 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.136472148203603 +p-value, i.e. P(X^2<=value) 0.00240062244217554 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybbA.txt b/validation/validation_results/Berges_2021/Berges_2021/ybbA.txt new file mode 100644 index 0000000..1c06c0e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybbA.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.157248 NA NA +3.67805555555556 0.258552 NA NA +4.09222222222222 0.350784 NA NA +4.565 0.433944 NA NA +0.05 NA 14.3701482371592 0.0263066098685597 +1.95 NA 13.9203156825855 0.419364252133795 +2.83333333333333 NA 13.2375280679518 0.793831471226797 +3.98333333333333 NA 11.8930283031867 1.44992959500157 +4.88333333333333 NA 9.24345756980004 2.05878355167584 +5.16666666666667 NA 8.4199886768514 2.55750800830806 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybbA_res/KEIO_ROBOT3_17.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybbA_res/KEIO_ROBOT3_17.pdf new file mode 100644 index 0000000..8a2d239 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybbA_res/KEIO_ROBOT3_17.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybbA_res/KEIO_ROBOT3_17_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybbA_res/KEIO_ROBOT3_17_log.txt new file mode 100644 index 0000000..b8eb3ae --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybbA_res/KEIO_ROBOT3_17_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.157248 NA NA + [2,] 0.258552 NA NA + [3,] 0.350784 NA NA + [4,] 0.433944 NA NA + [5,] NA 14.370148 0.02630661 + [6,] NA 13.920316 0.41936425 + [7,] NA 13.237528 0.79383147 + [8,] NA 11.893028 1.44992960 + [9,] NA 9.243458 2.05878355 +[10,] NA 8.419989 2.55750801 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03114404 14.55325914 0.16087716 0.58027422 -5.99587247 2.34163140 + +$result$lastp + X Glc Ace mu qGlc qAce + 3.030599e-09 -4.692585e-08 -8.397424e-08 -2.401953e-08 2.287653e-07 1.373314e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.009574804 0.389415513 0.167580989 0.073173778 0.685737739 0.293230759 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5662027 + +$result$laststep + X Glc Ace mu qGlc qAce + 3.030599e-09 -4.692585e-08 -8.397424e-08 -2.401953e-08 2.287653e-07 1.373314e-07 + +$result$normp +[1] 2.846635e-07 + +$result$res + [1] 0.404894217 0.232261447 -0.804211699 0.320405653 0.377472507 -0.093437618 -0.061434727 -0.575213190 0.344335985 0.008277044 0.691351796 0.027444739 -0.540356446 -0.733940540 0.569635012 -0.014134561 + +$result$prevres + [1] 0.404893984 0.232261329 -0.804211682 0.320405925 0.377472610 -0.093437470 -0.061434578 -0.575213124 0.344335817 0.008276746 0.691352213 0.027444989 -0.540356323 -0.733940640 0.569634701 -0.014134940 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 265.4535198 0.000000 0 2.378455e+01 0.000000000 0.00000000 + [2,] 422.5483594 0.000000 0 4.840270e+01 0.000000000 0.00000000 + [3,] 537.3416696 0.000000 0 6.848329e+01 0.000000000 0.00000000 + [4,] 706.9605848 0.000000 0 1.005104e+02 0.000000000 0.00000000 + [5,] -0.6612719 2.173913 0 -5.173565e-04 0.003434809 0.00000000 + [6,] -47.1808346 2.173913 0 -1.697257e+00 0.245068848 0.00000000 + [7,] -93.8131339 2.173913 0 -5.225276e+00 0.487288468 0.00000000 + [8,] -204.1586305 2.173913 0 -1.715653e+01 1.060450090 0.00000000 + [9,] -359.5780319 2.173913 0 -3.880431e+01 1.867736649 0.00000000 +[10,] -427.8482084 2.173913 0 -4.949676e+01 2.222348720 0.00000000 +[11,] 0.5939830 0.000000 5 4.647120e-04 0.000000000 0.00790006 +[12,] 42.3798641 0.000000 5 1.524549e+00 0.000000000 0.56365835 +[13,] 84.2670101 0.000000 5 4.693569e+00 0.000000000 1.12076348 +[14,] 183.3841026 0.000000 5 1.541074e+01 0.000000000 2.43903521 +[15,] 322.9885238 0.000000 5 3.485571e+01 0.000000000 4.29579429 +[16,] 384.3117461 0.000000 5 4.446013e+01 0.000000000 5.11140206 + +$result$retres +$result$retres$res + [1] 0.404893984 0.232261329 -0.804211682 0.320405925 0.377472610 -0.093437470 -0.061434578 -0.575213124 0.344335817 0.008276746 0.691352213 0.027444989 -0.540356323 -0.733940640 0.569634701 -0.014134940 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.16534588 13.166575 0.7024337 + [2,] 0.26319723 12.155494 1.0973017 + [3,] 0.33469977 11.416671 1.3858422 + [4,] 0.44035212 10.324983 1.8121903 + [5,] 0.03206088 14.543786 0.1645771 + [6,] 0.09655932 13.877334 0.4248532 + [7,] 0.16121407 13.209268 0.6857602 + [8,] 0.31420590 11.628430 1.3031415 + [9,] 0.52969179 9.401852 2.1727105 + [10,] 0.62434703 8.423796 2.5546810 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.008097880 NA NA + [2,] -0.004645227 NA NA + [3,] 0.016084234 NA NA + [4,] -0.006408119 NA NA + [5,] NA -0.173637401 -0.138270443 + [6,] NA 0.042981236 -0.005488998 + [7,] NA 0.028259906 0.108071265 + [8,] NA 0.264598037 0.146788128 + [9,] NA -0.158394476 -0.113926940 +[10,] NA -0.003807303 0.002826988 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybbA_res/KEIO_ROBOT3_17_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybbA_res/KEIO_ROBOT3_17_res.txt new file mode 100644 index 0000000..99100e8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybbA_res/KEIO_ROBOT3_17_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0311440390606217 0.031361806873661 0.0307822260412631 0.00405194672375391 0.0244365338617741 0.0394007459249918 +Glc 14.5532591413886 14.5241698325022 14.5333769731687 0.262079077066688 14.1010002822696 14.9902773574026 +Ace 0.160877163079448 0.153041735944549 0.142275108600896 0.0954614919021336 9.99999999996533e-07 0.38545437017634 +mu 0.580274216725679 0.580280612252078 0.583739173289177 0.0277337876260844 0.530534753651792 0.633486672477207 +qGlc -5.9958724701946 -5.93084630089484 -5.87199625370028 0.487211946147276 -7.09143048024888 -5.05201144219494 +qAce 2.34163140297454 2.35684829173716 2.40443696857368 0.202171871355845 1.92823469949155 2.73114074960394 +res 3.2058554052487 23.0658742255154 22.6767155145334 6.4136723899723 11.3736759448362 36.0751477022152 + + +Goodness of fit (khi2 test) + +khi2 value 3.20585540524953 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.320585540524953 +p-value, i.e. P(X^2<=value) 0.0238440404088727 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybcJ.txt b/validation/validation_results/Berges_2021/Berges_2021/ybcJ.txt new file mode 100644 index 0000000..f7557db --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybcJ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.039312 NA NA +1.195 0.066528 NA NA +1.61361111111111 0.081648 NA NA +2.36138888888889 0.127008 NA NA +3.28638888888889 0.201096 NA NA +3.81944444444444 0.288792 NA NA +4.41083333333333 0.397656 NA NA +0.283333333333333 NA 14.1608669897214 0.0487842701120136 +1.91666666666667 NA 13.6016404187441 0.389211385053695 +2.7 NA 13.521505151794 0.638015244304585 +3.61666666666667 NA 12.4980549672796 1.04273353068508 +4.05 NA 11.719327652436 1.42577889867036 +4.75 NA 10.1682750552157 1.91071447100489 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybcJ_res/KEIO_ROBOT4_13.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybcJ_res/KEIO_ROBOT4_13.pdf new file mode 100644 index 0000000..c541813 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybcJ_res/KEIO_ROBOT4_13.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybcJ_res/KEIO_ROBOT4_13_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybcJ_res/KEIO_ROBOT4_13_log.txt new file mode 100644 index 0000000..04b0f08 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybcJ_res/KEIO_ROBOT4_13_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.039312 NA NA + [2,] 0.066528 NA NA + [3,] 0.081648 NA NA + [4,] 0.127008 NA NA + [5,] 0.201096 NA NA + [6,] 0.288792 NA NA + [7,] 0.397656 NA NA + [8,] NA 14.16087 0.04878427 + [9,] NA 13.60164 0.38921139 +[10,] NA 13.52151 0.63801524 +[11,] NA 12.49805 1.04273353 +[12,] NA 11.71933 1.42577890 +[13,] NA 10.16828 1.91071447 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03322871 14.34436613 0.10269821 0.56220288 -5.09774985 2.37274045 + +$result$lastp + X Glc Ace mu qGlc qAce +-8.910765e-09 1.722776e-08 8.850420e-08 6.938116e-08 -4.683230e-07 -6.601785e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.004615101 0.240042286 0.104629584 0.035156822 0.571858544 0.250098705 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.356343 + +$result$laststep + X Glc Ace mu qGlc qAce +-8.910765e-09 1.722776e-08 8.850420e-08 6.938116e-08 -4.683230e-07 -6.601785e-08 + +$result$normp +[1] 4.865262e-07 + +$result$res + [1] -0.30416428 -0.07360520 0.03350582 -0.08362570 0.48648468 -0.21483030 -0.04745738 0.28580651 0.34556547 -0.54483884 -0.33499239 -0.02243597 0.27089522 0.39065183 -0.07400154 -0.17832052 -0.04474205 -0.48228283 0.38869512 + +$result$prevres + [1] -0.30416383 -0.07360460 0.03350646 -0.08362504 0.48648510 -0.21483025 -0.04745813 0.28580645 0.34556531 -0.54483902 -0.33499248 -0.02243593 0.27089566 0.39065142 -0.07400169 -0.17832052 -0.04474188 -0.48228262 0.38869530 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 97.891073 0.000000 0 3.88709050 0.00000000 0.00000000 + [3,] 123.865922 0.000000 0 6.64147240 0.00000000 0.00000000 + [4,] 188.595117 0.000000 0 14.79829275 0.00000000 0.00000000 + [5,] 317.234129 0.000000 0 34.64276223 0.00000000 0.00000000 + [6,] 428.086556 0.000000 0 54.33071779 0.00000000 0.00000000 + [7,] 596.933612 0.000000 0 87.49038708 0.00000000 0.00000000 + [8,] -3.403823 2.173913 0 -0.01644837 0.02218718 0.00000000 + [9,] -38.191529 2.173913 0 -1.43048178 0.24894432 0.00000000 +[10,] -70.230420 2.173913 0 -3.91846663 0.45778382 0.00000000 +[11,] -130.872086 2.173913 0 -10.36162871 0.85306515 0.00000000 +[12,] -172.412320 2.173913 0 -15.66502093 1.12383737 0.00000000 +[13,] -265.058728 2.173913 0 -29.28100788 1.72773561 0.00000000 +[14,] 3.643901 0.000000 5 0.01760851 0.00000000 0.05103051 +[15,] 40.885249 0.000000 5 1.53137634 0.00000000 0.57257194 +[16,] 75.183903 0.000000 5 4.19484340 0.00000000 1.05290279 +[17,] 140.102739 0.000000 5 11.09245376 0.00000000 1.96204985 +[18,] 184.572883 0.000000 5 16.76990414 0.00000000 2.58482596 +[19,] 283.753816 0.000000 5 31.34625211 0.00000000 3.97379191 + +$result$retres +$result$retres$res + [1] -0.30416383 -0.07360460 0.03350646 -0.08362504 0.48648510 -0.21483025 -0.04745813 0.28580645 0.34556531 -0.54483902 -0.33499248 -0.02243593 0.27089566 0.39065142 -0.07400169 -0.17832052 -0.04474188 -0.48228262 0.38869530 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03322872 14.34437 0.1026981 + [2,] 0.06505591 14.05577 0.2370227 + [3,] 0.08231813 13.89925 0.3098768 + [4,] 0.12533550 13.50919 0.4914288 + [5,] 0.21082570 12.73401 0.8522347 + [6,] 0.28449539 12.06602 1.1631528 + [7,] 0.39670684 11.04854 1.6367339 + [8,] 0.03896662 14.29234 0.1269146 + [9,] 0.09760903 13.76060 0.3744110 + [10,] 0.15161770 13.27088 0.6023511 + [11,] 0.25384271 12.34396 1.0337852 + [12,] 0.32386801 11.70901 1.3293224 + [13,] 0.48004412 10.29289 1.9884535 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0060832766 NA NA + [2,] 0.0014720920 NA NA + [3,] -0.0006701293 NA NA + [4,] 0.0016725009 NA NA + [5,] -0.0097297020 NA NA + [6,] 0.0042966050 NA NA + [7,] 0.0009491627 NA NA + [8,] NA -0.13147097 -0.078130284 + [9,] NA -0.15896004 0.014800338 +[10,] NA 0.25062595 0.035664104 +[11,] NA 0.15409654 0.008948377 +[12,] NA 0.01032053 0.096456525 +[13,] NA -0.12461200 -0.077739059 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybcJ_res/KEIO_ROBOT4_13_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybcJ_res/KEIO_ROBOT4_13_res.txt new file mode 100644 index 0000000..b2f14c9 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybcJ_res/KEIO_ROBOT4_13_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0332287144556285 0.0338961872802683 0.0336720029849051 0.00399033017813562 0.0267597329040102 0.0410545307911513 +Glc 14.3443661288834 14.3335980784813 14.3368937255463 0.209880986478869 13.9211405967763 14.7503139872873 +Ace 0.102698208666164 0.126255370994988 0.131161875723979 0.0693582327073024 1.000000000001e-06 0.26197541142103 +mu 0.562202880502101 0.559471511582778 0.559322305766074 0.0284139573564305 0.512447278860249 0.616171846672573 +qGlc -5.09774984998824 -5.03102291883967 -5.04565284787826 0.549116076378331 -6.08127733778831 -4.01974752039535 +qAce 2.37274044541511 2.29686795601782 2.30450802028482 0.22188212567565 1.81108256449696 2.69468593539311 +res 1.65074461483895 32.4494043307107 32.6000741813117 7.79148111271763 19.5098269379523 48.4295990971971 + + +Goodness of fit (khi2 test) + +khi2 value 1.65074461484174 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.126980354987826 +p-value, i.e. P(X^2<=value) 7.5427572587752e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybdH.txt b/validation/validation_results/Berges_2021/Berges_2021/ybdH.txt new file mode 100644 index 0000000..1f68e36 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybdH.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.099792 NA NA NA +3.34194444444444 0.154224 NA NA NA +3.9975 0.205632 NA NA NA +4.52333333333333 0.311472 NA NA NA +1.95 NA 13.4972486237711 0.409501932467997 0 +3.25 NA 12.8976928035861 1.12882703178052 0 +4.08333333333333 NA 11.3503974666385 1.85567122677379 0 +4.76666666666667 NA 9.83686340478682 2.60283546933473 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybdH_res/KEIO_ROBOT2_28.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybdH_res/KEIO_ROBOT2_28.pdf new file mode 100644 index 0000000..0d1f970 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybdH_res/KEIO_ROBOT2_28.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybdH_res/KEIO_ROBOT2_28_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybdH_res/KEIO_ROBOT2_28_log.txt new file mode 100644 index 0000000..121d3ea --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybdH_res/KEIO_ROBOT2_28_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.099792 NA NA NA +[2,] 0.154224 NA NA NA +[3,] 0.205632 NA NA NA +[4,] 0.311472 NA NA NA +[5,] NA 13.497249 0.4095019 0 +[6,] NA 12.897693 1.1288270 0 +[7,] NA 11.350397 1.8556712 0 +[8,] NA 9.836863 2.6028355 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.190953e-02 1.428914e+01 1.210804e-01 1.000000e-06 5.799618e-01 -7.862809e+00 4.527073e+00 -2.434964e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 3.979658e-09 3.922500e-08 -9.763163e-08 -2.117582e-22 -4.472873e-08 3.050849e-07 7.086678e-08 -4.347585e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.008656807 0.562676983 0.257404095 0.226601066 0.095146443 1.559792636 0.704976071 0.640873297 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4998525 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 3.979658e-09 3.922500e-08 -9.763163e-08 -2.117582e-22 -4.472873e-08 3.050849e-07 7.086678e-08 -4.347585e-13 + +$result$normp +[1] 3.334456e-07 + +$result$res + [1] -3.161404e-01 -1.017587e-01 8.477633e-01 -4.757820e-01 3.664185e-01 -5.818825e-01 1.392170e-01 7.624705e-02 3.523572e-01 -2.624927e-01 -3.972879e-01 3.074234e-01 4.034816e-06 2.431017e-06 5.487902e-07 -1.839627e-06 + +$result$prevres + [1] -3.161407e-01 -1.017589e-01 8.477633e-01 -4.757817e-01 3.664186e-01 -5.818824e-01 1.392170e-01 7.624689e-02 3.523574e-01 -2.624927e-01 -3.972880e-01 3.074233e-01 4.034816e-06 2.431017e-06 5.487913e-07 -1.839625e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.133072e+02 0.000000 0 0 1.169014e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.473120e+02 0.000000 0 0 2.543033e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.079691e+02 0.000000 0 0 4.448963e+01 0.0000000 0.0000000 0.0000000 + [4,] 6.890983e+02 0.000000 0 0 6.829246e+01 0.0000000 0.0000000 0.0000000 + [5,] -6.184922e+01 2.173913 0 0 -1.565090e+00 0.1723414 0.0000000 0.0000000 + [6,] -1.646211e+02 2.173913 0 0 -7.601660e+00 0.4587127 0.0000000 0.0000000 + [7,] -2.852347e+02 2.173913 0 0 -1.737949e+01 0.7947995 0.0000000 0.0000000 + [8,] -4.382850e+02 2.173913 0 0 -3.229315e+01 1.2212707 0.0000000 0.0000000 + [9,] 8.190339e+01 0.000000 5 0 2.072559e+00 0.0000000 0.3963852 0.0000000 +[10,] 2.179983e+02 0.000000 5 0 1.006644e+01 0.0000000 1.0550393 0.0000000 +[11,] 3.777199e+02 0.000000 5 0 2.301467e+01 0.0000000 1.8280389 0.0000000 +[12,] 5.803958e+02 0.000000 5 0 4.276397e+01 0.0000000 2.8089226 0.0000000 +[13,] -4.405314e-05 0.000000 0 5 -1.114762e-06 0.0000000 0.0000000 0.3963852 +[14,] -1.172541e-04 0.000000 0 5 -5.414410e-06 0.0000000 0.0000000 1.0550393 +[15,] -2.031632e-04 0.000000 0 5 -1.237883e-05 0.0000000 0.0000000 1.8280389 +[16,] -3.121758e-04 0.000000 0 5 -2.300134e-05 0.0000000 0.0000000 2.8089226 + +$result$retres +$result$retres$res + [1] -3.161407e-01 -1.017589e-01 8.477633e-01 -4.757817e-01 3.664186e-01 -5.818824e-01 1.392170e-01 7.624689e-02 3.523574e-01 -2.624927e-01 -3.972880e-01 3.074233e-01 4.034816e-06 2.431017e-06 5.487913e-07 -1.839625e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09346919 13.318974 0.6796617 6.995575e-07 + [2,] 0.15218882 12.522885 1.1380161 4.530237e-07 + [3,] 0.22258727 11.568461 1.6875331 1.574566e-07 + [4,] 0.30195637 10.492418 2.3070733 -1.757737e-07 + [5,] 0.06788718 13.665801 0.4799734 8.069633e-07 + [6,] 0.14428604 12.630027 1.0763285 4.862035e-07 + [7,] 0.23394810 11.414437 1.7762136 1.097583e-07 + [8,] 0.34772314 9.871937 2.6643201 -3.679251e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.006322814 NA NA NA +[2,] 0.002035178 NA NA NA +[3,] -0.016955266 NA NA NA +[4,] 0.009515634 NA NA NA +[5,] NA -0.16855254 -0.07047148 -8.069633e-07 +[6,] NA 0.26766593 0.05249854 -4.862035e-07 +[7,] NA -0.06403981 0.07945760 -1.097583e-07 +[8,] NA -0.03507357 -0.06148467 3.679251e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybdH_res/KEIO_ROBOT2_28_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybdH_res/KEIO_ROBOT2_28_res.txt new file mode 100644 index 0000000..6762d75 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybdH_res/KEIO_ROBOT2_28_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0219095318513257 0.0227174484752455 0.0225125905303037 0.00514783649729287 0.0143172713577112 0.0335764153676625 +Glc 14.2891413591458 14.3312876642561 14.2877853802545 0.36229384149091 13.7786275785129 15.1375852735224 +Ace 0.121080384641182 0.128757553093273 0.106514212777038 0.121345515390664 9.99999999973245e-07 0.416098197273039 +Lac 1e-06 0.0850863859941897 0.0714432154721596 0.0784615920434601 9.99999999982479e-07 0.257793786176107 +mu 0.57996183846291 0.576180803792893 0.575583750125133 0.0518887946695497 0.477809215742708 0.679637187773784 +qGlc -7.86280859515531 -7.93185895765221 -7.8819335709089 1.05841579050792 -10.0102256174797 -6.27922633140047 +qAce 4.52707326783488 4.49121215796645 4.42026541353818 0.425389381839747 3.76950875491172 5.46076168030536 +qLac -2.43496439084691e-06 -0.0108768698350068 -0.0204895411305725 0.233399419171387 -0.477406433031428 0.386017145667869 +res 1.99882043228971 20.9787421842909 19.6072590826722 6.82214104887569 10.0746993687566 36.4806775246496 + + +Goodness of fit (khi2 test) + +khi2 value 1.99882043229011 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.249852554036263 +p-value, i.e. P(X^2<=value) 0.0189520166423982 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybeL.txt b/validation/validation_results/Berges_2021/Berges_2021/ybeL.txt new file mode 100644 index 0000000..f7bdaf4 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybeL.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.046872 NA NA +1.18888888888889 0.078624 NA NA +2.27694444444444 0.12096 NA NA +3.12833333333333 0.187488 NA NA +3.77138888888889 0.273672 NA NA +4.41555555555556 0.394632 NA NA +4.82277777777778 0.58968 NA NA +0.0666666666666667 NA 14.6153277464247 0.0153550601206132 +1.71666666666667 NA 14.565904779378 0.346111724438148 +2.8 NA 13.5014575150146 0.73648238557672 +3.63333333333333 NA 12.6788566650425 1.16101061006176 +4.26666666666667 NA 11.7127013961542 1.6612023302101 +4.88333333333333 NA 9.66426363563845 2.08435777644132 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybeL_res/KEIO_ROBOT1_34.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybeL_res/KEIO_ROBOT1_34.pdf new file mode 100644 index 0000000..e6e1185 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybeL_res/KEIO_ROBOT1_34.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybeL_res/KEIO_ROBOT1_34_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybeL_res/KEIO_ROBOT1_34_log.txt new file mode 100644 index 0000000..bc5c106 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybeL_res/KEIO_ROBOT1_34_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.046872 NA NA + [2,] 0.078624 NA NA + [3,] 0.120960 NA NA + [4,] 0.187488 NA NA + [5,] 0.273672 NA NA + [6,] 0.394632 NA NA + [7,] 0.589680 NA NA + [8,] NA 14.615328 0.01535506 + [9,] NA 14.565905 0.34611172 +[10,] NA 13.501458 0.73648239 +[11,] NA 12.678857 1.16101061 +[12,] NA 11.712701 1.66120233 +[13,] NA 9.664264 2.08435778 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02644169 14.80638099 0.16890290 0.63235634 -5.71731731 2.35836771 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.235627e-08 1.030466e-07 -1.230541e-07 -1.069218e-07 5.897232e-07 -1.489625e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.009338371 0.604170215 0.262273702 0.079495590 1.365671516 0.590260248 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.9514258 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.235627e-08 1.030466e-07 -1.230541e-07 -1.069218e-07 5.897232e-07 -1.489625e-08 + +$result$normp +[1] 6.207586e-07 + +$result$res + [1] -1.02151547 -1.12730054 -0.46877463 0.18410286 0.67101323 1.84078983 -1.57570925 0.39295527 -0.49640636 0.30353030 -0.02630169 -0.47302094 0.29924342 0.78896996 0.08089305 -0.43449332 -0.54761398 -0.63207876 0.74432305 + +$result$prevres + [1] -1.02151609 -1.12730150 -0.46877588 0.18410159 0.67101231 1.84078993 -1.57570790 0.39295505 -0.49640632 0.30353051 -0.02630144 -0.47302085 0.29924305 0.78897056 0.08089332 -0.43449336 -0.54761423 -0.63207911 0.74432281 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.00000000 0.000000000 + [2,] 106.0408677 0.000000 0 3.333524e+00 0.00000000 0.000000000 + [3,] 211.0011352 0.000000 0 1.270358e+01 0.00000000 0.000000000 + [4,] 361.4937562 0.000000 0 2.990218e+01 0.00000000 0.000000000 + [5,] 542.8782614 0.000000 0 5.413683e+01 0.00000000 0.000000000 + [6,] 815.8479858 0.000000 0 9.525409e+01 0.00000000 0.000000000 + [7,] 1055.4659899 0.000000 0 1.345955e+02 0.00000000 0.000000000 + [8,] -0.8463105 2.173913 0 -7.511702e-04 0.00391405 0.000000000 + [9,] -38.5444701 2.173913 0 -1.030045e+00 0.17826199 0.000000000 +[10,] -95.8055463 2.173913 0 -4.542254e+00 0.44308528 0.000000000 +[11,] -175.9099426 2.173913 0 -1.143261e+01 0.81355527 0.000000000 +[12,] -272.2372983 2.173913 0 -2.154718e+01 1.25905384 0.000000000 +[13,] -411.4441082 2.173913 0 -3.846070e+01 1.90286300 0.000000000 +[14,] 0.8029282 0.000000 5 7.126646e-04 0.00000000 0.009002315 +[15,] 36.5686642 0.000000 5 9.772442e-01 0.00000000 0.410002581 +[16,] 90.8945135 0.000000 5 4.309416e+00 0.00000000 1.019096155 +[17,] 166.8927245 0.000000 5 1.084657e+01 0.00000000 1.871177118 +[18,] 258.2822992 0.000000 5 2.044266e+01 0.00000000 2.895823828 +[19,] 390.3533091 0.000000 5 3.648919e+01 0.00000000 4.376584911 + +$result$retres +$result$retres$res + [1] -1.02151609 -1.12730150 -0.46877588 0.18410159 0.67101231 1.84078993 -1.57570790 0.39295505 -0.49640632 0.30353051 -0.02630144 -0.47302085 0.29924305 0.78897056 0.08089332 -0.43449336 -0.54761423 -0.63207911 0.74432281 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02644168 14.806381 0.1689030 + [2,] 0.05607797 14.538431 0.2794313 + [3,] 0.11158448 14.036580 0.4864423 + [4,] 0.19117003 13.317024 0.7832559 + [5,] 0.28709225 12.449764 1.1409970 + [6,] 0.43144780 11.144603 1.6793697 + [7,] 0.55816584 9.998909 2.1519635 + [8,] 0.02758021 14.796087 0.1731492 + [9,] 0.07829523 14.337558 0.3622904 + [10,] 0.15532808 13.641082 0.6495837 + [11,] 0.26309186 12.666758 1.0514878 + [12,] 0.39268025 11.495112 1.5347865 + [13,] 0.57995402 9.801915 2.2332223 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.020430322 NA NA + [2,] 0.022546030 NA NA + [3,] 0.009375518 NA NA + [4,] -0.003682032 NA NA + [5,] -0.013420246 NA NA + [6,] -0.036815799 NA NA + [7,] 0.031514158 NA NA + [8,] NA -0.18075932 -0.15779411 + [9,] NA 0.22834691 -0.01617866 +[10,] NA -0.13962404 0.08689867 +[11,] NA 0.01209866 0.10952285 +[12,] NA 0.21758959 0.12641582 +[13,] NA -0.13765180 -0.14886456 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybeL_res/KEIO_ROBOT1_34_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybeL_res/KEIO_ROBOT1_34_res.txt new file mode 100644 index 0000000..04b38a9 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybeL_res/KEIO_ROBOT1_34_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0264416905954924 0.0263692203809594 0.0261428531560709 0.00319758907156598 0.0201180806960218 0.0328915162580176 +Glc 14.8063809919941 14.8129939421972 14.8045434449267 0.182401277261668 14.4579053354684 15.1380742953414 +Ace 0.168902895700486 0.181736073043649 0.182984631868623 0.0710277716258609 0.0555341505472968 0.324312996881095 +mu 0.632356344083671 0.63420533721946 0.634926761820142 0.026434685441494 0.583048412865195 0.690681529399772 +qGlc -5.71731731146385 -5.77710743997426 -5.78939745184019 0.42264643874317 -6.48672123870473 -5.04885416432227 +qAce 2.35836770946416 2.34414801738619 2.33315183148114 0.185051311016832 2.02373700861858 2.73293568261757 +res 11.7677436143546 33.2662551441294 32.539307665107 7.97497051403289 17.7226560216736 49.7491643759522 + + +Goodness of fit (khi2 test) + +khi2 value 11.7677436143637 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.905211047258749 +p-value, i.e. P(X^2<=value) 0.4532252460272 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybfE.txt b/validation/validation_results/Berges_2021/Berges_2021/ybfE.txt new file mode 100644 index 0000000..f5d65bd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybfE.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.195 0.058968 NA NA +1.61361111111111 0.06804 NA NA +2.36138888888889 0.10584 NA NA +3.28638888888889 0.190512 NA NA +3.81944444444444 0.270648 NA NA +4.41083333333333 0.349272 NA NA +0.283333333333333 NA 14.1416956733183 0.0351954215716336 +1.91666666666667 NA 13.9850632969595 0.40390307079693 +2.7 NA 13.3379379638135 0.651222181156563 +3.61666666666667 NA 12.8346659176308 1.18525591902738 +4.05 NA 12.0111891713715 1.45280922255735 +4.75 NA 10.6001656418343 2.07006839003538 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybfE_res/KEIO_ROBOT4_27.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybfE_res/KEIO_ROBOT4_27.pdf new file mode 100644 index 0000000..ea47c26 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybfE_res/KEIO_ROBOT4_27.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybfE_res/KEIO_ROBOT4_27_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybfE_res/KEIO_ROBOT4_27_log.txt new file mode 100644 index 0000000..b9e35e7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybfE_res/KEIO_ROBOT4_27_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.058968 NA NA + [3,] 0.068040 NA NA + [4,] 0.105840 NA NA + [5,] 0.190512 NA NA + [6,] 0.270648 NA NA + [7,] 0.349272 NA NA + [8,] NA 14.14170 0.03519542 + [9,] NA 13.98506 0.40390307 +[10,] NA 13.33794 0.65122218 +[11,] NA 12.83467 1.18525592 +[12,] NA 12.01119 1.45280922 +[13,] NA 10.60017 2.07006839 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03007843 14.38221250 0.09025321 0.56067373 -5.10330910 2.85932321 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.314777e-08 -3.972113e-07 -5.819951e-08 1.117047e-07 5.942627e-07 5.833245e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.005150846 0.269274370 0.118386517 0.043348241 0.712049683 0.317741960 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3995663 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.314777e-08 -3.972113e-07 -5.819951e-08 1.117047e-07 5.942627e-07 5.833245e-07 + +$result$normp +[1] 9.31252e-07 + +$result$res + [1] -0.083678466 -0.009365399 0.314511329 0.360199546 -0.031524523 -0.731208958 0.370537027 0.420392139 -0.284646271 0.160858573 -0.562161366 -0.015495308 0.281052232 0.407338878 -0.088846505 -0.086664451 -0.415217797 -0.150531413 0.333921288 + +$result$prevres + [1] -0.083677808 -0.009364507 0.314512284 0.360200526 -0.031523859 -0.731208824 0.370536035 0.420392948 -0.284645899 0.160858664 -0.562161631 -0.015495728 0.281051647 0.407339198 -0.088846055 -0.086664036 -0.415217673 -0.150531603 0.333920166 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 97.712352 0.000000 0 3.51214741 0.00000000 0.00000000 + [3,] 123.560657 0.000000 0 5.99700552 0.00000000 0.00000000 + [4,] 187.915324 0.000000 0 13.34704352 0.00000000 0.00000000 + [5,] 315.643861 0.000000 0 31.20122634 0.00000000 0.00000000 + [6,] 425.593533 0.000000 0 48.89343852 0.00000000 0.00000000 + [7,] 592.920835 0.000000 0 78.66340170 0.00000000 0.00000000 + [8,] -3.406778 2.173913 0 -0.01490085 0.02007924 0.00000000 + [9,] -38.167353 2.173913 0 -1.29353628 0.22495491 0.00000000 +[10,] -70.126774 2.173913 0 -3.53998482 0.41332083 0.00000000 +[11,] -130.538475 2.173913 0 -9.34998770 0.76938191 0.00000000 +[12,] -171.880405 2.173913 0 -14.12764043 1.01304750 0.00000000 +[13,] -264.002694 2.173913 0 -26.38285387 1.55600790 0.00000000 +[14,] 4.390185 0.000000 5 0.01920216 0.00000000 0.04618225 +[15,] 49.184823 0.000000 5 1.66693124 0.00000000 0.51739630 +[16,] 90.369719 0.000000 5 4.56184444 0.00000000 0.95063792 +[17,] 168.219991 0.000000 5 12.04897523 0.00000000 1.76957840 +[18,] 221.495772 0.000000 5 18.20575547 0.00000000 2.33000925 +[19,] 340.210279 0.000000 5 33.99858514 0.00000000 3.57881817 + +$result$retres +$result$retres$res + [1] -0.083677808 -0.009364507 0.314512284 0.360200526 -0.031523859 -0.731208824 0.370536035 0.420392948 -0.284645899 0.160858664 -0.562161631 -0.015495728 0.281051647 0.407339198 -0.088846055 -0.086664036 -0.415217673 -0.150531603 0.333920166 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03007844 14.38221 0.09025327 + [2,] 0.05878071 14.12096 0.23662905 + [3,] 0.07433025 13.97943 0.31592856 + [4,] 0.11304401 13.62705 0.51336097 + [5,] 0.18988152 12.92767 0.90521682 + [6,] 0.25602382 12.32563 1.24252924 + [7,] 0.35668272 11.40943 1.75586936 + [8,] 0.03525708 14.33508 0.11666326 + [9,] 0.08809653 13.85413 0.38613386 + [10,] 0.13667796 13.41193 0.63388937 + [11,] 0.22850963 12.57607 1.10221238 + [12,] 0.29135339 12.00406 1.42270290 + [13,] 0.43138823 10.72945 2.13685242 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0016735562 NA NA + [2,] 0.0001872901 NA NA + [3,] -0.0062902457 NA NA + [4,] -0.0072040105 NA NA + [5,] 0.0006304772 NA NA + [6,] 0.0146241765 NA NA + [7,] -0.0074107207 NA NA + [8,] NA -0.193380756 -0.08146784 + [9,] NA 0.130937113 0.01776921 +[10,] NA -0.073994986 0.01733281 +[11,] NA 0.258594350 0.08304353 +[12,] NA 0.007128035 0.03010632 +[13,] NA -0.129283758 -0.06678403 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybfE_res/KEIO_ROBOT4_27_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybfE_res/KEIO_ROBOT4_27_res.txt new file mode 100644 index 0000000..9bbaad8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybfE_res/KEIO_ROBOT4_27_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.030078430683945 0.0305136190538164 0.0302987764261197 0.00415101551981387 0.0239791965705472 0.0389278871922919 +Glc 14.3822124950273 14.3743944490997 14.3759261161225 0.196185257834805 14.0115790116291 14.7995721802079 +Ace 0.0902532135183574 0.112198388671386 0.115371748790348 0.0782612959490795 9.99999999998561e-07 0.279081137511572 +mu 0.56067373021973 0.559166383408391 0.560699402169823 0.032251752920056 0.49520955443262 0.619382201667703 +qGlc -5.10330910136598 -5.08723932064966 -5.08903040444274 0.639569161584843 -6.44103087056574 -4.05852727764648 +qAce 2.85932320691808 2.76964051191611 2.77611813820032 0.275604905526064 2.22374947303077 3.33828419667335 +res 2.0754916446245 31.1875379799389 29.8223356102603 8.33899970136635 18.1147226164122 48.6874025533819 + + +Goodness of fit (khi2 test) + +khi2 value 2.07549164463191 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.159653203433224 +p-value, i.e. P(X^2<=value) 0.000278752658970236 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgJ.txt b/validation/validation_results/Berges_2021/Berges_2021/ybgJ.txt new file mode 100644 index 0000000..4d1701a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybgJ.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 8.1647999999999998E-2 NA NA +2.2613888888888889 0.10130400000000001 NA NA +2.7741666666666664 0.12700800000000001 NA NA +3.2088888888888891 0.16783200000000001 NA NA +3.7063888888888892 0.22831199999999999 NA NA +4.2258333333333331 0.31600800000000001 NA NA +4.6355555555555554 0.41731200000000002 NA NA +4.9675000000000002 0.55792799999999998 NA NA +2.8 NA 12.0796452847492 0.717703747941942 +3.73333333333333 NA 11.6222307481209 1.3416899425554 +4.28333333333333 NA 10.9381454042475 1.86941898246375 +4.75 NA 9.80525271478514 2.41590323345763 +5.11666666666667 NA 9.0246676110643 2.95265094097849 +5.43333333333333 NA 8.07789105769978 3.47127196562077 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgJ_res/KEIO_ROBOT5_14.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybgJ_res/KEIO_ROBOT5_14.pdf new file mode 100644 index 0000000..a4ae81f Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybgJ_res/KEIO_ROBOT5_14.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgJ_res/KEIO_ROBOT5_14_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybgJ_res/KEIO_ROBOT5_14_log.txt new file mode 100644 index 0000000..394671f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybgJ_res/KEIO_ROBOT5_14_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.081648 NA NA + [2,] 0.101304 NA NA + [3,] 0.127008 NA NA + [4,] 0.167832 NA NA + [5,] 0.228312 NA NA + [6,] 0.316008 NA NA + [7,] 0.417312 NA NA + [8,] 0.557928 NA NA + [9,] NA 12.079645 0.7177037 +[10,] NA 11.622231 1.3416899 +[11,] NA 10.938145 1.8694190 +[12,] NA 9.805253 2.4159032 +[13,] NA 9.024668 2.9526509 +[14,] NA 8.077891 3.4712720 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0200457 12.9843772 0.3340699 0.6626183 -4.5475471 2.9923894 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.537019e-08 4.014004e-07 -3.899110e-07 -1.712811e-07 8.337727e-08 1.544213e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.003913093 0.482966441 0.217893011 0.043028052 0.704518235 0.312500264 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5360837 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.537019e-08 4.014004e-07 -3.899110e-07 -1.712811e-07 8.337727e-08 1.544213e-07 + +$result$normp +[1] 6.111661e-07 + +$result$res + [1] -0.71501137 -0.58028305 -0.05073837 0.01108105 0.26820199 0.68370920 0.76018354 -0.95029520 0.35366411 -0.28888595 -0.36233091 0.24889254 0.03133041 0.01732980 0.52324803 -0.11926823 -0.39603941 -0.32617243 -0.11242731 0.43065934 + +$result$prevres + [1] -0.71501289 -0.58028475 -0.05074020 0.01107923 0.26820045 0.68370850 0.76018413 -0.95029293 0.35366394 -0.28888582 -0.36233069 0.24889271 0.03133039 0.01732946 0.52324874 -0.11926815 -0.39603963 -0.32617276 -0.11242756 0.43065936 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 167.98565 0.000000 0 6.158577 0.0000000 0.0000000 + [2,] 223.73472 0.000000 0 10.142138 0.0000000 0.0000000 + [3,] 314.26517 0.000000 0 17.476306 0.0000000 0.0000000 + [4,] 419.17651 0.000000 0 26.963264 0.0000000 0.0000000 + [5,] 582.85870 0.000000 0 43.304708 0.0000000 0.0000000 + [6,] 822.32712 0.000000 0 69.659095 0.0000000 0.0000000 + [7,] 1078.82503 0.000000 0 100.247524 0.0000000 0.0000000 + [8,] 1344.23495 0.000000 0 133.854787 0.0000000 0.0000000 + [9,] -80.47337 2.173913 0 -2.919707 0.3547283 0.0000000 +[10,] -162.13331 2.173913 0 -8.345250 0.7146870 0.0000000 +[11,] -239.98483 2.173913 0 -14.626612 1.0578581 0.0000000 +[12,] -332.35319 2.173913 0 -23.011843 1.4650198 0.0000000 +[13,] -427.85937 2.173913 0 -32.470842 1.8860130 0.0000000 +[14,] -531.23379 2.173913 0 -43.413220 2.3416896 0.0000000 +[15,] 121.79261 0.000000 5 4.418837 0.0000000 0.8158751 +[16,] 245.38102 0.000000 5 12.630137 0.0000000 1.6437801 +[17,] 363.20558 0.000000 5 22.136679 0.0000000 2.4330737 +[18,] 503.00067 0.000000 5 34.827325 0.0000000 3.3695455 +[19,] 647.54470 0.000000 5 49.143067 0.0000000 4.3378299 +[20,] 803.99695 0.000000 5 65.703833 0.0000000 5.3858860 + +$result$retres +$result$retres$res + [1] -0.71501289 -0.58028475 -0.05074020 0.01107923 0.26820045 0.68370850 0.76018413 -0.95029293 0.35366394 -0.28888582 -0.36233069 0.24889271 0.03133039 0.01732946 0.52324874 -0.11926815 -0.39603963 -0.32617276 -0.11242756 0.43065936 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06734774 12.659743 0.5476867 + [2,] 0.08969830 12.506351 0.6486220 + [3,] 0.12599320 12.257260 0.8125300 + [4,] 0.16805358 11.968599 1.0024749 + [5,] 0.23367601 11.518233 1.2988262 + [6,] 0.32968217 10.859343 1.7323907 + [7,] 0.43251568 10.153597 2.1967875 + [8,] 0.53892214 9.423330 2.6773197 + [9,] 0.12816847 12.242331 0.8223535 + [10,] 0.23788550 11.489343 1.3178363 + [11,] 0.34248561 10.771473 1.7902111 + [12,] 0.46659031 9.919743 2.3506687 + [13,] 0.59491093 9.039080 2.9301654 + [14,] 0.73380321 8.085863 3.5574038 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0143002579 NA NA + [2,] 0.0116056951 NA NA + [3,] 0.0010148041 NA NA + [4,] -0.0002215845 NA NA + [5,] -0.0053640091 NA NA + [6,] -0.0136741699 NA NA + [7,] -0.0152036826 NA NA + [8,] 0.0190058587 NA NA + [9,] NA -0.162685414 -0.10464975 +[10,] NA 0.132887475 0.02385363 +[11,] NA 0.166672115 0.07920793 +[12,] NA -0.114490645 0.06523455 +[13,] NA -0.014411981 0.02248551 +[14,] NA -0.007971553 -0.08613187 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgJ_res/KEIO_ROBOT5_14_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybgJ_res/KEIO_ROBOT5_14_res.txt new file mode 100644 index 0000000..ee0cc27 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybgJ_res/KEIO_ROBOT5_14_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0200456979386878 0.0202745853987881 0.0200073113421261 0.00221727630987293 0.0167856365380373 0.024721041315041 +Glc 12.9843772081997 12.994035372779 12.9957925818435 0.203159253237994 12.6439672217899 13.4289195088588 +Ace 0.334069925274272 0.336303552727738 0.345420250635125 0.107188464120017 0.130905539454348 0.538739603335363 +mu 0.662618311443318 0.661545341401778 0.661745767338128 0.0223184285117812 0.617570340543564 0.700108264485015 +qGlc -4.54754711299036 -4.56067951380061 -4.61225428324306 0.41225230512152 -5.32173100930162 -3.79436451345911 +qAce 2.99238942510507 2.97942952747318 2.9682637166406 0.201686107220483 2.60366466892878 3.36187510217918 +res 4.02340036077513 36.4589707036205 36.0291613993088 7.56414301482667 23.6225346230842 53.0371801860671 + + +Goodness of fit (khi2 test) + +khi2 value 4.02340036079748 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.287385740056963 +p-value, i.e. P(X^2<=value) 0.00467621123442949 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgK.txt b/validation/validation_results/Berges_2021/Berges_2021/ybgK.txt new file mode 100644 index 0000000..301655c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybgK.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.114912 NA NA NA +3.34194444444444 0.16632 NA NA NA +3.9975 0.229824 NA NA NA +4.52333333333333 0.337176 NA NA NA +1.95 NA 13.4165012718718 0.353439951252108 0 +3.25 NA 12.6832589239717 0.885792121966531 0 +4.08333333333333 NA 12.1368426807205 1.41458478490299 0 +4.76666666666667 NA 10.6690753319846 1.9175389457116 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgK_res/KEIO_ROBOT2_15.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybgK_res/KEIO_ROBOT2_15.pdf new file mode 100644 index 0000000..3bb487e Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybgK_res/KEIO_ROBOT2_15.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgK_res/KEIO_ROBOT2_15_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybgK_res/KEIO_ROBOT2_15_log.txt new file mode 100644 index 0000000..2e6629e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybgK_res/KEIO_ROBOT2_15_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.114912 NA NA NA +[2,] 0.166320 NA NA NA +[3,] 0.229824 NA NA NA +[4,] 0.337176 NA NA NA +[5,] NA 13.41650 0.3534400 0 +[6,] NA 12.68326 0.8857921 0 +[7,] NA 12.13684 1.4145848 0 +[8,] NA 10.66908 1.9175389 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.560906e-02 1.393727e+01 1.446732e-01 1.000000e-06 5.640754e-01 -5.028081e+00 2.933540e+00 -2.195157e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 6.332277e-09 2.120787e-08 -9.911901e-08 0.000000e+00 -6.055452e-08 3.274287e-07 6.390176e-08 -4.492797e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.008712811 0.506212895 0.226068388 0.212393076 0.082151046 1.271512147 0.563300484 0.539470745 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4633467 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 6.332277e-09 2.120787e-08 -9.911901e-08 0.000000e+00 -6.055452e-08 3.274287e-07 6.390176e-08 -4.492797e-13 + +$result$normp +[1] 3.539411e-07 + +$result$res + [1] -4.958229e-01 1.184314e-01 7.169655e-01 -4.352766e-01 1.376238e-01 1.187448e-01 -5.558618e-01 2.994932e-01 2.906634e-01 -2.067808e-01 -3.515128e-01 2.676301e-01 4.001401e-06 2.381851e-06 5.116857e-07 -1.833410e-06 + +$result$prevres + [1] -4.958234e-01 1.184310e-01 7.169655e-01 -4.352762e-01 1.376238e-01 1.187449e-01 -5.558618e-01 2.994930e-01 2.906637e-01 -2.067808e-01 -3.515129e-01 2.676300e-01 4.001401e-06 2.381852e-06 5.116870e-07 -1.833408e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.049969e+02 0.000000 0 0 1.313173e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.293535e+02 0.000000 0 0 2.818740e+01 0.0000000 0.0000000 0.0000000 + [3,] 4.767129e+02 0.000000 0 0 4.880214e+01 0.0000000 0.0000000 0.0000000 + [4,] 6.413172e+02 0.000000 0 0 7.428907e+01 0.0000000 0.0000000 0.0000000 + [5,] -3.883350e+01 2.173913 0 0 -1.143899e+00 0.1977870 0.0000000 0.0000000 + [6,] -1.018145e+02 2.173913 0 0 -5.464392e+00 0.5185622 0.0000000 0.0000000 + [7,] -1.745415e+02 2.173913 0 0 -1.235402e+01 0.8889755 0.0000000 0.0000000 + [8,] -2.657375e+02 2.173913 0 0 -2.273949e+01 1.3534556 0.0000000 0.0000000 + [9,] 5.211037e+01 0.000000 5 0 1.534989e+00 0.0000000 0.4549101 0.0000000 +[10,] 1.366241e+02 0.000000 5 0 7.332625e+00 0.0000000 1.1926931 0.0000000 +[11,] 2.342158e+02 0.000000 5 0 1.657776e+01 0.0000000 2.0446436 0.0000000 +[12,] 3.565911e+02 0.000000 5 0 3.051394e+01 0.0000000 3.1129478 0.0000000 +[13,] -3.899398e-05 0.000000 0 5 -1.148626e-06 0.0000000 0.0000000 0.4549101 +[14,] -1.022353e-04 0.000000 0 5 -5.486974e-06 0.0000000 0.0000000 1.1926931 +[15,] -1.752628e-04 0.000000 0 5 -1.240507e-05 0.0000000 0.0000000 2.0446436 +[16,] -2.668357e-04 0.000000 0 5 -2.283346e-05 0.0000000 0.0000000 3.1129478 + +$result$retres +$result$retres$res + [1] -4.958234e-01 1.184310e-01 7.169655e-01 -4.352762e-01 1.376238e-01 1.187449e-01 -5.558618e-01 2.994930e-01 2.906637e-01 -2.067808e-01 -3.515129e-01 2.676300e-01 4.001401e-06 2.381852e-06 5.116870e-07 -1.833408e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10499553 13.22963 0.5575320 6.910595e-07 + [2,] 0.16868862 12.66188 0.8887754 4.431914e-07 + [3,] 0.24416331 11.98911 1.2812904 1.494739e-07 + [4,] 0.32847048 11.23761 1.7197397 -1.786159e-07 + [5,] 0.07692977 13.47981 0.4115727 8.002802e-07 + [6,] 0.16016282 12.73788 0.8444360 4.763704e-07 + [7,] 0.25627569 11.88115 1.3442822 1.023374e-07 + [8,] 0.37679652 10.80684 1.9710649 -3.666816e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.009916467 NA NA NA +[2,] -0.002368620 NA NA NA +[3,] -0.014339310 NA NA NA +[4,] 0.008705524 NA NA NA +[5,] NA -0.06330696 -0.05813274 -8.002802e-07 +[6,] NA -0.05462267 0.04135617 -4.763704e-07 +[7,] NA 0.25569641 0.07030257 -1.023374e-07 +[8,] NA -0.13776678 -0.05352600 3.666816e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgK_res/KEIO_ROBOT2_15_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybgK_res/KEIO_ROBOT2_15_res.txt new file mode 100644 index 0000000..981d25e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybgK_res/KEIO_ROBOT2_15_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0256090567713932 0.0255783343508947 0.025481078295733 0.00459549157044052 0.0165779871412903 0.0339267515310269 +Glc 13.9372732248333 13.9570498561334 14.0180909958427 0.380328002404298 13.3227275171529 14.6953226581379 +Ace 0.144673177825157 0.166086262974551 0.147753542295538 0.134273894054801 9.99999999973245e-07 0.495618486954049 +Lac 1e-06 0.0910587446347853 0.0721468956825276 0.0893290044990482 9.99999999993061e-07 0.282564338569644 +mu 0.564075356854053 0.568518703920813 0.567953267632975 0.0426785129314777 0.497263319524652 0.654288484182411 +qGlc -5.02808116675216 -5.10269377659003 -4.99698233957087 0.954373866593565 -7.10080807416181 -3.52544386361143 +qAce 2.93354049226213 2.89029995582418 2.88395846058915 0.389681394791131 1.98040800005945 3.45917294660236 +qLac -2.1951571178976e-06 -0.031787611813636 0.0105811831802394 0.222269957453531 -0.481046676704929 0.348522346066673 +res 1.71752139820497 19.532015702602 19.1390523845779 5.80968014401709 9.29824467384203 30.2456970348904 + + +Goodness of fit (khi2 test) + +khi2 value 1.71752139820573 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.214690174775716 +p-value, i.e. P(X^2<=value) 0.0115185503401559 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgS.txt b/validation/validation_results/Berges_2021/Berges_2021/ybgS.txt new file mode 100644 index 0000000..03f8dcf --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybgS.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.033264 NA NA +1.18888888888889 0.061992 NA NA +2.27694444444444 0.101304 NA NA +3.12833333333333 0.152712 NA NA +3.77138888888889 0.201096 NA NA +4.41555555555556 0.29484 NA NA +4.82277777777778 0.364392 NA NA +0.0666666666666667 NA 15.7889725785128 0.0140193309400806 +1.71666666666667 NA 15.2506803523456 0.340831112101821 +2.8 NA 13.4500392288649 0.71713907968748 +3.63333333333333 NA 12.8967271369171 1.19776472870001 +4.26666666666667 NA 11.6918641783141 1.66462046980478 +4.88333333333333 NA 10.6228426471551 2.3101950215882 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgS_res/KEIO_ROBOT1_40.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybgS_res/KEIO_ROBOT1_40.pdf new file mode 100644 index 0000000..24aeb2e Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybgS_res/KEIO_ROBOT1_40.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgS_res/KEIO_ROBOT1_40_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybgS_res/KEIO_ROBOT1_40_log.txt new file mode 100644 index 0000000..97a6edc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybgS_res/KEIO_ROBOT1_40_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.033264 NA NA + [2,] 0.061992 NA NA + [3,] 0.101304 NA NA + [4,] 0.152712 NA NA + [5,] 0.201096 NA NA + [6,] 0.294840 NA NA + [7,] 0.364392 NA NA + [8,] NA 15.78897 0.01401933 + [9,] NA 15.25068 0.34083111 +[10,] NA 13.45004 0.71713908 +[11,] NA 12.89673 1.19776473 +[12,] NA 11.69186 1.66462047 +[13,] NA 10.62284 2.31019502 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03351089 15.59832346 0.03115532 0.49084870 -7.71522882 3.36501443 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.124309e-09 4.739859e-08 -8.193043e-09 -8.371007e-09 -7.385124e-08 -9.379871e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.007260493 0.356428878 0.154993769 0.049961442 1.024273201 0.445619839 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5243597 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.124309e-09 4.739859e-08 -8.193043e-09 -8.371007e-09 -7.385124e-08 -9.379871e-09 + +$result$normp +[1] 8.903414e-08 + +$result$res + [1] 0.01234470 -0.09632647 0.05797071 0.14533614 0.61395782 -0.10565218 -0.34478908 -0.45254459 -0.75854505 1.28925783 0.20479882 0.33984878 -0.62281580 0.12388993 -0.02931772 -0.03834297 -0.14695438 0.01080999 0.07991514 + +$result$prevres + [1] 0.01234464 -0.09632654 0.05797064 0.14533608 0.61395780 -0.10565213 -0.34478896 -0.45254469 -0.75854510 1.28925783 0.20479885 0.33984884 -0.62281573 0.12388997 -0.02931771 -0.03834298 -0.14695440 0.01080998 0.07991515 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 89.620813 0.000000 0 3.570558452 0.000000000 0.00000000 + [3,] 152.880756 0.000000 0 11.665174925 0.000000000 0.00000000 + [4,] 232.191249 0.000000 0 24.341361702 0.000000000 0.00000000 + [5,] 318.366862 0.000000 0 40.236034628 0.000000000 0.00000000 + [6,] 436.763889 0.000000 0 64.627607170 0.000000000 0.00000000 + [7,] 533.403008 0.000000 0 86.206241454 0.000000000 0.00000000 + [8,] -1.136645 2.173913 0 -0.001276591 0.004936988 0.00000000 + [9,] -45.188020 2.173913 0 -1.480177814 0.196272974 0.00000000 +[10,] -100.890335 2.173913 0 -5.784849437 0.438214511 0.00000000 +[11,] -169.146091 2.173913 0 -13.207159593 0.734681593 0.00000000 +[12,] -243.277727 2.173913 0 -23.060511213 1.056670402 0.00000000 +[13,] -341.354028 2.173913 0 -38.147863164 1.482662233 0.00000000 +[14,] 1.140226 0.000000 5 0.001280612 0.000000000 0.01135507 +[15,] 45.330371 0.000000 5 1.484840663 0.000000000 0.45142784 +[16,] 101.208159 0.000000 5 5.803072844 0.000000000 1.00789338 +[17,] 169.678934 0.000000 5 13.248764728 0.000000000 1.68976766 +[18,] 244.044100 0.000000 5 23.133156332 0.000000000 2.43034192 +[19,] 342.429360 0.000000 5 38.268036391 0.000000000 3.41012314 + +$result$retres +$result$retres$res + [1] 0.01234464 -0.09632654 0.05797064 0.14533608 0.61395780 -0.10565213 -0.34478896 -0.45254469 -0.75854510 1.28925783 0.20479885 0.33984884 -0.62281573 0.12388997 -0.02931771 -0.03834298 -0.14695440 0.01080998 0.07991515 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03351089 15.59832 0.03115533 + [2,] 0.06006547 15.18093 0.21320029 + [3,] 0.10246341 14.51452 0.50385949 + [4,] 0.15561872 13.67902 0.86826583 + [5,] 0.21337516 12.77119 1.26421520 + [6,] 0.29272696 11.52393 1.80821165 + [7,] 0.35749622 10.50588 2.25223748 + [8,] 0.03462562 15.58080 0.03879733 + [9,] 0.07782745 14.90175 0.33496757 + [10,] 0.13245553 14.04310 0.70947048 + [11,] 0.19939495 12.99093 1.16837385 + [12,] 0.27209693 11.84819 1.66678246 + [13,] 0.36828180 10.33635 2.32617805 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0002468929 NA NA + [2,] 0.0019265307 NA NA + [3,] -0.0011594128 NA NA + [4,] -0.0029067216 NA NA + [5,] -0.0122791560 NA NA + [6,] 0.0021130425 NA NA + [7,] 0.0068957792 NA NA + [8,] NA 0.20817056 -0.024777995 + [9,] NA 0.34893075 0.005863542 +[10,] NA -0.59305860 0.007668597 +[11,] NA -0.09420747 0.029390880 +[12,] NA -0.15633047 -0.002161995 +[13,] NA 0.28649524 -0.015983029 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybgS_res/KEIO_ROBOT1_40_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybgS_res/KEIO_ROBOT1_40_res.txt new file mode 100644 index 0000000..c9683fc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybgS_res/KEIO_ROBOT1_40_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0335108939869771 0.0339087565431286 0.0336383270536805 0.00494677715766557 0.024219509495787 0.0441238064515878 +Glc 15.5983234641776 15.557870511098 15.5647310041998 0.223564680190815 15.174059815707 16.0235199793632 +Ace 0.0311553214800301 0.0819358465432826 0.077937862738154 0.0640160081943457 9.99999999979663e-07 0.221633068792158 +mu 0.490848700357153 0.490802528152467 0.487842652126811 0.0355432015918139 0.428248139275988 0.566436815545755 +qGlc -7.71522881546962 -7.69587346126564 -7.71548379317096 0.570674415682909 -8.7945655830605 -6.75423411568168 +qAce 3.36501443427435 3.27133362123905 3.26605974451585 0.234326445166618 2.83559502544801 3.71246914986039 +res 3.57439000449648 32.3544478734923 32.0355619162041 8.01812710107639 17.0202722373644 51.6228542109159 + + +Goodness of fit (khi2 test) + +khi2 value 3.57439000449652 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.274953077268963 +p-value, i.e. P(X^2<=value) 0.00506599022671696 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybhC.txt b/validation/validation_results/Berges_2021/Berges_2021/ybhC.txt new file mode 100644 index 0000000..9b88561 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybhC.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.18888888888889 0.061992 NA NA +2.27694444444444 0.108864 NA NA +3.12833333333333 0.163296 NA NA +3.77138888888889 0.229824 NA NA +4.41555555555556 0.314496 NA NA +4.82277777777778 0.452088 NA NA +0.0666666666666667 NA 15.1724537692799 0.00924842802087092 +1.71666666666667 NA 15.1783014053895 0.369839593471127 +2.8 NA 14.0549409948794 0.759688518918676 +3.63333333333333 NA 12.5492025652656 1.16181059218255 +4.26666666666667 NA 11.5233977511109 1.61805401818168 +4.88333333333333 NA 9.99249338828517 2.04848663627186 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybhC_res/KEIO_ROBOT1_3.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybhC_res/KEIO_ROBOT1_3.pdf new file mode 100644 index 0000000..5b6b758 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybhC_res/KEIO_ROBOT1_3.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybhC_res/KEIO_ROBOT1_3_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybhC_res/KEIO_ROBOT1_3_log.txt new file mode 100644 index 0000000..f46770c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybhC_res/KEIO_ROBOT1_3_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.061992 NA NA + [3,] 0.108864 NA NA + [4,] 0.163296 NA NA + [5,] 0.229824 NA NA + [6,] 0.314496 NA NA + [7,] 0.452088 NA NA + [8,] NA 15.172454 0.009248428 + [9,] NA 15.178301 0.369839593 +[10,] NA 14.054941 0.759688519 +[11,] NA 12.549203 1.161810592 +[12,] NA 11.523398 1.618054018 +[13,] NA 9.992493 2.048486636 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02836716 15.41061874 0.14259753 0.56314186 -7.51977720 2.74693593 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.494950e-09 2.364931e-08 -2.093893e-08 -1.246672e-08 5.560277e-08 1.935077e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008195079 0.463716069 0.200107089 0.065718083 1.255561139 0.530378444 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.703229 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.494950e-09 2.364931e-08 -2.093893e-08 -1.246672e-08 5.560277e-08 1.935077e-08 + +$result$normp +[1] 6.798164e-08 + +$result$res + [1] -0.169241945 -0.329141036 -0.330423404 0.093306634 0.370643723 1.324072125 -1.161192507 0.486247099 -0.836653966 -0.214512160 0.672351788 0.171851513 -0.279284274 0.693213488 -0.008950303 -0.429115998 -0.434657580 -0.421759198 0.601269591 + +$result$prevres + [1] -0.169242020 -0.329141141 -0.330423529 0.093306521 0.370643656 1.324072165 -1.161192348 0.486247049 -0.836653973 -0.214512137 0.672351822 0.171851536 -0.279284296 0.693213591 -0.008950252 -0.429115994 -0.434657615 -0.421759256 0.601269525 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.00000000 0.000000000 + [2,] 97.6643026 0.000000 0 3.293768e+00 0.00000000 0.000000000 + [3,] 180.2357566 0.000000 0 1.164151e+01 0.00000000 0.000000000 + [4,] 291.1150301 0.000000 0 2.583411e+01 0.00000000 0.000000000 + [5,] 418.1540847 0.000000 0 4.473563e+01 0.00000000 0.000000000 + [6,] 601.0073764 0.000000 0 7.528024e+01 0.00000000 0.000000000 + [7,] 755.9166289 0.000000 0 1.034158e+02 0.00000000 0.000000000 + [8,] -1.1105387 2.173913 0 -1.056665e-03 0.00418933 0.000000000 + [9,] -47.2973543 2.173913 0 -1.334341e+00 0.17842172 0.000000000 +[10,] -111.4541483 2.173913 0 -5.544005e+00 0.42044299 0.000000000 +[11,] -195.5824321 2.173913 0 -1.329801e+01 0.73780351 0.000000000 +[12,] -291.8384827 2.173913 0 -2.413481e+01 1.10091410 0.000000000 +[13,] -425.0625647 2.173913 0 -4.149191e+01 1.60348069 0.000000000 +[14,] 0.9330504 0.000000 5 8.877866e-04 0.00000000 0.009635459 +[15,] 39.7382039 0.000000 5 1.121085e+00 0.00000000 0.410369958 +[16,] 93.6413408 0.000000 5 4.657952e+00 0.00000000 0.967018871 +[17,] 164.3240871 0.000000 5 1.117269e+01 0.00000000 1.696948077 +[18,] 245.1963182 0.000000 5 2.027754e+01 0.00000000 2.532102433 +[19,] 357.1282817 0.000000 5 3.486060e+01 0.00000000 3.688005585 + +$result$retres +$result$retres$res + [1] -0.169242020 -0.329141141 -0.330423529 0.093306521 0.370643656 1.324072165 -1.161192348 0.486247049 -0.836653973 -0.214512137 0.672351822 0.171851536 -0.279284296 0.693213591 -0.008950252 -0.429115994 -0.434657615 -0.421759256 0.601269525 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02836716 15.410619 0.1425975 + [2,] 0.05540918 15.049520 0.2745051 + [3,] 0.10225553 14.423968 0.5030158 + [4,] 0.16516213 13.583961 0.8098664 + [5,] 0.23723687 12.621528 1.1614380 + [6,] 0.34097744 11.236254 1.6674716 + [7,] 0.42886415 10.062680 2.0961720 + [8,] 0.02945239 15.396127 0.1478911 + [9,] 0.07458646 14.793441 0.3680495 + [10,] 0.13728092 13.956265 0.6738653 + [11,] 0.21949166 12.858484 1.0748791 + [12,] 0.31355374 11.602449 1.5337022 + [13,] 0.44374123 9.864023 2.1687405 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.003384840 NA NA + [2,] 0.006582823 NA NA + [3,] 0.006608471 NA NA + [4,] -0.001866130 NA NA + [5,] -0.007412873 NA NA + [6,] -0.026481443 NA NA + [7,] 0.023223847 NA NA + [8,] NA -0.22367364 -0.13864272 + [9,] NA 0.38486083 0.00179005 +[10,] NA 0.09867558 0.08582320 +[11,] NA -0.30928184 0.08693152 +[12,] NA -0.07905171 0.08435185 +[13,] NA 0.12847078 -0.12025391 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybhC_res/KEIO_ROBOT1_3_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybhC_res/KEIO_ROBOT1_3_res.txt new file mode 100644 index 0000000..5ead5cc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybhC_res/KEIO_ROBOT1_3_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0283671610910483 0.0287996519878213 0.0282363129855644 0.00400032384158994 0.0220913185623638 0.0376107483019928 +Glc 15.4106187368003 15.4003814344763 15.4037801283288 0.227830984042548 14.9639649312919 15.8739110826286 +Ace 0.142597527589566 0.146897778069367 0.145457883441227 0.0740706443738212 0.00467351741778465 0.291895034755503 +mu 0.56314185525744 0.561284865350897 0.563277287114233 0.0302658429944232 0.503289874778956 0.623618839074341 +qGlc -7.51977719645843 -7.48959155947562 -7.49864923927137 0.626642444178732 -8.81026910774908 -6.34497272649083 +qAce 2.74693592535785 2.72619105597243 2.71997322775329 0.215353625154339 2.33695794624118 3.16624809353695 +res 6.4289040957413 31.6164260063225 30.8255122298751 7.70712135929764 19.9666749834792 50.6878484358354 + + +Goodness of fit (khi2 test) + +khi2 value 6.42890409574143 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.494531084287802 +p-value, i.e. P(X^2<=value) 0.0708580364804748 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiB.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiB.txt new file mode 100644 index 0000000..3829518 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiB.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.107352 NA NA NA +3.34194444444444 0.161784 NA NA NA +3.9975 0.214704 NA NA NA +4.52333333333333 0.314496 NA NA NA +1.95 NA 13.6352943789264 0.39039522949506 0 +3.25 NA 12.5774665397727 0.973752850335694 0 +4.08333333333333 NA 11.5861306424075 1.4523411520089 0 +4.76666666666667 NA 10.7192098194515 2.08272417235889 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiB_res/KEIO_ROBOT2_16.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybiB_res/KEIO_ROBOT2_16.pdf new file mode 100644 index 0000000..5b7ee12 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybiB_res/KEIO_ROBOT2_16.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiB_res/KEIO_ROBOT2_16_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiB_res/KEIO_ROBOT2_16_log.txt new file mode 100644 index 0000000..69f7c67 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiB_res/KEIO_ROBOT2_16_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.107352 NA NA NA +[2,] 0.161784 NA NA NA +[3,] 0.214704 NA NA NA +[4,] 0.314496 NA NA NA +[5,] NA 13.63529 0.3903952 0 +[6,] NA 12.57747 0.9737529 0 +[7,] NA 11.58613 1.4523412 0 +[8,] NA 10.71921 2.0827242 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.663762e-02 1.403394e+01 1.327965e-01 1.000000e-06 5.389879e-01 -5.770102e+00 3.308622e+00 -2.290181e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 8.360186e-10 3.017354e-08 -1.246152e-08 0.000000e+00 -7.858339e-09 -3.570856e-08 5.807931e-09 -7.806976e-14 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.008238255 0.458114446 0.205727131 0.189966372 0.074924778 1.188532624 0.528514439 0.500405990 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4070296 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 8.360186e-10 3.017354e-08 -1.246152e-08 0.000000e+00 -7.858339e-09 -3.570856e-08 5.807931e-09 -7.806976e-14 + +$result$normp +[1] 4.936616e-08 + +$result$res + [1] -2.391133e-01 -2.156885e-02 7.515754e-01 -4.742707e-01 -2.868089e-01 2.126232e-01 3.415317e-01 -2.673460e-01 2.331958e-01 -3.094282e-01 -3.017992e-02 1.064123e-01 3.947055e-06 2.303693e-06 4.540414e-07 -1.822216e-06 + +$result$prevres + [1] -2.391133e-01 -2.156889e-02 7.515754e-01 -4.742706e-01 -2.868089e-01 2.126232e-01 3.415317e-01 -2.673460e-01 2.331958e-01 -3.094282e-01 -3.017994e-02 1.064123e-01 3.947055e-06 2.303693e-06 4.540416e-07 -1.822216e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 1.925280e+02 0.000000 0 0 1.282834e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.028661e+02 0.000000 0 0 2.696157e+01 0.0000000 0.0000000 0.0000000 + [3,] 4.312238e+02 0.000000 0 0 4.591838e+01 0.0000000 0.0000000 0.0000000 + [4,] 5.725184e+02 0.000000 0 0 6.898323e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.330084e+01 2.173913 0 0 -1.318058e+00 0.1998979 0.0000000 0.0000000 + [6,] -1.108817e+02 2.173913 0 0 -6.134105e+00 0.5118844 0.0000000 0.0000000 + [7,] -1.869459e+02 2.173913 0 0 -1.362638e+01 0.8630340 0.0000000 0.0000000 + [8,] -2.805537e+02 2.173913 0 0 -2.471224e+01 1.2951734 0.0000000 0.0000000 + [9,] 5.710680e+01 0.000000 5 0 1.738306e+00 0.0000000 0.4597652 0.0000000 +[10,] 1.462350e+02 0.000000 5 0 8.089891e+00 0.0000000 1.1773340 0.0000000 +[11,] 2.465514e+02 0.000000 5 0 1.797099e+01 0.0000000 1.9849783 0.0000000 +[12,] 3.700049e+02 0.000000 5 0 3.259145e+01 0.0000000 2.9788987 0.0000000 +[13,] -3.952850e-05 0.000000 0 5 -1.203230e-06 0.0000000 0.0000000 0.4597652 +[14,] -1.012218e-04 0.000000 0 5 -5.599706e-06 0.0000000 0.0000000 1.1773340 +[15,] -1.706593e-04 0.000000 0 5 -1.243926e-05 0.0000000 0.0000000 1.9849783 +[16,] -2.561120e-04 0.000000 0 5 -2.255933e-05 0.0000000 0.0000000 2.9788987 + +$result$retres +$result$retres$res + [1] -2.391133e-01 -2.156889e-02 7.515754e-01 -4.742706e-01 -2.868089e-01 2.126232e-01 3.415317e-01 -2.673460e-01 2.331958e-01 -3.094282e-01 -3.017994e-02 1.064123e-01 3.947055e-06 2.303693e-06 4.540416e-07 -1.822216e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.1025697 13.22105 0.5989121 6.773615e-07 + [2,] 0.1613526 12.59176 0.9597558 4.275908e-07 + [3,] 0.2297355 11.85969 1.3795299 1.370292e-07 + [4,] 0.3050106 11.05384 1.8416122 -1.828175e-07 + [5,] 0.0761992 13.50336 0.4370344 7.894109e-07 + [6,] 0.1535514 12.67527 0.9118672 4.607385e-07 + [7,] 0.2406135 11.74324 1.4463052 9.080832e-08 + [8,] 0.3477557 10.59623 2.1040066 -3.644431e-07 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.0047822664 NA NA NA +[2,] 0.0004313778 NA NA NA +[3,] -0.0150315083 NA NA NA +[4,] 0.0094854128 NA NA NA +[5,] NA 0.13193209 -0.046639166 -7.894109e-07 +[6,] NA -0.09780668 0.061885640 -4.607385e-07 +[7,] NA -0.15710457 0.006035987 -9.080832e-08 +[8,] NA 0.12297916 -0.021282461 3.644431e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiB_res/KEIO_ROBOT2_16_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiB_res/KEIO_ROBOT2_16_res.txt new file mode 100644 index 0000000..2436079 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiB_res/KEIO_ROBOT2_16_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0266376219964614 0.0269037215266619 0.0263453631922348 0.00520598980509837 0.0181551320738363 0.0385158221471277 +Glc 14.0339407961349 13.9955000814228 13.9613194351194 0.409152343951424 13.3529478405047 14.9381761623137 +Ace 0.132796495984356 0.132406483704348 0.102090117245517 0.117917263220362 9.99999999952081e-07 0.368541504229691 +Lac 1e-06 0.0965703253742598 0.0823741354772248 0.0820460977207956 9.99999999999339e-07 0.262366061107215 +mu 0.538987893900298 0.541239545502743 0.537564289164808 0.0451184097067906 0.454348366983078 0.620835700927614 +qGlc -5.7701023792801 -5.67186985861464 -5.5956601109538 1.1963553974937 -8.18066501503478 -3.59396504301349 +qAce 3.30862225955078 3.32180595537653 3.32555304196655 0.388933901168045 2.53092921398051 4.00514107466072 +qLac -2.2901805020393e-06 -0.0479258016085189 -0.0250949186658543 0.221513957981221 -0.471603249899153 0.315472782492611 +res 1.32538488563974 20.4147535663842 20.1551754696209 5.69061481677224 10.6184677910274 32.9966491938996 + + +Goodness of fit (khi2 test) + +khi2 value 1.32538488563975 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.165673110704968 +p-value, i.e. P(X^2<=value) 0.0047581138188236 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiC.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiC.txt new file mode 100644 index 0000000..a91c234 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiC.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.099792 NA NA NA +3.34194444444444 0.1512 NA NA NA +3.9975 0.216216 NA NA NA +4.52333333333333 0.300888 NA NA NA +1.95 NA 13.549637195701 0.414172382079061 0 +3.25 NA 12.6608383630957 0.979887934459837 0 +4.08333333333333 NA 11.4605338604977 1.5054590285525 0 +4.76666666666667 NA 10.1379635075061 2.06028905182974 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiC_res/KEIO_ROBOT2_42.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybiC_res/KEIO_ROBOT2_42.pdf new file mode 100644 index 0000000..25bbbb0 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybiC_res/KEIO_ROBOT2_42.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiC_res/KEIO_ROBOT2_42_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiC_res/KEIO_ROBOT2_42_log.txt new file mode 100644 index 0000000..f49a376 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiC_res/KEIO_ROBOT2_42_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.099792 NA NA NA +[2,] 0.151200 NA NA NA +[3,] 0.216216 NA NA NA +[4,] 0.300888 NA NA NA +[5,] NA 13.54964 0.4141724 0 +[6,] NA 12.66084 0.9798879 0 +[7,] NA 11.46053 1.5054590 0 +[8,] NA 10.13796 2.0602891 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.406540e-02 1.417447e+01 1.853536e-01 1.000000e-06 5.552566e-01 -7.123409e+00 3.380550e+00 -2.404378e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 1.497845e-09 3.077106e-08 -3.646129e-08 -4.235165e-22 -1.559598e-08 3.477259e-08 5.356435e-08 -3.050519e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.004539908 0.270060309 0.118841216 0.109678787 0.045594063 0.734593852 0.322161429 0.304490738 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.2377775 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 1.497845e-09 3.077106e-08 -3.646129e-08 -4.235165e-22 -1.559598e-08 3.477259e-08 5.356435e-08 -3.050519e-13 + +$result$normp +[1] 8.12406e-08 + +$result$res + [1] -1.639017e-01 1.358364e-01 2.640968e-01 -2.143814e-01 4.768004e-02 -1.173065e-01 9.207353e-02 -2.244706e-02 2.864862e-01 -2.530249e-01 -2.612833e-01 2.278220e-01 3.982516e-06 2.354444e-06 4.912853e-07 -1.829668e-06 + +$result$prevres + [1] -1.639018e-01 1.358364e-01 2.640968e-01 -2.143812e-01 4.768002e-02 -1.173065e-01 9.207354e-02 -2.244708e-02 2.864863e-01 -2.530249e-01 -2.612834e-01 2.278219e-01 3.982516e-06 2.354444e-06 4.912860e-07 -1.829667e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.005243e+02 0.000000 0 0 1.207095e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.197885e+02 0.000000 0 0 2.571906e+01 0.0000000 0.0000000 0.0000000 + [3,] 4.602000e+02 0.000000 0 0 4.427190e+01 0.0000000 0.0000000 0.0000000 + [4,] 6.162383e+02 0.000000 0 0 6.708112e+01 0.0000000 0.0000000 0.0000000 + [5,] -5.446178e+01 2.173913 0 0 -1.504098e+00 0.1839912 0.0000000 0.0000000 + [6,] -1.416059e+02 2.173913 0 0 -7.119297e+00 0.4783948 0.0000000 0.0000000 + [7,] -2.413332e+02 2.173913 0 0 -1.599606e+01 0.8153090 0.0000000 0.0000000 + [8,] -3.655644e+02 2.173913 0 0 -2.928981e+01 1.2350060 0.0000000 0.0000000 + [9,] 5.944551e+01 0.000000 5 0 1.641737e+00 0.0000000 0.4231797 0.0000000 +[10,] 1.545641e+02 0.000000 5 0 7.770776e+00 0.0000000 1.1003081 0.0000000 +[11,] 2.634174e+02 0.000000 5 0 1.745984e+01 0.0000000 1.8752107 0.0000000 +[12,] 3.990168e+02 0.000000 5 0 3.197008e+01 0.0000000 2.8405139 0.0000000 +[13,] -4.227994e-05 0.000000 0 5 -1.167666e-06 0.0000000 0.0000000 0.4231797 +[14,] -1.099319e-04 0.000000 0 5 -5.526875e-06 0.0000000 0.0000000 1.1003081 +[15,] -1.873526e-04 0.000000 0 5 -1.241811e-05 0.0000000 0.0000000 1.8752107 +[16,] -2.837961e-04 0.000000 0 5 -2.273836e-05 0.0000000 0.0000000 2.8405139 + +$result$retres +$result$retres$res + [1] -1.639018e-01 1.358364e-01 2.640968e-01 -2.143812e-01 4.768002e-02 -1.173065e-01 9.207354e-02 -2.244708e-02 2.864863e-01 -2.530249e-01 -2.612834e-01 2.278219e-01 3.982516e-06 2.354444e-06 4.912860e-07 -1.829667e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09651396 13.24502 0.6264398 6.862825e-07 + [2,] 0.15391673 12.50860 0.9759231 4.377166e-07 + [3,] 0.22149794 11.64160 1.3873755 1.450758e-07 + [4,] 0.29660038 10.67810 1.8446191 -1.801335e-07 + [5,] 0.07106006 13.57157 0.4714696 7.965033e-07 + [6,] 0.14625607 12.60688 0.9292830 4.708888e-07 + [7,] 0.23231002 11.50289 1.4532024 9.825719e-08 + [8,] 0.33950821 10.12764 2.1058534 -3.659334e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.003278035 NA NA NA +[2,] -0.002716727 NA NA NA +[3,] -0.005281936 NA NA NA +[4,] 0.004287625 NA NA NA +[5,] NA -0.02193281 -0.05729727 -7.965033e-07 +[6,] NA 0.05396098 0.05060497 -4.708888e-07 +[7,] NA -0.04235383 0.05225667 -9.825719e-08 +[8,] NA 0.01032566 -0.04556438 3.659334e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiC_res/KEIO_ROBOT2_42_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiC_res/KEIO_ROBOT2_42_res.txt new file mode 100644 index 0000000..e115017 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiC_res/KEIO_ROBOT2_42_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0240653992770026 0.0243556777049506 0.0240811336135545 0.00502394934353078 0.0140702292479244 0.0341330102981906 +Glc 14.1744664064864 14.1616927089736 14.1262442125737 0.35736713165889 13.5139117190477 14.9482687230346 +Ace 0.185353623782547 0.190799490789404 0.169503750196435 0.156075210931619 9.99999999976541e-07 0.483601010264772 +Lac 1e-06 0.0901025011949625 0.077174152578257 0.0790646115982294 9.9999999998777e-07 0.249371859188835 +mu 0.555256579034822 0.558368843822618 0.558140442741155 0.0520687278918793 0.467876145440594 0.670748399180983 +qGlc -7.1234091223943 -7.06811530071411 -6.83537828435636 1.06470171930041 -9.7433560505079 -5.51450734691435 +qAce 3.38054993112479 3.38058195054508 3.44064678416982 0.473839792035455 2.37150220933434 4.21941061537608 +qLac -2.40437754145451e-06 -0.00642024611272548 -0.0243578344833437 0.227681277839773 -0.403314216562057 0.431372853939594 +res 0.452305160897407 20.0053495111331 19.672225281256 5.86396229532617 10.4731056350081 34.0311535071598 + + +Goodness of fit (khi2 test) + +khi2 value 0.452305160897458 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.0565381451121822 +p-value, i.e. P(X^2<=value) 9.10167878111842e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiH.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiH.txt new file mode 100644 index 0000000..7de28f3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiH.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.176904 NA NA +3.67805555555556 0.282744 NA NA +4.09222222222222 0.35532 NA NA +4.565 0.46116 NA NA +0.05 NA 14.3269793812272 0.020144487443013 +1.95 NA 14.1156966906156 0.444939875961519 +2.83333333333333 NA 13.7052961811136 0.784314830247369 +3.98333333333333 NA 11.8407119871537 1.44617383115738 +4.88333333333333 NA 9.16027037801367 2.22695418020307 +5.16666666666667 NA 8.31269299647365 2.4621736319432 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiH_res/KEIO_ROBOT3_28.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybiH_res/KEIO_ROBOT3_28.pdf new file mode 100644 index 0000000..d85ad11 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybiH_res/KEIO_ROBOT3_28.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiH_res/KEIO_ROBOT3_28_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiH_res/KEIO_ROBOT3_28_log.txt new file mode 100644 index 0000000..fcfc074 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiH_res/KEIO_ROBOT3_28_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.176904 NA NA + [2,] 0.282744 NA NA + [3,] 0.355320 NA NA + [4,] 0.461160 NA NA + [5,] NA 14.326979 0.02014449 + [6,] NA 14.115697 0.44493988 + [7,] NA 13.705296 0.78431483 + [8,] NA 11.840712 1.44617383 + [9,] NA 9.160270 2.22695418 +[10,] NA 8.312693 2.46217363 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03502792 14.77229397 0.15765897 0.56546688 -5.90982217 2.21590918 + +$result$lastp + X Glc Ace mu qGlc qAce + 4.025156e-09 3.454407e-07 1.092555e-07 -2.807830e-08 -5.584479e-07 -2.836687e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01031807 0.39918683 0.17119971 0.07022034 0.65756460 0.27962630 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5771347 + +$result$laststep + X Glc Ace mu qGlc qAce + 4.025156e-09 3.454407e-07 1.092555e-07 -2.807830e-08 -5.584479e-07 -2.836687e-07 + +$result$normp +[1] 7.241565e-07 + +$result$res + [1] 0.06529650 -0.12074829 -0.05068902 0.08678456 0.94525313 -0.17397177 -0.83491466 -0.40031347 0.40464545 0.05930132 0.70725399 -0.05540484 -0.41288111 -0.60131037 -0.17419695 0.53653928 + +$result$prevres + [1] 0.06529620 -0.12074845 -0.05068902 0.08678487 0.94525238 -0.17397223 -0.83491491 -0.40031331 0.40464602 0.05930204 0.70725344 -0.05540533 -0.41288149 -0.60131040 -0.17419638 0.53654014 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 254.3827123 0.000000 0 2.563500e+01 0.000000000 0.000000000 + [2,] 400.1508874 0.000000 0 5.155329e+01 0.000000000 0.000000000 + [3,] 505.7483620 0.000000 0 7.249499e+01 0.000000000 0.000000000 + [4,] 660.7525573 0.000000 0 1.056559e+02 0.000000000 0.000000000 + [5,] -0.6515391 2.173913 0 -5.732399e-04 0.003861717 0.000000000 + [6,] -45.7165903 2.173913 0 -1.842607e+00 0.270965349 0.000000000 + [7,] -90.0560169 2.173913 0 -5.614016e+00 0.533768154 0.000000000 + [8,] -193.3691096 2.173913 0 -1.817219e+01 1.146111899 0.000000000 + [9,] -336.7429743 2.173913 0 -4.062764e+01 1.995898573 0.000000000 +[10,] -399.2046841 2.173913 0 -5.163013e+01 2.366113387 0.000000000 +[11,] 0.5618831 0.000000 5 4.943584e-04 0.000000000 0.008881948 +[12,] 39.4256906 0.000000 5 1.589052e+00 0.000000000 0.623220302 +[13,] 77.6637241 0.000000 5 4.841491e+00 0.000000000 1.227666754 +[14,] 166.7602642 0.000000 5 1.567158e+01 0.000000000 2.636057369 +[15,] 290.4049539 0.000000 5 3.503701e+01 0.000000000 4.590566717 +[16,] 344.2715268 0.000000 5 4.452549e+01 0.000000000 5.442060789 + +$result$retres +$result$retres$res + [1] 0.06529620 -0.12074845 -0.05068902 0.08678487 0.94525238 -0.17397223 -0.83491491 -0.40031331 0.40464602 0.05930204 0.70725344 -0.05540533 -0.41288149 -0.60131040 -0.17419638 0.53654014 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.17820992 13.275866 0.7187498 + [2,] 0.28032903 12.208597 1.1189265 + [3,] 0.35430622 11.435444 1.4088228 + [4,] 0.46289570 10.300551 1.8343552 + [5,] 0.03603241 14.761795 0.1615952 + [6,] 0.10551001 14.035669 0.4338588 + [7,] 0.17386890 13.321235 0.7017385 + [8,] 0.33314856 11.656568 1.3259118 + [9,] 0.55419063 9.346408 2.1921149 + [10,] 0.65048897 8.339972 2.5694817 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.001305924 NA NA + [2,] 0.002414969 NA NA + [3,] 0.001013780 NA NA + [4,] -0.001735697 NA NA + [5,] NA -0.43481610 -0.14145069 + [6,] NA 0.08002723 0.01108107 + [7,] NA 0.38406086 0.08257630 + [8,] NA 0.18414412 0.12026208 + [9,] NA -0.18613717 0.03483928 +[10,] NA -0.02727894 -0.10730803 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiH_res/KEIO_ROBOT3_28_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiH_res/KEIO_ROBOT3_28_res.txt new file mode 100644 index 0000000..7a8d3b3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiH_res/KEIO_ROBOT3_28_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.035027919714055 0.034937658310772 0.0345471225838324 0.00373303951449532 0.028761596618927 0.0424646196772773 +Glc 14.7722939699054 14.7746116857046 14.7608527229711 0.276695183425185 14.2873866803938 15.294603253762 +Ace 0.157658966533171 0.178251369053979 0.17056901250802 0.10432939491135 1.000000000001e-06 0.393653399247234 +mu 0.56546687626547 0.566778951395996 0.567777969160022 0.023183554324336 0.523383946496345 0.607464742429182 +qGlc -5.90982216578887 -5.94799307271836 -5.98809065255077 0.457995639796747 -6.82523626929866 -5.0945248697824 +qAce 2.21590918147457 2.18174917912211 2.18666210014988 0.191657256594497 1.76312058205945 2.52547963237466 +res 3.33084416247923 23.5861276892864 22.5492286688225 7.03768550103834 11.728827193321 38.7233865843335 + + +Goodness of fit (khi2 test) + +khi2 value 3.33084416248282 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.333084416248282 +p-value, i.e. P(X^2<=value) 0.0274677465473763 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiJ.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiJ.txt new file mode 100644 index 0000000..efa0631 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiJ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.04536 NA NA +1.18888888888889 0.069552 NA NA +2.27694444444444 0.108864 NA NA +3.12833333333333 0.16632 NA NA +3.77138888888889 0.2268 NA NA +4.41555555555556 0.353808 NA NA +4.82277777777778 0.464184 NA NA +0.0666666666666667 NA 15.9638944003128 0.0101694965853752 +1.71666666666667 NA 15.3323602271337 0.383110525112282 +2.8 NA 13.731101227635 0.833394488028364 +3.63333333333333 NA 12.3859248674319 1.23532899439753 +4.26666666666667 NA 11.5278664739984 1.80887425775963 +4.88333333333333 NA 9.78163641657413 2.36628121876008 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiJ_res/KEIO_ROBOT1_36.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybiJ_res/KEIO_ROBOT1_36.pdf new file mode 100644 index 0000000..66432d2 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybiJ_res/KEIO_ROBOT1_36.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiJ_res/KEIO_ROBOT1_36_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiJ_res/KEIO_ROBOT1_36_log.txt new file mode 100644 index 0000000..af64477 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiJ_res/KEIO_ROBOT1_36_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.045360 NA NA + [2,] 0.069552 NA NA + [3,] 0.108864 NA NA + [4,] 0.166320 NA NA + [5,] 0.226800 NA NA + [6,] 0.353808 NA NA + [7,] 0.464184 NA NA + [8,] NA 15.963894 0.0101695 + [9,] NA 15.332360 0.3831105 +[10,] NA 13.731101 0.8333945 +[11,] NA 12.385925 1.2353290 +[12,] NA 11.527866 1.8088743 +[13,] NA 9.781636 2.3662812 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03114227 15.74527410 0.11397642 0.55242806 -7.94504952 3.00334527 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.021351e-08 3.067934e-07 -1.024533e-07 -7.856570e-08 -7.316565e-08 -1.326379e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008467915 0.472489483 0.204038769 0.061958634 1.214384199 0.514440513 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7116455 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.021351e-08 3.067934e-07 -1.024533e-07 -7.856570e-08 -7.316565e-08 -1.326379e-08 + +$result$normp +[1] 3.412109e-07 + +$result$res + [1] -0.710886538 -0.474607324 0.034480662 0.451159718 1.166579007 0.161511178 -0.853718342 -0.511788996 -0.642135676 0.779539752 1.030415611 -0.139558208 -0.516472483 0.550792826 -0.006938609 -0.467914053 -0.153224539 -0.381942846 0.459227220 + +$result$prevres + [1] -0.710887049 -0.474608029 0.034479846 0.451158998 1.166578611 0.161511516 -0.853717203 -0.511789651 -0.642135943 0.779539804 1.030415883 -0.139557860 -0.516472233 0.550793328 -0.006938425 -0.467914123 -0.153224768 -0.381943107 0.459227095 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 96.428200 0.000000 0 3.570223788 0.000000000 0.00000000 + [3,] 175.892181 0.000000 0 12.472372693 0.000000000 0.00000000 + [4,] 281.519687 0.000000 0 27.426595731 0.000000000 0.00000000 + [5,] 401.595100 0.000000 0 47.167171614 0.000000000 0.00000000 + [6,] 573.237526 0.000000 0 78.826107073 0.000000000 0.00000000 + [7,] 717.850390 0.000000 0 107.815525643 0.000000000 0.00000000 + [8,] -1.172922 2.173913 0 -0.001225055 0.004597511 0.00000000 + [9,] -49.443238 2.173913 0 -1.527466755 0.193802963 0.00000000 +[10,] -115.569529 2.173913 0 -6.288704927 0.452998590 0.00000000 +[11,] -201.414950 2.173913 0 -14.973373875 0.789487415 0.00000000 +[12,] -298.881164 2.173913 0 -27.018814689 1.171526331 0.00000000 +[13,] -432.881291 2.173913 0 -46.183508947 1.696767451 0.00000000 +[14,] 1.019778 0.000000 5 0.001065104 0.000000000 0.01057428 +[15,] 42.987620 0.000000 5 1.328031149 0.000000000 0.44574681 +[16,] 100.480049 0.000000 5 5.467612309 0.000000000 1.04189676 +[17,] 175.116956 0.000000 5 13.018356602 0.000000000 1.81582106 +[18,] 259.857371 0.000000 5 23.491069383 0.000000000 2.69451056 +[19,] 376.361605 0.000000 5 40.153501384 0.000000000 3.90256514 + +$result$retres +$result$retres$res + [1] -0.710887049 -0.474608029 0.034479846 0.451158998 1.166578611 0.161511516 -0.853717203 -0.511789651 -0.642135943 0.779539804 1.030415883 -0.139557860 -0.516472233 0.550793328 -0.006938425 -0.467914123 -0.153224768 -0.381943107 0.459227095 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03114226 15.745274 0.1139765 + [2,] 0.06005984 15.329380 0.2711906 + [3,] 0.10955360 14.617558 0.5402697 + [4,] 0.17534318 13.671369 0.8979430 + [5,] 0.25013157 12.595758 1.3045395 + [6,] 0.35703823 11.058221 1.8857511 + [7,] 0.44710966 9.762810 2.3754357 + [8,] 0.03231056 15.728471 0.1203282 + [9,] 0.08039088 15.036978 0.3817228 + [10,] 0.14625688 14.089690 0.7398117 + [11,] 0.23176439 12.859916 1.2046840 + [12,] 0.32884695 11.463670 1.7324856 + [13,] 0.46231962 9.544059 2.4581266 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0142177410 NA NA + [2,] 0.0094921606 NA NA + [3,] -0.0006895969 NA NA + [4,] -0.0090231800 NA NA + [5,] -0.0233315722 NA NA + [6,] -0.0032302303 NA NA + [7,] 0.0170743441 NA NA + [8,] NA 0.23542324 -0.110158666 + [9,] NA 0.29538253 0.001387685 +[10,] NA -0.35858831 0.093582825 +[11,] NA -0.47399131 0.030644954 +[12,] NA 0.06419662 0.076388621 +[13,] NA 0.23757723 -0.091845419 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiJ_res/KEIO_ROBOT1_36_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiJ_res/KEIO_ROBOT1_36_res.txt new file mode 100644 index 0000000..6134b5d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiJ_res/KEIO_ROBOT1_36_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0311422692362925 0.0312267646853046 0.0312194184898471 0.00376713418227379 0.0250495946776361 0.0377943828528155 +Glc 15.7452740959438 15.7474128401521 15.7345505901732 0.175407722287395 15.4519902824429 16.1012723429694 +Ace 0.113976419792839 0.122575568712464 0.119946078669535 0.0771325135525305 9.99999999996533e-07 0.253051406391491 +mu 0.552428064449329 0.552857098209378 0.551776381061335 0.0280080406938565 0.508873933389625 0.603759451566649 +qGlc -7.9450495245811 -8.00672608599448 -7.99818083250973 0.462363255430552 -8.97001362407258 -7.16151903540286 +qAce 3.00334526520896 3.00980208192987 3.01720434892384 0.186920225042694 2.65930226467816 3.4088312972091 +res 6.58371049624292 32.6196490646734 31.6581533434039 7.90976732076754 19.8810044933127 48.3654324952583 + + +Goodness of fit (khi2 test) + +khi2 value 6.58371049624799 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.506439268942153 +p-value, i.e. P(X^2<=value) 0.0776874486361725 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiT.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiT.txt new file mode 100644 index 0000000..0b49a2b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiT.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.17388 NA NA +3.67805555555556 0.285768 NA NA +4.09222222222222 0.390096 NA NA +4.565 0.541296 NA NA +0.05 NA 14.3189444673889 0.0240365718024159 +1.95 NA 14.2071853938769 0.431866817658686 +2.83333333333333 NA 13.3405155031835 0.680913889674489 +3.98333333333333 NA 11.6903725230143 1.37466138629946 +4.88333333333333 NA 9.11829288237042 2.10349630225521 +5.16666666666667 NA 8.46725540367133 2.53166409764046 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiT_res/KEIO_ROBOT3_25.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybiT_res/KEIO_ROBOT3_25.pdf new file mode 100644 index 0000000..220171f Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybiT_res/KEIO_ROBOT3_25.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiT_res/KEIO_ROBOT3_25_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiT_res/KEIO_ROBOT3_25_log.txt new file mode 100644 index 0000000..1336529 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiT_res/KEIO_ROBOT3_25_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.173880 NA NA + [2,] 0.285768 NA NA + [3,] 0.390096 NA NA + [4,] 0.541296 NA NA + [5,] NA 14.318944 0.02403657 + [6,] NA 14.207185 0.43186682 + [7,] NA 13.340516 0.68091389 + [8,] NA 11.690373 1.37466139 + [9,] NA 9.118293 2.10349630 +[10,] NA 8.467255 2.53166410 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02521863 14.48333351 0.18282595 0.66946476 -5.37297299 2.06282212 + +$result$lastp + X Glc Ace mu qGlc qAce +-3.411197e-08 -5.058935e-07 2.038892e-07 3.218967e-07 -4.620973e-07 1.577328e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.006740029 0.346036386 0.149100851 0.063111101 0.542943812 0.232762574 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.526203 + +$result$laststep + X Glc Ace mu qGlc qAce +-3.411197e-08 -5.058935e-07 2.038892e-07 3.218967e-07 -4.620973e-07 1.577328e-07 + +$result$normp +[1] 8.004334e-07 + +$result$res + [1] -0.041368243 0.504971092 0.015387160 -0.276714165 0.342390064 -0.582995902 -0.008044933 0.179020989 0.535228724 -0.465598942 0.807172397 -0.200300332 -0.289550077 -0.755811150 0.222909191 0.215579971 + +$result$prevres + [1] -0.041364552 0.504973587 0.015387851 -0.276717294 0.342391145 -0.582995851 -0.008045514 0.179019911 0.535228562 -0.465598253 0.807171394 -0.200300415 -0.289549592 -0.755810197 0.222909380 0.215579429 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 343.1044773 0.000000 0 2.489315e+01 0.000000000 0.000000000 + [2,] 586.6042483 0.000000 0 5.441085e+01 0.000000000 0.000000000 + [3,] 774.0374468 0.000000 0 7.988095e+01 0.000000000 0.000000000 + [4,] 1062.2325615 0.000000 0 1.222876e+02 0.000000000 0.000000000 + [5,] -0.5939032 2.173913 0 -3.765251e-04 0.002787553 0.000000000 + [6,] -46.9223546 2.173913 0 -1.397909e+00 0.220235436 0.000000000 + [7,] -98.8329081 2.173913 0 -4.585532e+00 0.463883554 0.000000000 + [8,] -233.6617138 2.173913 0 -1.642298e+01 1.096717968 0.000000000 + [9,] -441.2567507 2.173913 0 -3.986783e+01 2.071089008 0.000000000 +[10,] -537.0638079 2.173913 0 -5.201967e+01 2.520770385 0.000000000 +[11,] 0.5244338 0.000000 5 3.324825e-04 0.000000000 0.006411371 +[12,] 41.4337995 0.000000 5 1.234394e+00 0.000000000 0.506541503 +[13,] 87.2723232 0.000000 5 4.049157e+00 0.000000000 1.066932174 +[14,] 206.3300677 0.000000 5 1.450197e+01 0.000000000 2.522451327 +[15,] 389.6425039 0.000000 5 3.520445e+01 0.000000000 4.763504719 +[16,] 474.2429130 0.000000 5 4.593488e+01 0.000000000 5.797771885 + +$result$retres +$result$retres$res + [1] -0.041364552 0.504973587 0.015387851 -0.276717294 0.342391145 -0.582995851 -0.008045514 0.179019911 0.535228562 -0.465598253 0.807171394 -0.200300415 -0.289549592 -0.755810197 0.222909380 0.215579429 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.17305271 13.296851 0.6383471 + [2,] 0.29586747 12.311167 1.0167764 + [3,] 0.39040376 11.552440 1.3080712 + [4,] 0.53576165 10.385830 1.7559628 + [5,] 0.02607710 14.476444 0.1854709 + [6,] 0.09304097 13.939007 0.3918067 + [7,] 0.16807329 13.336815 0.6230040 + [8,] 0.36295695 11.772722 1.2234993 + [9,] 0.66301806 9.364498 2.1480782 + [10,] 0.80149908 8.253080 2.5747800 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.000827291 NA NA + [2,] -0.010099472 NA NA + [3,] -0.000307757 NA NA + [4,] 0.005534346 NA NA + [5,] NA -0.157499927 -0.16143428 + [6,] NA 0.268178091 0.04006008 + [7,] NA 0.003700936 0.05790992 + [8,] NA -0.082349159 0.15116204 + [9,] NA -0.246205139 -0.04458188 +[10,] NA 0.214175196 -0.04311589 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiT_res/KEIO_ROBOT3_25_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiT_res/KEIO_ROBOT3_25_res.txt new file mode 100644 index 0000000..454bd7a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiT_res/KEIO_ROBOT3_25_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0252186267308202 0.0252729660967095 0.0250333479818215 0.00259214023397812 0.0208845419194634 0.0300139454480185 +Glc 14.4833335122822 14.4754090131225 14.4931108076928 0.234424599674361 14.0880735040255 14.9282722128621 +Ace 0.182825951068403 0.195464546359756 0.188429408393167 0.120131119370691 9.99999999998398e-07 0.426190704040441 +mu 0.669464759335296 0.670175095141353 0.669828820368168 0.0219347510325162 0.630589095681991 0.711310738398983 +qGlc -5.37297298910308 -5.37156046218389 -5.3540303520757 0.411277950164599 -6.1608944777346 -4.59051928596695 +qAce 2.06282212085986 2.05031632204741 2.03172333738313 0.197878579204181 1.65105300308383 2.38676102147058 +res 2.7688956786614 23.9900244904534 23.0954816956137 6.06737121611635 12.6244875110069 36.0381575306627 + + +Goodness of fit (khi2 test) + +khi2 value 2.76889567869755 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.276889567869755 +p-value, i.e. P(X^2<=value) 0.0136482522624836 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiU.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiU.txt new file mode 100644 index 0000000..5c3122a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiU.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.03024 NA NA +1.18888888888889 0.054432 NA NA +2.27694444444444 0.092232 NA NA +3.12833333333333 0.133056 NA NA +3.77138888888889 0.175392 NA NA +4.41555555555556 0.261576 NA NA +4.82277777777778 0.379512 NA NA +0.0666666666666667 NA 16.1477460715663 0.0136413681684281 +1.71666666666667 NA 15.1845013815184 0.336393964993759 +2.8 NA 13.507280302755 0.739541940112951 +3.63333333333333 NA 12.9557238684356 1.1625930503366 +4.26666666666667 NA 11.9383082728535 1.70115941132939 +4.88333333333333 NA 10.6108691138264 2.23910680957277 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiU_res/KEIO_ROBOT1_38.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybiU_res/KEIO_ROBOT1_38.pdf new file mode 100644 index 0000000..6fdb70f Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybiU_res/KEIO_ROBOT1_38.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiU_res/KEIO_ROBOT1_38_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiU_res/KEIO_ROBOT1_38_log.txt new file mode 100644 index 0000000..9ee5e83 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiU_res/KEIO_ROBOT1_38_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.030240 NA NA + [2,] 0.054432 NA NA + [3,] 0.092232 NA NA + [4,] 0.133056 NA NA + [5,] 0.175392 NA NA + [6,] 0.261576 NA NA + [7,] 0.379512 NA NA + [8,] NA 16.14775 0.01364137 + [9,] NA 15.18450 0.33639396 +[10,] NA 13.50728 0.73954194 +[11,] NA 12.95572 1.16259305 +[12,] NA 11.93831 1.70115941 +[13,] NA 10.61087 2.23910681 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02499554 15.65248374 0.08363944 0.54816931 -8.63196559 3.61970146 + +$result$lastp + X Glc Ace mu qGlc qAce + 3.782320e-09 1.350985e-07 -3.699641e-08 -3.656498e-08 -9.225707e-08 -3.630550e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.01002653 0.56560633 0.24537849 0.09142702 1.85832375 0.80136303 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.8471311 + +$result$laststep + X Glc Ace mu qGlc qAce + 3.782320e-09 1.350985e-07 -3.699641e-08 -3.656498e-08 -9.225707e-08 -3.630550e-08 + +$result$normp +[1] 1.755024e-07 + +$result$res + [1] -0.26222283 -0.32349780 -0.25750693 0.29080851 1.10854674 0.98265427 -1.39732019 -1.10850530 -0.31970030 1.54825995 0.44805405 0.05733180 -0.62544019 0.38070702 0.02578156 -0.27495570 -0.17265062 -0.35544129 0.39655904 + +$result$prevres + [1] -0.26222302 -0.32349806 -0.25750723 0.29080825 1.10854660 0.98265441 -1.39731975 -1.10850559 -0.31970043 1.54825996 0.44805416 0.05733196 -0.62544006 0.38070720 0.02578161 -0.27495575 -0.17265072 -0.35544138 0.39655904 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 95.941195 0.000000 0 2.851076753 0.000000000 0.00000000 + [3,] 174.194789 0.000000 0 9.914027344 0.000000000 0.00000000 + [4,] 277.793892 0.000000 0 21.721921141 0.000000000 0.00000000 + [5,] 395.196372 0.000000 0 37.254332348 0.000000000 0.00000000 + [6,] 562.558544 0.000000 0 62.089133134 0.000000000 0.00000000 + [7,] 703.256680 0.000000 0 84.776139371 0.000000000 0.00000000 + [8,] -1.274149 2.173913 0 -0.001068067 0.003689548 0.00000000 + [9,] -53.491667 2.173913 0 -1.325027931 0.154895555 0.00000000 +[10,] -124.631255 2.173913 0 -5.435508700 0.360894106 0.00000000 +[11,] -216.617328 2.173913 0 -12.904088156 0.627257720 0.00000000 +[12,] -320.735713 2.173913 0 -23.231534507 0.928752812 0.00000000 +[13,] -463.501557 2.173913 0 -39.619336864 1.342159159 0.00000000 +[14,] 1.228885 0.000000 5 0.001030124 0.000000000 0.00848596 +[15,] 51.591366 0.000000 5 1.277956087 0.000000000 0.35625978 +[16,] 120.203708 0.000000 5 5.242411320 0.000000000 0.83005644 +[17,] 208.921960 0.000000 5 12.445668210 0.000000000 1.44269276 +[18,] 309.341522 0.000000 5 22.406230257 0.000000000 2.13613147 +[19,] 447.035585 0.000000 5 38.211853122 0.000000000 3.08696607 + +$result$retres +$result$retres$res + [1] -0.26222302 -0.32349806 -0.25750723 0.29080825 1.10854660 0.98265441 -1.39731975 -1.10850559 -0.31970043 1.54825996 0.44805416 0.05733196 -0.62544006 0.38070720 0.02578161 -0.27495575 -0.17265072 -0.35544138 0.39655904 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02499554 15.65248 0.08363948 + [2,] 0.04796204 15.29083 0.23529311 + [3,] 0.08708186 14.67482 0.49361120 + [4,] 0.13887216 13.85928 0.83559578 + [5,] 0.19756293 12.93508 1.22314583 + [6,] 0.28122909 11.61760 1.77561472 + [7,] 0.35156561 10.51002 2.24006461 + [8,] 0.02592589 15.63783 0.08978281 + [9,] 0.06405368 15.03744 0.34155029 + [10,] 0.11599784 14.21948 0.68455079 + [11,] 0.18316353 13.16183 1.12806291 + [12,] 0.25918790 11.96468 1.63007113 + [13,] 0.36343157 10.32317 2.31841862 + + +$result$it +[1] 9 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.005244460 NA NA + [2,] 0.006469961 NA NA + [3,] 0.005150145 NA NA + [4,] -0.005816165 NA NA + [5,] -0.022170932 NA NA + [6,] -0.019653088 NA NA + [7,] 0.027946395 NA NA + [8,] NA 0.5099126 -0.076141440 + [9,] NA 0.1470622 -0.005156323 +[10,] NA -0.7121996 0.054991150 +[11,] NA -0.2061049 0.034530144 +[12,] NA -0.0263727 0.071088277 +[13,] NA 0.2877024 -0.079311808 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybiU_res/KEIO_ROBOT1_38_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybiU_res/KEIO_ROBOT1_38_res.txt new file mode 100644 index 0000000..ad6b32f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybiU_res/KEIO_ROBOT1_38_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0249955434508096 0.0250852575824536 0.0247321084641886 0.00422963600762194 0.0185800114296251 0.0341436038491705 +Glc 15.6524837384102 15.650019987203 15.6765305145185 0.197729196253275 15.2967588905369 15.9860272153359 +Ace 0.0836394421256246 0.104084211434569 0.0869517581257231 0.0766030261494348 1.00000000000048e-06 0.255140915717327 +mu 0.548169309615138 0.550024051444061 0.550447345567361 0.0378559728782927 0.477329978874255 0.616129577560846 +qGlc -8.63196559434993 -8.64180236370866 -8.6023059292231 0.683071785269401 -9.83978175690708 -7.33857755427374 +qAce 3.61970146203361 3.56009943024836 3.56406936384785 0.27768213946127 3.06641986560646 4.11073186365155 +res 9.32920496336539 31.427736178925 31.1967625919776 7.12741941813025 20.8155981763665 47.3426757454645 + + +Goodness of fit (khi2 test) + +khi2 value 9.32920496336613 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.717631151028164 +p-value, i.e. P(X^2<=value) 0.252349443191528 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjP_2.txt b/validation/validation_results/Berges_2021/Berges_2021/ybjP_2.txt new file mode 100644 index 0000000..7af3b2e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybjP_2.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 5.5944000000000001E-2 NA NA +2.2613888888888889 7.4088000000000001E-2 NA NA +2.7741666666666664 9.2231999999999995E-2 NA NA +3.2088888888888891 0.111888 NA NA +3.7063888888888892 0.15271200000000001 NA NA +4.2258333333333331 0.192024 NA NA +4.6355555555555554 0.26006399999999996 NA NA +4.9675000000000002 0.27820800000000001 NA NA +2.8 NA 12.6105444647865 0.627527432976143 +3.73333333333333 NA 11.9721799503859 1.22233058750634 +4.28333333333333 NA 11.077209101886 1.73035276754826 +4.75 NA 10.47525130666 2.38144539879694 +5.11666666666667 NA 9.67062965958776 2.97997870407792 +5.43333333333333 NA 8.97399527048699 3.63933447360756 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjP_2_res/KEIO_ROBOT5_17.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybjP_2_res/KEIO_ROBOT5_17.pdf new file mode 100644 index 0000000..709d75e Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybjP_2_res/KEIO_ROBOT5_17.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjP_2_res/KEIO_ROBOT5_17_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybjP_2_res/KEIO_ROBOT5_17_log.txt new file mode 100644 index 0000000..12c8537 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybjP_2_res/KEIO_ROBOT5_17_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.055944 NA NA + [2,] 0.074088 NA NA + [3,] 0.092232 NA NA + [4,] 0.111888 NA NA + [5,] 0.152712 NA NA + [6,] 0.192024 NA NA + [7,] 0.260064 NA NA + [8,] 0.278208 NA NA + [9,] NA 12.610544 0.6275274 +[10,] NA 11.972180 1.2223306 +[11,] NA 11.077209 1.7303528 +[12,] NA 10.475251 2.3814454 +[13,] NA 9.670630 2.9799787 +[14,] NA 8.973995 3.6393345 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0195870 13.5311003 0.0000010 0.5449931 -6.9735892 5.4089860 + +$result$lastp + X Glc Ace mu qGlc qAce +-5.051547e-10 -1.782514e-08 -2.775558e-17 5.139036e-09 -1.563646e-08 5.475102e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.004053915 0.405787295 0.199383732 0.046532670 0.912102770 0.426228011 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.392048 + +$result$laststep + X Glc Ace mu qGlc qAce +-5.051547e-10 -1.782514e-08 -2.775558e-17 5.139036e-09 -1.563646e-08 5.475102e-08 + +$result$normp +[1] 5.9888e-08 + +$result$res + [1] -0.14373601 -0.34562780 -0.16990586 0.03473900 -0.25326052 0.19685850 -0.75376200 0.76815384 0.03994406 -0.23401408 0.25485386 -0.06539495 0.07935997 -0.07474885 0.36120277 0.35162113 0.41025528 0.06061508 -0.06981112 -0.38998144 + +$result$prevres + [1] -0.14373596 -0.34562775 -0.16990581 0.03473905 -0.25326047 0.19685854 -0.75376198 0.76815385 0.03994407 -0.23401408 0.25485385 -0.06539496 0.07935997 -0.07474885 0.36120280 0.35162115 0.41025529 0.06061506 -0.06981117 -0.38998152 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 135.4706 0.000000 0 4.852891 0.0000000 0.000000 + [2,] 171.4796 0.000000 0 7.595490 0.0000000 0.000000 + [3,] 226.7674 0.000000 0 12.322000 0.0000000 0.000000 + [4,] 287.3915 0.000000 0 18.063282 0.0000000 0.000000 + [5,] 376.8999 0.000000 0 27.361821 0.0000000 0.000000 + [6,] 500.2326 0.000000 0 41.404962 0.0000000 0.000000 + [7,] 625.3860 0.000000 0 56.782950 0.0000000 0.000000 + [8,] 749.4027 0.000000 0 72.915716 0.0000000 0.000000 + [9,] -100.1309 2.173913 0 -3.418420 0.2812417 0.000000 +[10,] -184.9681 2.173913 0 -8.912122 0.5195275 0.000000 +[11,] -259.3399 2.173913 0 -14.771128 0.7284186 0.000000 +[12,] -342.4998 2.173913 0 -22.144206 0.9619931 0.000000 +[13,] -424.4124 2.173913 0 -30.069147 1.1920644 0.000000 +[14,] -509.5980 2.173913 0 -38.878246 1.4313288 0.000000 +[15,] 178.6304 0.000000 5 6.098355 0.0000000 0.646856 +[16,] 329.9774 0.000000 5 15.898951 0.0000000 1.194913 +[17,] 462.6544 0.000000 5 26.351236 0.0000000 1.675363 +[18,] 611.0090 0.000000 5 39.504579 0.0000000 2.212584 +[19,] 757.1386 0.000000 5 53.642430 0.0000000 2.741748 +[20,] 909.1071 0.000000 5 69.357589 0.0000000 3.292056 + +$result$retres +$result$retres$res + [1] -0.14373596 -0.34562775 -0.16990581 0.03473905 -0.25326047 0.19685854 -0.75376198 0.76815385 0.03994407 -0.23401408 0.25485385 -0.06539496 0.07935997 -0.07474885 0.36120280 0.35162115 0.41025529 0.06061506 -0.06981117 -0.38998152 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05306928 13.102670 0.3323082 + [2,] 0.06717544 12.922171 0.4723101 + [3,] 0.08883388 12.645035 0.6872673 + [4,] 0.11258278 12.341151 0.9229720 + [5,] 0.14764679 11.892481 1.2709777 + [6,] 0.19596117 11.274263 1.7504916 + [7,] 0.24498876 10.646919 2.2370841 + [8,] 0.29357108 10.025272 2.7192572 + [9,] 0.09009342 12.628919 0.6997680 + [10,] 0.14983091 11.864533 1.2926548 + [11,] 0.20219926 11.194442 1.8124038 + [12,] 0.26075565 10.445170 2.3935684 + [13,] 0.31843380 9.707135 2.9660165 + [14,] 0.37841662 8.939611 3.5613382 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.002874719 NA NA + [2,] 0.006912555 NA NA + [3,] 0.003398116 NA NA + [4,] -0.000694781 NA NA + [5,] 0.005065209 NA NA + [6,] -0.003937171 NA NA + [7,] 0.015075240 NA NA + [8,] -0.015363077 NA NA + [9,] NA -0.01837427 -0.07224056 +[10,] NA 0.10764648 -0.07032423 +[11,] NA -0.11723277 -0.08205106 +[12,] NA 0.03008168 -0.01212301 +[13,] NA -0.03650559 0.01396223 +[14,] NA 0.03438447 0.07799630 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjP_2_res/KEIO_ROBOT5_17_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybjP_2_res/KEIO_ROBOT5_17_res.txt new file mode 100644 index 0000000..6379cef --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybjP_2_res/KEIO_ROBOT5_17_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0195870045384002 0.0191073480362612 0.0189055726284183 0.00270482905006267 0.014263992000395 0.0251827154582824 +Glc 13.5311003021063 13.5281371748329 13.4865083927178 0.26705544170974 13.0547977932124 14.0160764359967 +Ace 9.99999999994061e-07 0.0459000821856204 1.00000000001488e-06 0.0676867350072682 9.99999999910794e-07 0.197550438062319 +mu 0.544993148930527 0.551921101201135 0.552886768780196 0.0286995246318528 0.494755729490993 0.609930699927248 +qGlc -6.97358919879183 -7.08208459189972 -7.14000551721944 0.64544765156824 -8.25225159818897 -5.90107850943997 +qAce 5.40898601749857 5.36234007525952 5.42798294740974 0.317416477658447 4.70183357280515 5.88311066147866 +res 2.15182312541161 37.5147139009868 37.5277160738871 8.37301946213707 22.5844335963256 54.6586143540494 + + +Goodness of fit (khi2 test) + +khi2 value 2.15182312541164 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.153701651815117 +p-value, i.e. P(X^2<=value) 0.000130129932124814 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjS.txt b/validation/validation_results/Berges_2021/Berges_2021/ybjS.txt new file mode 100644 index 0000000..023a1e8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybjS.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.066528 NA NA +1.61361111111111 0.081648 NA NA +2.36138888888889 0.133056 NA NA +3.28638888888889 0.223776 NA NA +3.81944444444444 0.322056 NA NA +4.41083333333333 0.482328 NA NA +0.283333333333333 NA 14.1330041645542 0.0397151678221417 +1.91666666666667 NA 13.8886984498606 0.454876374532712 +2.7 NA 13.0176283146058 0.740965085114364 +3.61666666666667 NA 12.418732714215 1.3774427694778 +4.05 NA 11.4206095572602 1.67369630262202 +4.75 NA 9.76792840981849 2.38632487049567 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjS_res/KEIO_ROBOT4_30.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybjS_res/KEIO_ROBOT4_30.pdf new file mode 100644 index 0000000..48dd3e8 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybjS_res/KEIO_ROBOT4_30.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjS_res/KEIO_ROBOT4_30_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybjS_res/KEIO_ROBOT4_30_log.txt new file mode 100644 index 0000000..d36e730 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybjS_res/KEIO_ROBOT4_30_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.066528 NA NA + [3,] 0.081648 NA NA + [4,] 0.133056 NA NA + [5,] 0.223776 NA NA + [6,] 0.322056 NA NA + [7,] 0.482328 NA NA + [8,] NA 14.133004 0.03971517 + [9,] NA 13.888698 0.45487637 +[10,] NA 13.017628 0.74096509 +[11,] NA 12.418733 1.37744277 +[12,] NA 11.420610 1.67369630 +[13,] NA 9.767928 2.38632487 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02972867 14.27409799 0.15047455 0.62814888 -5.03331755 2.64076655 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.925523e-09 -1.066453e-08 3.943959e-08 1.698610e-08 -5.887695e-08 -6.204817e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.004925927 0.290344320 0.127238590 0.041366832 0.632391759 0.279752941 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4437522 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.925523e-09 -1.066453e-08 3.943959e-08 1.698610e-08 -5.887695e-08 -6.204817e-08 + +$result$normp +[1] 9.632196e-08 + +$result$res + [1] -0.25236659 -0.17761243 0.01342262 -0.10136993 0.52445462 0.26898335 -0.37929120 0.20584931 -0.37047069 0.42590408 -0.47033706 0.12850597 0.08054839 0.67552564 -0.06394450 -0.17031647 -0.70012565 -0.28566144 0.54452243 + +$result$prevres + [1] -0.25236650 -0.17761229 0.01342277 -0.10136977 0.52445472 0.26898335 -0.37929144 0.20584932 -0.37047070 0.42590405 -0.47033709 0.12850596 0.08054846 0.67552546 -0.06394460 -0.17031651 -0.70012559 -0.28566134 0.54452258 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 105.917544 0.000000 0 3.76280131 0.00000000 0.00000000 + [3,] 137.773495 0.000000 0 6.60906513 0.00000000 0.00000000 + [4,] 220.374144 0.000000 0 15.47047455 0.00000000 0.00000000 + [5,] 394.005339 0.000000 0 38.49431017 0.00000000 0.00000000 + [6,] 550.706887 0.000000 0 62.53111697 0.00000000 0.00000000 + [7,] 798.458475 0.000000 0 104.70042968 0.00000000 0.00000000 + [8,] -3.393236 2.173913 0 -0.01471450 0.02004173 0.00000000 + [9,] -40.644126 2.173913 0 -1.38487658 0.24005953 0.00000000 +[10,] -77.553142 2.173913 0 -3.95281150 0.45805809 0.00000000 +[11,] -151.494832 2.173913 0 -10.99157936 0.89478557 0.00000000 +[12,] -204.339103 2.173913 0 -17.02913012 1.20690376 0.00000000 +[13,] -326.804810 2.173913 0 -33.14148093 1.93023238 0.00000000 +[14,] 4.094658 0.000000 5 0.01775616 0.00000000 0.04609598 +[15,] 49.045743 0.000000 5 1.67114679 0.00000000 0.55213691 +[16,] 93.584286 0.000000 5 4.76990396 0.00000000 1.05353360 +[17,] 182.810589 0.000000 5 13.26366762 0.00000000 2.05800682 +[18,] 246.578391 0.000000 5 20.54925087 0.00000000 2.77587864 +[19,] 394.359194 0.000000 5 39.99221342 0.00000000 4.43953447 + +$result$retres +$result$retres$res + [1] -0.25236650 -0.17761229 0.01342277 -0.10136977 0.52445472 0.26898335 -0.37929144 0.20584932 -0.37047070 0.42590405 -0.47033709 0.12850596 0.08054846 0.67552546 -0.06394460 -0.17031651 -0.70012559 -0.28566134 0.54452258 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02972867 14.274098 0.1504745 + [2,] 0.06297575 14.007691 0.2902468 + [3,] 0.08191646 13.855921 0.3698744 + [4,] 0.13102860 13.462388 0.5763441 + [5,] 0.23426509 12.635160 1.0103550 + [6,] 0.32743567 11.888590 1.4020484 + [7,] 0.47474217 10.708233 2.0213317 + [8,] 0.03551970 14.227695 0.1748203 + [9,] 0.09909350 13.718282 0.4420875 + [10,] 0.16208386 13.213544 0.7069018 + [11,] 0.28827560 12.202378 1.2374177 + [12,] 0.37846167 11.479722 1.6165640 + [13,] 0.58746638 9.804981 2.4952294 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0050473299 NA NA + [2,] 0.0035522459 NA NA + [3,] -0.0002684554 NA NA + [4,] 0.0020273954 NA NA + [5,] -0.0104890944 NA NA + [6,] -0.0053796670 NA NA + [7,] 0.0075858288 NA NA + [8,] NA -0.09469069 -0.13510509 + [9,] NA 0.17041652 0.01278892 +[10,] NA -0.19591586 0.03406330 +[11,] NA 0.21635506 0.14002512 +[12,] NA -0.05911274 0.05713227 +[13,] NA -0.03705229 -0.10890452 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjS_res/KEIO_ROBOT4_30_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybjS_res/KEIO_ROBOT4_30_res.txt new file mode 100644 index 0000000..759a30a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybjS_res/KEIO_ROBOT4_30_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0297286681320115 0.0297225472342946 0.0299764886359806 0.00381007411213421 0.0233787513961142 0.0371327148774777 +Glc 14.2740979867044 14.3034003121008 14.3061916303571 0.193192850794312 13.8895448076864 14.658397589187 +Ace 0.150474551820207 0.162646776368853 0.167134209191703 0.0755007584146333 0.0262947766304424 0.301589394528885 +mu 0.628148883169576 0.630318090686855 0.628783334052494 0.0306593659953304 0.570801093849164 0.68534855903271 +qGlc -5.0333175468257 -5.06938050742061 -5.11535137846568 0.493591274490723 -5.86097317721038 -4.09336765624692 +qAce 2.64076654534923 2.64187133256783 2.65528108801945 0.217026295704766 2.23964269301945 3.03361091068794 +res 2.55990768857741 32.4564757409941 32.5036646466378 7.27634043938822 20.3820259014517 49.0879739670533 + + +Goodness of fit (khi2 test) + +khi2 value 2.55990768857767 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.196915976044436 +p-value, i.e. P(X^2<=value) 0.000887240993195517 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjX.txt b/validation/validation_results/Berges_2021/Berges_2021/ybjX.txt new file mode 100644 index 0000000..f890625 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybjX.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.123984 NA NA NA +3.34194444444444 0.179928 NA NA NA +3.9975 0.250992 NA NA NA +4.52333333333333 0.374976 NA NA NA +1.95 NA 13.9070915991529 0.442018719073139 0 +3.25 NA 13.0804249700635 1.13739169478258 0 +4.08333333333333 NA 11.8982448189565 1.83066557934566 0 +4.76666666666667 NA 10.1970080735335 2.61340578205637 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjX_res/KEIO_ROBOT2_5.pdf b/validation/validation_results/Berges_2021/Berges_2021/ybjX_res/KEIO_ROBOT2_5.pdf new file mode 100644 index 0000000..0f4e705 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ybjX_res/KEIO_ROBOT2_5.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjX_res/KEIO_ROBOT2_5_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ybjX_res/KEIO_ROBOT2_5_log.txt new file mode 100644 index 0000000..d895e56 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybjX_res/KEIO_ROBOT2_5_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.123984 NA NA NA +[2,] 0.179928 NA NA NA +[3,] 0.250992 NA NA NA +[4,] 0.374976 NA NA NA +[5,] NA 13.90709 0.4420187 0 +[6,] NA 13.08042 1.1373917 0 +[7,] NA 11.89824 1.8306656 0 +[8,] NA 10.19701 2.6134058 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.588741e-02 1.461432e+01 1.503265e-01 1.000000e-06 5.848077e-01 -6.426926e+00 3.717311e+00 -2.027985e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 3.182076e-09 3.186679e-08 -5.659424e-08 2.117582e-22 -3.002131e-08 1.557543e-07 1.456108e-08 -2.114244e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.00827909 0.52334230 0.23632019 0.21560009 0.07699061 1.21565530 0.54351608 0.50843912 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4771739 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 3.182076e-09 3.186679e-08 -5.659424e-08 2.117582e-22 -3.002131e-08 1.557543e-07 1.456108e-08 -2.114244e-13 + +$result$normp +[1] 1.720501e-07 + +$result$res + [1] -6.098889e-01 1.413973e-01 8.576187e-01 -5.144964e-01 2.213713e-01 -1.846122e-01 -2.130047e-01 1.762456e-01 2.923291e-01 -2.537464e-01 -2.635016e-01 2.249189e-01 4.044854e-06 2.445957e-06 5.601951e-07 -1.841390e-06 + +$result$prevres + [1] -6.098892e-01 1.413971e-01 8.576187e-01 -5.144962e-01 2.213713e-01 -1.846122e-01 -2.130047e-01 1.762455e-01 2.923292e-01 -2.537464e-01 -2.635016e-01 2.249189e-01 4.044854e-06 2.445957e-06 5.601957e-07 -1.841389e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.159084e+02 0.000000 0 0 1.398104e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.529823e+02 0.000000 0 0 3.053801e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.179049e+02 0.000000 0 0 5.359536e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.043695e+02 0.000000 0 0 8.247983e+01 0.0000000 0.0000000 0.0000000 + [5,] -5.083842e+01 2.173913 0 0 -1.521929e+00 0.2047752 0.0000000 0.0000000 + [6,] -1.359410e+02 2.173913 0 0 -7.429672e+00 0.5475650 0.0000000 0.0000000 + [7,] -2.363121e+02 2.173913 0 0 -1.704454e+01 0.9518561 0.0000000 0.0000000 + [8,] -3.641384e+02 2.173913 0 0 -3.176237e+01 1.4667353 0.0000000 0.0000000 + [9,] 6.763094e+01 0.000000 5 0 2.024640e+00 0.0000000 0.4709829 0.0000000 +[10,] 1.808438e+02 0.000000 5 0 9.883779e+00 0.0000000 1.2593995 0.0000000 +[11,] 3.143688e+02 0.000000 5 0 2.267455e+01 0.0000000 2.1892690 0.0000000 +[12,] 4.844175e+02 0.000000 5 0 4.225385e+01 0.0000000 3.3734911 0.0000000 +[13,] -3.689616e-05 0.000000 0 5 -1.104545e-06 0.0000000 0.0000000 0.4709829 +[14,] -9.865965e-05 0.000000 0 5 -5.392111e-06 0.0000000 0.0000000 1.2593995 +[15,] -1.715044e-04 0.000000 0 5 -1.237014e-05 0.0000000 0.0000000 2.1892690 +[16,] -2.642747e-04 0.000000 0 5 -2.305165e-05 0.0000000 0.0000000 3.3734911 + +$result$retres +$result$retres$res + [1] -6.098892e-01 1.413971e-01 8.576187e-01 -5.144962e-01 2.213713e-01 -1.846122e-01 -2.130047e-01 1.762455e-01 2.923292e-01 -2.537464e-01 -2.635016e-01 2.249189e-01 4.044854e-06 2.445957e-06 5.601957e-07 -1.841389e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.1117862 13.67031 0.6963395 7.021218e-07 + [2,] 0.1827559 12.89036 1.1474562 4.560143e-07 + [3,] 0.2681444 11.95196 1.6902250 1.599060e-07 + [4,] 0.3646861 10.89098 2.3038891 -1.748795e-07 + [5,] 0.0809743 14.00892 0.5004846 8.089708e-07 + [6,] 0.1731887 12.99550 1.0866424 4.891914e-07 + [7,] 0.2819477 11.80026 1.7779653 1.120391e-07 + [8,] 0.4204561 10.27808 2.6583896 -3.682777e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.012197783 NA NA NA +[2,] -0.002827943 NA NA NA +[3,] -0.017152374 NA NA NA +[4,] 0.010289923 NA NA NA +[5,] NA -0.10183080 -0.05846584 -8.089708e-07 +[6,] NA 0.08492159 0.05074929 -4.891914e-07 +[7,] NA 0.09798214 0.05270033 -1.120391e-07 +[8,] NA -0.08107293 -0.04498377 3.682777e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ybjX_res/KEIO_ROBOT2_5_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ybjX_res/KEIO_ROBOT2_5_res.txt new file mode 100644 index 0000000..c5cebb5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ybjX_res/KEIO_ROBOT2_5_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0258874149800371 0.0259577428370608 0.0251953586335254 0.00483835297513963 0.0183952432730065 0.036710601533177 +Glc 14.614316963906 14.6364538698232 14.6489989950072 0.394950085526943 13.9215891841613 15.2860031561847 +Ace 0.150326523045557 0.190075832707798 0.176812099078662 0.138055698906867 9.99999999965959e-07 0.467353705264397 +Lac 1e-06 0.0986609493233759 0.0841281703522097 0.0861791674019562 9.99999999986122e-07 0.301138225216244 +mu 0.584807656050613 0.589049960228493 0.591704767329552 0.0419126667904248 0.50156884211973 0.664961676400353 +qGlc -6.42692636349099 -6.46044566394544 -6.54648561576598 0.914570736578555 -8.21820329890997 -4.76807084489007 +qAce 3.71731077021325 3.65936682964538 3.65379647648914 0.400095805822658 2.84513983964392 4.31023037192675 +qLac -2.02798498649911e-06 -0.0521372282801786 -0.0295441700655251 0.201153195593723 -0.425467327503779 0.260488428526286 +res 1.82155967628701 20.5360076853126 20.0762273053048 6.10238393039788 10.1290302445481 33.0220398285868 + + +Goodness of fit (khi2 test) + +khi2 value 1.82155967628722 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.227694959535902 +p-value, i.e. P(X^2<=value) 0.0139979402353719 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycaC.txt b/validation/validation_results/Berges_2021/Berges_2021/ycaC.txt new file mode 100644 index 0000000..722ec9f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycaC.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.107352 NA NA NA +3.34194444444444 0.17388 NA NA NA +3.9975 0.235872 NA NA NA +4.52333333333333 0.337176 NA NA NA +1.95 NA 13.9037945322368 0.477895473576096 0 +3.25 NA 12.4933857308924 1.29622840515378 0 +4.08333333333333 NA 11.3588706257904 2.01280725020975 0 +4.76666666666667 NA 9.36842480939882 2.7169760460164 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycaC_res/KEIO_ROBOT2_19.pdf b/validation/validation_results/Berges_2021/Berges_2021/ycaC_res/KEIO_ROBOT2_19.pdf new file mode 100644 index 0000000..9dbc201 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ycaC_res/KEIO_ROBOT2_19.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycaC_res/KEIO_ROBOT2_19_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ycaC_res/KEIO_ROBOT2_19_log.txt new file mode 100644 index 0000000..a91d21a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycaC_res/KEIO_ROBOT2_19_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.107352 NA NA NA +[2,] 0.173880 NA NA NA +[3,] 0.235872 NA NA NA +[4,] 0.337176 NA NA NA +[5,] NA 13.903795 0.4778955 0 +[6,] NA 12.493386 1.2962284 0 +[7,] NA 11.358871 2.0128073 0 +[8,] NA 9.368425 2.7169760 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.714053e-02 1.465781e+01 1.902340e-01 1.000000e-06 5.521897e-01 -8.246722e+00 4.115895e+00 -2.153392e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 5.222700e-09 1.179355e-07 -1.703172e-07 -2.117582e-22 -4.912290e-08 1.204157e-07 2.593947e-07 -7.312080e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.008355001 0.510114351 0.227367245 0.203234030 0.074410480 1.236466483 0.547557226 0.504954053 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4396346 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 5.222700e-09 1.179355e-07 -1.703172e-07 -2.117582e-22 -4.912290e-08 1.204157e-07 2.593947e-07 -7.312080e-13 + +$result$normp +[1] 3.565707e-07 + +$result$res + [1] 3.314633e-02 -1.032740e-01 5.442806e-01 -3.641846e-01 -6.603064e-02 2.843623e-01 -3.474307e-01 1.290991e-01 5.191238e-01 -4.551254e-01 -4.816210e-01 4.176226e-01 3.975893e-06 2.344895e-06 4.842249e-07 -1.828317e-06 + +$result$prevres + [1] 3.314596e-02 -1.032743e-01 5.442806e-01 -3.641841e-01 -6.603069e-02 2.843623e-01 -3.474307e-01 1.290990e-01 5.191243e-01 -4.551254e-01 -4.816211e-01 4.176222e-01 3.975893e-06 2.344896e-06 4.842267e-07 -1.828315e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 1.989919e+02 0.000000 0 0 1.350937e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.165276e+02 0.000000 0 0 2.870973e+01 0.0000000 0.0000000 0.0000000 + [3,] 4.545925e+02 0.000000 0 0 4.932068e+01 0.0000000 0.0000000 0.0000000 + [4,] 6.077485e+02 0.000000 0 0 7.461065e+01 0.0000000 0.0000000 0.0000000 + [5,] -6.282860e+01 2.173913 0 0 -1.955328e+00 0.2067732 0.0000000 0.0000000 + [6,] -1.628898e+02 2.173913 0 0 -9.225582e+00 0.5360814 0.0000000 0.0000000 + [7,] -2.770412e+02 2.173913 0 0 -2.068405e+01 0.9117616 0.0000000 0.0000000 + [8,] -4.189149e+02 2.173913 0 0 -3.780517e+01 1.3786775 0.0000000 0.0000000 + [9,] 7.212206e+01 0.000000 5 0 2.244556e+00 0.0000000 0.4755784 0.0000000 +[10,] 1.869840e+02 0.000000 5 0 1.059021e+01 0.0000000 1.2329872 0.0000000 +[11,] 3.180205e+02 0.000000 5 0 2.374358e+01 0.0000000 2.0970516 0.0000000 +[12,] 4.808798e+02 0.000000 5 0 4.339722e+01 0.0000000 3.1709584 0.0000000 +[13,] -3.773348e-05 0.000000 0 5 -1.174327e-06 0.0000000 0.0000000 0.4755784 +[14,] -9.782802e-05 0.000000 0 5 -5.540682e-06 0.0000000 0.0000000 1.2329872 +[15,] -1.663849e-04 0.000000 0 5 -1.242239e-05 0.0000000 0.0000000 2.0970516 +[16,] -2.515911e-04 0.000000 0 5 -2.270495e-05 0.0000000 0.0000000 3.1709584 + +$result$retres +$result$retres$res + [1] 3.314596e-02 -1.032743e-01 5.442806e-01 -3.641841e-01 -6.603069e-02 2.843623e-01 -3.474307e-01 1.290990e-01 5.191243e-01 -4.551254e-01 -4.816211e-01 4.176222e-01 3.975893e-06 2.344896e-06 4.842267e-07 -1.828315e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10801492 13.44999 0.7930533 6.846116e-07 + [2,] 0.17181451 12.49717 1.2686007 4.358103e-07 + [3,] 0.24675761 11.37792 1.8272093 1.435524e-07 + [4,] 0.32989232 10.13634 2.4468763 -1.806506e-07 + [5,] 0.07966243 13.87342 0.5817203 7.951787e-07 + [6,] 0.16330910 12.62419 1.2052033 4.689792e-07 + [7,] 0.25873460 11.19905 1.9164830 9.684535e-08 + [8,] 0.37733465 9.42781 2.8005005 -3.656630e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] -0.0006629191 NA NA NA +[2,] 0.0020654851 NA NA NA +[3,] -0.0108856129 NA NA NA +[4,] 0.0072836824 NA NA NA +[5,] NA 0.03037412 -0.10382486 -7.951787e-07 +[6,] NA -0.13080668 0.09102507 -4.689792e-07 +[7,] NA 0.15981811 0.09632423 -9.684535e-08 +[8,] NA -0.05938555 -0.08352444 3.656630e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycaC_res/KEIO_ROBOT2_19_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ycaC_res/KEIO_ROBOT2_19_res.txt new file mode 100644 index 0000000..9fcebbc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycaC_res/KEIO_ROBOT2_19_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0271405338253949 0.0278342625825982 0.0270837218565457 0.00541090567293958 0.0200804160971204 0.0429570508061741 +Glc 14.6578131580985 14.7010834898062 14.698098452274 0.360874556942936 14.0133011800627 15.3986663048307 +Ace 0.190234004669811 0.191324680142557 0.160499943415334 0.144523598616047 9.99999999987122e-07 0.500136182571306 +Lac 1e-06 0.0822816201015648 0.0720093316425484 0.0814406670890302 9.9999999999653e-07 0.274782713229911 +mu 0.552189669346768 0.551789002025417 0.557596665964346 0.0438020439361778 0.446666191219396 0.625601941171451 +qGlc -8.24672231914933 -8.34815158244283 -8.36268481361555 1.00983519089542 -10.6182967826836 -6.51340767190618 +qAce 4.11589524017011 4.07970348679747 4.06221302677846 0.427340208348327 3.31020996252185 4.9867910777058 +qLac -2.1533922964001e-06 -0.00629278635532117 -0.0101095341454508 0.207932254831934 -0.43502304770229 0.363483911599023 +res 1.5462287110673 19.9519944024029 19.1273453049765 6.16507029184569 9.83832113564668 33.1616970346544 + + +Goodness of fit (khi2 test) + +khi2 value 1.54622871106816 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.193278588883521 +p-value, i.e. P(X^2<=value) 0.00808673532958881 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycbZ.txt b/validation/validation_results/Berges_2021/Berges_2021/ycbZ.txt new file mode 100644 index 0000000..81a031e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycbZ.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.10584 NA NA NA +3.34194444444444 0.167832 NA NA NA +3.9975 0.223776 NA NA NA +4.52333333333333 0.31752 NA NA NA +1.95 NA 13.9907576313227 0.254202682618522 0 +3.25 NA 13.5925632492612 0.674859963718235 0 +4.08333333333333 NA 12.8250522971963 1.0614865727115 0 +4.76666666666667 NA 12.378333762988 1.55136704938532 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycbZ_res/KEIO_ROBOT2_32.pdf b/validation/validation_results/Berges_2021/Berges_2021/ycbZ_res/KEIO_ROBOT2_32.pdf new file mode 100644 index 0000000..869e749 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ycbZ_res/KEIO_ROBOT2_32.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycbZ_res/KEIO_ROBOT2_32_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ycbZ_res/KEIO_ROBOT2_32_log.txt new file mode 100644 index 0000000..1114375 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycbZ_res/KEIO_ROBOT2_32_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.105840 NA NA NA +[2,] 0.167832 NA NA NA +[3,] 0.223776 NA NA NA +[4,] 0.317520 NA NA NA +[5,] NA 13.99076 0.2542027 0 +[6,] NA 13.59256 0.6748600 0 +[7,] NA 12.82505 1.0614866 0 +[8,] NA 12.37833 1.5513670 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.667811e-02 1.429116e+01 4.750761e-02 1.000000e-06 5.436999e-01 -3.268169e+00 2.502221e+00 -2.252053e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 9.931738e-10 2.013153e-08 -1.294462e-08 -4.235165e-22 -9.218119e-09 -2.196844e-08 9.449010e-09 -2.060034e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.00557205 0.29916789 0.13432697 0.12799858 0.05058189 0.77157625 0.34278816 0.33192703 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.2751964 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 9.931738e-10 2.013153e-08 -1.294462e-08 -4.235165e-22 -9.218119e-09 -2.196844e-08 9.449010e-09 -2.060034e-13 + +$result$normp +[1] 3.50813e-08 + +$result$res + [1] -9.482160e-02 -1.834641e-01 5.341838e-01 -2.732548e-01 -4.784568e-03 -1.732748e-01 3.256640e-01 -1.476046e-01 1.249317e-01 -1.572953e-01 -3.087693e-02 6.324054e-02 3.957409e-06 2.318416e-06 4.647752e-07 -1.824448e-06 + +$result$prevres + [1] -9.482168e-02 -1.834642e-01 5.341838e-01 -2.732547e-01 -4.784590e-03 -1.732748e-01 3.256640e-01 -1.476046e-01 1.249318e-01 -1.572953e-01 -3.087695e-02 6.324052e-02 3.957409e-06 2.318416e-06 4.647756e-07 -1.824447e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 1.948106e+02 0.000000 0 0 1.300016e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.076731e+02 0.000000 0 0 2.743113e+01 0.0000000 0.0000000 0.0000000 + [3,] 4.394234e+02 0.000000 0 0 4.686263e+01 0.0000000 0.0000000 0.0000000 + [4,] 5.848521e+02 0.000000 0 0 7.057642e+01 0.0000000 0.0000000 0.0000000 + [5,] -2.465797e+01 2.173913 0 0 -7.526481e-01 0.2012833 0.0000000 0.0000000 + [6,] -6.342122e+01 2.173913 0 0 -3.519919e+00 0.5177082 0.0000000 0.0000000 + [7,] -1.072610e+02 2.173913 0 0 -7.844992e+00 0.8755732 0.0000000 0.0000000 + [8,] -1.614027e+02 2.173913 0 0 -1.426693e+01 1.3175318 0.0000000 0.0000000 + [9,] 4.342164e+01 0.000000 5 0 1.325381e+00 0.0000000 0.4629516 0.0000000 +[10,] 1.116821e+02 0.000000 5 0 6.198429e+00 0.0000000 1.1907288 0.0000000 +[11,] 1.888822e+02 0.000000 5 0 1.381470e+01 0.0000000 2.0138182 0.0000000 +[12,] 2.842233e+02 0.000000 5 0 2.512346e+01 0.0000000 3.0303232 0.0000000 +[13,] -3.908041e-05 0.000000 0 5 -1.192872e-06 0.0000000 0.0000000 0.4629516 +[14,] -1.005163e-04 0.000000 0 5 -5.578719e-06 0.0000000 0.0000000 1.1907288 +[15,] -1.699980e-04 0.000000 0 5 -1.243353e-05 0.0000000 0.0000000 2.0138182 +[16,] -2.558070e-04 0.000000 0 5 -2.261166e-05 0.0000000 0.0000000 3.0303232 + +$result$retres +$result$retres$res + [1] -9.482168e-02 -1.834642e-01 5.341838e-01 -2.732547e-01 -4.784590e-03 -1.732748e-01 3.256640e-01 -1.476046e-01 1.249318e-01 -1.572953e-01 -3.087695e-02 6.324052e-02 3.957409e-06 2.318416e-06 4.647756e-07 -1.824447e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10394357 13.82672 0.4030994 6.799597e-07 + [2,] 0.16416272 13.46474 0.6802406 4.305268e-07 + [3,] 0.23445968 13.04219 1.0037619 1.393506e-07 + [4,] 0.31205491 12.57576 1.3608714 -1.820556e-07 + [5,] 0.07701945 13.98856 0.2791890 7.914817e-07 + [6,] 0.15615794 13.51286 0.6434009 4.636832e-07 + [7,] 0.24566067 12.97486 1.0553112 9.295512e-08 + [8,] 0.35619540 12.31044 1.5640152 -3.648894e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.001896434 NA NA NA +[2,] 0.003669284 NA NA NA +[3,] -0.010683675 NA NA NA +[4,] 0.005465094 NA NA NA +[5,] NA 0.002200911 -0.024986351 -7.914817e-07 +[6,] NA 0.079706391 0.031459066 -4.636832e-07 +[7,] NA -0.149805430 0.006175389 -9.295512e-08 +[8,] NA 0.067898128 -0.012648105 3.648894e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycbZ_res/KEIO_ROBOT2_32_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ycbZ_res/KEIO_ROBOT2_32_res.txt new file mode 100644 index 0000000..50b3ff4 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycbZ_res/KEIO_ROBOT2_32_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0266781057647893 0.0266072211473764 0.0263504116511977 0.00490354826726784 0.0174363353516986 0.037581568819522 +Glc 14.2911575826544 14.3000148135912 14.3405703572974 0.371673629440451 13.5849245216418 14.9457309278833 +Ace 0.0475076057076054 0.0810763865607373 0.0562359559578715 0.0914051172192583 9.99999999848344e-07 0.312393752320048 +Lac 1e-06 0.0955058661252253 0.0725317645627876 0.0857719970709571 9.99999999986122e-07 0.301449094301954 +mu 0.543699910640933 0.548687200822724 0.546910803023039 0.0440346133002185 0.470863945392715 0.639054541419065 +qGlc -3.26816941965065 -3.29948431231668 -3.37107857305652 0.878503654268589 -4.74854511446642 -1.45181276034798 +qAce 2.50222076616563 2.42468677302036 2.45701295621418 0.315551972222548 1.8071693735466 3.0448409995353 +qLac -2.25205268280496e-06 -0.039639666546825 -0.000678484016712981 0.212328106160496 -0.39662855586131 0.368736943177937 +res 0.605864375178886 18.9408564377741 18.1670116563535 6.16290797681204 9.52903744614972 31.2184044665555 + + +Goodness of fit (khi2 test) + +khi2 value 0.605864375178901 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.0757330468973627 +p-value, i.e. P(X^2<=value) 0.000275715818533893 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yccJ.txt b/validation/validation_results/Berges_2021/Berges_2021/yccJ.txt new file mode 100644 index 0000000..882f82d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yccJ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.18888888888889 0.058968 NA NA +2.27694444444444 0.101304 NA NA +3.12833333333333 0.15876 NA NA +3.77138888888889 0.216216 NA NA +4.41555555555556 0.3402 NA NA +4.82277777777778 0.433944 NA NA +0.0666666666666667 NA 16.0343028553029 0 +1.71666666666667 NA 14.813258962501 0.378859374020614 +2.8 NA 13.5598976778992 0.879546003468164 +3.63333333333333 NA 12.6140416025677 1.43484606158601 +4.26666666666667 NA 11.4393679090908 2.04689957872656 +4.88333333333333 NA 9.82283071764603 2.82444865654303 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yccJ_res/KEIO_ROBOT1_27.pdf b/validation/validation_results/Berges_2021/Berges_2021/yccJ_res/KEIO_ROBOT1_27.pdf new file mode 100644 index 0000000..6c5d50a Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yccJ_res/KEIO_ROBOT1_27.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yccJ_res/KEIO_ROBOT1_27_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yccJ_res/KEIO_ROBOT1_27_log.txt new file mode 100644 index 0000000..cb95bc4 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yccJ_res/KEIO_ROBOT1_27_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.058968 NA NA + [3,] 0.101304 NA NA + [4,] 0.158760 NA NA + [5,] 0.216216 NA NA + [6,] 0.340200 NA NA + [7,] 0.433944 NA NA + [8,] NA 16.034303 0.0000000 + [9,] NA 14.813259 0.3788594 +[10,] NA 13.559898 0.8795460 +[11,] NA 12.614042 1.4348461 +[12,] NA 11.439368 2.0468996 +[13,] NA 9.822831 2.8244487 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02874555 15.56115282 0.07152583 0.55777465 -8.12083941 3.84174011 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.248239e-09 5.089022e-08 -1.557875e-08 -1.058849e-08 -5.357901e-08 -2.092866e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.006605258 0.379283054 0.165751040 0.052283699 1.040958185 0.461299332 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5723443 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.248239e-09 5.089022e-08 -1.557875e-08 -1.058849e-08 -5.357901e-08 -2.092866e-09 + +$result$normp +[1] 7.629729e-08 + +$result$res + [1] -0.15032274 -0.15884353 0.05284441 0.29092636 0.96840440 -0.13833694 -0.52320656 -1.06305551 0.16540643 0.92304270 0.41278687 0.04130532 -0.47948581 0.39513309 0.05239677 -0.31074460 -0.29476413 -0.17231060 0.33028947 + +$result$prevres + [1] -0.15032280 -0.15884362 0.05284431 0.29092628 0.96840436 -0.13833688 -0.52320640 -1.06305562 0.16540638 0.92304269 0.41278690 0.04130538 -0.47948574 0.39513317 0.05239679 -0.31074461 -0.29476416 -0.17231064 0.33028945 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.000000000 + [2,] 97.043089 0.000000 0 3.316472590 0.000000000 0.000000000 + [3,] 178.046529 0.000000 0 11.653502565 0.000000000 0.000000000 + [4,] 286.267892 0.000000 0 25.742824377 0.000000000 0.000000000 + [5,] 409.774968 0.000000 0 44.423960439 0.000000000 0.000000000 + [6,] 586.931427 0.000000 0 74.497765821 0.000000000 0.000000000 + [7,] 736.600902 0.000000 0 102.117465808 0.000000000 0.000000000 + [8,] -1.199089 2.173913 0 -0.001156070 0.004244447 0.000000000 + [9,] -50.806126 2.173913 0 -1.450609924 0.179839750 0.000000000 +[10,] -119.236284 2.173913 0 -5.999549493 0.422063742 0.000000000 +[11,] -208.518458 2.173913 0 -14.337555963 0.738098149 0.000000000 +[12,] -310.277534 2.173913 0 -25.946203156 1.098297367 0.000000000 +[13,] -450.647200 2.173913 0 -44.477520720 1.595167485 0.000000000 +[14,] 1.304687 0.000000 5 0.001257879 0.000000000 0.009762227 +[15,] 55.280375 0.000000 5 1.578358099 0.000000000 0.413631425 +[16,] 129.736845 0.000000 5 6.527900699 0.000000000 0.970746607 +[17,] 226.881667 0.000000 5 15.600194932 0.000000000 1.697625743 +[18,] 337.602171 0.000000 5 28.231159343 0.000000000 2.526083945 +[19,] 490.333512 0.000000 5 48.394440105 0.000000000 3.668885215 + +$result$retres +$result$retres$res + [1] -0.15032280 -0.15884362 0.05284431 0.29092628 0.96840436 -0.13833688 -0.52320640 -1.06305562 0.16540638 0.92304269 0.41278690 0.04130538 -0.47948574 0.39513317 0.05239679 -0.31074461 -0.29476416 -0.17231064 0.33028945 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02874554 15.561153 0.07152585 + [2,] 0.05579113 15.167387 0.25780556 + [3,] 0.10236089 14.489361 0.57856038 + [4,] 0.16457853 13.583512 1.00709186 + [5,] 0.23558409 12.549717 1.49615122 + [6,] 0.33743326 11.066859 2.19764968 + [7,] 0.42347987 9.814075 2.79030606 + [8,] 0.02983457 15.545297 0.07902663 + [9,] 0.07488817 14.889346 0.38933873 + [10,] 0.13703712 13.984497 0.81739708 + [11,] 0.21812407 12.803924 1.37589323 + [12,] 0.31054267 11.458368 2.01243745 + [13,] 0.43802778 9.602267 2.89050655 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.003006456 NA NA + [2,] 0.003176872 NA NA + [3,] -0.001056886 NA NA + [4,] -0.005818526 NA NA + [5,] -0.019368087 NA NA + [6,] 0.002766738 NA NA + [7,] 0.010464128 NA NA + [8,] NA 0.48900558 -0.07902663 + [9,] NA -0.07608693 -0.01047936 +[10,] NA -0.42459964 0.06214892 +[11,] NA -0.18988198 0.05895283 +[12,] NA -0.01900047 0.03446213 +[13,] NA 0.22056344 -0.06605789 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yccJ_res/KEIO_ROBOT1_27_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yccJ_res/KEIO_ROBOT1_27_res.txt new file mode 100644 index 0000000..9f1936f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yccJ_res/KEIO_ROBOT1_27_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0287455451849989 0.0282340671380678 0.0281304065943309 0.00359771381447259 0.0223050656611632 0.0354234607148045 +Glc 15.5611528187509 15.5772778096766 15.5954381813215 0.184372122609096 15.1727529842218 15.8988522033893 +Ace 0.0715258294952547 0.0981641485060682 0.0922485516692038 0.0775253831112043 9.99999999994885e-07 0.270658086763027 +mu 0.557774646985962 0.563689054932921 0.56290985016921 0.0293870732087105 0.509902107109065 0.620195696403594 +qGlc -8.12083941112367 -8.24299286137968 -8.2825437662066 0.532839674780389 -9.27611711328609 -7.16076817409569 +qAce 3.84174011379481 3.8246056235608 3.80953566320376 0.265010082809643 3.38320536009933 4.34400969441784 +res 4.25851380535437 31.2815588866184 31.1334753260968 7.50663935344418 18.9841277243852 47.8594565331822 + + +Goodness of fit (khi2 test) + +khi2 value 4.25851380535449 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.327577985027268 +p-value, i.e. P(X^2<=value) 0.0118822649993308 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yccU.txt b/validation/validation_results/Berges_2021/Berges_2021/yccU.txt new file mode 100644 index 0000000..76ac4ce --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yccU.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.195 0.065016 NA NA +1.61361111111111 0.084672 NA NA +2.36138888888889 0.116424 NA NA +3.28638888888889 0.214704 NA NA +3.81944444444444 0.328104 NA NA +4.41083333333333 0.412776 NA NA +0.283333333333333 NA 14.0992938992388 0.0452837541079639 +1.91666666666667 NA 13.4609951142845 0.408008995262568 +2.7 NA 12.8343155411592 0.689164023227013 +3.61666666666667 NA 12.0654733839531 1.13979048996528 +4.05 NA 11.6527105738767 1.53242613589798 +4.75 NA 10.2807339207277 2.17070311298599 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yccU_res/KEIO_ROBOT4_11.pdf b/validation/validation_results/Berges_2021/Berges_2021/yccU_res/KEIO_ROBOT4_11.pdf new file mode 100644 index 0000000..28d2688 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yccU_res/KEIO_ROBOT4_11.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yccU_res/KEIO_ROBOT4_11_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yccU_res/KEIO_ROBOT4_11_log.txt new file mode 100644 index 0000000..1eb5e1d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yccU_res/KEIO_ROBOT4_11_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.065016 NA NA + [3,] 0.084672 NA NA + [4,] 0.116424 NA NA + [5,] 0.214704 NA NA + [6,] 0.328104 NA NA + [7,] 0.412776 NA NA + [8,] NA 14.09929 0.04528375 + [9,] NA 13.46100 0.40800900 +[10,] NA 12.83432 0.68916402 +[11,] NA 12.06547 1.13979049 +[12,] NA 11.65271 1.53242614 +[13,] NA 10.28073 2.17070311 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03406862 13.99270004 0.08914485 0.57092001 -4.46725881 2.54623525 + +$result$lastp + X Glc Ace mu qGlc qAce +-6.952833e-10 2.642447e-09 -1.436603e-09 5.070457e-09 -3.747445e-08 2.117796e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006518372 0.342604303 0.150397224 0.048338189 0.771388219 0.342915540 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5126247 + +$result$laststep + X Glc Ace mu qGlc qAce +-6.952833e-10 2.642447e-09 -1.436603e-09 5.070457e-09 -3.747445e-08 2.117796e-08 + +$result$normp +[1] 4.345204e-08 + +$result$res + [1] -0.110969246 0.119135877 0.046118237 0.737605310 0.386625905 -1.327127187 0.495077157 -0.333475856 0.004400468 0.390538249 0.200298638 -0.184815748 -0.076945751 0.352694450 -0.084791350 -0.210807738 -0.023433815 -0.305420599 0.271759052 + +$result$prevres + [1] -0.110969211 0.119135925 0.046118289 0.737605365 0.386625946 -1.327127171 0.495077115 -0.333475863 0.004400455 0.390538236 0.200298633 -0.184815743 -0.076945717 0.352694459 -0.084791334 -0.210807721 -0.023433808 -0.305420604 0.271759007 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 98.916139 0.000000 0 4.02707343 0.00000000 0.00000000 + [3,] 125.620551 0.000000 0 6.90580098 0.00000000 0.00000000 + [4,] 192.517518 0.000000 0 15.48789011 0.00000000 0.00000000 + [5,] 326.453708 0.000000 0 36.55064521 0.00000000 0.00000000 + [6,] 442.579555 0.000000 0 57.58986150 0.00000000 0.00000000 + [7,] 620.332721 0.000000 0 93.21800964 0.00000000 0.00000000 + [8,] -2.986622 2.173913 0 -0.01480304 0.02277685 0.00000000 + [9,] -33.798843 2.173913 0 -1.30084981 0.25775982 0.00000000 +[10,] -62.453049 2.173913 0 -3.58267033 0.47628513 0.00000000 +[11,] -117.096760 2.173913 0 -9.53642231 0.89301398 0.00000000 +[12,] -154.739171 2.173913 0 -14.46382948 1.18008596 0.00000000 +[13,] -239.118528 2.173913 0 -27.17929495 1.82358750 0.00000000 +[14,] 3.915304 0.000000 5 0.01940601 0.00000000 0.05238675 +[15,] 44.308504 0.000000 5 1.70534560 0.00000000 0.59284758 +[16,] 81.872659 0.000000 5 4.69669217 0.00000000 1.09545580 +[17,] 153.507687 0.000000 5 12.50174753 0.00000000 2.05393215 +[18,] 202.854905 0.000000 5 18.96131889 0.00000000 2.71419771 +[19,] 313.471800 0.000000 5 35.63062461 0.00000000 4.19425126 + +$result$retres +$result$retres$res + [1] -0.110969211 0.119135925 0.046118289 0.737605365 0.386625946 -1.327127171 0.495077115 -0.333475863 0.004400455 0.390538236 0.200298633 -0.184815743 -0.076945717 0.352694459 -0.084791334 -0.210807721 -0.023433808 -0.305420604 0.271759007 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03406862 13.99270 0.08914485 + [2,] 0.06739872 13.73190 0.23779314 + [3,] 0.08559437 13.58953 0.31894356 + [4,] 0.13117611 13.23287 0.52223270 + [5,] 0.22243652 12.51878 0.92924327 + [6,] 0.30156146 11.89966 1.28213107 + [7,] 0.42267754 10.95196 1.82229439 + [8,] 0.04005034 13.94590 0.11582265 + [9,] 0.10176232 13.46302 0.39105073 + [10,] 0.15915214 13.01396 0.64700248 + [11,] 0.26859480 12.15761 1.13510373 + [12,] 0.34398657 11.56770 1.47134202 + [13,] 0.51298500 10.24534 2.22505491 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0022193842 NA NA + [2,] -0.0023827185 NA NA + [3,] -0.0009223658 NA NA + [4,] -0.0147521073 NA NA + [5,] -0.0077325189 NA NA + [6,] 0.0265425434 NA NA + [7,] -0.0099015423 NA NA + [8,] NA 0.153398897 -0.070538892 + [9,] NA -0.002024209 0.016958267 +[10,] NA -0.179647588 0.042161544 +[11,] NA -0.092137371 0.004686762 +[12,] NA 0.085015242 0.061084121 +[13,] NA 0.035395030 -0.054351801 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yccU_res/KEIO_ROBOT4_11_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yccU_res/KEIO_ROBOT4_11_res.txt new file mode 100644 index 0000000..5dc8a45 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yccU_res/KEIO_ROBOT4_11_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0340686150863086 0.0340293028815575 0.0334451713097875 0.00401319854244842 0.0271923188860039 0.0416827843968166 +Glc 13.9927000370448 14.0216845646353 14.0127669316499 0.203599396900989 13.6353686178765 14.3854414929166 +Ace 0.0891448475880089 0.109314620349973 0.101269459967833 0.0746417506429939 9.9999999999662e-07 0.267889384495465 +mu 0.570920006917912 0.571851325895166 0.571964185760522 0.0283846425295949 0.519079038678116 0.622217478363416 +qGlc -4.46725880703114 -4.52733341846999 -4.49762425987867 0.605562969567504 -5.5513689151292 -3.43652209207527 +qAce 2.54623525318828 2.5684580162014 2.57808993267656 0.221039737244655 2.20774355544146 3.04644653731681 +res 3.41619297403077 32.4636790511833 31.5334314854762 7.97967770159115 19.9160787095382 50.5923824353456 + + +Goodness of fit (khi2 test) + +khi2 value 3.41619297403078 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.262784074925445 +p-value, i.e. P(X^2<=value) 0.00403378135416319 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycdX.txt b/validation/validation_results/Berges_2021/Berges_2021/ycdX.txt new file mode 100644 index 0000000..9ef8663 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycdX.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.107352 NA NA NA +3.34194444444444 0.157248 NA NA NA +3.9975 0.246456 NA NA NA +4.52333333333333 0.374976 NA NA NA +1.95 NA 13.4356604206081 0.390106761389206 0 +3.25 NA 12.9629713247571 1.03641883995434 0 +4.08333333333333 NA 12.2656484863726 1.69330949843917 0 +4.76666666666667 NA 10.7746207723897 2.33446165882051 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycdX_res/KEIO_ROBOT2_7.pdf b/validation/validation_results/Berges_2021/Berges_2021/ycdX_res/KEIO_ROBOT2_7.pdf new file mode 100644 index 0000000..5748a1f Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ycdX_res/KEIO_ROBOT2_7.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycdX_res/KEIO_ROBOT2_7_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ycdX_res/KEIO_ROBOT2_7_log.txt new file mode 100644 index 0000000..d35b96e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycdX_res/KEIO_ROBOT2_7_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.107352 NA NA NA +[2,] 0.157248 NA NA NA +[3,] 0.246456 NA NA NA +[4,] 0.374976 NA NA NA +[5,] NA 13.43566 0.3901068 0 +[6,] NA 12.96297 1.0364188 0 +[7,] NA 12.26565 1.6933095 0 +[8,] NA 10.77462 2.3344617 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 1.747424e-02 1.391015e+01 2.426325e-01 1.000000e-06 6.729955e-01 -4.877853e+00 3.526647e+00 -2.227834e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 1.115376e-09 -3.907407e-08 -5.649324e-08 0.000000e+00 -1.580652e-08 2.058443e-07 1.178018e-07 -4.003326e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.007083896 0.544026390 0.247854010 0.229872529 0.096578290 1.430956572 0.645420257 0.608580357 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5385585 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 1.115376e-09 -3.907407e-08 -5.649324e-08 0.000000e+00 -1.580652e-08 2.058443e-07 1.178018e-07 -4.003326e-13 + +$result$normp +[1] 2.474237e-07 + +$result$res + [1] -6.635717e-01 4.198058e-01 5.523008e-01 -4.070710e-01 2.840031e-01 -1.189513e-01 -4.482670e-01 2.832152e-01 5.056135e-01 -3.471305e-01 -5.631785e-01 4.046956e-01 4.214789e-06 2.712056e-06 7.737000e-07 -1.862845e-06 + +$result$prevres + [1] -6.635718e-01 4.198057e-01 5.523007e-01 -4.070709e-01 2.840032e-01 -1.189513e-01 -4.482670e-01 2.832151e-01 5.056137e-01 -3.471305e-01 -5.631786e-01 4.046954e-01 4.214789e-06 2.712056e-06 7.737008e-07 -1.862844e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.691978e+02 0.000000 0 0 1.176660e+01 0.0000000 0.0000000 0.0000000 + [2,] 4.739665e+02 0.000000 0 0 2.767867e+01 0.0000000 0.0000000 0.0000000 + [3,] 7.368045e+02 0.000000 0 0 5.146822e+01 0.0000000 0.0000000 0.0000000 + [4,] 1.049644e+03 0.000000 0 0 8.296575e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.277661e+01 2.173913 0 0 -8.838120e-01 0.1532414 0.0000000 0.0000000 + [6,] -1.246422e+02 2.173913 0 0 -4.737103e+00 0.4465137 0.0000000 0.0000000 + [7,] -2.302396e+02 2.173913 0 0 -1.157446e+01 0.8248020 0.0000000 0.0000000 + [8,] -3.738729e+02 2.173913 0 0 -2.274618e+01 1.3393486 0.0000000 0.0000000 + [9,] 7.113238e+01 0.000000 5 0 1.469674e+00 0.0000000 0.3524551 0.0000000 +[10,] 2.072651e+02 0.000000 5 0 7.877236e+00 0.0000000 1.0269815 0.0000000 +[11,] 3.828610e+02 0.000000 5 0 1.924694e+01 0.0000000 1.8970446 0.0000000 +[12,] 6.217059e+02 0.000000 5 0 3.782418e+01 0.0000000 3.0805017 0.0000000 +[13,] -4.493535e-05 0.000000 0 5 -9.284140e-07 0.0000000 0.0000000 0.3524551 +[14,] -1.309323e-04 0.000000 0 5 -4.976163e-06 0.0000000 0.0000000 1.0269815 +[15,] -2.418588e-04 0.000000 0 5 -1.215857e-05 0.0000000 0.0000000 1.8970446 +[16,] -3.927406e-04 0.000000 0 5 -2.389408e-05 0.0000000 0.0000000 3.0805017 + +$result$retres +$result$retres$res + [1] -6.635718e-01 4.198057e-01 5.523007e-01 -4.070709e-01 2.840032e-01 -1.189513e-01 -4.482670e-01 2.832151e-01 5.056137e-01 -3.471305e-01 -5.631786e-01 4.046954e-01 4.214789e-06 2.712056e-06 7.737008e-07 -1.862844e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09408056 13.35491 0.6440668 7.464083e-07 + [2,] 0.16564411 12.83622 1.0190757 5.095097e-07 + [3,] 0.25750201 12.17043 1.5004316 2.054303e-07 + [4,] 0.36683458 11.37799 2.0733587 -1.564959e-07 + [5,] 0.06491438 13.56630 0.4912295 8.429578e-07 + [6,] 0.15570503 12.90825 0.9669927 5.424113e-07 + [7,] 0.27281475 12.05945 1.5806738 1.547402e-07 + [8,] 0.43210701 10.90490 2.4154007 -3.725688e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.013271436 NA NA NA +[2,] -0.008396114 NA NA NA +[3,] -0.011046015 NA NA NA +[4,] 0.008141417 NA NA NA +[5,] NA -0.13064147 -0.10112274 -8.429578e-07 +[6,] NA 0.05471759 0.06942610 -5.424113e-07 +[7,] NA 0.20620281 0.11263572 -1.547402e-07 +[8,] NA -0.13027894 -0.08093908 3.725688e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycdX_res/KEIO_ROBOT2_7_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ycdX_res/KEIO_ROBOT2_7_res.txt new file mode 100644 index 0000000..1db9e7e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycdX_res/KEIO_ROBOT2_7_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0174742444093979 0.0173515388606086 0.0172573804214824 0.00331745539569275 0.0115451322598542 0.0237545470615398 +Glc 13.9101467047199 13.9329724073874 13.9711348498987 0.288210251356479 13.2771683022363 14.4613206356685 +Ace 0.242632522021351 0.251374895295122 0.254303726398883 0.133323362063087 1.00000000002737e-06 0.489273919976977 +Lac 1e-06 0.087049962622814 0.0813361655524168 0.0721471050789434 9.99999999994709e-07 0.240596278137757 +mu 0.672995496354984 0.678707907260477 0.677530270135822 0.0457063329230098 0.597245423574118 0.762386206972658 +qGlc -4.87785302335237 -4.94732094502402 -4.99218620562316 0.861243807081074 -6.64109959094647 -3.23482605621603 +qAce 3.52664669947983 3.49096079860014 3.51562756200968 0.424860817425703 2.65621139681048 4.40423781848911 +qLac -2.22783365967648e-06 -0.0134538089335158 -0.0364028281961123 0.219463015706793 -0.40577045325202 0.458625503346194 +res 2.32036169756134 19.5155957090976 18.4702259503196 6.41311642358342 9.79215981912143 35.5197044773262 + + +Goodness of fit (khi2 test) + +khi2 value 2.32036169756149 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.290045212195186 +p-value, i.e. P(X^2<=value) 0.0304178767459805 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycdY.txt b/validation/validation_results/Berges_2021/Berges_2021/ycdY.txt new file mode 100644 index 0000000..4c67fd7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycdY.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.039312 NA NA +1.18888888888889 0.06804 NA NA +2.27694444444444 0.114912 NA NA +3.12833333333333 0.16632 NA NA +3.77138888888889 0.240408 NA NA +4.41555555555556 0.349272 NA NA +4.82277777777778 0.473256 NA NA +0.0666666666666667 NA 15.5278027855446 0.0103674127639184 +1.71666666666667 NA 14.8041665450283 0.350113897544456 +2.8 NA 13.3508981173071 0.707163297792848 +3.63333333333333 NA 12.4770145577351 1.08121603661172 +4.26666666666667 NA 11.50371343231 1.52900691357399 +4.88333333333333 NA 9.94368259596718 1.98050933180573 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycdY_res/KEIO_ROBOT1_35.pdf b/validation/validation_results/Berges_2021/Berges_2021/ycdY_res/KEIO_ROBOT1_35.pdf new file mode 100644 index 0000000..f6430f7 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ycdY_res/KEIO_ROBOT1_35.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycdY_res/KEIO_ROBOT1_35_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ycdY_res/KEIO_ROBOT1_35_log.txt new file mode 100644 index 0000000..7114773 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycdY_res/KEIO_ROBOT1_35_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.039312 NA NA + [2,] 0.068040 NA NA + [3,] 0.114912 NA NA + [4,] 0.166320 NA NA + [5,] 0.240408 NA NA + [6,] 0.349272 NA NA + [7,] 0.473256 NA NA + [8,] NA 15.527803 0.01036741 + [9,] NA 14.804167 0.35011390 +[10,] NA 13.350898 0.70716330 +[11,] NA 12.477015 1.08121604 +[12,] NA 11.503713 1.52900691 +[13,] NA 9.943683 1.98050933 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03104856 15.25310635 0.11829494 0.55640127 -6.96117160 2.47625710 + +$result$lastp + X Glc Ace mu qGlc qAce + 6.203618e-09 1.714447e-07 -5.965849e-08 -4.756878e-08 -5.440760e-08 1.536348e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.007504585 0.413573844 0.178490424 0.055061738 1.034794056 0.437109441 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6275274 + +$result$laststep + X Glc Ace mu qGlc qAce + 6.203618e-09 1.714447e-07 -5.965849e-08 -4.756878e-08 -5.440760e-08 1.536348e-08 + +$result$normp +[1] 1.960865e-07 + +$result$res + [1] -0.41317203 -0.39386757 -0.23477175 0.53410030 0.63679367 0.64959860 -0.94338510 -0.62907820 -0.37439474 0.96940586 0.50350606 -0.07419622 -0.39524276 0.56574697 -0.05428414 -0.35416896 -0.28894185 -0.32410634 0.45575432 + +$result$prevres + [1] -0.41317234 -0.39386800 -0.23477226 0.53409985 0.63679341 0.64959879 -0.94338443 -0.62907856 -0.37439490 0.96940589 0.50350620 -0.07419602 -0.39524261 0.56574727 -0.05428401 -0.35416898 -0.28894197 -0.32410650 0.45575420 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.000000000 0.00000000 + [2,] 96.8847720 0.000000 0 3.576335e+00 0.000000000 0.00000000 + [3,] 177.4906452 0.000000 0 1.254785e+01 0.000000000 0.00000000 + [4,] 285.0406518 0.000000 0 2.768606e+01 0.000000000 0.00000000 + [5,] 407.6580741 0.000000 0 4.773520e+01 0.000000000 0.00000000 + [6,] 583.3830215 0.000000 0 7.997984e+01 0.000000000 0.00000000 + [7,] 731.7383006 0.000000 0 1.095707e+02 0.000000000 0.00000000 + [8,] -1.0278101 2.173913 0 -1.070310e-03 0.004584288 0.00000000 + [9,] -43.4915793 2.173913 0 -1.340817e+00 0.193983240 0.00000000 +[10,] -101.9638177 2.173913 0 -5.538972e+00 0.454783940 0.00000000 +[11,] -178.1556626 2.173913 0 -1.322437e+01 0.794618483 0.00000000 +[12,] -264.9092777 2.173913 0 -2.391398e+01 1.181561144 0.00000000 +[13,] -384.4774245 2.173913 0 -4.096362e+01 1.714864762 0.00000000 +[14,] 0.8409189 0.000000 5 8.756908e-04 0.000000000 0.01054386 +[15,] 35.5833153 0.000000 5 1.097011e+00 0.000000000 0.44616145 +[16,] 83.4232911 0.000000 5 4.531796e+00 0.000000000 1.04600306 +[17,] 145.7608399 0.000000 5 1.081972e+01 0.000000000 1.82762251 +[18,] 216.7396660 0.000000 5 1.956560e+01 0.000000000 2.71759063 +[19,] 314.5662141 0.000000 5 3.351503e+01 0.000000000 3.94418895 + +$result$retres +$result$retres$res + [1] -0.41317234 -0.39386800 -0.23477226 0.53409985 0.63679341 0.64959879 -0.94338443 -0.62907856 -0.37439490 0.96940589 0.50350620 -0.07419602 -0.39524261 0.56574727 -0.05428401 -0.35416898 -0.28894197 -0.32410650 0.45575420 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03104855 15.253106 0.1182950 + [2,] 0.06016264 14.888858 0.2478669 + [3,] 0.11021655 14.262630 0.4706312 + [4,] 0.17700200 13.427074 0.7678590 + [5,] 0.25314387 12.474458 1.1067274 + [6,] 0.36226398 11.109249 1.5923651 + [7,] 0.45438831 9.956676 2.0023633 + [8,] 0.03222188 15.238427 0.1235169 + [9,] 0.08069752 14.631945 0.3392571 + [10,] 0.14744805 13.796825 0.6363295 + [11,] 0.23442687 12.708627 1.0234276 + [12,] 0.33346276 11.469583 1.4641856 + [13,] 0.46995894 9.761871 2.0716602 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.008263447 NA NA + [2,] 0.007877360 NA NA + [3,] 0.004695445 NA NA + [4,] -0.010681997 NA NA + [5,] -0.012735868 NA NA + [6,] -0.012991976 NA NA + [7,] 0.018867689 NA NA + [8,] NA 0.28937614 -0.11314945 + [9,] NA 0.17222165 0.01085680 +[10,] NA -0.44592671 0.07083380 +[11,] NA -0.23161285 0.05778839 +[12,] NA 0.03413017 0.06482130 +[13,] NA 0.18181160 -0.09115084 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycdY_res/KEIO_ROBOT1_35_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ycdY_res/KEIO_ROBOT1_35_res.txt new file mode 100644 index 0000000..c37ea8c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycdY_res/KEIO_ROBOT1_35_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0310485594214067 0.030844700018112 0.0312543759502453 0.00428419125426406 0.0231596984101115 0.040779860045681 +Glc 15.2531063453601 15.2619268488966 15.2435923772491 0.213789137501622 14.9024022938973 15.6538788907646 +Ace 0.118294943491968 0.138105069913098 0.135261870068553 0.0752639948462798 0.0126337019868936 0.279795760945192 +mu 0.55640127453897 0.560018629400111 0.556098710587587 0.0309429284436981 0.491494976751645 0.620384333070724 +qGlc -6.96117159524727 -7.01011532532184 -6.94834272575664 0.508972239429557 -8.05389996378737 -6.21588501849019 +qAce 2.47625710101387 2.43047933722297 2.41839241112846 0.21551717296274 2.10537620306206 2.86102196884186 +res 5.1192788390352 31.9311768655772 31.340112523904 8.14848004083245 19.3630266075087 51.7474026569408 + + +Goodness of fit (khi2 test) + +khi2 value 5.11927883903702 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.393790679925924 +p-value, i.e. P(X^2<=value) 0.0275273950642234 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yceB.txt b/validation/validation_results/Berges_2021/Berges_2021/yceB.txt new file mode 100644 index 0000000..54ed431 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yceB.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.18888888888889 0.065016 NA NA +2.27694444444444 0.099792 NA NA +3.12833333333333 0.154224 NA NA +3.77138888888889 0.205632 NA NA +4.41555555555556 0.311472 NA NA +4.82277777777778 0.367416 NA NA +0.0666666666666667 NA 15.559624228597 0.0215317327507714 +1.71666666666667 NA 14.71704580933 0.344988399768314 +2.8 NA 13.2770323566347 0.754812985353216 +3.63333333333333 NA 12.3574367897689 1.26887550643715 +4.26666666666667 NA 11.7294043923184 2.02108010043818 +4.88333333333333 NA 10.094382496042 2.82432936256191 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yceB_res/KEIO_ROBOT1_28.pdf b/validation/validation_results/Berges_2021/Berges_2021/yceB_res/KEIO_ROBOT1_28.pdf new file mode 100644 index 0000000..d9c5408 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yceB_res/KEIO_ROBOT1_28.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yceB_res/KEIO_ROBOT1_28_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yceB_res/KEIO_ROBOT1_28_log.txt new file mode 100644 index 0000000..6a5dc5a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yceB_res/KEIO_ROBOT1_28_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.065016 NA NA + [3,] 0.099792 NA NA + [4,] 0.154224 NA NA + [5,] 0.205632 NA NA + [6,] 0.311472 NA NA + [7,] 0.367416 NA NA + [8,] NA 15.55962 0.02153173 + [9,] NA 14.71705 0.34498840 +[10,] NA 13.27703 0.75481299 +[11,] NA 12.35744 1.26887551 +[12,] NA 11.72940 2.02108010 +[13,] NA 10.09438 2.82432936 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03248045 15.26447304 0.00000100 0.50384511 -7.66352584 4.04347183 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.106033e-09 4.349320e-08 6.938894e-18 -8.093767e-09 -5.251889e-08 -4.906722e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006847542 0.349302705 0.153618802 0.048459244 0.993876862 0.451762560 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5171749 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.106033e-09 4.349320e-08 6.938894e-18 -8.093767e-09 -5.251889e-08 -4.906722e-08 + +$result$normp +[1] 8.440508e-08 + +$result$res + [1] -0.19037771 -0.29454927 0.12517439 0.14341627 0.57856835 -0.54940291 0.07504176 -0.67832034 -0.28650019 0.99216034 0.69429277 -0.45864081 -0.26299177 -0.06313220 0.06692496 0.26503724 0.48220892 -0.22285492 -0.16313249 + +$result$prevres + [1] -0.19037776 -0.29454934 0.12517431 0.14341620 0.57856831 -0.54940288 0.07504185 -0.67832043 -0.28650024 0.99216033 0.69429280 -0.45864076 -0.26299171 -0.06313220 0.06692493 0.26503721 0.48220890 -0.22285491 -0.16313242 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.0000000 + [2,] 91.016323 0.000000 0 3.514653560 0.000000000 0.0000000 + [3,] 157.472422 0.000000 0 11.646056952 0.000000000 0.0000000 + [4,] 241.826006 0.000000 0 24.571857694 0.000000000 0.0000000 + [5,] 334.360210 0.000000 0 40.957918100 0.000000000 0.0000000 + [6,] 462.561312 0.000000 0 66.340177060 0.000000000 0.0000000 + [7,] 567.906074 0.000000 0 88.960196179 0.000000000 0.0000000 + [8,] -1.129520 2.173913 0 -0.001229756 0.004787262 0.0000000 + [9,] -45.459948 2.173913 0 -1.447841973 0.192673630 0.0000000 +[10,] -102.472821 2.173913 0 -5.720631952 0.434312205 0.0000000 +[11,] -173.191936 2.173913 0 -13.176056684 0.734042172 0.0000000 +[12,] -250.722321 2.173913 0 -23.165369938 1.062640450 0.0000000 +[13,] -354.130585 2.173913 0 -38.585176808 1.500917357 0.0000000 +[14,] 1.370716 0.000000 5 0.001492357 0.000000000 0.0110107 +[15,] 55.167408 0.000000 5 1.757012305 0.000000000 0.4431493 +[16,] 124.354736 0.000000 5 6.942208414 0.000000000 0.9989181 +[17,] 210.175122 0.000000 5 15.989655049 0.000000000 1.6882970 +[18,] 304.261247 0.000000 5 28.112073534 0.000000000 2.4440730 +[19,] 429.751179 0.000000 5 46.824606327 0.000000000 3.4521099 + +$result$retres +$result$retres$res + [1] -0.19037776 -0.29454934 0.12517431 0.14341620 0.57856831 -0.54940288 0.07504185 -0.67832043 -0.28650024 0.99216033 0.69429280 -0.45864076 -0.26299171 -0.06313220 0.06692493 0.26503721 0.48220890 -0.22285491 -0.16313242 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03248044 15.264473 0.000001000 + [2,] 0.05912501 14.859207 0.213829733 + [3,] 0.10229549 14.202580 0.560282617 + [4,] 0.15709232 13.369116 1.000039727 + [5,] 0.21720337 12.454822 1.482444538 + [6,] 0.30048394 11.188118 2.150790139 + [7,] 0.36891684 10.147248 2.699979713 + [8,] 0.03358998 15.247597 0.008905293 + [9,] 0.07713617 14.585256 0.358373386 + [10,] 0.13314044 13.733426 0.807820428 + [11,] 0.20260848 12.676811 1.365317286 + [12,] 0.27876730 11.518430 1.976509119 + [13,] 0.38034619 9.973406 2.791702879 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.003807555 NA NA + [2,] 0.005890987 NA NA + [3,] -0.002503486 NA NA + [4,] -0.002868324 NA NA + [5,] -0.011571366 NA NA + [6,] 0.010988058 NA NA + [7,] -0.001500837 NA NA + [8,] NA 0.3120274 0.01262644 + [9,] NA 0.1317901 -0.01338499 +[10,] NA -0.4563938 -0.05300744 +[11,] NA -0.3193747 -0.09644178 +[12,] NA 0.2109747 0.04457098 +[13,] NA 0.1209762 0.03262648 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yceB_res/KEIO_ROBOT1_28_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yceB_res/KEIO_ROBOT1_28_res.txt new file mode 100644 index 0000000..63749cf --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yceB_res/KEIO_ROBOT1_28_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0324804458207697 0.0319349277918067 0.0319608790058939 0.00441261324476232 0.0235067416137232 0.0396313508015786 +Glc 15.2644730352908 15.2313711551332 15.2225370993227 0.219584599330961 14.8681926594335 15.6522716727096 +Ace 1.000000000001e-06 0.0478114272232141 0.0305440834352988 0.0514279993304951 9.99999999987122e-07 0.153335154814223 +mu 0.503845109723636 0.509612474257774 0.506500632108341 0.0324771793010818 0.456015957024759 0.576854391812678 +qGlc -7.66352584355849 -7.73068968398683 -7.73562551359114 0.620427499882684 -8.7008011123492 -6.51334680829923 +qAce 4.04347183315101 3.95551075550335 3.91058386443284 0.246108364588054 3.55382631295792 4.43140160875637 +res 3.47710877476784 30.9473400080143 30.0660840920896 8.37829492949244 16.355452854229 48.6266260871744 + + +Goodness of fit (khi2 test) + +khi2 value 3.4771087747679 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.267469905751377 +p-value, i.e. P(X^2<=value) 0.00441058877723694 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yceD.txt b/validation/validation_results/Berges_2021/Berges_2021/yceD.txt new file mode 100644 index 0000000..6021b67 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yceD.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.18888888888889 0.063504 NA NA +2.27694444444444 0.10584 NA NA +3.12833333333333 0.160272 NA NA +3.77138888888889 0.208656 NA NA +4.41555555555556 0.303912 NA NA +4.82277777777778 0.403704 NA NA +0.0666666666666667 NA 14.5879870804845 0.0122345489871367 +1.71666666666667 NA 15.049885457895 0.339761539062991 +2.8 NA 13.3116690533774 0.663342501189371 +3.63333333333333 NA 12.8636685983638 1.06566686361899 +4.26666666666667 NA 11.8251049423497 1.441464688624 +4.88333333333333 NA 10.4176248556825 1.88067071716377 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yceD_res/KEIO_ROBOT1_39.pdf b/validation/validation_results/Berges_2021/Berges_2021/yceD_res/KEIO_ROBOT1_39.pdf new file mode 100644 index 0000000..d44608c Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yceD_res/KEIO_ROBOT1_39.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yceD_res/KEIO_ROBOT1_39_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yceD_res/KEIO_ROBOT1_39_log.txt new file mode 100644 index 0000000..d9b57b2 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yceD_res/KEIO_ROBOT1_39_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.063504 NA NA + [3,] 0.105840 NA NA + [4,] 0.160272 NA NA + [5,] 0.208656 NA NA + [6,] 0.303912 NA NA + [7,] 0.403704 NA NA + [8,] NA 14.58799 0.01223455 + [9,] NA 15.04989 0.33976154 +[10,] NA 13.31167 0.66334250 +[11,] NA 12.86367 1.06566686 +[12,] NA 11.82510 1.44146469 +[13,] NA 10.41762 1.88067072 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03026723 14.94141371 0.10368565 0.53003438 -6.40470858 2.64144687 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.737847e-09 1.015071e-08 -1.879019e-08 -1.351185e-08 9.452203e-08 9.424228e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.008305391 0.429991010 0.186599828 0.062820013 1.186069870 0.511810499 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6475955 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.737847e-09 1.015071e-08 -1.879019e-08 -1.351185e-08 9.452203e-08 9.424228e-09 + +$result$normp +[1] 9.831037e-08 + +$result$res + [1] -0.30103832 -0.33326418 -0.23288129 -0.06927620 0.73795543 0.52119244 -0.68213754 0.73972189 -1.41574906 0.83092710 -0.14278415 -0.06093401 0.04881824 0.48438169 -0.06112044 -0.22576049 -0.38991932 -0.20491334 0.39733191 + +$result$prevres + [1] -0.30103840 -0.33326430 -0.23288142 -0.06927632 0.73795536 0.52119248 -0.68213739 0.73972187 -1.41574905 0.83092713 -0.14278412 -0.06093401 0.04881818 0.48438178 -0.06112040 -0.22576050 -0.38991936 -0.20491339 0.39733186 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.000000000 0.00000000 + [2,] 93.8948004 0.000000 0 3.378746e+00 0.000000000 0.00000000 + [3,] 167.1483734 0.000000 0 1.151933e+01 0.000000000 0.00000000 + [4,] 262.4727527 0.000000 0 2.485249e+01 0.000000000 0.00000000 + [5,] 369.0709276 0.000000 0 4.212926e+01 0.000000000 0.00000000 + [6,] 519.2675869 0.000000 0 6.939837e+01 0.000000000 0.00000000 + [7,] 644.3622816 0.000000 0 9.405894e+01 0.000000000 0.00000000 + [8,] -0.9448131 2.173913 0 -9.588432e-04 0.004464977 0.00000000 + [9,] -38.9841030 2.173913 0 -1.164291e+00 0.184230220 0.00000000 +[10,] -89.6017195 2.173913 0 -4.703168e+00 0.423437842 0.00000000 +[11,] -153.9493707 2.173913 0 -1.102758e+01 0.727530563 0.00000000 +[12,] -225.8388972 2.173913 0 -1.966085e+01 1.067264511 0.00000000 +[13,] -323.3036119 2.173913 0 -3.320650e+01 1.527861124 0.00000000 +[14,] 0.8962233 0.000000 5 9.095317e-04 0.000000000 0.01026945 +[15,] 36.9792313 0.000000 5 1.104414e+00 0.000000000 0.42372951 +[16,] 84.9936886 0.000000 5 4.461294e+00 0.000000000 0.97390704 +[17,] 146.0320734 0.000000 5 1.046045e+01 0.000000000 1.67332029 +[18,] 214.2244704 0.000000 5 1.864973e+01 0.000000000 2.45470838 +[19,] 306.6767767 0.000000 5 3.149876e+01 0.000000000 3.51408059 + +$result$retres +$result$retres$res + [1] -0.30103840 -0.33326430 -0.23288142 -0.06927632 0.73795536 0.52119248 -0.68213739 0.73972187 -1.41574905 0.83092713 -0.14278412 -0.06093401 0.04881818 0.48438178 -0.06112040 -0.22576050 -0.38991936 -0.20491339 0.39733186 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03026723 14.94141 0.1036857 + [2,] 0.05683871 14.62034 0.2361057 + [3,] 0.10118237 14.08451 0.4570940 + [4,] 0.15888647 13.38723 0.7446646 + [5,] 0.22341511 12.60750 1.0662455 + [6,] 0.31433585 11.50885 1.5193526 + [7,] 0.39006125 10.59382 1.8967330 + [8,] 0.03135586 14.92826 0.1091109 + [9,] 0.07518547 14.39864 0.3275375 + [10,] 0.13350808 13.69390 0.6181904 + [11,] 0.20765069 12.79799 0.9876830 + [12,] 0.29048321 11.79708 1.4004820 + [13,] 0.40278395 10.44008 1.9601371 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.006020768 NA NA + [2,] 0.006665286 NA NA + [3,] 0.004657628 NA NA + [4,] 0.001385526 NA NA + [5,] -0.014759107 NA NA + [6,] -0.010423850 NA NA + [7,] 0.013642748 NA NA + [8,] NA -0.34027206 -0.09687636 + [9,] NA 0.65124456 0.01222408 +[10,] NA -0.38222648 0.04515210 +[11,] NA 0.06568070 0.07798387 +[12,] NA 0.02802964 0.04098268 +[13,] NA -0.02245636 -0.07946637 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yceD_res/KEIO_ROBOT1_39_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yceD_res/KEIO_ROBOT1_39_res.txt new file mode 100644 index 0000000..eb42e64 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yceD_res/KEIO_ROBOT1_39_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0302672336482256 0.0300629349720577 0.0301757884855595 0.00396422270275909 0.022718059738982 0.0371960537553268 +Glc 14.9414137138593 14.930202247314 14.9330397357436 0.199633442230246 14.5445748537647 15.2718208665664 +Ace 0.103685646486452 0.124373039625407 0.116321143153435 0.068096088644919 1.00000000000759e-06 0.279996464876946 +mu 0.530034383538321 0.533408363265637 0.530254016219009 0.0301805817043892 0.483675403323234 0.593738866841573 +qGlc -6.4047085817761 -6.41429110619278 -6.33757525542597 0.5303475045113 -7.37784891573602 -5.30574033009375 +qAce 2.64144686708914 2.60453231064197 2.59306056864739 0.230988894919573 2.23984726660242 3.06610112622529 +res 5.45193890669637 31.4041272545184 31.496731433367 6.97014686907521 18.0252917885208 44.0816346645365 + + +Goodness of fit (khi2 test) + +khi2 value 5.45193890669646 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.419379915899728 +p-value, i.e. P(X^2<=value) 0.036148130039151 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycfH.txt b/validation/validation_results/Berges_2021/Berges_2021/ycfH.txt new file mode 100644 index 0000000..59811b0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycfH.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.114912 NA NA NA +3.34194444444444 0.18144 NA NA NA +3.9975 0.276696 NA NA NA +4.52333333333333 0.379512 NA NA NA +1.95 NA 13.790091257838 0.430033716030711 0 +3.25 NA 12.6607738080546 1.1009927982608 0 +4.08333333333333 NA 11.7808057923058 1.81683424728487 0 +4.76666666666667 NA 10.7042083589446 2.66027363795312 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycfH_res/KEIO_ROBOT2_12.pdf b/validation/validation_results/Berges_2021/Berges_2021/ycfH_res/KEIO_ROBOT2_12.pdf new file mode 100644 index 0000000..a089fbb Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ycfH_res/KEIO_ROBOT2_12.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycfH_res/KEIO_ROBOT2_12_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ycfH_res/KEIO_ROBOT2_12_log.txt new file mode 100644 index 0000000..a00d5ca --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycfH_res/KEIO_ROBOT2_12_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.114912 NA NA NA +[2,] 0.181440 NA NA NA +[3,] 0.276696 NA NA NA +[4,] 0.379512 NA NA NA +[5,] NA 13.79009 0.4300337 0 +[6,] NA 12.66077 1.1009928 0 +[7,] NA 11.78081 1.8168342 0 +[8,] NA 10.70421 2.6602736 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.567029e-02 1.411722e+01 1.182850e-01 1.000000e-06 5.943109e-01 -5.069373e+00 3.724809e+00 -1.981519e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-4.696725e-09 1.814206e-07 -2.254079e-08 -2.117582e-22 4.188020e-08 -8.117308e-07 2.982135e-07 -1.773159e-12 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.004331415 0.273627647 0.126036277 0.114980498 0.040574532 0.625889829 0.283927183 0.265550237 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.2561318 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-4.696725e-09 1.814206e-07 -2.254079e-08 -2.117582e-22 4.188020e-08 -8.117308e-07 2.982135e-07 -1.773159e-12 + +$result$normp +[1] 8.848931e-07 + +$result$res + [1] -6.983950e-02 2.815491e-01 -2.526017e-02 -1.000373e-01 -3.296205e-01 3.577755e-01 1.656927e-01 -1.938478e-01 2.001109e-01 -1.674321e-01 -1.891676e-01 1.564888e-01 4.064327e-06 2.475173e-06 5.826740e-07 -1.844666e-06 + +$result$prevres + [1] -6.983905e-02 2.815495e-01 -2.525995e-02 -1.000374e-01 -3.296208e-01 3.577753e-01 1.656928e-01 -1.938472e-01 2.001111e-01 -1.674319e-01 -1.891676e-01 1.564885e-01 4.064328e-06 2.475175e-06 5.826776e-07 -1.844661e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.211023e+02 0.000000 0 0 1.419729e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.643725e+02 0.000000 0 0 3.125904e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.379580e+02 0.000000 0 0 5.520364e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.353076e+02 0.000000 0 0 8.538046e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.054352e+01 2.173913 0 0 -1.206492e+00 0.2053043 0.0000000 0.0000000 + [6,] -1.094029e+02 2.173913 0 0 -5.948859e+00 0.5539948 0.0000000 0.0000000 + [7,] -1.914065e+02 2.173913 0 0 -1.373950e+01 0.9692447 0.0000000 0.0000000 + [8,] -2.965853e+02 2.173913 0 0 -2.574914e+01 1.5018490 0.0000000 0.0000000 + [9,] 6.851712e+01 0.000000 5 0 2.038930e+00 0.0000000 0.4721999 0.0000000 +[10,] 1.848871e+02 0.000000 5 0 1.005336e+01 0.0000000 1.2741880 0.0000000 +[11,] 3.234703e+02 0.000000 5 0 2.321928e+01 0.0000000 2.2292628 0.0000000 +[12,] 5.012187e+02 0.000000 5 0 4.351514e+01 0.0000000 3.4542526 0.0000000 +[13,] -3.644961e-05 0.000000 0 5 -1.084666e-06 0.0000000 0.0000000 0.4721999 +[14,] -9.835592e-05 0.000000 0 5 -5.348169e-06 0.0000000 0.0000000 1.2741880 +[15,] -1.720792e-04 0.000000 0 5 -1.235215e-05 0.0000000 0.0000000 2.2292628 +[16,] -2.666374e-04 0.000000 0 5 -2.314910e-05 0.0000000 0.0000000 3.4542526 + +$result$retres +$result$retres$res + [1] -6.983905e-02 2.815495e-01 -2.525995e-02 -1.000374e-01 -3.296208e-01 3.577753e-01 1.656928e-01 -1.938472e-01 2.001111e-01 -1.674319e-01 -1.891676e-01 1.564885e-01 4.064328e-06 2.475175e-06 5.826776e-07 -1.844661e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.1135152 13.36791 0.6688481 7.071125e-07 + [2,] 0.1870710 12.74050 1.1298547 4.618670e-07 + [3,] 0.2761908 11.98032 1.6884080 1.647289e-07 + [4,] 0.3775113 11.11607 2.3234281 -1.730880e-07 + [5,] 0.0817970 13.63847 0.4700559 8.128656e-07 + [6,] 0.1771230 12.82535 1.0675064 4.950350e-07 + [7,] 0.2906453 11.85702 1.7790007 1.165355e-07 + [8,] 0.4362502 10.61504 2.6915713 -3.689321e-07 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.001396781 NA NA NA +[2,] -0.005630991 NA NA NA +[3,] 0.000505199 NA NA NA +[4,] 0.002000748 NA NA NA +[5,] NA 0.15162559 -0.04002222 -8.128656e-07 +[6,] NA -0.16457665 0.03348638 -4.950350e-07 +[7,] NA -0.07621867 0.03783353 -1.165355e-07 +[8,] NA 0.08916973 -0.03129769 3.689321e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycfH_res/KEIO_ROBOT2_12_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ycfH_res/KEIO_ROBOT2_12_res.txt new file mode 100644 index 0000000..72cc32c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycfH_res/KEIO_ROBOT2_12_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0256702890165889 0.0267378583726409 0.0267243396041246 0.00468674525069704 0.0186988857643205 0.0363129368440534 +Glc 14.1172172770101 14.1709900265089 14.1717032339747 0.317452955593528 13.5927427784808 14.7866368397581 +Ace 0.118285003013407 0.139290000451462 0.108585244450633 0.140830799983238 9.99999999945489e-07 0.439748760959868 +Lac 1e-06 0.0730375259785977 0.0520023380176476 0.0779813025975911 9.99999999994709e-07 0.29075354213377 +mu 0.594310860656136 0.58825159161792 0.587026865056793 0.0411303152642651 0.518316497276784 0.663427883350867 +qGlc -5.06937307353856 -5.20689700941023 -5.24620108019936 0.832810738281412 -6.7540048695094 -3.66590274464301 +qAce 3.72480939393561 3.63280573967649 3.65380180721581 0.356142443098334 2.99992010456006 4.17690733410318 +qLac -1.98151885490483e-06 0.0118184235776971 0.0293850829218795 0.188494042295761 -0.459022047752018 0.305293426747279 +res 0.524828045085872 19.9334779391384 19.2295265565033 5.94960191931822 11.0788373293245 34.5429453213815 + + +Goodness of fit (khi2 test) + +khi2 value 0.524828045086938 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.0656035056358672 +p-value, i.e. P(X^2<=value) 0.000160313357814763 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycgJ.txt b/validation/validation_results/Berges_2021/Berges_2021/ycgJ.txt new file mode 100644 index 0000000..0f06685 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycgJ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.195 0.054432 NA NA +1.61361111111111 0.066528 NA NA +2.36138888888889 0.093744 NA NA +3.28638888888889 0.148176 NA NA +3.81944444444444 0.21168 NA NA +4.41083333333333 0.291816 NA NA +0.283333333333333 NA 13.8071895508623 0.0387173800123003 +1.91666666666667 NA 14.1191986287769 0.377328934831423 +2.7 NA 13.5474684260314 0.662050779501799 +3.61666666666667 NA 12.8795638128504 1.21555757034447 +4.05 NA 12.2782709091485 1.56623627679534 +4.75 NA 11.3811616027503 2.36017181505283 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycgJ_res/KEIO_ROBOT4_38.pdf b/validation/validation_results/Berges_2021/Berges_2021/ycgJ_res/KEIO_ROBOT4_38.pdf new file mode 100644 index 0000000..a28bc32 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ycgJ_res/KEIO_ROBOT4_38.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycgJ_res/KEIO_ROBOT4_38_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ycgJ_res/KEIO_ROBOT4_38_log.txt new file mode 100644 index 0000000..a2154aa --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycgJ_res/KEIO_ROBOT4_38_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.054432 NA NA + [3,] 0.066528 NA NA + [4,] 0.093744 NA NA + [5,] 0.148176 NA NA + [6,] 0.211680 NA NA + [7,] 0.291816 NA NA + [8,] NA 13.80719 0.03871738 + [9,] NA 14.11920 0.37732893 +[10,] NA 13.54747 0.66205078 +[11,] NA 12.87956 1.21555757 +[12,] NA 12.27827 1.56623628 +[13,] NA 11.38116 2.36017182 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02608918 14.20418020 0.02146313 0.54601874 -4.70322810 3.97223950 + +$result$lastp + X Glc Ace mu qGlc qAce +-4.769613e-09 5.761760e-08 4.256933e-08 4.666033e-08 -5.015493e-07 6.662548e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.004625173 0.239865305 0.108204733 0.044987673 0.761263090 0.361313786 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3547176 + +$result$laststep + X Glc Ace mu qGlc qAce +-4.769613e-09 5.761760e-08 4.256933e-08 4.666033e-08 -5.015493e-07 6.662548e-08 + +$result$normp +[1] 5.131496e-07 + +$result$res + [1] -0.283141015 -0.216619941 -0.178138851 0.048601396 0.438882718 -0.085035702 -0.090258001 0.781285315 -0.717947773 -0.217617567 -0.151700486 0.215858327 0.090122184 0.072506758 -0.025828079 -0.006990951 -0.082085425 -0.010280572 0.052678268 + +$result$prevres + [1] -0.283140777 -0.216619623 -0.178138513 0.048601740 0.438882949 -0.085035654 -0.090258334 0.781285184 -0.717947920 -0.217617689 -0.151700507 0.215858403 0.090122530 0.072506571 -0.025828093 -0.006990882 -0.082085311 -0.010280482 0.052678196 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.0000000 0.00000000 + [2,] 96.016048 0.000000 0 2.99345155 0.0000000 0.00000000 + [3,] 120.673051 0.000000 0 5.08006972 0.0000000 0.00000000 + [4,] 181.523564 0.000000 0 11.18306961 0.0000000 0.00000000 + [5,] 300.802157 0.000000 0 25.79053805 0.0000000 0.00000000 + [6,] 402.425931 0.000000 0 40.10021105 0.0000000 0.00000000 + [7,] 555.806629 0.000000 0 63.95947253 0.0000000 0.00000000 + [8,] -3.133016 2.173913 0 -0.01187798 0.0173791 0.00000000 + [9,] -34.600175 2.173913 0 -1.01328306 0.1919300 0.00000000 +[10,] -63.062602 2.173913 0 -2.74803213 0.3498134 0.00000000 +[11,] -116.189957 2.173913 0 -7.17841224 0.6445151 0.00000000 +[12,] -152.204865 2.173913 0 -10.78823124 0.8442927 0.00000000 +[13,] -231.777053 2.173913 0 -19.96868773 1.2856861 0.00000000 +[14,] 6.085972 0.000000 5 0.02307330 0.0000000 0.03997192 +[15,] 67.211804 0.000000 5 1.96833058 0.0000000 0.44143894 +[16,] 122.500862 0.000000 5 5.33812899 0.0000000 0.80457073 +[17,] 225.702230 0.000000 5 13.94426582 0.0000000 1.48238474 +[18,] 295.662192 0.000000 5 20.95643983 0.0000000 1.94187324 +[19,] 450.233385 0.000000 5 38.78973240 0.0000000 2.95707800 + +$result$retres +$result$retres$res + [1] -0.283140777 -0.216619623 -0.178138513 0.048601740 0.438882949 -0.085035654 -0.090258334 0.781285184 -0.717947920 -0.217617689 -0.151700507 0.215858403 0.090122530 0.072506571 -0.025828093 -0.006990882 -0.082085311 -0.010280482 0.052678196 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02608918 14.20418 0.02146309 + [2,] 0.05009961 13.99736 0.19613687 + [3,] 0.06296523 13.88654 0.28973317 + [4,] 0.09471603 13.61305 0.52071757 + [5,] 0.15695366 13.07696 0.97349098 + [6,] 0.20997929 12.62021 1.35924791 + [7,] 0.29001083 11.93084 1.94147059 + [8,] 0.03045427 14.16658 0.05321869 + [9,] 0.07429597 13.78894 0.37216332 + [10,] 0.11395132 13.44736 0.66065260 + [11,] 0.18797114 12.80978 1.19914051 + [12,] 0.23814900 12.37757 1.56418018 + [13,] 0.34901316 11.42262 2.37070745 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0056628155 NA NA + [2,] 0.0043323925 NA NA + [3,] 0.0035627703 NA NA + [4,] -0.0009720348 NA NA + [5,] -0.0087776590 NA NA + [6,] 0.0017007131 NA NA + [7,] 0.0018051667 NA NA + [8,] NA -0.35939118 -0.014501314 + [9,] NA 0.33025604 0.005165619 +[10,] NA 0.10010414 0.001398176 +[11,] NA 0.06978223 0.016417062 +[12,] NA -0.09929487 0.002056096 +[13,] NA -0.04145636 -0.010535639 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycgJ_res/KEIO_ROBOT4_38_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ycgJ_res/KEIO_ROBOT4_38_res.txt new file mode 100644 index 0000000..7e29ded --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycgJ_res/KEIO_ROBOT4_38_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0260891796970982 0.0251781555150304 0.0251746171034363 0.00404900868334148 0.0184339328415641 0.033810864756164 +Glc 14.204180201336 14.197198221052 14.1856841850633 0.195935363241444 13.8088457631368 14.5245408381525 +Ace 0.0214631289574233 0.0592329660979421 0.0416899094900756 0.0662886276758362 9.99999999994061e-07 0.212400338998413 +mu 0.546018736635224 0.557142237230507 0.554704803134538 0.039333018800997 0.482707564029749 0.632687384536826 +qGlc -4.7032281041939 -4.68480311197248 -4.67090983556428 0.747165132830873 -6.0315042227655 -3.45780886295012 +qAce 3.9722394960142 3.94858636221956 3.93776515848091 0.346063114301008 3.27056365650159 4.73613403648913 +res 1.63571911416458 31.3639702274916 30.7909765462147 8.52307138698936 17.0654346571256 46.8357510891238 + + +Goodness of fit (khi2 test) + +khi2 value 1.63571911416542 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.125824547243494 +p-value, i.e. P(X^2<=value) 7.15330007839247e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycgM.txt b/validation/validation_results/Berges_2021/Berges_2021/ycgM.txt new file mode 100644 index 0000000..81aa20f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycgM.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.114912 NA NA NA +3.34194444444444 0.179928 NA NA NA +3.9975 0.25704 NA NA NA +4.52333333333333 0.356832 NA NA NA +1.95 NA 13.9609876180909 0.385401613161975 0 +3.25 NA 12.5477138407315 0.872064244939514 0 +4.08333333333333 NA 11.7833732729286 1.37375162744232 0 +4.76666666666667 NA 10.5786376687642 1.92847715231013 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycgM_res/KEIO_ROBOT2_13.pdf b/validation/validation_results/Berges_2021/Berges_2021/ycgM_res/KEIO_ROBOT2_13.pdf new file mode 100644 index 0000000..780f6c2 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ycgM_res/KEIO_ROBOT2_13.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycgM_res/KEIO_ROBOT2_13_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ycgM_res/KEIO_ROBOT2_13_log.txt new file mode 100644 index 0000000..afdc526 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycgM_res/KEIO_ROBOT2_13_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.114912 NA NA NA +[2,] 0.179928 NA NA NA +[3,] 0.257040 NA NA NA +[4,] 0.356832 NA NA NA +[5,] NA 13.96099 0.3854016 0 +[6,] NA 12.54771 0.8720642 0 +[7,] NA 11.78337 1.3737516 0 +[8,] NA 10.57864 1.9284772 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.794185e-02 1.430878e+01 1.518005e-01 1.000000e-06 5.603099e-01 -5.692215e+00 2.689789e+00 -2.036874e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 1.682501e-09 9.614048e-08 -2.741676e-08 -2.117582e-22 -1.522471e-08 -1.613977e-07 2.723378e-08 -2.878900e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.006325829 0.367674098 0.161111426 0.152758475 0.054692957 0.853517931 0.373122350 0.359700442 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3323645 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 1.682501e-09 9.614048e-08 -2.741676e-08 -2.117582e-22 -1.522471e-08 -1.613977e-07 2.723378e-08 -2.878900e-13 + +$result$normp +[1] 1.924063e-07 + +$result$res + [1] -7.130496e-02 9.126463e-02 2.692394e-01 -2.246433e-01 -4.670364e-01 6.330404e-01 2.593339e-02 -1.919374e-01 1.613016e-01 -1.284876e-01 -1.711972e-01 1.383832e-01 3.993367e-06 2.370158e-06 5.029575e-07 -1.831838e-06 + +$result$prevres + [1] -7.130508e-02 9.126455e-02 2.692394e-01 -2.246432e-01 -4.670365e-01 6.330404e-01 2.593343e-02 -1.919373e-01 1.613016e-01 -1.284876e-01 -1.711972e-01 1.383831e-01 3.993367e-06 2.370159e-06 5.029582e-07 -1.831837e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.030751e+02 0.000000 0 0 1.419362e+01 0.0000000 0.000000 0.000000 + [2,] 3.252349e+02 0.000000 0 0 3.037047e+01 0.0000000 0.000000 0.000000 + [3,] 4.695910e+02 0.000000 0 0 5.245215e+01 0.0000000 0.000000 0.000000 + [4,] 6.304864e+02 0.000000 0 0 7.968737e+01 0.0000000 0.000000 0.000000 + [5,] -4.377291e+01 2.173913 0 0 -1.405476e+00 0.2148717 0.000000 0.000000 + [6,] -1.143573e+02 2.173913 0 0 -6.687618e+00 0.5613550 0.000000 0.000000 + [7,] -1.955515e+02 2.173913 0 0 -1.507954e+01 0.9599199 0.000000 0.000000 + [8,] -2.970788e+02 2.173913 0 0 -2.769436e+01 1.4582955 0.000000 0.000000 + [9,] 4.757406e+01 0.000000 5 0 1.527524e+00 0.0000000 0.494205 0.000000 +[10,] 1.242878e+02 0.000000 5 0 7.268356e+00 0.0000000 1.291117 0.000000 +[11,] 2.125328e+02 0.000000 5 0 1.638902e+01 0.0000000 2.207816 0.000000 +[12,] 3.228765e+02 0.000000 5 0 3.009927e+01 0.0000000 3.354080 0.000000 +[13,] -3.602600e-05 0.000000 0 5 -1.156735e-06 0.0000000 0.000000 0.494205 +[14,] -9.411838e-05 0.000000 0 5 -5.504046e-06 0.0000000 0.000000 1.291117 +[15,] -1.609429e-04 0.000000 0 5 -1.241077e-05 0.0000000 0.000000 2.207816 +[16,] -2.445020e-04 0.000000 0 5 -2.279302e-05 0.0000000 0.000000 3.354080 + +$result$retres +$result$retres$res + [1] -7.130508e-02 9.126455e-02 2.692394e-01 -2.246432e-01 -4.670365e-01 6.330404e-01 2.593343e-02 -1.919373e-01 1.613016e-01 -1.284876e-01 -1.711972e-01 1.383831e-01 3.993367e-06 2.370159e-06 5.029582e-07 -1.831837e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.11348590 13.43973 0.5624580 6.890249e-07 + [2,] 0.18175329 12.74620 0.8901781 4.408550e-07 + [3,] 0.26242479 11.92665 1.2774447 1.475930e-07 + [4,] 0.35233914 11.01321 1.7090819 -1.792693e-07 + [5,] 0.08332344 13.74615 0.4176619 7.986734e-07 + [6,] 0.17262694 12.83891 0.8463667 4.740317e-07 + [7,] 0.27535407 11.79530 1.3395122 1.005916e-07 + [8,] 0.40380668 10.49035 1.9561538 -3.663673e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.001426102 NA NA NA +[2,] -0.001825291 NA NA NA +[3,] -0.005384789 NA NA NA +[4,] 0.004492864 NA NA NA +[5,] NA 0.21483678 -0.03226033 -7.986734e-07 +[6,] NA -0.29119857 0.02569751 -4.740317e-07 +[7,] NA -0.01192938 0.03423944 -1.005916e-07 +[8,] NA 0.08829116 -0.02767663 3.663673e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycgM_res/KEIO_ROBOT2_13_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ycgM_res/KEIO_ROBOT2_13_res.txt new file mode 100644 index 0000000..80be251 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycgM_res/KEIO_ROBOT2_13_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0279418502334196 0.0290107906048241 0.0286393644080609 0.00608039831493717 0.0198113832963162 0.0432038286234678 +Glc 14.3087751298146 14.3034980339314 14.282640068748 0.366450422678616 13.7213112368611 15.0563763423314 +Ace 0.151800499658329 0.171541121599341 0.155899839733944 0.139292032715874 9.99999999987122e-07 0.438508735732614 +Lac 1e-06 0.106720306447122 0.0938177557401172 0.0794978092354539 9.99999999993061e-07 0.28841498950816 +mu 0.560309930481265 0.556227821600841 0.554339291093996 0.047765669319844 0.45673999116708 0.649109324777115 +qGlc -5.69221525870033 -5.66441338800187 -5.71586891375288 0.81059514263494 -7.05260610310024 -4.15251878189139 +qAce 2.6897889709902 2.63799615439976 2.64242808988531 0.415964879559361 1.82179024009294 3.41827567408522 +qLac -2.03687401940419e-06 -0.0566506430192241 -0.0596461868943821 0.186177392719222 -0.377342074376209 0.312259224534095 +res 0.883729358613601 20.3874004173671 19.5164279820294 6.60834318418149 10.3167984331005 33.5745649630379 + + +Goodness of fit (khi2 test) + +khi2 value 0.883729358613678 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.11046616982671 +p-value, i.e. P(X^2<=value) 0.00111837088054084 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciK.txt b/validation/validation_results/Berges_2021/Berges_2021/yciK.txt new file mode 100644 index 0000000..6c94fdd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yciK.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.15876 NA NA +3.67805555555556 0.244944 NA NA +4.09222222222222 0.322056 NA NA +4.565 0.40068 NA NA +0.05 NA 14.8602406261967 0.0193168634643637 +1.95 NA 14.4254429186305 0.428953986746089 +2.83333333333333 NA 13.1108011487154 0.729344508256235 +3.98333333333333 NA 12.1012867075662 1.39100131403763 +4.88333333333333 NA 9.83460273558639 2.1179320316505 +5.16666666666667 NA 8.89984839993595 2.2943412690886 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciK_res/KEIO_ROBOT3_20.pdf b/validation/validation_results/Berges_2021/Berges_2021/yciK_res/KEIO_ROBOT3_20.pdf new file mode 100644 index 0000000..87c7fde Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yciK_res/KEIO_ROBOT3_20.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciK_res/KEIO_ROBOT3_20_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yciK_res/KEIO_ROBOT3_20_log.txt new file mode 100644 index 0000000..0f4e3ad --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yciK_res/KEIO_ROBOT3_20_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.158760 NA NA + [2,] 0.244944 NA NA + [3,] 0.322056 NA NA + [4,] 0.400680 NA NA + [5,] NA 14.860241 0.01931686 + [6,] NA 14.425443 0.42895399 + [7,] NA 13.110801 0.72934451 + [8,] NA 12.101287 1.39100131 + [9,] NA 9.834603 2.11793203 +[10,] NA 8.899848 2.29434127 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03645623 14.92348420 0.12679750 0.52527061 -6.11377939 2.33178549 + +$result$lastp + X Glc Ace mu qGlc qAce + 5.807080e-09 5.946993e-08 -1.119261e-07 -4.065440e-08 7.308807e-08 1.728394e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01036207 0.36191314 0.15526576 0.06802115 0.66080059 0.28098334 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5125086 + +$result$laststep + X Glc Ace mu qGlc qAce + 5.807080e-09 5.946993e-08 -1.119261e-07 -4.065440e-08 7.308807e-08 1.728394e-07 + +$result$normp +[1] 2.301433e-07 + +$result$res + [1] 0.323073543 0.335900360 -0.461665806 0.016227984 0.112938417 -0.563943030 0.777170797 -0.417616492 -0.008022484 0.099472792 0.558936740 -0.066321786 -0.237710098 -0.572771490 -0.244179737 0.562046371 + +$result$prevres + [1] 0.323073194 0.335900237 -0.461665695 0.016228511 0.112938292 -0.563942993 0.777170908 -0.417616359 -0.008022507 0.099472660 0.558937294 -0.066321497 -0.237709988 -0.572771655 -0.244180108 0.562045952 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 226.6025256 0.000000 0 2.376665e+01 0.000000000 0.000000000 + [2,] 345.1564012 0.000000 0 4.628134e+01 0.000000000 0.000000000 + [3,] 429.0387525 0.000000 0 6.400700e+01 0.000000000 0.000000000 + [4,] 549.9808939 0.000000 0 9.152929e+01 0.000000000 0.000000000 + [5,] -0.6733447 2.173913 0 -6.163765e-04 0.004015128 0.000000000 + [6,] -45.1676276 2.173913 0 -1.874875e+00 0.269332794 0.000000000 + [7,] -86.7737701 2.173913 0 -5.554183e+00 0.517428591 0.000000000 + [8,] -179.7450983 2.173913 0 -1.730136e+01 1.071812978 0.000000000 + [9,] -303.6739941 2.173913 0 -3.749067e+01 1.810796127 0.000000000 +[10,] -356.4655091 2.173913 0 -4.716844e+01 2.125589862 0.000000000 +[11,] 0.5906689 0.000000 5 5.406954e-04 0.000000000 0.009234795 +[12,] 39.6217736 0.000000 5 1.644671e+00 0.000000000 0.619465425 +[13,] 76.1193547 0.000000 5 4.872219e+00 0.000000000 1.190085759 +[14,] 157.6753076 0.000000 5 1.517703e+01 0.000000000 2.465169848 +[15,] 266.3877396 0.000000 5 3.288742e+01 0.000000000 4.164831091 +[16,] 312.6973105 0.000000 5 4.137692e+01 0.000000000 4.888856683 + +$result$retres +$result$retres$res + [1] 0.323073194 0.335900237 -0.461665695 0.016228511 0.112938292 -0.563942993 0.777170908 -0.417616359 -0.008022507 0.099472660 0.558937294 -0.066321497 -0.237709988 -0.572771655 -0.244180108 0.562045952 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.16522146 13.424748 0.6984132 + [2,] 0.25166200 12.418641 1.0821407 + [3,] 0.31282269 11.706774 1.3536456 + [4,] 0.40100457 10.680399 1.7451033 + [5,] 0.03742638 14.912192 0.1311043 + [6,] 0.10153363 14.166029 0.4156897 + [7,] 0.16147965 13.468300 0.6818025 + [8,] 0.29543250 11.909183 1.2764470 + [9,] 0.47398894 9.830912 2.0690960 + [10,] 0.55005082 8.945606 2.4067505 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0064614639 NA NA + [2,] -0.0067180047 NA NA + [3,] 0.0092333139 NA NA + [4,] -0.0003245702 NA NA + [5,] NA -0.051951614 -0.11178746 + [6,] NA 0.259413777 0.01326430 + [7,] NA -0.357498618 0.04754200 + [8,] NA 0.192103525 0.11455433 + [9,] NA 0.003690353 0.04883602 +[10,] NA -0.045757424 -0.11240919 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciK_res/KEIO_ROBOT3_20_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yciK_res/KEIO_ROBOT3_20_res.txt new file mode 100644 index 0000000..78ceee1 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yciK_res/KEIO_ROBOT3_20_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0364562331643664 0.0367541329082295 0.0363664616414578 0.00422954543088551 0.0304251565652116 0.0467573879838343 +Glc 14.9234842000709 14.895491917758 14.8870311276499 0.227346606351062 14.5309483160436 15.321874749434 +Ace 0.126797498450576 0.134295332203327 0.133910861332984 0.0919283659520596 9.99999999990418e-07 0.290364533386899 +mu 0.525270612986394 0.524292877561998 0.5257716675708 0.0257672505667825 0.46752361572947 0.565815303597985 +qGlc -6.11377938931646 -6.09950933241622 -6.06001388260529 0.457701461514649 -6.92370412332234 -5.32460428754822 +qAce 2.33178549276477 2.33121992249368 2.33506616663106 0.182185153882648 1.98714498573324 2.63716730093932 +res 2.62665023198719 24.0868302630584 21.964504391907 7.06982695161236 14.6446394679913 38.8677183444408 + + +Goodness of fit (khi2 test) + +khi2 value 2.62665023198847 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.262665023198847 +p-value, i.e. P(X^2<=value) 0.0111012044667803 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciO.txt b/validation/validation_results/Berges_2021/Berges_2021/yciO.txt new file mode 100644 index 0000000..ab79179 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yciO.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.065016 NA NA +1.61361111111111 0.074088 NA NA +2.36138888888889 0.104328 NA NA +3.28638888888889 0.176904 NA NA +3.81944444444444 0.222264 NA NA +4.41083333333333 0.3402 NA NA +0.283333333333333 NA 14.1367070212309 0.0450748656217376 +1.91666666666667 NA 13.8160143660819 0.386908304279855 +2.7 NA 13.4266398389715 0.684847244954476 +3.61666666666667 NA 13.0062384144005 1.19269822482367 +4.05 NA 12.226708601525 1.4506791386098 +4.75 NA 10.6964462204203 1.83019754078841 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciO_res/KEIO_ROBOT4_9.pdf b/validation/validation_results/Berges_2021/Berges_2021/yciO_res/KEIO_ROBOT4_9.pdf new file mode 100644 index 0000000..f46faad Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yciO_res/KEIO_ROBOT4_9.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciO_res/KEIO_ROBOT4_9_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yciO_res/KEIO_ROBOT4_9_log.txt new file mode 100644 index 0000000..466532d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yciO_res/KEIO_ROBOT4_9_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.065016 NA NA + [3,] 0.074088 NA NA + [4,] 0.104328 NA NA + [5,] 0.176904 NA NA + [6,] 0.222264 NA NA + [7,] 0.340200 NA NA + [8,] NA 14.13671 0.04507487 + [9,] NA 13.81601 0.38690830 +[10,] NA 13.42664 0.68484724 +[11,] NA 13.00624 1.19269822 +[12,] NA 12.22671 1.45067914 +[13,] NA 10.69645 1.83019754 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0298555 14.3673947 0.1366224 0.5439401 -5.0972825 2.7336457 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.830003e-09 -1.430589e-08 -3.893762e-08 -2.494254e-08 1.945353e-07 5.592272e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.00744054 0.37701990 0.16535614 0.06333887 1.05549067 0.46851117 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5552492 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.830003e-09 -1.430589e-08 -3.893762e-08 -2.494254e-08 1.945353e-07 5.592272e-08 + +$result$normp +[1] 2.081401e-07 + +$result$res + [1] -0.24602514 -0.39130488 -0.11370984 0.17654014 0.07425879 0.80641712 -0.56756247 0.40015077 0.08170666 0.01167815 -0.78205921 -0.24349119 0.53201481 0.58274357 0.12629906 -0.23291948 -0.66582155 -0.52974918 0.71944758 + +$result$prevres + [1] -0.24602528 -0.39130507 -0.11371004 0.17653995 0.07425867 0.80641713 -0.56756222 0.40015081 0.08170673 0.01167821 -0.78205918 -0.24349122 0.53201465 0.58274375 0.12629913 -0.23291947 -0.66582161 -0.52974928 0.71944747 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 95.777846 0.000000 0 3.41709644 0.00000000 0.00000000 + [3,] 120.268984 0.000000 0 5.79397722 0.00000000 0.00000000 + [4,] 180.634757 0.000000 0 12.73482847 0.00000000 0.00000000 + [5,] 298.754346 0.000000 0 29.31280987 0.00000000 0.00000000 + [6,] 399.243670 0.000000 0 45.52631541 0.00000000 0.00000000 + [7,] 550.734066 0.000000 0 72.52485263 0.00000000 0.00000000 + [8,] -3.394488 2.173913 0 -0.01472571 0.01988199 0.00000000 + [9,] -37.411745 2.173913 0 -1.25311471 0.21912580 0.00000000 +[10,] -68.109440 2.173913 0 -3.39410496 0.39892648 0.00000000 +[11,] -125.306736 2.173913 0 -8.85221790 0.73393900 0.00000000 +[12,] -164.028656 2.173913 0 -13.29362004 0.96073868 0.00000000 +[13,] -249.478639 2.173913 0 -24.57521344 1.46123113 0.00000000 +[14,] 4.187025 0.000000 5 0.01816384 0.00000000 0.04572857 +[15,] 46.146557 0.000000 5 1.54568920 0.00000000 0.50398934 +[16,] 84.011484 0.000000 5 4.18655317 0.00000000 0.91753090 +[17,] 154.563079 0.000000 5 10.91901442 0.00000000 1.68805970 +[18,] 202.325709 0.000000 5 16.39738542 0.00000000 2.20969896 +[19,] 307.726367 0.000000 5 30.31298062 0.00000000 3.36083159 + +$result$retres +$result$retres$res + [1] -0.24602528 -0.39130507 -0.11371004 0.17653995 0.07425867 0.80641713 -0.56756222 0.40015081 0.08170673 0.01167821 -0.78205918 -0.24349122 0.53201465 0.58274375 0.12629913 -0.23291947 -0.66582161 -0.52974928 0.71944747 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02985549 14.36739 0.1366225 + [2,] 0.05718990 14.11124 0.2739953 + [3,] 0.07181380 13.97420 0.3474897 + [4,] 0.10785880 13.63642 0.5286388 + [5,] 0.17838917 12.97548 0.8830989 + [6,] 0.23839234 12.41319 1.1846531 + [7,] 0.32884876 11.56552 1.6392542 + [8,] 0.03483021 14.32078 0.1616236 + [9,] 0.08468349 13.85360 0.4121681 + [10,] 0.12967186 13.43201 0.6382634 + [11,] 0.21349616 12.64649 1.0595339 + [12,] 0.27024426 12.11470 1.3447293 + [13,] 0.39547370 10.94117 1.9740870 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.004920506 NA NA + [2,] 0.007826101 NA NA + [3,] 0.002274201 NA NA + [4,] -0.003530799 NA NA + [5,] -0.001485173 NA NA + [6,] -0.016128343 NA NA + [7,] 0.011351244 NA NA + [8,] NA -0.184069372 -0.11654875 + [9,] NA -0.037585095 -0.02525983 +[10,] NA -0.005371977 0.04658389 +[11,] NA 0.359747225 0.13316432 +[12,] NA 0.112005959 0.10594986 +[13,] NA -0.244726741 -0.14388949 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciO_res/KEIO_ROBOT4_9_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yciO_res/KEIO_ROBOT4_9_res.txt new file mode 100644 index 0000000..d09fe2c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yciO_res/KEIO_ROBOT4_9_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0298554971345589 0.0298236951930002 0.0296236838260288 0.00427334004108708 0.023222194503247 0.0377378899276574 +Glc 14.3673946660992 14.3395391188206 14.3490568965552 0.197974730237221 14.0164151533551 14.6965294243538 +Ace 0.136622436760278 0.140329653961821 0.138080912752682 0.0785997110113801 9.99999999998355e-07 0.285050701612983 +mu 0.543940057918775 0.546082213695003 0.54675457372199 0.0348350257964219 0.486739822216103 0.607636168456294 +qGlc -5.09728246235458 -5.07583775525681 -5.0749438851624 0.666037449004818 -6.31665494655193 -3.83895904652425 +qAce 2.73364574487987 2.75357620730588 2.73638292487452 0.283577778289795 2.2471438110225 3.27514105901238 +res 4.00792200959864 31.8833474348162 30.6797689303657 7.87462511521994 19.4530861561361 49.3114599867031 + + +Goodness of fit (khi2 test) + +khi2 value 4.00792200959897 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.308301693046075 +p-value, i.e. P(X^2<=value) 0.00889317384480033 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciW.txt b/validation/validation_results/Berges_2021/Berges_2021/yciW.txt new file mode 100644 index 0000000..6b622e4 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yciW.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.195 0.06804 NA NA +1.61361111111111 0.084672 NA NA +2.36138888888889 0.130032 NA NA +3.28638888888889 0.222264 NA NA +3.81944444444444 0.306936 NA NA +4.41083333333333 0.427896 NA NA +0.283333333333333 NA 14.1164104316706 0.0439113202268244 +1.91666666666667 NA 13.9508608314002 0.423599994204055 +2.7 NA 13.3042729429434 0.689357548277228 +3.61666666666667 NA 12.0034227850537 1.2230539796854 +4.05 NA 11.624179494965 1.5018870244879 +4.75 NA 10.1799998178291 2.03227924092051 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciW_res/KEIO_ROBOT4_12.pdf b/validation/validation_results/Berges_2021/Berges_2021/yciW_res/KEIO_ROBOT4_12.pdf new file mode 100644 index 0000000..03a42da Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yciW_res/KEIO_ROBOT4_12.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciW_res/KEIO_ROBOT4_12_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yciW_res/KEIO_ROBOT4_12_log.txt new file mode 100644 index 0000000..8cf58b3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yciW_res/KEIO_ROBOT4_12_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.068040 NA NA + [3,] 0.084672 NA NA + [4,] 0.130032 NA NA + [5,] 0.222264 NA NA + [6,] 0.306936 NA NA + [7,] 0.427896 NA NA + [8,] NA 14.11641 0.04391132 + [9,] NA 13.95086 0.42359999 +[10,] NA 13.30427 0.68935755 +[11,] NA 12.00342 1.22305398 +[12,] NA 11.62418 1.50188702 +[13,] NA 10.18000 2.03227924 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03489014 14.31553820 0.12946026 0.56747439 -4.93288765 2.36528502 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.863623e-08 2.827318e-07 -2.382751e-07 -2.140325e-07 4.249423e-07 7.986946e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.004800247 0.251456712 0.109714567 0.034786024 0.560768198 0.245809499 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3745609 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.863623e-08 2.827318e-07 -2.382751e-07 -2.140325e-07 4.249423e-07 7.986946e-08 + +$result$normp +[1] 6.085206e-07 + +$result$res + [1] -0.06989324 0.03501632 0.12501711 0.16093182 0.14856513 -0.10702563 -0.07775918 0.31787918 -0.50432718 -0.19380066 0.55195859 -0.05476753 -0.11694239 0.55457860 -0.04020840 -0.16128356 -0.53347165 -0.34929628 0.52968129 + +$result$prevres + [1] -0.06989467 0.03501438 0.12501504 0.16092972 0.14856381 -0.10702568 -0.07775655 0.31787864 -0.50432716 -0.19380038 0.55195898 -0.05476727 -0.11694281 0.55457969 -0.04020808 -0.16128367 -0.53347216 -0.34929683 0.52968106 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 98.509713 0.000000 0 4.10723219 0.00000000 0.00000000 + [3,] 124.924096 0.000000 0 7.03310965 0.00000000 0.00000000 + [4,] 190.957563 0.000000 0 15.73282364 0.00000000 0.00000000 + [5,] 322.778143 0.000000 0 37.01053544 0.00000000 0.00000000 + [6,] 436.793573 0.000000 0 58.20747136 0.00000000 0.00000000 + [7,] 610.976736 0.000000 0 94.02592580 0.00000000 0.00000000 + [8,] -3.296269 2.173913 0 -0.01672910 0.02331437 0.00000000 + [9,] -37.176826 2.173913 0 -1.46407333 0.26295010 0.00000000 +[10,] -68.563920 2.173913 0 -4.02359976 0.48494968 0.00000000 +[11,] -128.242035 2.173913 0 -10.68217223 0.90705043 0.00000000 +[12,] -169.261347 2.173913 0 -16.18101282 1.19717828 0.00000000 +[13,] -261.026518 2.173913 0 -30.34247269 1.84622941 0.00000000 +[14,] 3.635237 0.000000 5 0.01844942 0.00000000 0.05362306 +[15,] 40.999858 0.000000 5 1.61462945 0.00000000 0.60478524 +[16,] 75.614604 0.000000 5 4.43736152 0.00000000 1.11538426 +[17,] 141.429642 0.000000 5 11.78065984 0.00000000 2.08621600 +[18,] 186.667123 0.000000 5 17.84496672 0.00000000 2.75351004 +[19,] 287.868848 0.000000 5 33.46270232 0.00000000 4.24632764 + +$result$retres +$result$retres$res + [1] -0.06989467 0.03501438 0.12501504 0.16092972 0.14856381 -0.10702568 -0.07775655 0.31787864 -0.50432716 -0.19380038 0.55195898 -0.05476727 -0.11694281 0.55457969 -0.04020808 -0.16128367 -0.53347216 -0.34929683 0.52968106 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03489011 14.31554 0.1294605 + [2,] 0.06874029 14.02129 0.2705511 + [3,] 0.08717230 13.86106 0.3473774 + [4,] 0.13325059 13.46052 0.5394358 + [5,] 0.22523528 12.66092 0.9228362 + [6,] 0.30479549 11.96933 1.2544503 + [7,] 0.42634087 10.91277 1.7610623 + [8,] 0.04097605 14.26263 0.1548273 + [9,] 0.10353016 13.71887 0.4155584 + [10,] 0.16148055 13.21512 0.6571008 + [11,] 0.27166502 12.25732 1.1163595 + [12,] 0.34739951 11.59899 1.4320277 + [13,] 0.51682672 10.12621 2.1382155 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0013978934 NA NA + [2,] -0.0007002876 NA NA + [3,] -0.0025003007 NA NA + [4,] -0.0032185943 NA NA + [5,] -0.0029712761 NA NA + [6,] 0.0021405136 NA NA + [7,] 0.0015551311 NA NA + [8,] NA -0.14622418 -0.110915937 + [9,] NA 0.23199049 0.008041617 +[10,] NA 0.08914817 0.032256734 +[11,] NA -0.25390113 0.106694431 +[12,] NA 0.02519295 0.069859367 +[13,] NA 0.05379369 -0.105936212 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yciW_res/KEIO_ROBOT4_12_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yciW_res/KEIO_ROBOT4_12_res.txt new file mode 100644 index 0000000..31cdf1b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yciW_res/KEIO_ROBOT4_12_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0348901352030196 0.0348773533194798 0.0345655280825381 0.00429125884964612 0.0285998264679146 0.0449186972958199 +Glc 14.3155381978691 14.2625350149052 14.2634175584801 0.202483250381771 13.8668890320768 14.6382067444576 +Ace 0.129460256808763 0.152716937145994 0.148614610626975 0.0727396843702776 0.0158754746685427 0.28905998921592 +mu 0.567474385296316 0.570184701664403 0.572400424098008 0.0297915101212325 0.510903865256036 0.617744909955589 +qGlc -4.93288764804306 -4.80389192904729 -4.7481599333446 0.497432177509378 -5.80373466003298 -3.94048108589678 +qAce 2.36528501551032 2.32754516112715 2.31622246610593 0.236148474937182 1.91779688848579 2.7315703702134 +res 1.82384585839848 32.2464726063998 32.5983583967965 7.94534247183111 18.3708176207627 46.805771547064 + + +Goodness of fit (khi2 test) + +khi2 value 1.8238458584244 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.140295835263415 +p-value, i.e. P(X^2<=value) 0.0001339467285235 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycjW.txt b/validation/validation_results/Berges_2021/Berges_2021/ycjW.txt new file mode 100644 index 0000000..d1e19c3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycjW.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.1512 NA NA +3.67805555555556 0.231336 NA NA +4.09222222222222 0.30996 NA NA +4.565 0.388584 NA NA +0.05 NA 14.5572270429628 0.0151390546249419 +1.95 NA 13.947454455017 0.429547130036194 +2.83333333333333 NA 12.872133836164 0.754822524886305 +3.98333333333333 NA 12.2168097019368 1.48329242755575 +4.88333333333333 NA 9.85168690470855 2.01174092137088 +5.16666666666667 NA 9.15358277027717 2.65459164439776 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycjW_res/KEIO_ROBOT3_22.pdf b/validation/validation_results/Berges_2021/Berges_2021/ycjW_res/KEIO_ROBOT3_22.pdf new file mode 100644 index 0000000..f994977 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ycjW_res/KEIO_ROBOT3_22.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycjW_res/KEIO_ROBOT3_22_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ycjW_res/KEIO_ROBOT3_22_log.txt new file mode 100644 index 0000000..1e33403 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycjW_res/KEIO_ROBOT3_22_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.151200 NA NA + [2,] 0.231336 NA NA + [3,] 0.309960 NA NA + [4,] 0.388584 NA NA + [5,] NA 14.557227 0.01513905 + [6,] NA 13.947454 0.42954713 + [7,] NA 12.872134 0.75482252 + [8,] NA 12.216810 1.48329243 + [9,] NA 9.851687 2.01174092 +[10,] NA 9.153583 2.65459164 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03232078 14.51029546 0.11671234 0.54498204 -5.75266470 2.64460919 + +$result$lastp + X Glc Ace mu qGlc qAce + 6.941228e-09 7.737281e-08 -9.348608e-08 -5.348593e-08 9.034292e-08 9.668971e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.01166640 0.43050837 0.18827378 0.08619866 0.82478184 0.36208296 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6195272 + +$result$laststep + X Glc Ace mu qGlc qAce + 6.941228e-09 7.737281e-08 -9.348608e-08 -5.348593e-08 9.034292e-08 9.668971e-08 + +$result$normp +[1] 1.874723e-07 + +$result$res + [1] 0.19130517 0.42775028 -0.46623246 0.02029673 -0.12251290 -0.18131797 0.82903475 -0.77374263 0.25184610 -0.00330734 0.52952921 -0.07871323 -0.30166383 -0.74298606 0.96682073 -0.37298683 + +$result$prevres + [1] 0.19130469 0.42775007 -0.46623240 0.02029730 -0.12251307 -0.18131795 0.82903486 -0.77374248 0.25184610 -0.00330747 0.52952968 -0.07871304 -0.30166381 -0.74298626 0.96682048 -0.37298704 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 239.8242121 0.000000 0 2.230007e+01 0.00000000 0.00000000 + [2,] 371.1095916 0.000000 0 4.411662e+01 0.00000000 0.00000000 + [3,] 465.0806495 0.000000 0 6.151333e+01 0.00000000 0.00000000 + [4,] 601.7645479 0.000000 0 8.878696e+01 0.00000000 0.00000000 + [5,] -0.6338869 2.173913 0 -5.145191e-04 0.00356143 0.00000000 + [6,] -43.4669380 2.173913 0 -1.607927e+00 0.24421468 0.00000000 + [7,] -84.5334241 2.173913 0 -4.829242e+00 0.47494265 0.00000000 + [8,] -178.2005749 2.173913 0 -1.532826e+01 1.00120225 0.00000000 + [9,] -305.5484671 2.173913 0 -3.372660e+01 1.71669374 0.00000000 +[10,] -360.3977454 2.173913 0 -4.264123e+01 2.02485897 0.00000000 +[11,] 0.6702426 0.000000 5 5.440285e-04 0.00000000 0.00819129 +[12,] 45.9599239 0.000000 5 1.700148e+00 0.00000000 0.56169376 +[13,] 89.3817215 0.000000 5 5.106217e+00 0.00000000 1.09236811 +[14,] 188.4210220 0.000000 5 1.620740e+01 0.00000000 2.30276517 +[15,] 323.0727760 0.000000 5 3.566094e+01 0.00000000 3.94839560 +[16,] 381.0678586 0.000000 5 4.508686e+01 0.00000000 4.65717562 + +$result$retres +$result$retres$res + [1] 0.19130469 0.42775007 -0.46623240 0.02029730 -0.12251307 -0.18131795 0.82903486 -0.77374248 0.25184610 -0.00330747 0.52952968 -0.07871304 -0.30166381 -0.74298626 0.96682048 -0.37298704 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15502609 13.215055 0.7121588 + [2,] 0.23989100 12.319247 1.1239788 + [3,] 0.30063535 11.678049 1.4187500 + [4,] 0.38898995 10.745404 1.8475042 + [5,] 0.03321360 14.500871 0.1210450 + [6,] 0.09354338 13.864048 0.4138045 + [7,] 0.15138499 13.253490 0.6944898 + [8,] 0.28331393 11.860888 1.3346952 + [9,] 0.46268175 9.967536 2.2051050 + [10,] 0.53993624 9.152061 2.5799942 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.003826094 NA NA + [2,] -0.008555001 NA NA + [3,] 0.009324648 NA NA + [4,] -0.000405946 NA NA + [5,] NA 0.056356011 -0.10590594 + [6,] NA 0.083406255 0.01574261 + [7,] NA -0.381356037 0.06033276 + [8,] NA 0.355921539 0.14859725 + [9,] NA -0.115849204 -0.19336410 +[10,] NA 0.001521436 0.07459741 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycjW_res/KEIO_ROBOT3_22_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ycjW_res/KEIO_ROBOT3_22_res.txt new file mode 100644 index 0000000..83fc52c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycjW_res/KEIO_ROBOT3_22_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0323207831751712 0.0328006369229599 0.0321574582121978 0.00487962309130827 0.0251413451487073 0.0432527458190126 +Glc 14.5102954580954 14.4957470760368 14.4925979081 0.248452403910754 14.0386043799226 14.9178084171349 +Ace 0.116712344418286 0.137497965859685 0.134235780357532 0.0974756219021714 9.99999999997531e-07 0.324991246418944 +mu 0.544982037848727 0.544038690480224 0.543885269301976 0.0315470564947901 0.480846931864123 0.599072107590925 +qGlc -5.7526646994753 -5.70391445776576 -5.68431556326328 0.45377049327783 -6.510654215701 -4.86826160338258 +qAce 2.64460918654347 2.59636708272594 2.60486083830081 0.245529984973222 2.15737079342971 3.0802614818639 +res 3.83813974559936 23.3437347749837 22.5187679863127 6.49383191834346 11.6885602267519 38.0787597707898 + + +Goodness of fit (khi2 test) + +khi2 value 3.83813974560049 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.383813974560049 +p-value, i.e. P(X^2<=value) 0.0456465215466213 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycjX.txt b/validation/validation_results/Berges_2021/Berges_2021/ycjX.txt new file mode 100644 index 0000000..fc49747 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycjX.txt @@ -0,0 +1,14 @@ +time X Glc Ace +1.8288888888888888 5.1408000000000002E-2 NA NA +2.2613888888888889 6.1992000000000005E-2 NA NA +2.7741666666666664 8.3159999999999998E-2 NA NA +3.2088888888888891 9.6768000000000007E-2 NA NA +3.7063888888888892 0.125496 NA NA +4.2258333333333331 0.160272 NA NA +4.9675000000000002 0.258552 NA NA +2.8 NA 12.7131866601612 0.581183903420994 +3.73333333333333 NA 11.7078725414553 1.01320243897091 +4.28333333333333 NA 11.4781433617575 1.39717622990341 +4.75 NA 10.7117265869643 1.78512511479223 +5.11666666666667 NA 9.8344712383905 2.09950872563035 +5.43333333333333 NA 9.08600448133257 2.44682068819493 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycjX_res/KEIO_ROBOT5_11.pdf b/validation/validation_results/Berges_2021/Berges_2021/ycjX_res/KEIO_ROBOT5_11.pdf new file mode 100644 index 0000000..b91ef69 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ycjX_res/KEIO_ROBOT5_11.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycjX_res/KEIO_ROBOT5_11_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ycjX_res/KEIO_ROBOT5_11_log.txt new file mode 100644 index 0000000..9ae5f2b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycjX_res/KEIO_ROBOT5_11_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.051408 NA NA + [2,] 0.061992 NA NA + [3,] 0.083160 NA NA + [4,] 0.096768 NA NA + [5,] 0.125496 NA NA + [6,] 0.160272 NA NA + [7,] 0.258552 NA NA + [8,] NA 12.713187 0.5811839 + [9,] NA 11.707873 1.0132024 +[10,] NA 11.478143 1.3971762 +[11,] NA 10.711727 1.7851251 +[12,] NA 9.834471 2.0995087 +[13,] NA 9.086004 2.4468207 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01783251 13.57328128 0.15389293 0.53347342 -7.71507740 4.07360268 + +$result$lastp + X Glc Ace mu qGlc qAce + 5.222402e-09 1.511508e-07 -1.630678e-07 -6.928974e-08 5.863439e-08 2.112974e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.003342204 0.327361365 0.147635013 0.042927906 0.845336680 0.377377888 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3046774 + +$result$laststep + X Glc Ace mu qGlc qAce + 5.222402e-09 1.511508e-07 -1.630678e-07 -6.928974e-08 5.863439e-08 2.112974e-07 + +$result$normp +[1] 3.199228e-07 + +$result$res + [1] -0.20498261 -0.12031974 -0.24135640 0.10052558 0.16534361 0.48295379 -0.30713001 -0.06647870 0.50780392 -0.39360789 -0.28475689 0.09568333 0.14135622 0.21495078 0.01149864 -0.20719331 -0.25576669 0.02628180 0.21022878 + +$result$prevres + [1] -0.20498300 -0.12032015 -0.24135680 0.10052523 0.16534338 0.48295379 -0.30712936 -0.06647871 0.50780401 -0.39360780 -0.28475684 0.09568329 0.14135606 0.21495107 0.01149870 -0.20719336 -0.25576680 0.02628168 0.21022870 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 132.6464 0.000000 0 4.326085 0.0000000 0.0000000 + [2,] 167.0702 0.000000 0 6.737310 0.0000000 0.0000000 + [3,] 219.6351 0.000000 0 10.865421 0.0000000 0.0000000 + [4,] 276.9620 0.000000 0 15.848462 0.0000000 0.0000000 + [5,] 361.1463 0.000000 0 23.869676 0.0000000 0.0000000 + [6,] 476.4644 0.000000 0 35.905020 0.0000000 0.0000000 + [7,] 707.7229 0.000000 0 62.692188 0.0000000 0.0000000 + [8,] -108.5798 2.173913 0 -3.361769 0.2509695 0.0000000 + [9,] -198.9307 2.173913 0 -8.687104 0.4598051 0.0000000 +[10,] -277.4852 2.173913 0 -14.320882 0.6413747 0.0000000 +[11,] -364.8129 2.173913 0 -21.369623 0.8432226 0.0000000 +[12,] -450.4227 2.173913 0 -28.910150 1.0410996 0.0000000 +[13,] -539.1051 2.173913 0 -37.259234 1.2460786 0.0000000 +[14,] 131.8606 0.000000 5 4.082574 0.0000000 0.5772299 +[15,] 241.5839 0.000000 5 10.549727 0.0000000 1.0575518 +[16,] 336.9814 0.000000 5 17.391456 0.0000000 1.4751617 +[17,] 443.0333 0.000000 5 25.951536 0.0000000 1.9394120 +[18,] 546.9989 0.000000 5 35.108844 0.0000000 2.3945291 +[19,] 654.6959 0.000000 5 45.248075 0.0000000 2.8659809 + +$result$retres +$result$retres$res + [1] -0.20498300 -0.12032015 -0.24135680 0.10052523 0.16534338 0.48295379 -0.30712936 -0.06647871 0.50780401 -0.39360780 -0.28475684 0.09568329 0.14135606 0.21495107 0.01149870 -0.20719336 -0.25576680 0.02628168 0.21022870 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.04730834 13.147002 0.3789705 + [2,] 0.05958560 12.969449 0.4727196 + [3,] 0.07833286 12.698327 0.6158737 + [4,] 0.09877850 12.402643 0.7719966 + [5,] 0.12880287 11.968431 1.0012626 + [6,] 0.16993108 11.373636 1.3153175 + [7,] 0.25240941 10.180837 1.9451219 + [8,] 0.07941987 12.682606 0.6241741 + [9,] 0.13066767 11.941462 1.0155022 + [10,] 0.17522444 11.297084 1.3557376 + [11,] 0.22475748 10.580738 1.7339718 + [12,] 0.27331607 9.878486 2.1047651 + [13,] 0.32361747 9.151028 2.4888664 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.004099660 NA NA + [2,] 0.002406403 NA NA + [3,] 0.004827136 NA NA + [4,] -0.002010505 NA NA + [5,] -0.003306868 NA NA + [6,] -0.009659076 NA NA + [7,] 0.006142587 NA NA + [8,] NA 0.03058021 -0.042990213 + [9,] NA -0.23358984 -0.002299741 +[10,] NA 0.18105959 0.041438671 +[11,] NA 0.13098815 0.051153360 +[12,] NA -0.04401432 -0.005256336 +[13,] NA -0.06502379 -0.042045741 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ycjX_res/KEIO_ROBOT5_11_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ycjX_res/KEIO_ROBOT5_11_res.txt new file mode 100644 index 0000000..4c161a3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ycjX_res/KEIO_ROBOT5_11_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0178325092500709 0.0183592995190549 0.0184550171396416 0.0039674652038556 0.0118989077256237 0.026032795018102 +Glc 13.5732812787785 13.5577394137708 13.5689963226631 0.285402004544128 12.9585098729975 14.1291097750898 +Ace 0.153892927130115 0.161402563314212 0.150655511367206 0.11632195612608 9.99999999994061e-07 0.371768280819381 +mu 0.533473420820518 0.53147943270819 0.523005020010298 0.043982876778787 0.453955684869016 0.618525939771214 +qGlc -7.71507740459228 -7.68281856363858 -7.77525091268092 0.966705275496111 -9.41241185906493 -5.91634510897855 +qAce 4.07360268314257 4.07435041815882 4.07396892551769 0.35612791270999 3.43420427365229 4.82961754929412 +res 1.20676810804083 32.5919016303454 31.1435047001942 7.84404207696175 17.609190507711 49.2263008929828 + + +Goodness of fit (khi2 test) + +khi2 value 1.20676810804211 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.0928283160032395 +p-value, i.e. P(X^2<=value) 1.1904993726407e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydbC.txt b/validation/validation_results/Berges_2021/Berges_2021/ydbC.txt new file mode 100644 index 0000000..3286cbc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydbC.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.108864 NA NA NA +3.34194444444444 0.167832 NA NA NA +3.9975 0.247968 NA NA NA +4.52333333333333 0.374976 NA NA NA +1.95 NA 13.6659005676694 0.392662523873551 0 +3.25 NA 12.8629473963873 0.961475148473047 0 +4.08333333333333 NA 11.3498025448378 1.41082498029099 0 +4.76666666666667 NA 10.1322329800833 1.94394289691752 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydbC_res/KEIO_ROBOT2_31.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydbC_res/KEIO_ROBOT2_31.pdf new file mode 100644 index 0000000..c8ef4d0 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydbC_res/KEIO_ROBOT2_31.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydbC_res/KEIO_ROBOT2_31_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydbC_res/KEIO_ROBOT2_31_log.txt new file mode 100644 index 0000000..01138cd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydbC_res/KEIO_ROBOT2_31_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.108864 NA NA NA +[2,] 0.167832 NA NA NA +[3,] 0.247968 NA NA NA +[4,] 0.374976 NA NA NA +[5,] NA 13.66590 0.3926625 0 +[6,] NA 12.86295 0.9614751 0 +[7,] NA 11.34980 1.4108250 0 +[8,] NA 10.13223 1.9439429 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.013984e-02 1.417397e+01 2.706868e-01 1.000000e-06 6.411445e-01 -6.508739e+00 2.717528e+00 -2.156602e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-9.774825e-09 -3.107539e-07 2.038460e-07 -2.117582e-22 1.191087e-07 3.362703e-08 -2.361842e-07 1.087142e-12 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.006924555 0.499555325 0.216357815 0.206143037 0.082213649 1.253658137 0.543468758 0.524139991 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4735182 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-9.774825e-09 -3.107539e-07 2.038460e-07 -2.117582e-22 1.191087e-07 3.362703e-08 -2.361842e-07 1.087142e-12 + +$result$normp +[1] 4.575121e-07 + +$result$res + [1] -4.367885e-01 1.901426e-01 6.666779e-01 -4.455611e-01 -2.736077e-03 -2.764624e-01 4.910466e-01 -2.118481e-01 4.533933e-01 -4.515668e-01 -2.765109e-01 2.746843e-01 4.156198e-06 2.617346e-06 6.954273e-07 -1.857379e-06 + +$result$prevres + [1] -4.367876e-01 1.901434e-01 6.666780e-01 -4.455621e-01 -2.735790e-03 -2.764624e-01 4.910464e-01 -2.118482e-01 4.533928e-01 -4.515668e-01 -2.765106e-01 2.746847e-01 4.156198e-06 2.617345e-06 6.954245e-07 -1.857383e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.485824e+02 0.000000 0 0 1.252298e+01 0.0000000 0.0000000 0.0000000 + [2,] 4.261077e+02 0.000000 0 0 2.867971e+01 0.0000000 0.0000000 0.0000000 + [3,] 6.487178e+02 0.000000 0 0 5.222765e+01 0.0000000 0.0000000 0.0000000 + [4,] 9.088072e+02 0.000000 0 0 8.279165e+01 0.0000000 0.0000000 0.0000000 + [5,] -5.497729e+01 2.173913 0 0 -1.298852e+00 0.1701150 0.0000000 0.0000000 + [6,] -1.552401e+02 2.173913 0 0 -6.729225e+00 0.4803559 0.0000000 0.0000000 + [7,] -2.804613e+02 2.173913 0 0 -1.606946e+01 0.8678251 0.0000000 0.0000000 + [8,] -4.467875e+02 2.173913 0 0 -3.097556e+01 1.3824847 0.0000000 0.0000000 + [9,] 5.279447e+01 0.000000 5 0 1.247282e+00 0.0000000 0.3912645 0.0000000 +[10,] 1.490764e+02 0.000000 5 0 6.462047e+00 0.0000000 1.1048185 0.0000000 +[11,] 2.693258e+02 0.000000 5 0 1.543143e+01 0.0000000 1.9959978 0.0000000 +[12,] 4.290483e+02 0.000000 5 0 2.974570e+01 0.0000000 3.1797148 0.0000000 +[13,] -4.189716e-05 0.000000 0 5 -9.898304e-07 0.0000000 0.0000000 0.3912645 +[14,] -1.183055e-04 0.000000 0 5 -5.128215e-06 0.0000000 0.0000000 1.1048185 +[15,] -2.137343e-04 0.000000 0 5 -1.224623e-05 0.0000000 0.0000000 1.9959978 +[16,] -3.404884e-04 0.000000 0 5 -2.360589e-05 0.0000000 0.0000000 3.1797148 + +$result$retres +$result$retres$res + [1] -4.367876e-01 1.901434e-01 6.666780e-01 -4.455621e-01 -2.735790e-03 -2.764624e-01 4.910464e-01 -2.118482e-01 4.533928e-01 -4.515668e-01 -2.765106e-01 2.746847e-01 4.156198e-06 2.617345e-06 6.954245e-07 -1.857383e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10012825 13.36195 0.6097222 7.309448e-07 + [2,] 0.17163487 12.63603 0.9128072 4.904196e-07 + [3,] 0.26130156 11.72576 1.2928648 1.888097e-07 + [4,] 0.36606476 10.66223 1.7369098 -1.635800e-07 + [5,] 0.07031126 13.66464 0.4833411 8.312395e-07 + [6,] 0.16180950 12.73577 0.8711618 5.234689e-07 + [7,] 0.27608443 11.57568 1.3555229 1.390849e-07 + [8,] 0.42787114 10.03478 1.9988798 -3.714767e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.008735752 NA NA NA +[2,] -0.003802867 NA NA NA +[3,] -0.013333561 NA NA NA +[4,] 0.008911241 NA NA NA +[5,] NA 0.001258463 -0.09067856 -8.312395e-07 +[6,] NA 0.127172722 0.09031336 -5.234689e-07 +[7,] NA -0.225881349 0.05530213 -1.390849e-07 +[8,] NA 0.097450163 -0.05493693 3.714767e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydbC_res/KEIO_ROBOT2_31_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydbC_res/KEIO_ROBOT2_31_res.txt new file mode 100644 index 0000000..f185e87 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydbC_res/KEIO_ROBOT2_31_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0201398375460333 0.0203893734212257 0.0204986586134641 0.00454588380486823 0.0130161230328249 0.0294740596040543 +Glc 14.1739695295929 14.2291857645197 14.2340090024882 0.351262104493357 13.5260407217738 15.0184503066027 +Ace 0.270686781018409 0.270070419932278 0.282442591185614 0.143348899082357 9.99999999995709e-07 0.510342495674033 +Lac 1e-06 0.083680334337042 0.0785465460817224 0.0732029096318095 9.9999999998777e-07 0.28213777208646 +mu 0.641144543927124 0.644018041577925 0.634329610577633 0.053183480809199 0.552267125841663 0.748429638106734 +qGlc -6.50873932686511 -6.71898652232562 -6.69351581212077 0.934816816561429 -8.44786749763572 -4.99704504324349 +qAce 2.71752844492203 2.69420203311803 2.69385610530547 0.369513560158897 2.0053914677321 3.47470495680315 +qLac -2.15660220107422e-06 -0.000451515764507183 -0.0184711627182295 0.206600839955494 -0.371645865442015 0.371520576024728 +res 1.79375562220923 19.2815438709098 17.9185886470361 6.4375632851952 9.58811739968651 34.264646471818 + + +Goodness of fit (khi2 test) + +khi2 value 1.79375562221243 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.224219452776554 +p-value, i.e. P(X^2<=value) 0.0133050514412937 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydbL.txt b/validation/validation_results/Berges_2021/Berges_2021/ydbL.txt new file mode 100644 index 0000000..4337d80 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydbL.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.195 0.065016 NA NA +1.61361111111111 0.081648 NA NA +2.36138888888889 0.127008 NA NA +3.28638888888889 0.199584 NA NA +3.81944444444444 0.30996 NA NA +4.41083333333333 0.397656 NA NA +0.283333333333333 NA 14.5424613755221 0.0424514793611834 +1.91666666666667 NA 13.4886014247737 0.398846625783488 +2.7 NA 13.4932339216344 0.667101239324003 +3.61666666666667 NA 12.5977582555031 1.12614209441127 +4.05 NA 11.7714619018929 1.40421195513424 +4.75 NA 10.598185079174 2.10218548130665 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydbL_res/KEIO_ROBOT4_14.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydbL_res/KEIO_ROBOT4_14.pdf new file mode 100644 index 0000000..cf595ae Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydbL_res/KEIO_ROBOT4_14.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydbL_res/KEIO_ROBOT4_14_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydbL_res/KEIO_ROBOT4_14_log.txt new file mode 100644 index 0000000..11d97a3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydbL_res/KEIO_ROBOT4_14_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.065016 NA NA + [3,] 0.081648 NA NA + [4,] 0.127008 NA NA + [5,] 0.199584 NA NA + [6,] 0.309960 NA NA + [7,] 0.397656 NA NA + [8,] NA 14.54246 0.04245148 + [9,] NA 13.48860 0.39884663 +[10,] NA 13.49323 0.66710124 +[11,] NA 12.59776 1.12614209 +[12,] NA 11.77146 1.40421196 +[13,] NA 10.59819 2.10218548 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03410687 14.39175951 0.08057552 0.56000101 -4.73755189 2.52642029 + +$result$lastp + X Glc Ace mu qGlc qAce + 7.122471e-09 7.706696e-08 -4.350887e-08 -5.429581e-08 7.746215e-08 -3.436274e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006148289 0.317884468 0.139251046 0.045652919 0.740307952 0.327561156 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4725563 + +$result$laststep + X Glc Ace mu qGlc qAce + 7.122471e-09 7.706696e-08 -4.350887e-08 -5.429581e-08 7.746215e-08 -3.436274e-08 + +$result$normp +[1] 1.342099e-07 + +$result$res + [1] -0.10905669 0.07918449 0.12729539 0.04863118 0.76265221 -1.01958122 0.27996436 -0.43546896 0.75583248 -0.26456093 -0.22654511 0.26414480 -0.09340228 0.32290947 -0.11024914 -0.21232737 -0.16648321 0.04453776 0.12161249 + +$result$prevres + [1] -0.10905705 0.07918402 0.12729488 0.04863066 0.76265188 -1.01958124 0.27996498 -0.43546911 0.75583247 -0.26456087 -0.22654502 0.26414487 -0.09340235 0.32290966 -0.11024912 -0.21232744 -0.16648333 0.04453767 0.12161255 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 97.633852 0.000000 0 3.97933090 0.00000000 0.00000000 + [3,] 123.426636 0.000000 0 6.79281044 0.00000000 0.00000000 + [4,] 187.617120 0.000000 0 15.11059991 0.00000000 0.00000000 + [5,] 314.946969 0.000000 0 35.30190266 0.00000000 0.00000000 + [6,] 424.501674 0.000000 0 55.29951611 0.00000000 0.00000000 + [7,] 591.164521 0.000000 0 88.93459585 0.00000000 0.00000000 + [8,] -3.162302 2.173913 0 -0.01568352 0.02276623 0.00000000 + [9,] -35.405034 2.173913 0 -1.36038854 0.25488998 0.00000000 +[10,] -65.027308 2.173913 0 -3.72138856 0.46814837 0.00000000 +[11,] -120.988790 2.173913 0 -9.82412394 0.87102951 0.00000000 +[12,] -159.268671 2.173913 0 -14.84037877 1.14661626 0.00000000 +[13,] -244.534483 2.173913 0 -27.70256451 1.76046684 0.00000000 +[14,] 3.878670 0.000000 5 0.01923637 0.00000000 0.05236233 +[15,] 43.425465 0.000000 5 1.66856227 0.00000000 0.58624695 +[16,] 79.758179 0.000000 5 4.56440817 0.00000000 1.07674124 +[17,] 148.396818 0.000000 5 12.04961827 0.00000000 2.00336788 +[18,] 195.348379 0.000000 5 18.20222344 0.00000000 2.63721740 +[19,] 299.929763 0.000000 5 33.97812662 0.00000000 4.04907373 + +$result$retres +$result$retres$res + [1] -0.10905705 0.07918402 0.12729488 0.04863066 0.76265188 -1.01958124 0.27996498 -0.43546911 0.75583247 -0.26456087 -0.22654502 0.26414487 -0.09340235 0.32290966 -0.11024912 -0.21232744 -0.16648333 0.04453767 0.12161255 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03410686 14.39176 0.08057556 + [2,] 0.06659968 14.11687 0.22716550 + [3,] 0.08419390 13.96803 0.30654105 + [4,] 0.12798061 13.59760 0.50408290 + [5,] 0.21483704 12.86280 0.89593187 + [6,] 0.28956838 12.23058 1.23307903 + [7,] 0.40325530 11.26880 1.74597262 + [8,] 0.03997145 14.34215 0.10703341 + [9,] 0.09976664 13.83628 0.37679680 + [10,] 0.15470211 13.37154 0.62463575 + [11,] 0.25848449 12.49355 1.09284543 + [12,] 0.32947577 11.89297 1.41311949 + [13,] 0.48760398 10.55522 2.12650799 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0021811410 NA NA + [2,] -0.0015836803 NA NA + [3,] -0.0025458976 NA NA + [4,] -0.0009726133 NA NA + [5,] -0.0152530376 NA NA + [6,] 0.0203916247 NA NA + [7,] -0.0055992995 NA NA + [8,] NA 0.20031579 -0.064581933 + [9,] NA -0.34768294 0.022049823 +[10,] NA 0.12169800 0.042465487 +[11,] NA 0.10421071 0.033296666 +[12,] NA -0.12150664 -0.008907533 +[13,] NA 0.04296508 -0.024322511 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydbL_res/KEIO_ROBOT4_14_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydbL_res/KEIO_ROBOT4_14_res.txt new file mode 100644 index 0000000..b3a8868 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydbL_res/KEIO_ROBOT4_14_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0341068661412457 0.0343580516947823 0.03452528247475 0.00438354779103649 0.0269574953624906 0.0420885589895225 +Glc 14.3917595147465 14.3736240635849 14.382689379819 0.21485060520978 14.0081464069358 14.7648841214814 +Ace 0.0805755177325966 0.090534793595531 0.0821955337823634 0.0751156578279101 9.99999999994061e-07 0.250891214562701 +mu 0.560001007631421 0.559164739738566 0.557540402070521 0.0315404700167216 0.506166229198874 0.618213791951273 +qGlc -4.73755188741049 -4.7305946684886 -4.75827822927358 0.565168445710674 -5.98625569228922 -3.72322270303966 +qAce 2.5264202890914 2.52353485684445 2.52866020858814 0.208172289707475 2.11159460363262 2.88327764323736 +res 2.90302270086771 32.8759730222061 32.3944619052588 7.42821247628134 19.3675523852665 45.8511808926504 + + +Goodness of fit (khi2 test) + +khi2 value 2.90302270086918 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.223309438528399 +p-value, i.e. P(X^2<=value) 0.00173811838533262 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcH.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcH.txt new file mode 100644 index 0000000..1aa0bf5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcH.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.061992 NA NA +1.61361111111111 0.080136 NA NA +2.36138888888889 0.12852 NA NA +3.28638888888889 0.216216 NA NA +3.81944444444444 0.319032 NA NA +4.41083333333333 0.449064 NA NA +0.283333333333333 NA 13.99042746806 0.0399367051802503 +1.91666666666667 NA 13.7534802924685 0.415458495608456 +2.7 NA 13.4186128263691 0.722866410067539 +3.61666666666667 NA 12.4282739407315 1.1721387885519 +4.05 NA 11.2163322093381 1.46408492068005 +4.75 NA 9.85710882404138 2.03935743528089 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcH_res/KEIO_ROBOT4_34.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydcH_res/KEIO_ROBOT4_34.pdf new file mode 100644 index 0000000..14fe4b9 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydcH_res/KEIO_ROBOT4_34.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcH_res/KEIO_ROBOT4_34_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcH_res/KEIO_ROBOT4_34_log.txt new file mode 100644 index 0000000..bf94cc6 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcH_res/KEIO_ROBOT4_34_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.061992 NA NA + [3,] 0.080136 NA NA + [4,] 0.128520 NA NA + [5,] 0.216216 NA NA + [6,] 0.319032 NA NA + [7,] 0.449064 NA NA + [8,] NA 13.990427 0.03993671 + [9,] NA 13.753480 0.41545850 +[10,] NA 13.418613 0.72286641 +[11,] NA 12.428274 1.17213879 +[12,] NA 11.216332 1.46408492 +[13,] NA 9.857109 2.03935744 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0302834 14.2764351 0.1542366 0.6112150 -5.1766802 2.3205386 + +$result$lastp + X Glc Ace mu qGlc qAce +-7.397219e-09 -1.946876e-07 -6.759207e-08 6.106005e-08 1.569628e-07 3.671971e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.005215314 0.296681921 0.129141791 0.043141891 0.669088418 0.291658118 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4496696 + +$result$laststep + X Glc Ace mu qGlc qAce +-7.397219e-09 -1.946876e-07 -6.759207e-08 6.106005e-08 1.569628e-07 3.671971e-07 + +$result$normp +[1] 4.535702e-07 + +$result$res + [1] -0.224630076 0.043687912 0.052988040 -0.013919492 0.475140003 -0.318831177 -0.013424845 0.516330791 -0.104760177 -0.481694796 -0.510239640 0.582229615 -0.001865792 0.680194078 -0.025981469 -0.423844153 -0.421091129 -0.290803049 0.481525722 + +$result$prevres + [1] -0.224629706 0.043688450 0.052988631 -0.013918851 0.475140495 -0.318831004 -0.013425408 0.516331186 -0.104760009 -0.481694773 -0.510239789 0.582229404 -0.001866019 0.680194424 -0.025981110 -0.423843858 -0.421091081 -0.290803237 0.481524862 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 103.795738 0.000000 0 3.75622970 0.00000000 0.00000000 + [3,] 134.059843 0.000000 0 6.55092004 0.00000000 0.00000000 + [4,] 211.735799 0.000000 0 15.14141718 0.00000000 0.00000000 + [5,] 372.677385 0.000000 0 37.08998944 0.00000000 0.00000000 + [6,] 516.215681 0.000000 0 59.70849269 0.00000000 0.00000000 + [7,] 740.992433 0.000000 0 98.97810576 0.00000000 0.00000000 + [8,] -3.481279 2.173913 0 -0.01536606 0.02036536 0.00000000 + [9,] -40.999970 2.173913 0 -1.41706252 0.23984844 0.00000000 +[10,] -77.485546 2.173913 0 -4.00195896 0.45328784 0.00000000 +[11,] -149.520232 2.173913 0 -10.98460271 0.87468833 0.00000000 +[12,] -200.445374 2.173913 0 -16.91105141 1.17259870 0.00000000 +[13,] -317.305706 2.173913 0 -32.57039452 1.85622771 0.00000000 +[14,] 3.589252 0.000000 5 0.01584265 0.00000000 0.04684033 +[15,] 42.271606 0.000000 5 1.46101348 0.00000000 0.55165142 +[16,] 79.888802 0.000000 5 4.12608189 0.00000000 1.04256203 +[17,] 154.157683 0.000000 5 11.32529613 0.00000000 2.01178316 +[18,] 206.662296 0.000000 5 17.43555686 0.00000000 2.69697701 +[19,] 327.147115 0.000000 5 33.58058302 0.00000000 4.26932374 + +$result$retres +$result$retres$res + [1] -0.224629706 0.043688450 0.052988631 -0.013918851 0.475140495 -0.318831004 -0.013425408 0.516331186 -0.104760009 -0.481694773 -0.510239789 0.582229404 -0.001866019 0.680194424 -0.025981110 -0.423843858 -0.421091081 -0.290803237 0.481524862 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03028341 14.27644 0.1542366 + [2,] 0.06286577 14.00048 0.2779388 + [3,] 0.08119577 13.84523 0.3475305 + [4,] 0.12824162 13.44678 0.5261447 + [5,] 0.22571881 12.62120 0.8962265 + [6,] 0.31265538 11.88489 1.2262898 + [7,] 0.44879549 10.73185 1.7431592 + [8,] 0.03600931 14.22794 0.1759756 + [9,] 0.09771893 13.70529 0.4102623 + [10,] 0.15772931 13.19703 0.6380976 + [11,] 0.27620981 12.19356 1.0879206 + [12,] 0.35996996 11.48416 1.4059243 + [13,] 0.55217833 9.85625 2.1356624 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0044925941 NA NA + [2,] -0.0008737690 NA NA + [3,] -0.0010597726 NA NA + [4,] 0.0002783770 NA NA + [5,] -0.0095028099 NA NA + [6,] 0.0063766201 NA NA + [7,] 0.0002685082 NA NA + [8,] NA -0.2375123456 -0.136038885 + [9,] NA 0.0481896039 0.005196222 +[10,] NA 0.2215795956 0.084768772 +[11,] NA 0.2347103031 0.084218216 +[12,] NA -0.2678255259 0.058160647 +[13,] NA 0.0008583686 -0.096304972 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcH_res/KEIO_ROBOT4_34_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcH_res/KEIO_ROBOT4_34_res.txt new file mode 100644 index 0000000..de0d2f9 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcH_res/KEIO_ROBOT4_34_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0302833984758504 0.0304948175343881 0.0304911598635273 0.00361722550273864 0.0242300197489837 0.0376974388582382 +Glc 14.276435106471 14.2850299473618 14.2809903955048 0.196660517691918 13.9606064298283 14.6229893715837 +Ace 0.15423656536138 0.168891494628399 0.160968537667513 0.0807587633296634 0.0234217468729511 0.327370610553098 +mu 0.611215041080458 0.611206451566334 0.609695531184048 0.0285325052276576 0.554964758458854 0.66308049194495 +qGlc -5.17668017581414 -5.20084941610434 -5.22788758250299 0.564792229829698 -6.2313232140528 -4.14044609813421 +qAce 2.32053857920079 2.30084249186022 2.29857699552218 0.213691392034231 1.88742579195487 2.73827492828721 +res 2.62863577036101 32.5886762840153 32.6104481708939 7.69337879100354 18.7855097581454 45.887530404773 + + +Goodness of fit (khi2 test) + +khi2 value 2.62863577036412 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.202202751566471 +p-value, i.e. P(X^2<=value) 0.00102373712654554 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcI.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcI.txt new file mode 100644 index 0000000..f5a3300 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcI.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.195 0.058968 NA NA +1.61361111111111 0.074088 NA NA +2.36138888888889 0.111888 NA NA +3.28638888888889 0.190512 NA NA +3.81944444444444 0.2646 NA NA +4.41083333333333 0.37044 NA NA +0.283333333333333 NA 14.2075431970974 0.0362503857945569 +1.91666666666667 NA 14.2541154607933 0.34900477725699 +2.7 NA 13.5065055036334 0.622280585244065 +3.61666666666667 NA 12.80261001675 1.04137354932284 +4.05 NA 12.3221641511158 1.25312751569365 +4.75 NA 10.6562475965489 1.69193559900367 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcI_res/KEIO_ROBOT4_10.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydcI_res/KEIO_ROBOT4_10.pdf new file mode 100644 index 0000000..df58f10 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydcI_res/KEIO_ROBOT4_10.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcI_res/KEIO_ROBOT4_10_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcI_res/KEIO_ROBOT4_10_log.txt new file mode 100644 index 0000000..679cfa9 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcI_res/KEIO_ROBOT4_10_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.058968 NA NA + [3,] 0.074088 NA NA + [4,] 0.111888 NA NA + [5,] 0.190512 NA NA + [6,] 0.264600 NA NA + [7,] 0.370440 NA NA + [8,] NA 14.20754 0.03625039 + [9,] NA 14.25412 0.34900478 +[10,] NA 13.50651 0.62228059 +[11,] NA 12.80261 1.04137355 +[12,] NA 12.32216 1.25312752 +[13,] NA 10.65625 1.69193560 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0292953 14.5277073 0.1266283 0.5747114 -5.0639213 2.2768969 + +$result$lastp + X Glc Ace mu qGlc qAce + 7.723009e-10 -1.361651e-07 -9.070641e-08 -7.433898e-09 4.709846e-07 2.784202e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.00498819 0.26478869 0.11526376 0.04298323 0.68896357 0.30037742 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3953256 + +$result$laststep + X Glc Ace mu qGlc qAce + 7.723009e-10 -1.361651e-07 -9.070641e-08 -7.433898e-09 4.709846e-07 2.784202e-07 + +$result$normp +[1] 5.711119e-07 + +$result$res + [1] -0.122835117 -0.037463308 -0.001725067 0.096178773 0.157867474 -0.075378051 -0.042700885 0.596774240 -0.532449935 0.132767290 -0.173775785 -0.397703927 0.374388118 0.554513151 0.053828582 -0.319742273 -0.515728288 -0.262805263 0.489934089 + +$result$prevres + [1] -0.12283516 -0.03746336 -0.00172512 0.09617872 0.15786746 -0.07537802 -0.04270077 0.59677453 -0.53244972 0.13276742 -0.17377582 -0.39770408 0.37438768 0.55451359 0.05382887 -0.31974211 -0.51572837 -0.26280550 0.48993351 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 99.365323 0.000000 0 3.47856929 0.00000000 0.00000000 + [3,] 126.391444 0.000000 0 5.97467733 0.00000000 0.00000000 + [4,] 194.248884 0.000000 0 13.43766937 0.00000000 0.00000000 + [5,] 330.546828 0.000000 0 31.82363985 0.00000000 0.00000000 + [6,] 449.035285 0.000000 0 50.24334782 0.00000000 0.00000000 + [7,] 630.794059 0.000000 0 81.50910904 0.00000000 0.00000000 + [8,] -3.387394 2.173913 0 -0.01443961 0.01959641 0.00000000 + [9,] -38.477675 2.173913 0 -1.27467038 0.22259722 0.00000000 +[10,] -71.248187 2.173913 0 -3.51883866 0.41217793 0.00000000 +[11,] -133.945993 2.173913 0 -9.39348690 0.77489104 0.00000000 +[12,] -177.242219 2.173913 0 -14.26698906 1.02536407 0.00000000 +[13,] -274.509230 2.173913 0 -26.87132915 1.58806351 0.00000000 +[14,] 3.503078 0.000000 5 0.01493274 0.00000000 0.04507175 +[15,] 39.791744 0.000000 5 1.31820225 0.00000000 0.51197361 +[16,] 73.681418 0.000000 5 3.63901219 0.00000000 0.94800924 +[17,] 138.520446 0.000000 5 9.71428831 0.00000000 1.78224940 +[18,] 183.295302 0.000000 5 14.75422776 0.00000000 2.35833735 +[19,] 283.884124 0.000000 5 27.78902463 0.00000000 3.65254608 + +$result$retres +$result$retres$res + [1] -0.12283516 -0.03746336 -0.00172512 0.09617872 0.15786746 -0.07537802 -0.04270077 0.59677453 -0.53244972 0.13276742 -0.17377582 -0.39770408 0.37438768 0.55451359 0.05382887 -0.31974211 -0.51572837 -0.26280550 0.48993351 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02929530 14.52771 0.1266284 + [2,] 0.05821873 14.27286 0.2412175 + [3,] 0.07405350 14.13333 0.3039518 + [4,] 0.11381157 13.78301 0.4614656 + [5,] 0.19366935 13.07937 0.7778468 + [6,] 0.26309244 12.46766 1.0528878 + [7,] 0.36958598 11.52932 1.4747948 + [8,] 0.03447595 14.48206 0.1471531 + [9,] 0.08814272 14.00919 0.3597706 + [10,] 0.13826165 13.56758 0.5583322 + [11,] 0.23415113 12.72267 0.9382279 + [12,] 0.30036799 12.13922 1.2005664 + [13,] 0.44912731 10.82847 1.7899223 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0024567031 NA NA + [2,] 0.0007492672 NA NA + [3,] 0.0000345024 NA NA + [4,] -0.0019235745 NA NA + [5,] -0.0031573491 NA NA + [6,] 0.0015075605 NA NA + [7,] 0.0008540153 NA NA + [8,] NA -0.27451628 -0.11090272 + [9,] NA 0.24492687 -0.01076577 +[10,] NA -0.06107301 0.06394842 +[11,] NA 0.07993688 0.10314567 +[12,] NA 0.18294388 0.05256110 +[13,] NA -0.17221833 -0.09798670 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcI_res/KEIO_ROBOT4_10_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcI_res/KEIO_ROBOT4_10_res.txt new file mode 100644 index 0000000..fb603dd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcI_res/KEIO_ROBOT4_10_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0292952976530054 0.0301461623539683 0.0298536982732652 0.0039218593912551 0.0226478101244989 0.0379601427402495 +Glc 14.5277073087856 14.5595422630372 14.5488121871248 0.182332275676085 14.263163585749 14.9147709571263 +Ace 0.126628269626235 0.139857126720452 0.131466873618803 0.0806494189916846 1.00000000000066e-06 0.325766363824916 +mu 0.574711445054875 0.569588989309994 0.567653275203222 0.0309875164680523 0.514399138539243 0.634402951097772 +qGlc -5.06392129749565 -5.08702326456366 -5.03842938401035 0.586894613444123 -6.20946852173557 -4.10676068904435 +qAce 2.27689686905812 2.2498030789687 2.23543339676991 0.235105819305887 1.85251251341557 2.70578966452534 +res 2.03167029009032 31.8805170703335 30.4992588950639 7.7535841067275 19.3642625988134 50.0869996660008 + + +Goodness of fit (khi2 test) + +khi2 value 2.03167029009141 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.156282330007032 +p-value, i.e. P(X^2<=value) 0.000247218842337235 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcJ.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcJ.txt new file mode 100644 index 0000000..a907deb --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcJ.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.1992000000000005E-2 NA NA +2.2613888888888889 8.0135999999999999E-2 NA NA +2.7741666666666664 0.10886399999999999 NA NA +3.2088888888888891 0.13910400000000001 NA NA +3.7063888888888892 0.185976 NA NA +4.2258333333333331 0.28576800000000002 NA NA +4.6355555555555554 0.36892799999999998 NA NA +4.9675000000000002 0.50349600000000005 NA NA +2.8 NA 12.3340476792856 0.72013989236879 +3.73333333333333 NA 11.7155922721535 1.37549176990552 +4.28333333333333 NA 10.834394566381 1.88412768065121 +4.75 NA 9.93273493765846 2.48922347602994 +5.11666666666667 NA 8.62534169715793 2.9184150328111 +5.43333333333333 NA 8.14771334544394 3.55285728629418 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcJ_res/KEIO_ROBOT5_2.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydcJ_res/KEIO_ROBOT5_2.pdf new file mode 100644 index 0000000..21631de Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydcJ_res/KEIO_ROBOT5_2.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcJ_res/KEIO_ROBOT5_2_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcJ_res/KEIO_ROBOT5_2_log.txt new file mode 100644 index 0000000..a5bd209 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcJ_res/KEIO_ROBOT5_2_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.061992 NA NA + [2,] 0.080136 NA NA + [3,] 0.108864 NA NA + [4,] 0.139104 NA NA + [5,] 0.185976 NA NA + [6,] 0.285768 NA NA + [7,] 0.368928 NA NA + [8,] 0.503496 NA NA + [9,] NA 12.334048 0.7201399 +[10,] NA 11.715592 1.3754918 +[11,] NA 10.834395 1.8841277 +[12,] NA 9.932735 2.4892235 +[13,] NA 8.625342 2.9184150 +[14,] NA 8.147713 3.5528573 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0145274 13.0604222 0.4181185 0.7069624 -5.4982699 3.4195696 + +$result$lastp + X Glc Ace mu qGlc qAce +-5.238850e-09 -2.755313e-07 2.268133e-07 8.106526e-08 1.537629e-07 -2.046983e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.003520695 0.494477541 0.224081530 0.053074076 0.838132976 0.372994334 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5607842 + +$result$laststep + X Glc Ace mu qGlc qAce +-5.238850e-09 -2.755313e-07 2.268133e-07 8.106526e-08 1.537629e-07 -2.046983e-07 + +$result$normp +[1] 4.466601e-07 + +$result$res + [1] -0.45304161 -0.41367849 -0.28010633 0.06553718 0.68118943 0.11997646 0.80277019 -0.83433474 0.04664478 -0.27041335 0.01056661 -0.01257627 0.74113535 -0.51535712 0.68196062 -0.21806529 -0.42293212 -0.61143533 0.23003056 0.34044156 + +$result$prevres + [1] -0.45304105 -0.41367786 -0.28010563 0.06553789 0.68119003 0.11997672 0.80276990 -0.83433576 0.04664501 -0.27041331 0.01056654 -0.01257638 0.74113526 -0.51535712 0.68196008 -0.21806547 -0.42293208 -0.61143514 0.23003082 0.34044179 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 182.1770 0.000000 0 4.840262 0.0000000 0.0000000 + [2,] 247.3340 0.000000 0 8.125446 0.0000000 0.0000000 + [3,] 355.4037 0.000000 0 14.323284 0.0000000 0.0000000 + [4,] 483.2754 0.000000 0 22.528768 0.0000000 0.0000000 + [5,] 686.9767 0.000000 0 36.989724 0.0000000 0.0000000 + [6,] 991.8065 0.000000 0 60.887399 0.0000000 0.0000000 + [7,] 1325.0245 0.000000 0 89.230596 0.0000000 0.0000000 + [8,] 1675.4858 0.000000 0 120.911256 0.0000000 0.0000000 + [9,] -105.4855 2.173913 0 -2.810909 0.2787114 0.0000000 +[10,] -219.8574 2.173913 0 -8.323220 0.5809022 0.0000000 +[11,] -332.3804 2.173913 0 -14.904570 0.8782080 0.0000000 +[12,] -468.8997 2.173913 0 -23.887751 1.2389164 0.0000000 +[13,] -612.6589 2.173913 0 -34.207282 1.6187537 0.0000000 +[14,] -770.6234 2.173913 0 -46.325977 2.0361240 0.0000000 +[15,] 150.8919 0.000000 5 4.020870 0.0000000 0.6410363 +[16,] 314.4954 0.000000 5 11.905966 0.0000000 1.3360751 +[17,] 475.4541 0.000000 5 21.320271 0.0000000 2.0198783 +[18,] 670.7385 0.000000 5 34.170278 0.0000000 2.8495078 +[19,] 876.3790 0.000000 5 48.931871 0.0000000 3.7231334 +[20,] 1102.3397 0.000000 5 66.267080 0.0000000 4.6830852 + +$result$retres +$result$retres$res + [1] -0.45304105 -0.41367786 -0.28010563 0.06553789 0.68119003 0.11997672 0.80276990 -0.83433576 0.04664501 -0.27041331 0.01056654 -0.01257638 0.74113526 -0.51535712 0.68196008 -0.21806547 -0.42293208 -0.61143514 0.23003082 0.34044179 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05293118 12.761744 0.6038769 + [2,] 0.07186244 12.614510 0.6954473 + [3,] 0.10326189 12.370306 0.8473261 + [4,] 0.14041476 12.081357 1.0270341 + [5,] 0.19959980 11.621056 1.3133116 + [6,] 0.28816753 10.932237 1.7417128 + [7,] 0.38498340 10.179269 2.2100102 + [8,] 0.48680928 9.387337 2.7025410 + [9,] 0.10516511 12.355504 0.8565319 + [10,] 0.20343836 11.591202 1.3318787 + [11,] 0.30012299 10.839255 1.7995413 + [12,] 0.41742635 9.926950 2.3669364 + [13,] 0.54095043 8.966264 2.9644212 + [14,] 0.67668039 7.910649 3.6209456 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.009060821 NA NA + [2,] 0.008273557 NA NA + [3,] 0.005602113 NA NA + [4,] -0.001310758 NA NA + [5,] -0.013623801 NA NA + [6,] -0.002399534 NA NA + [7,] -0.016055398 NA NA + [8,] 0.016686715 NA NA + [9,] NA -0.021456706 -0.13639202 +[10,] NA 0.124390124 0.04361309 +[11,] NA -0.004860607 0.08458642 +[12,] NA 0.005785134 0.12228703 +[13,] NA -0.340922220 -0.04600616 +[14,] NA 0.237064274 -0.06808836 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcJ_res/KEIO_ROBOT5_2_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcJ_res/KEIO_ROBOT5_2_res.txt new file mode 100644 index 0000000..437bfc0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcJ_res/KEIO_ROBOT5_2_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0145274014764651 0.0142951055972443 0.0142888191120177 0.00185155564972945 0.0114521459150048 0.0175700504871105 +Glc 13.0604221953422 13.0409319909564 13.039427890064 0.193023690803814 12.6800735487867 13.46950078159 +Ace 0.418118487282525 0.429554533232839 0.435284758701086 0.10171437689485 0.252417814911237 0.60547732197849 +mu 0.706962426372778 0.711802101097802 0.711239597252843 0.0259730090922817 0.668590814321066 0.755326257574953 +qGlc -5.49826986469006 -5.54660845306557 -5.57681392282222 0.476678355588264 -6.41491090756885 -4.68407078089708 +qAce 3.41956963009771 3.40842536940913 3.42568835044317 0.227833539077964 2.96579235739321 3.94479377823151 +res 4.4027046160999 35.2280676133898 35.2233866832735 9.15779835540326 22.3801150530468 53.6066228189219 + + +Goodness of fit (khi2 test) + +khi2 value 4.40270461610391 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.314478901150279 +p-value, i.e. P(X^2<=value) 0.00748496869012593 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcL.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcL.txt new file mode 100644 index 0000000..1de2066 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcL.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.18888888888889 0.061992 NA NA +2.27694444444444 0.096768 NA NA +3.12833333333333 0.134568 NA NA +3.77138888888889 0.190512 NA NA +4.41555555555556 0.269136 NA NA +4.82277777777778 0.346248 NA NA +0.0666666666666667 NA 15.4778947496306 0.0181581444183399 +1.71666666666667 NA 15.2580903565761 0.344189790724828 +2.8 NA 13.626224935021 0.734696101585912 +3.63333333333333 NA 12.9967577370014 1.1886682973416 +4.26666666666667 NA 11.9552611462585 1.65213376174966 +4.88333333333333 NA 11.0488637435718 2.22344201091661 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcL_res/KEIO_ROBOT1_33.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydcL_res/KEIO_ROBOT1_33.pdf new file mode 100644 index 0000000..176faa8 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydcL_res/KEIO_ROBOT1_33.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcL_res/KEIO_ROBOT1_33_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcL_res/KEIO_ROBOT1_33_log.txt new file mode 100644 index 0000000..5d2e77a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcL_res/KEIO_ROBOT1_33_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.061992 NA NA + [3,] 0.096768 NA NA + [4,] 0.134568 NA NA + [5,] 0.190512 NA NA + [6,] 0.269136 NA NA + [7,] 0.346248 NA NA + [8,] NA 15.47789 0.01815814 + [9,] NA 15.25809 0.34418979 +[10,] NA 13.62622 0.73469610 +[11,] NA 12.99676 1.18866830 +[12,] NA 11.95526 1.65213376 +[13,] NA 11.04886 2.22344201 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03099828 15.43728220 0.05549351 0.49328576 -7.31439567 3.47704746 + +$result$lastp + X Glc Ace mu qGlc qAce + 3.173171e-09 1.011713e-07 -2.966381e-08 -2.525668e-08 -1.139045e-07 -1.182367e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.007196412 0.353792874 0.154509540 0.053508554 1.082665393 0.479170963 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5223246 + +$result$laststep + X Glc Ace mu qGlc qAce + 3.173171e-09 1.011713e-07 -2.966381e-08 -2.525668e-08 -1.139045e-07 -1.182367e-08 + +$result$normp +[1] 1.577262e-07 + +$result$res + [1] -0.18888619 -0.31344843 -0.07298996 0.52421140 0.43434693 0.22860566 -0.58234326 -0.12169438 -0.94159748 0.95974083 0.30633454 0.37073041 -0.57351392 0.22320161 0.01192863 -0.14073208 -0.20003951 -0.11229074 0.21793209 + +$result$prevres + [1] -0.18888635 -0.31344863 -0.07299018 0.52421123 0.43434686 0.22860579 -0.58234293 -0.12169459 -0.94159757 0.95974083 0.30633462 0.37073052 -0.57351380 0.22320175 0.01192867 -0.14073212 -0.20003958 -0.11229080 0.21793208 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 89.880858 0.000000 0 3.312424404 0.000000000 0.00000000 + [3,] 153.731462 0.000000 0 10.850573424 0.000000000 0.00000000 + [4,] 233.968235 0.000000 0 22.688585472 0.000000000 0.00000000 + [5,] 321.306508 0.000000 0 37.562832924 0.000000000 0.00000000 + [6,] 441.489298 0.000000 0 60.428669547 0.000000000 0.00000000 + [7,] 539.709327 0.000000 0 80.685347446 0.000000000 0.00000000 + [8,] -1.077680 2.173913 0 -0.001119644 0.004567189 0.00000000 + [9,] -42.942549 2.173913 0 -1.301926624 0.181989727 0.00000000 +[10,] -96.048576 2.173913 0 -5.098627209 0.407052086 0.00000000 +[11,] -161.271989 2.173913 0 -11.659680274 0.683467704 0.00000000 +[12,] -232.234881 2.173913 0 -20.384813811 0.984207130 0.00000000 +[13,] -326.261844 2.173913 0 -33.764937336 1.382691657 0.00000000 +[14,] 1.178284 0.000000 5 0.001224165 0.000000000 0.01050454 +[15,] 46.951323 0.000000 5 1.423464110 0.000000000 0.41857637 +[16,] 105.014905 0.000000 5 5.574594381 0.000000000 0.93621980 +[17,] 176.327055 0.000000 5 12.748135032 0.000000000 1.57197572 +[18,] 253.914477 0.000000 5 22.287777447 0.000000000 2.26367640 +[19,] 356.719047 0.000000 5 36.916962591 0.000000000 3.18019081 + +$result$retres +$result$retres$res + [1] -0.18888635 -0.31344863 -0.07299018 0.52421123 0.43434686 0.22860579 -0.58234293 -0.12169459 -0.94159757 0.95974083 0.30633462 0.37073052 -0.57351380 0.22320175 0.01192867 -0.14073212 -0.20003958 -0.11229080 0.21793208 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03099827 15.43728 0.05549354 + [2,] 0.05572303 15.07067 0.22977212 + [3,] 0.09530820 14.48370 0.50879803 + [4,] 0.14505222 13.74610 0.85943118 + [5,] 0.19919894 12.94322 1.24109774 + [6,] 0.27370812 11.83840 1.76629421 + [7,] 0.33460114 10.93549 2.19551384 + [8,] 0.03203462 15.42192 0.06279850 + [9,] 0.07229383 14.82496 0.34657552 + [10,] 0.12336306 14.06771 0.70654968 + [11,] 0.18608493 13.13767 1.14866038 + [12,] 0.25432615 12.12580 1.62967560 + [13,] 0.34474686 10.78505 2.26702843 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.003777727 NA NA + [2,] 0.006268973 NA NA + [3,] 0.001459804 NA NA + [4,] -0.010484225 NA NA + [5,] -0.008686937 NA NA + [6,] -0.004572116 NA NA + [7,] 0.011646859 NA NA + [8,] NA 0.05597951 -0.044640351 + [9,] NA 0.43313488 -0.002385734 +[10,] NA -0.44148078 0.028146423 +[11,] NA -0.14091392 0.040007916 +[12,] NA -0.17053604 0.022458161 +[13,] NA 0.26381635 -0.043586415 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcL_res/KEIO_ROBOT1_33_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcL_res/KEIO_ROBOT1_33_res.txt new file mode 100644 index 0000000..19fd44d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcL_res/KEIO_ROBOT1_33_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0309982762031511 0.0317204615613833 0.0311669822944179 0.00427107361297943 0.0253692216374844 0.0419613857054266 +Glc 15.4372822034971 15.4197101947849 15.4250310201862 0.207027984453205 14.9764278352145 15.7588247304697 +Ace 0.0554935119524576 0.0871724717431024 0.083275212715945 0.0701552787587455 9.99999999997531e-07 0.242170545772475 +mu 0.493285756302652 0.491243608194452 0.493662927409541 0.0301045442890661 0.42736104043673 0.536999871992701 +qGlc -7.31439566823108 -7.19192462592217 -7.21618439103576 0.635120127139561 -8.43132151993082 -6.18849346428143 +qAce 3.47704746059736 3.36207272091617 3.34285753938281 0.26843572363494 2.88517805625183 3.89132165099605 +res 3.54669858701524 32.7116018512856 31.9911198681084 7.16362750717771 19.7565241920043 48.0943583376728 + + +Goodness of fit (khi2 test) + +khi2 value 3.54669858701566 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.272822968231974 +p-value, i.e. P(X^2<=value) 0.00487251842525504 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcP.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcP.txt new file mode 100644 index 0000000..0a6cb9d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcP.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.18888888888889 0.072576 NA NA +2.27694444444444 0.123984 NA NA +3.12833333333333 0.179928 NA NA +3.77138888888889 0.250992 NA NA +4.41555555555556 0.374976 NA NA +4.82277777777778 0.517104 NA NA +0.0666666666666667 NA 15.5027807784449 0.022261494161035 +1.71666666666667 NA 13.7035066126948 0.331145638950881 +2.8 NA 13.48090749895 0.749274479954118 +3.63333333333333 NA 12.3847382486559 1.13740428626231 +4.26666666666667 NA 11.3269383933929 1.59017918830562 +4.88333333333333 NA 9.98419906231454 2.04614778354927 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcP_res/KEIO_ROBOT1_5.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydcP_res/KEIO_ROBOT1_5.pdf new file mode 100644 index 0000000..ae1c28f Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydcP_res/KEIO_ROBOT1_5.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcP_res/KEIO_ROBOT1_5_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcP_res/KEIO_ROBOT1_5_log.txt new file mode 100644 index 0000000..dd6314c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcP_res/KEIO_ROBOT1_5_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.072576 NA NA + [3,] 0.123984 NA NA + [4,] 0.179928 NA NA + [5,] 0.250992 NA NA + [6,] 0.374976 NA NA + [7,] 0.517104 NA NA + [8,] NA 15.502781 0.02226149 + [9,] NA 13.703507 0.33114564 +[10,] NA 13.480907 0.74927448 +[11,] NA 12.384738 1.13740429 +[12,] NA 11.326938 1.59017919 +[13,] NA 9.984199 2.04614778 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03128413 14.84175180 0.13419882 0.57224631 -6.01583303 2.40834866 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.049193e-08 2.602960e-07 -9.879879e-08 -7.905583e-08 -7.245340e-08 1.359306e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.009607286 0.541656957 0.234890407 0.069779476 1.259648023 0.542124160 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.8316405 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.049193e-08 2.602960e-07 -9.879879e-08 -7.905583e-08 -7.245340e-08 1.359306e-08 + +$result$normp +[1] 2.988467e-07 + +$result$res + [1] -0.3257934 -0.5402058 -0.4425724 0.3740017 0.9889630 0.8244557 -1.1455083 -1.4648219 1.2799401 0.1239971 0.3382457 0.1401343 -0.4174953 0.5852862 0.1151318 -0.4655830 -0.4093311 -0.3734188 0.5479150 + +$result$prevres + [1] -0.3257939 -0.5402065 -0.4425733 0.3740009 0.9889625 0.8244560 -1.1455071 -1.4648224 1.2799398 0.1239971 0.3382459 0.1401346 -0.4174950 0.5852867 0.1151320 -0.4655831 -0.4093313 -0.3734191 0.5479148 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.000000000 0.00000000 + [2,] 98.7271889 0.000000 0 3.671994e+00 0.000000000 0.00000000 + [3,] 184.0111294 0.000000 0 1.310752e+01 0.000000000 0.00000000 + [4,] 299.5257704 0.000000 0 2.931374e+01 0.000000000 0.00000000 + [5,] 432.7614612 0.000000 0 5.105918e+01 0.000000000 0.00000000 + [6,] 625.6610227 0.000000 0 8.642680e+01 0.000000000 0.00000000 + [7,] 789.8477246 0.000000 0 1.191694e+02 0.000000000 0.00000000 + [8,] -0.8887040 2.173913 0 -9.326366e-04 0.004621525 0.00000000 + [9,] -38.1824896 2.173913 0 -1.190510e+00 0.198560313 0.00000000 +[10,] -90.6005750 2.173913 0 -4.985041e+00 0.471149963 0.00000000 +[11,] -159.9241705 2.173913 0 -1.203266e+01 0.831653298 0.00000000 +[12,] -239.7626343 2.173913 0 -2.194616e+01 1.246837078 0.00000000 +[13,] -350.8933894 2.173913 0 -3.791465e+01 1.824750090 0.00000000 +[14,] 0.8182925 0.000000 5 8.587443e-04 0.000000000 0.01062951 +[15,] 35.1573123 0.000000 5 1.096187e+00 0.000000000 0.45668872 +[16,] 83.4223422 0.000000 5 4.590079e+00 0.000000000 1.08364491 +[17,] 147.2534682 0.000000 5 1.107932e+01 0.000000000 1.91280259 +[18,] 220.7663753 0.000000 5 2.020738e+01 0.000000000 2.86772528 +[19,] 323.0923030 0.000000 5 3.491069e+01 0.000000000 4.19692521 + +$result$retres +$result$retres$res + [1] -0.3257939 -0.5402065 -0.4425733 0.3740009 0.9889625 0.8244560 -1.1455071 -1.4648224 1.2799398 0.1239971 0.3382459 0.1401346 -0.4174950 0.5852867 0.1151320 -0.4655831 -0.4093313 -0.3734191 0.5479148 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03128412 14.841752 0.1341989 + [2,] 0.06177187 14.521244 0.2625092 + [3,] 0.11513253 13.960282 0.4870822 + [4,] 0.18740802 13.200474 0.7912599 + [5,] 0.27077125 12.324104 1.1421013 + [6,] 0.39146512 11.055290 1.6500519 + [7,] 0.49419386 9.975338 2.0823948 + [8,] 0.03250066 14.828962 0.1393188 + [9,] 0.08355182 14.292279 0.3541720 + [10,] 0.15530650 13.537946 0.6561579 + [11,] 0.25020300 12.540331 1.0555380 + [12,] 0.35949321 11.391400 1.5154954 + [13,] 0.51161918 9.792151 2.1557307 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.006515878 NA NA + [2,] 0.010804131 NA NA + [3,] 0.008851466 NA NA + [4,] -0.007480017 NA NA + [5,] -0.019779250 NA NA + [6,] -0.016489120 NA NA + [7,] 0.022910143 NA NA + [8,] NA 0.67381831 -0.11705733 + [9,] NA -0.58877232 -0.02302641 +[10,] NA -0.05703868 0.09311661 +[11,] NA -0.15559313 0.08186627 +[12,] NA -0.06446190 0.07468382 +[13,] NA 0.19204772 -0.10958296 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcP_res/KEIO_ROBOT1_5_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcP_res/KEIO_ROBOT1_5_res.txt new file mode 100644 index 0000000..f6790a8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcP_res/KEIO_ROBOT1_5_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0312841328468915 0.0313841606982059 0.0307747070398635 0.00379336860141058 0.0248378668324097 0.0394032472569283 +Glc 14.8417518009082 14.8527326683992 14.8602662890094 0.196541079739537 14.46177487428 15.2265719748273 +Ace 0.134198815164828 0.147386501582211 0.141052393922202 0.0845133232051579 0.00528669362828601 0.328447320591004 +mu 0.572246309846033 0.573317439434702 0.575295877310065 0.0263113037013919 0.52320679707155 0.622834712485909 +qGlc -6.01583302850634 -5.98639592169537 -5.93459224792398 0.520694899843371 -7.01130914841176 -5.05173723335606 +qAce 2.4083486595128 2.38603160498107 2.38954273127918 0.216724586110347 1.97631270701454 2.85921502036341 +res 8.99113770243264 32.2552795092318 31.2306379014034 9.57407644474717 19.7907077729283 52.1243096754978 + + +Goodness of fit (khi2 test) + +khi2 value 8.99113770243801 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.691625977110616 +p-value, i.e. P(X^2<=value) 0.226387460894162 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcS.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcS.txt new file mode 100644 index 0000000..efb8618 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcS.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.099792 NA NA NA +3.34194444444444 0.157248 NA NA NA +3.9975 0.21168 NA NA NA +4.52333333333333 0.320544 NA NA NA +1.95 NA 13.3842895637964 0.402156460013089 0 +3.25 NA 13.1428566496856 0.848561798109363 0 +4.08333333333333 NA 11.9920662465255 1.46876203606816 0 +4.76666666666667 NA 11.027020985036 2.06326575296067 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcS_2.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcS_2.txt new file mode 100644 index 0000000..c03ec2b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcS_2.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 5.4431999999999994E-2 NA NA +2.2613888888888889 6.9552000000000003E-2 NA NA +2.7741666666666664 8.4671999999999997E-2 NA NA +3.2088888888888891 0.1134 NA NA +3.7063888888888892 0.157248 NA NA +4.2258333333333331 0.192024 NA NA +4.6355555555555554 0.26006399999999996 NA NA +4.9675000000000002 0.33717600000000003 NA NA +2.8 NA 12.4807614861131 0.617586980040094 +3.73333333333333 NA 11.8177463087443 1.03577227963538 +4.28333333333333 NA 11.3685837039516 1.39218182842489 +4.75 NA 10.7139280891487 1.80101188328769 +5.11666666666667 NA 10.1762000059622 2.17010758504405 +5.43333333333333 NA 9.42077649862271 2.53041798522943 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcS_2_res/KEIO_ROBOT5_12.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydcS_2_res/KEIO_ROBOT5_12.pdf new file mode 100644 index 0000000..ec522b4 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydcS_2_res/KEIO_ROBOT5_12.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcS_2_res/KEIO_ROBOT5_12_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcS_2_res/KEIO_ROBOT5_12_log.txt new file mode 100644 index 0000000..507227c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcS_2_res/KEIO_ROBOT5_12_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.054432 NA NA + [2,] 0.069552 NA NA + [3,] 0.084672 NA NA + [4,] 0.113400 NA NA + [5,] 0.157248 NA NA + [6,] 0.192024 NA NA + [7,] 0.260064 NA NA + [8,] 0.337176 NA NA + [9,] NA 12.480761 0.617587 +[10,] NA 11.817746 1.035772 +[11,] NA 11.368584 1.392182 +[12,] NA 10.713928 1.801012 +[13,] NA 10.176200 2.170108 +[14,] NA 9.420776 2.530418 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01622448 13.08296206 0.25708620 0.60382379 -5.27077778 3.36988963 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.750306e-09 8.469152e-08 -7.732768e-08 -3.851521e-08 -1.348272e-08 6.717190e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.002894207 0.315120080 0.143150464 0.039692501 0.701229273 0.312231787 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3297419 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.750306e-09 8.469152e-08 -7.732768e-08 -3.851521e-08 -1.348272e-08 6.717190e-08 + +$result$normp +[1] 1.390577e-07 + +$result$res + [1] -0.27398190 -0.29954575 0.09782488 -0.03840796 -0.25748677 0.80547502 0.32453836 -0.57316538 -0.05270453 0.12477409 -0.05430930 0.03788317 -0.13637117 0.08072775 0.20009365 -0.03231243 -0.11514759 -0.20208665 -0.07233056 0.22178359 + +$result$prevres + [1] -0.27398214 -0.29954601 0.09782461 -0.03840822 -0.25748698 0.80547495 0.32453848 -0.57316503 -0.05270457 0.12477410 -0.05430927 0.03788320 -0.13637116 0.08072771 0.20009379 -0.03231240 -0.11514762 -0.20208671 -0.07233062 0.22178356 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 150.85961 0.000000 0 4.476421 0.0000000 0.000000 + [2,] 195.88025 0.000000 0 7.186816 0.0000000 0.000000 + [3,] 266.96857 0.000000 0 12.016094 0.0000000 0.000000 + [4,] 347.10474 0.000000 0 18.071152 0.0000000 0.000000 + [5,] 468.73095 0.000000 0 28.186765 0.0000000 0.000000 + [6,] 641.41833 0.000000 0 43.976874 0.0000000 0.000000 + [7,] 821.45891 0.000000 0 61.781472 0.0000000 0.000000 + [8,] 1003.76969 0.000000 0 80.898892 0.0000000 0.000000 + [9,] -83.93715 2.173913 0 -2.419843 0.2583748 0.000000 +[10,] -161.83543 2.173913 0 -6.603556 0.4981608 0.000000 +[11,] -233.05647 2.173913 0 -11.252837 0.7173929 0.000000 +[12,] -315.09130 2.173913 0 -17.278960 0.9699120 0.000000 +[13,] -397.88156 2.173913 0 -23.914633 1.2247564 0.000000 +[14,] -485.71961 2.173913 0 -31.439360 1.4951389 0.000000 +[15,] 123.43065 0.000000 5 3.558410 0.0000000 0.594262 +[16,] 237.98107 0.000000 5 9.710614 0.0000000 1.145770 +[17,] 342.71251 0.000000 5 16.547441 0.0000000 1.650004 +[18,] 463.34577 0.000000 5 25.408931 0.0000000 2.230798 +[19,] 585.08991 0.000000 5 35.166773 0.0000000 2.816940 +[20,] 714.25689 0.000000 5 46.231980 0.0000000 3.438820 + +$result$retres +$result$retres$res + [1] -0.27398214 -0.29954601 0.09782461 -0.03840822 -0.25748698 0.80547495 0.32453848 -0.57316503 -0.05270457 0.12477410 -0.05430927 0.03788320 -0.13637116 0.08072771 0.20009379 -0.03231240 -0.11514762 -0.20208671 -0.07233062 0.22178356 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.04895236 12.797280 0.4397378 + [2,] 0.06356108 12.669761 0.5212679 + [3,] 0.08662849 12.468405 0.6500051 + [4,] 0.11263184 12.241422 0.7951276 + [5,] 0.15209826 11.896920 1.0153863 + [6,] 0.20813350 11.407788 1.3281143 + [7,] 0.26655477 10.897829 1.6541584 + [8,] 0.32571270 10.381439 1.9843138 + [9,] 0.08799039 12.456517 0.6576057 + [10,] 0.15459309 11.875142 1.0293098 + [11,] 0.21548678 11.343601 1.3691523 + [12,] 0.28562622 10.731354 1.7605945 + [13,] 0.35641155 10.113469 2.1556415 + [14,] 0.43151271 9.457911 2.5747747 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0054796428 NA NA + [2,] 0.0059909203 NA NA + [3,] -0.0019564922 NA NA + [4,] 0.0007681644 NA NA + [5,] 0.0051497396 NA NA + [6,] -0.0161094990 NA NA + [7,] -0.0064907697 NA NA + [8,] 0.0114633005 NA NA + [9,] NA 0.02424410 -0.04001876 +[10,] NA -0.05739609 0.00646248 +[11,] NA 0.02498226 0.02302952 +[12,] NA -0.01742627 0.04041734 +[13,] NA 0.06273074 0.01446612 +[14,] NA -0.03713475 -0.04435671 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcS_2_res/KEIO_ROBOT5_12_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcS_2_res/KEIO_ROBOT5_12_res.txt new file mode 100644 index 0000000..af0c8bd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcS_2_res/KEIO_ROBOT5_12_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.016224476536336 0.0165976926851888 0.0165916977017763 0.00278299815999293 0.0121288458500897 0.0218732908945399 +Glc 13.0829620566873 13.067975601663 13.0576548751346 0.253820654622005 12.5693210735534 13.5853453684018 +Ace 0.257086196231788 0.250995968522838 0.243461131709576 0.120908422338757 0.015710862586341 0.459237187634776 +mu 0.603823790990043 0.601837460696881 0.59785050803981 0.0348752906075892 0.542055183639526 0.667558052007494 +qGlc -5.27077777724271 -5.17347600959577 -5.16348195023749 0.681932668615009 -6.38162895173431 -3.80579087882325 +qAce 3.36988963069857 3.3890561059651 3.39565778360807 0.299211843986513 2.82244358134346 4.00363256781228 +res 1.52221602239683 35.8733153442541 34.9671766900996 8.17768200041431 23.3094692370143 54.7165340065097 + + +Goodness of fit (khi2 test) + +khi2 value 1.52221602239733 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.108729715885524 +p-value, i.e. P(X^2<=value) 1.5137540188658e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcS_res/KEIO_ROBOT2_10.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydcS_res/KEIO_ROBOT2_10.pdf new file mode 100644 index 0000000..a053b7b Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydcS_res/KEIO_ROBOT2_10.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcS_res/KEIO_ROBOT2_10_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcS_res/KEIO_ROBOT2_10_log.txt new file mode 100644 index 0000000..4dbadc3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcS_res/KEIO_ROBOT2_10_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.099792 NA NA NA +[2,] 0.157248 NA NA NA +[3,] 0.211680 NA NA NA +[4,] 0.320544 NA NA NA +[5,] NA 13.38429 0.4021565 0 +[6,] NA 13.14286 0.8485618 0 +[7,] NA 11.99207 1.4687620 0 +[8,] NA 11.02702 2.0632658 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.068129e-02 1.393311e+01 1.544961e-01 1.000000e-06 6.002998e-01 -5.079785e+00 3.419876e+00 -2.410836e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-6.994395e-09 -8.215372e-09 1.089993e-07 2.117582e-22 8.203302e-08 -5.005426e-07 -2.890118e-09 9.372720e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.007468193 0.477313786 0.216903890 0.200550375 0.086774528 1.330269391 0.597434549 0.564348508 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4485552 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-6.994395e-09 -8.215372e-09 1.089993e-07 2.117582e-22 8.203302e-08 -5.005426e-07 -2.890118e-09 9.372720e-13 + +$result$normp +[1] 5.1892e-07 + +$result$res + [1] -3.479017e-01 -1.743616e-01 8.112379e-01 -4.024970e-01 3.470212e-01 -5.782693e-01 1.859357e-01 4.531250e-02 7.178610e-02 8.521332e-02 -3.253625e-01 1.683631e-01 4.076455e-06 2.493526e-06 5.969145e-07 -1.846609e-06 + +$result$prevres + [1] -3.479010e-01 -1.743611e-01 8.112380e-01 -4.024975e-01 3.470211e-01 -5.782695e-01 1.859357e-01 4.531276e-02 7.178588e-02 8.521336e-02 -3.253624e-01 1.683632e-01 4.076455e-06 2.493525e-06 5.969123e-07 -1.846612e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.244395e+02 0.000000 0 0 1.161069e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.717388e+02 0.000000 0 0 2.569300e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.509925e+02 0.000000 0 0 4.555246e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.554992e+02 0.000000 0 0 7.067574e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.091004e+01 2.173913 0 0 -9.823012e-01 0.1665568 0.0000000 0.0000000 + [6,] -1.110287e+02 2.173913 0 0 -4.874049e+00 0.4520305 0.0000000 0.0000000 + [7,] -1.950425e+02 2.173913 0 0 -1.130504e+01 0.7940751 0.0000000 0.0000000 + [8,] -3.032827e+02 2.173913 0 0 -2.126276e+01 1.2347528 0.0000000 0.0000000 + [9,] 6.334653e+01 0.000000 5 0 1.521029e+00 0.0000000 0.3830807 0.0000000 +[10,] 1.719207e+02 0.000000 5 0 7.547146e+00 0.0000000 1.0396701 0.0000000 +[11,] 3.020105e+02 0.000000 5 0 1.750512e+01 0.0000000 1.8263728 0.0000000 +[12,] 4.696133e+02 0.000000 5 0 3.292399e+01 0.0000000 2.8399314 0.0000000 +[13,] -4.465606e-05 0.000000 0 5 -1.072248e-06 0.0000000 0.0000000 0.3830807 +[14,] -1.211953e-04 0.000000 0 5 -5.320352e-06 0.0000000 0.0000000 1.0396701 +[15,] -2.129019e-04 0.000000 0 5 -1.234021e-05 0.0000000 0.0000000 1.8263728 +[16,] -3.310534e-04 0.000000 0 5 -2.320973e-05 0.0000000 0.0000000 2.8399314 + +$result$retres +$result$retres$res + [1] -3.479010e-01 -1.743611e-01 8.112380e-01 -4.024975e-01 3.470211e-01 -5.782695e-01 1.859357e-01 4.531276e-02 7.178588e-02 8.521336e-02 -3.253624e-01 1.683632e-01 4.076455e-06 2.493525e-06 5.969123e-07 -1.846612e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09283398 13.32255 0.5655460 7.102308e-07 + [2,] 0.15376078 12.80698 0.9126427 4.655453e-07 + [3,] 0.22790476 12.17957 1.3350370 1.677790e-07 + [4,] 0.31249405 11.46377 1.8169377 -1.719364e-07 + [5,] 0.06667394 13.54392 0.4165136 8.152910e-07 + [6,] 0.14550403 12.87685 0.8656045 4.987049e-07 + [7,] 0.23995551 12.07760 1.4036896 1.193825e-07 + [8,] 0.36164330 11.04786 2.0969384 -3.693225e-07 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.006958021 NA NA NA +[2,] 0.003487223 NA NA NA +[3,] -0.016224760 NA NA NA +[4,] 0.008049949 NA NA NA +[5,] NA -0.15962969 -0.01435718 -8.152910e-07 +[6,] NA 0.26600396 -0.01704267 -4.987049e-07 +[7,] NA -0.08553040 0.06507248 -1.193825e-07 +[8,] NA -0.02084387 -0.03367263 3.693225e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcS_res/KEIO_ROBOT2_10_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcS_res/KEIO_ROBOT2_10_res.txt new file mode 100644 index 0000000..9b4b45a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcS_res/KEIO_ROBOT2_10_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0206812877828299 0.0201478520206737 0.0197622899419946 0.00402566889936402 0.0125287643575115 0.0290801197328312 +Glc 13.9331126730311 13.8679971758069 13.8706482890202 0.353346254276895 13.2357086915945 14.6059420652089 +Ace 0.154496110262948 0.184264598283469 0.173728728106714 0.14760534684383 9.99999999987122e-07 0.501526775982086 +Lac 1e-06 0.102232561395134 0.0884458799041271 0.0791406335274377 9.99999999998678e-07 0.256055238009145 +mu 0.600299810775309 0.611784486992718 0.614065421716886 0.047686078561972 0.527465965438626 0.721124019535998 +qGlc -5.07978495269022 -4.99463722177465 -4.99578332340814 1.0178402952934 -7.15813545371083 -3.01304760952438 +qAce 3.41987558684639 3.36449966873259 3.3909003936297 0.459603701079244 2.50336736356652 4.11550346027326 +qLac -2.41083637457776e-06 -0.0569709263332368 -0.0809010845884791 0.206145376583128 -0.412052655000965 0.382286038153626 +res 1.60961414670512 20.5867688503121 19.9495224520183 6.73490879693567 9.8202627651091 33.5493401301939 + + +Goodness of fit (khi2 test) + +khi2 value 1.60961414670624 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.20120176833828 +p-value, i.e. P(X^2<=value) 0.0092653944717633 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcY.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcY.txt new file mode 100644 index 0000000..c911b2c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcY.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.05292 NA NA +1.18888888888889 0.0756 NA NA +2.27694444444444 0.110376 NA NA +3.12833333333333 0.167832 NA NA +3.77138888888889 0.21924 NA NA +4.41555555555556 0.346248 NA NA +4.82277777777778 0.43092 NA NA +0.0666666666666667 NA 15.4534654206327 0.00617280415298425 +1.71666666666667 NA 15.2126958356339 0.339055519890531 +2.8 NA 13.6044997677315 0.718336054401776 +3.63333333333333 NA 12.9480135191829 1.19486736206779 +4.26666666666667 NA 11.4121675497342 1.65279945490713 +4.88333333333333 NA 10.1330398572084 2.26315930915145 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcY_res/KEIO_ROBOT1_29.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydcY_res/KEIO_ROBOT1_29.pdf new file mode 100644 index 0000000..d2d2532 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydcY_res/KEIO_ROBOT1_29.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcY_res/KEIO_ROBOT1_29_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcY_res/KEIO_ROBOT1_29_log.txt new file mode 100644 index 0000000..589cb78 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcY_res/KEIO_ROBOT1_29_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.052920 NA NA + [2,] 0.075600 NA NA + [3,] 0.110376 NA NA + [4,] 0.167832 NA NA + [5,] 0.219240 NA NA + [6,] 0.346248 NA NA + [7,] 0.430920 NA NA + [8,] NA 15.45347 0.006172804 + [9,] NA 15.21270 0.339055520 +[10,] NA 13.60450 0.718336054 +[11,] NA 12.94801 1.194867362 +[12,] NA 11.41217 1.652799455 +[13,] NA 10.13304 2.263159309 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03417157 15.52425853 0.05694566 0.52090029 -7.21755715 2.92719604 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.122242e-08 1.870692e-07 -8.280573e-08 -7.776594e-08 2.614132e-07 -8.513288e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008095578 0.417140666 0.180820657 0.054315671 1.063162300 0.456773748 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6230335 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.122242e-08 1.870692e-07 -8.280573e-08 -7.776594e-08 2.614132e-07 -8.513288e-08 + +$result$normp +[1] 3.515816e-07 + +$result$res + [1] -0.93742157 -0.60612174 0.07535732 0.32484468 1.22267797 -0.26963352 -0.47604624 0.11752593 -0.81045127 0.77710975 -0.20126111 0.46771058 -0.35063389 0.28779225 -0.02276262 -0.13889668 -0.27768441 -0.07692813 0.22847959 + +$result$prevres + [1] -0.93742213 -0.60612249 0.07535647 0.32484393 1.22267754 -0.26963326 -0.47604526 0.11752553 -0.81045135 0.77710988 -0.20126089 0.46771076 -0.35063394 0.28779266 -0.02276251 -0.13889679 -0.27768463 -0.07692832 0.22847960 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 92.8806804 0.000000 0 3.773387702 0.000000000 0.00000000 + [3,] 163.7079748 0.000000 0 12.737583495 0.000000000 0.00000000 + [4,] 255.0789188 0.000000 0 27.267942107 0.000000000 0.00000000 + [5,] 356.5736666 0.000000 0 45.953157491 0.000000000 0.00000000 + [6,] 498.7412925 0.000000 0 75.253283343 0.000000000 0.00000000 + [7,] 616.5933397 0.000000 0 101.615709511 0.000000000 0.00000000 + [8,] -1.0643973 2.173913 0 -0.001219421 0.005039394 0.00000000 + [9,] -43.5379963 2.173913 0 -1.464823412 0.206130836 0.00000000 +[10,] -99.3890407 2.173913 0 -5.871607735 0.470557852 0.00000000 +[11,] -169.7842748 2.173913 0 -13.681633775 0.803844399 0.00000000 +[12,] -247.9142792 2.173913 0 -24.273840055 1.173751250 0.00000000 +[13,] -353.2374586 2.173913 0 -40.798834759 1.672404308 0.00000000 +[14,] 0.9928718 0.000000 5 0.001137478 0.000000000 0.01159061 +[15,] 40.6123246 0.000000 5 1.366390024 0.000000000 0.47410092 +[16,] 92.7102834 0.000000 5 5.477046699 0.000000000 1.08228306 +[17,] 158.3750898 0.000000 5 12.762253628 0.000000000 1.84884212 +[18,] 231.2549043 0.000000 5 22.642683497 0.000000000 2.69962787 +[19,] 329.5005635 0.000000 5 38.057229528 0.000000000 3.84652991 + +$result$retres +$result$retres$res + [1] -0.93742213 -0.60612249 0.07535647 0.32484393 1.22267754 -0.26963326 -0.47604526 0.11752553 -0.81045135 0.77710988 -0.20126089 0.46771076 -0.35063394 0.28779266 -0.02276251 -0.13889679 -0.27768463 -0.07692832 0.22847960 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03417156 15.524258 0.05694574 + [2,] 0.06347755 15.118197 0.22163057 + [3,] 0.11188313 14.447492 0.49364540 + [4,] 0.17432888 13.582249 0.84455887 + [5,] 0.24369355 12.621137 1.23435318 + [6,] 0.34085533 11.274870 1.78035318 + [7,] 0.42139909 10.158862 2.23296830 + [8,] 0.03537907 15.507527 0.06373134 + [9,] 0.08356343 14.839888 0.33450302 + [10,] 0.14692389 13.961970 0.69055670 + [11,] 0.22678406 12.855434 1.13933044 + [12,] 0.31541899 11.627315 1.63741379 + [13,] 0.43490332 9.971748 2.30885523 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.018748443 NA NA + [2,] 0.012122450 NA NA + [3,] -0.001507129 NA NA + [4,] -0.006496879 NA NA + [5,] -0.024453551 NA NA + [6,] 0.005392665 NA NA + [7,] 0.009520905 NA NA + [8,] NA -0.05406175 -0.057558532 + [9,] NA 0.37280762 0.004552503 +[10,] NA -0.35747055 0.027779358 +[11,] NA 0.09258001 0.055536925 +[12,] NA -0.21514695 0.015385664 +[13,] NA 0.16129161 -0.045695919 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydcY_res/KEIO_ROBOT1_29_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydcY_res/KEIO_ROBOT1_29_res.txt new file mode 100644 index 0000000..acef34e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydcY_res/KEIO_ROBOT1_29_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0341715686894335 0.0337592707369168 0.0335167774718285 0.00391387903874572 0.0270521511526025 0.0412533521075005 +Glc 15.5242585259574 15.5353385781617 15.5510676054736 0.209674625256637 15.1078635749796 15.8858465382092 +Ace 0.0569456576642422 0.0868270634067039 0.0785380023034312 0.0695947420026541 9.99999999994061e-07 0.23504451386166 +mu 0.520900287984813 0.525908518434756 0.523665718265157 0.0271962944457028 0.481508089863954 0.575084576517426 +qGlc -7.21755715436173 -7.29978089240499 -7.25302241639208 0.491646267145049 -8.25157753846212 -6.4354139101997 +qAce 2.92719603858013 2.88066643164948 2.89195225194955 0.200960282478453 2.45904836693025 3.2152268228038 +res 5.04622004385385 32.2022345735585 30.7959709987179 7.60427923750416 17.4667333881048 47.3174322221493 + + +Goodness of fit (khi2 test) + +khi2 value 5.04622004385802 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.388170772604463 +p-value, i.e. P(X^2<=value) 0.0258384789439947 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yddE.txt b/validation/validation_results/Berges_2021/Berges_2021/yddE.txt new file mode 100644 index 0000000..c5ab2c4 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yddE.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.3504000000000005E-2 NA NA +2.2613888888888889 9.2231999999999995E-2 NA NA +2.7741666666666664 0.119448 NA NA +3.2088888888888891 0.14666400000000002 NA NA +3.7063888888888892 0.192024 NA NA +4.2258333333333331 0.27972000000000002 NA NA +4.6355555555555554 0.34776000000000001 NA NA +4.9675000000000002 0.40975200000000001 NA NA +2.8 NA 12.0010830847629 0.659969530921884 +3.73333333333333 NA 11.2452160406717 1.1152860985231 +4.28333333333333 NA 10.8819069929927 1.52510021355059 +4.75 NA 9.58000442055282 1.84272660283614 +5.11666666666667 NA 8.84243764521291 2.20664138711043 +5.43333333333333 NA 7.8582933064267 2.52885355216718 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yddE_res/KEIO_ROBOT5_13.pdf b/validation/validation_results/Berges_2021/Berges_2021/yddE_res/KEIO_ROBOT5_13.pdf new file mode 100644 index 0000000..3df983a Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yddE_res/KEIO_ROBOT5_13.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yddE_res/KEIO_ROBOT5_13_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yddE_res/KEIO_ROBOT5_13_log.txt new file mode 100644 index 0000000..d11f113 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yddE_res/KEIO_ROBOT5_13_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.063504 NA NA + [2,] 0.092232 NA NA + [3,] 0.119448 NA NA + [4,] 0.146664 NA NA + [5,] 0.192024 NA NA + [6,] 0.279720 NA NA + [7,] 0.347760 NA NA + [8,] 0.409752 NA NA + [9,] NA 12.001083 0.6599695 +[10,] NA 11.245216 1.1152861 +[11,] NA 10.881907 1.5251002 +[12,] NA 9.580004 1.8427266 +[13,] NA 8.842438 2.2066414 +[14,] NA 7.858293 2.5288536 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02374935 13.08196681 0.31733444 0.57586516 -5.71781275 2.52156483 + +$result$lastp + X Glc Ace mu qGlc qAce +-6.261675e-10 -4.260057e-08 -4.548142e-09 5.940760e-09 4.442550e-08 2.467915e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.003505645 0.359289831 0.156421775 0.033013644 0.601542541 0.261724798 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3640251 + +$result$laststep + X Glc Ace mu qGlc qAce +-6.261675e-10 -4.260057e-08 -4.548142e-09 5.940760e-09 4.442550e-08 2.467915e-08 + +$result$normp +[1] 6.673728e-08 + +$result$res + [1] 0.22902163 -0.24459247 -0.10525082 0.20294092 0.43504614 -0.45026655 -0.25034887 0.26005241 0.29157065 0.10517433 -0.74472435 0.22327120 -0.03114458 0.15585276 0.37444086 -0.04638644 -0.43230213 -0.13156975 -0.06674798 0.30256545 + +$result$prevres + [1] 0.22902169 -0.24459241 -0.10525077 0.20294098 0.43504618 -0.45026653 -0.25034889 0.26005235 0.29157069 0.10517434 -0.74472435 0.22327119 -0.03114460 0.15585273 0.37444089 -0.04638641 -0.43230211 -0.13156975 -0.06674801 0.30256539 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 143.33956 0.000000 0 6.225943 0.0000000 0.0000000 + [2,] 183.87902 0.000000 0 9.875502 0.0000000 0.0000000 + [3,] 247.04461 0.000000 0 16.276450 0.0000000 0.0000000 + [4,] 317.31986 0.000000 0 24.182639 0.0000000 0.0000000 + [5,] 422.59032 0.000000 0 37.198231 0.0000000 0.0000000 + [6,] 569.94118 0.000000 0 57.199754 0.0000000 0.0000000 + [7,] 721.60501 0.000000 0 79.442534 0.0000000 0.0000000 + [8,] 873.60921 0.000000 0 103.063963 0.0000000 0.0000000 + [9,] -86.66243 2.173913 0 -3.624195 0.3599587 0.0000000 +[10,] -163.69972 2.173913 0 -9.676959 0.6799387 0.0000000 +[11,] -232.74165 2.173913 0 -16.273190 0.9667094 0.0000000 +[12,] -311.15336 2.173913 0 -24.703689 1.2923981 0.0000000 +[13,] -389.37958 2.173913 0 -33.880921 1.6173164 0.0000000 +[14,] -471.59011 2.173913 0 -44.189469 1.9587838 0.0000000 +[15,] 87.90203 0.000000 5 3.676035 0.0000000 0.8279051 +[16,] 166.04124 0.000000 5 9.815376 0.0000000 1.5638590 +[17,] 236.07073 0.000000 5 16.505958 0.0000000 2.2234315 +[18,] 315.60403 0.000000 5 25.057045 0.0000000 2.9725157 +[19,] 394.94917 0.000000 5 34.365546 0.0000000 3.7198277 +[20,] 478.33562 0.000000 5 44.821545 0.0000000 4.5052028 + +$result$retres +$result$retres$res + [1] 0.22902169 -0.24459241 -0.10525077 0.20294098 0.43504618 -0.45026653 -0.25034889 0.26005235 0.29157069 0.10517434 -0.74472435 0.22327119 -0.03114460 0.15585273 0.37444089 -0.04638641 -0.43230211 -0.13156975 -0.06674801 0.30256539 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06808443 12.641760 0.5114663 + [2,] 0.08734015 12.450569 0.5957821 + [3,] 0.11734298 12.152668 0.7271568 + [4,] 0.15072282 11.821237 0.8733185 + [5,] 0.20072492 11.324762 1.0922648 + [6,] 0.27071467 10.629828 1.3987318 + [7,] 0.34275302 9.914553 1.7141691 + [8,] 0.41495305 9.197673 2.0303144 + [9,] 0.11910169 12.135206 0.7348577 + [10,] 0.20386373 11.293596 1.1060088 + [11,] 0.27982870 10.539334 1.4386398 + [12,] 0.36610300 9.682709 1.8164127 + [13,] 0.45217319 8.828111 2.1932918 + [14,] 0.54262722 7.929986 2.5893666 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.004580434 NA NA + [2,] 0.004891848 NA NA + [3,] 0.002105015 NA NA + [4,] -0.004058820 NA NA + [5,] -0.008700924 NA NA + [6,] 0.009005331 NA NA + [7,] 0.005006978 NA NA + [8,] -0.005201047 NA NA + [9,] NA -0.13412252 -0.074888179 +[10,] NA -0.04838020 0.009277282 +[11,] NA 0.34257320 0.086460423 +[12,] NA -0.10270475 0.026313951 +[13,] NA 0.01432652 0.013349601 +[14,] NA -0.07169226 -0.060513078 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yddE_res/KEIO_ROBOT5_13_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yddE_res/KEIO_ROBOT5_13_res.txt new file mode 100644 index 0000000..99eb2b3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yddE_res/KEIO_ROBOT5_13_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0237493509574687 0.02446602763889 0.0242188445539616 0.00282028646273919 0.0194159040986009 0.0303004257194796 +Glc 13.0819668132787 13.0951915859002 13.1127819935083 0.249181829359508 12.6121214255737 13.4959231234038 +Ace 0.317334442574479 0.32649476847443 0.337098138321404 0.103425213182784 0.0990729331585429 0.521441037293596 +mu 0.575865158557788 0.570714342979884 0.570657882733514 0.0241027344279882 0.526459076269987 0.615362400060009 +qGlc -5.71781275187705 -5.72138215500569 -5.76907159520252 0.505138343203285 -6.69507112339112 -4.71642473422649 +qAce 2.52156482709804 2.49107839727499 2.48420082975872 0.220127383839585 2.13430430143372 2.94307474279168 +res 1.85520012933215 35.4805314338859 34.2639958698351 8.2152121890937 22.5405641639676 51.7882645999031 + + +Goodness of fit (khi2 test) + +khi2 value 1.85520012933219 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.132514294952299 +p-value, i.e. P(X^2<=value) 5.23575923068512e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yddM.txt b/validation/validation_results/Berges_2021/Berges_2021/yddM.txt new file mode 100644 index 0000000..3494375 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yddM.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.195 0.063504 NA NA +1.61361111111111 0.080136 NA NA +2.36138888888889 0.123984 NA NA +3.28638888888889 0.207144 NA NA +3.81944444444444 0.306936 NA NA +4.41083333333333 0.406728 NA NA +0.283333333333333 NA 14.2311623411494 0.043838692043064 +1.91666666666667 NA 13.5637188904027 0.365103377470869 +2.7 NA 13.4210343114782 0.716623777667717 +3.61666666666667 NA 12.2614802266628 1.2139411482998 +4.05 NA 11.8409004777119 1.53740259995908 +4.75 NA 9.90783136607123 2.00643938979535 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yddM_res/KEIO_ROBOT4_28.pdf b/validation/validation_results/Berges_2021/Berges_2021/yddM_res/KEIO_ROBOT4_28.pdf new file mode 100644 index 0000000..70bf18b Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yddM_res/KEIO_ROBOT4_28.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yddM_res/KEIO_ROBOT4_28_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yddM_res/KEIO_ROBOT4_28_log.txt new file mode 100644 index 0000000..8c7ac46 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yddM_res/KEIO_ROBOT4_28_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.063504 NA NA + [3,] 0.080136 NA NA + [4,] 0.123984 NA NA + [5,] 0.207144 NA NA + [6,] 0.306936 NA NA + [7,] 0.406728 NA NA + [8,] NA 14.231162 0.04383869 + [9,] NA 13.563719 0.36510338 +[10,] NA 13.421034 0.71662378 +[11,] NA 12.261480 1.21394115 +[12,] NA 11.840900 1.53740260 +[13,] NA 9.907831 2.00643939 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0330171 14.3493012 0.1240754 0.5714233 -5.2324385 2.4737584 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.772447e-10 -8.748056e-09 -1.057540e-08 -1.513277e-09 3.198961e-08 2.735937e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006122452 0.324729793 0.141655578 0.046836685 0.758328132 0.332240304 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4836253 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.772447e-10 -8.748056e-09 -1.057540e-08 -1.513277e-09 3.198961e-08 2.735937e-08 + +$result$normp +[1] 4.430079e-08 + +$result$res + [1] -0.16354476 0.09268930 0.14419655 0.16472975 0.43919852 -0.70598812 0.19070779 0.14131503 0.39995910 -0.39929055 0.00486735 -0.53937190 0.39252098 0.52678501 0.21696539 -0.33426177 -0.51928911 -0.55060712 0.66040760 + +$result$prevres + [1] -0.163544769 0.092689292 0.144196542 0.164729737 0.439198515 -0.705988110 0.190707816 0.141315046 0.399959113 -0.399290540 0.004867349 -0.539371912 0.392520944 0.526785060 0.216965427 -0.334261756 -0.519289121 -0.550607144 0.660407534 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 98.975647 0.000000 0 3.90512770 0.00000000 0.00000000 + [3,] 125.722609 0.000000 0 6.69809414 0.00000000 0.00000000 + [4,] 192.746451 0.000000 0 15.02771297 0.00000000 0.00000000 + [5,] 326.994103 0.000000 0 35.48116412 0.00000000 0.00000000 + [6,] 443.431126 0.000000 0 55.91976764 0.00000000 0.00000000 + [7,] 621.711324 0.000000 0 90.54165139 0.00000000 0.00000000 + [8,] -3.498445 2.173913 0 -0.01680507 0.02207547 0.00000000 + [9,] -39.610635 2.173913 0 -1.47767001 0.24994627 0.00000000 +[10,] -73.212416 2.173913 0 -4.07092153 0.46197619 0.00000000 +[11,] -137.318942 2.173913 0 -10.84019424 0.86649348 0.00000000 +[12,] -181.494319 2.173913 0 -16.44430455 1.14524363 0.00000000 +[13,] -280.546957 2.173913 0 -30.91030891 1.77027368 0.00000000 +[14,] 3.804136 0.000000 5 0.01827348 0.00000000 0.05077357 +[15,] 43.071776 0.000000 5 1.60678748 0.00000000 0.57487641 +[16,] 79.609651 0.000000 5 4.42663497 0.00000000 1.06254523 +[17,] 149.317746 0.000000 5 11.78740060 0.00000000 1.99293500 +[18,] 197.353129 0.000000 5 17.88119300 0.00000000 2.63406036 +[19,] 305.060896 0.000000 5 33.61122373 0.00000000 4.07162947 + +$result$retres +$result$retres$res + [1] -0.163544769 0.092689292 0.144196542 0.164729737 0.439198515 -0.705988110 0.190707816 0.141315046 0.399959113 -0.399290540 0.004867349 -0.539371912 0.392520944 0.526785060 0.216965427 -0.334261756 -0.519289121 -0.550607144 0.660407534 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03301710 14.34930 0.1240754 + [2,] 0.06535779 14.05316 0.2640820 + [3,] 0.08301993 13.89143 0.3405435 + [4,] 0.12727859 13.48616 0.5321444 + [5,] 0.21592797 12.67441 0.9159180 + [6,] 0.29281624 11.97036 1.2487763 + [7,] 0.41054216 10.89236 1.7584256 + [8,] 0.03881975 14.29617 0.1491957 + [9,] 0.09871666 13.74770 0.4084965 + [10,] 0.15444972 13.23736 0.6497714 + [11,] 0.26077900 12.26372 1.1100833 + [12,] 0.33404979 11.59279 1.4272812 + [13,] 0.49834188 10.08839 2.1385209 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.003270895 NA NA + [2,] -0.001853786 NA NA + [3,] -0.002883931 NA NA + [4,] -0.003294595 NA NA + [5,] -0.008783970 NA NA + [6,] 0.014119762 NA NA + [7,] -0.003814156 NA NA + [8,] NA -0.065004921 -0.10535701 + [9,] NA -0.183981192 -0.04339309 +[10,] NA 0.183673649 0.06685235 +[11,] NA -0.002238981 0.10385782 +[12,] NA 0.248111079 0.11012143 +[13,] NA -0.180559634 -0.13208151 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yddM_res/KEIO_ROBOT4_28_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yddM_res/KEIO_ROBOT4_28_res.txt new file mode 100644 index 0000000..6a4cb0d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yddM_res/KEIO_ROBOT4_28_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0330171047966288 0.0332012879788968 0.0331925650348049 0.00357762628379896 0.0268044402907315 0.0399764146195035 +Glc 14.3493011750335 14.3664587461338 14.3571146720576 0.181462177250394 14.0106794905851 14.7076768351747 +Ace 0.124075382300643 0.134860468664874 0.126024207726011 0.0763136637929761 0.00225838669406945 0.282300613609482 +mu 0.571423282756617 0.572011075182236 0.571251624303209 0.0257606083174716 0.524614181847831 0.618653431485756 +qGlc -5.23243850408571 -5.21302855588701 -5.16751133383169 0.53621897799921 -6.15790753983157 -4.32895697106538 +qAce 2.47375840964762 2.45758637743375 2.5084666461769 0.229032461755186 2.02936535611403 2.85180550968467 +res 3.04061430174956 32.6002878293496 32.505114702063 7.80239970769437 19.9258046732275 50.7592371363734 + + +Goodness of fit (khi2 test) + +khi2 value 3.04061430174958 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.233893407826891 +p-value, i.e. P(X^2<=value) 0.00221607589920214 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydeI.txt b/validation/validation_results/Berges_2021/Berges_2021/ydeI.txt new file mode 100644 index 0000000..d7b9d0f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydeI.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.10584 NA NA NA +3.34194444444444 0.157248 NA NA NA +3.9975 0.214704 NA NA NA +4.52333333333333 0.297864 NA NA NA +1.95 NA 14.23440500919 0.38788851141066 0 +3.25 NA 12.5384366613795 0.894036310031323 0 +4.08333333333333 NA 12.1306594937962 1.37192764912841 0 +4.76666666666667 NA 11.0962635959685 1.8960346493585 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydeI_res/KEIO_ROBOT2_2.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydeI_res/KEIO_ROBOT2_2.pdf new file mode 100644 index 0000000..ede1f88 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydeI_res/KEIO_ROBOT2_2.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydeI_res/KEIO_ROBOT2_2_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydeI_res/KEIO_ROBOT2_2_log.txt new file mode 100644 index 0000000..87badcb --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydeI_res/KEIO_ROBOT2_2_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.105840 NA NA NA +[2,] 0.157248 NA NA NA +[3,] 0.214704 NA NA NA +[4,] 0.297864 NA NA NA +[5,] NA 14.23441 0.3878885 0 +[6,] NA 12.53844 0.8940363 0 +[7,] NA 12.13066 1.3719276 0 +[8,] NA 11.09626 1.8960346 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.919934e-02 1.447323e+01 1.246967e-01 1.000000e-06 5.082991e-01 -5.933002e+00 3.045075e+00 -2.305444e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 2.114774e-09 1.005299e-07 -2.670512e-08 0.000000e+00 -1.838356e-08 -1.690262e-07 1.191152e-08 -1.620241e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.01168413 0.60447263 0.26789582 0.24943437 0.09737445 1.56319494 0.68846561 0.65671372 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5223732 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 2.114774e-09 1.005299e-07 -2.670512e-08 0.000000e+00 -1.838356e-08 -1.690262e-07 1.191152e-08 -1.620241e-13 + +$result$normp +[1] 1.996838e-07 + +$result$res + [1] -8.570877e-02 1.190605e-01 4.025444e-01 -3.427726e-01 -7.362536e-01 1.081417e+00 -7.090168e-02 -2.742616e-01 1.660231e-01 -1.581797e-01 -1.409256e-01 1.330823e-01 3.877982e-06 2.207401e-06 3.852655e-07 -1.806210e-06 + +$result$prevres + [1] -8.570891e-02 1.190604e-01 4.025444e-01 -3.427725e-01 -7.362537e-01 1.081417e+00 -7.090164e-02 -2.742615e-01 1.660231e-01 -1.581797e-01 -1.409257e-01 1.330823e-01 3.877983e-06 2.207401e-06 3.852659e-07 -1.806210e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 1.783017e+02 0.000000 0 0 1.302296e+01 0.0000000 0.0000000 0.0000000 + [2,] 2.733439e+02 0.000000 0 0 2.667360e+01 0.0000000 0.0000000 0.0000000 + [3,] 3.814382e+02 0.000000 0 0 4.452313e+01 0.0000000 0.0000000 0.0000000 + [4,] 4.983136e+02 0.000000 0 0 6.581643e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.299507e+01 2.173913 0 0 -1.423015e+00 0.2116007 0.0000000 0.0000000 + [6,] -1.070108e+02 2.173913 0 0 -6.415824e+00 0.5266549 0.0000000 0.0000000 + [7,] -1.768340e+02 2.173913 0 0 -1.395118e+01 0.8702905 0.0000000 0.0000000 + [8,] -2.608101e+02 2.173913 0 0 -2.484989e+01 1.2835799 0.0000000 0.0000000 + [9,] 5.075396e+01 0.000000 5 0 1.679812e+00 0.0000000 0.4866817 0.0000000 +[10,] 1.263220e+02 0.000000 5 0 7.573624e+00 0.0000000 1.2113063 0.0000000 +[11,] 2.087454e+02 0.000000 5 0 1.646881e+01 0.0000000 2.0016681 0.0000000 +[12,] 3.078759e+02 0.000000 5 0 2.933430e+01 0.0000000 2.9522337 0.0000000 +[13,] -3.842612e-05 0.000000 0 5 -1.271796e-06 0.0000000 0.0000000 0.4866817 +[14,] -9.563911e-05 0.000000 0 5 -5.734036e-06 0.0000000 0.0000000 1.2113063 +[15,] -1.580424e-04 0.000000 0 5 -1.246864e-05 0.0000000 0.0000000 2.0016681 +[16,] -2.330946e-04 0.000000 0 5 -2.220918e-05 0.0000000 0.0000000 2.9522337 + +$result$retres +$result$retres$res + [1] -8.570891e-02 1.190604e-01 4.025444e-01 -3.427725e-01 -7.362537e-01 1.081417e+00 -7.090164e-02 -2.742615e-01 1.660231e-01 -1.581797e-01 -1.409257e-01 1.330823e-01 3.877983e-06 2.207401e-06 3.852659e-07 -1.806210e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10412582 13.59866 0.5735598 6.601631e-07 + [2,] 0.15962921 12.95081 0.9060647 4.084217e-07 + [3,] 0.22275489 12.21399 1.2842326 1.221085e-07 + [4,] 0.29100855 11.41732 1.6931207 -1.874631e-07 + [5,] 0.07867532 13.89573 0.4210931 7.755965e-07 + [6,] 0.15234054 13.03589 0.8624004 4.414802e-07 + [7,] 0.23268859 12.09804 1.3437425 7.705318e-08 + [8,] 0.32932292 10.97010 1.9226511 -3.612420e-07 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.001714178 NA NA NA +[2,] -0.002381208 NA NA NA +[3,] -0.008050888 NA NA NA +[4,] 0.006855449 NA NA NA +[5,] NA 0.33867670 -0.03320462 -7.755965e-07 +[6,] NA -0.49745174 0.03163595 -4.414802e-07 +[7,] NA 0.03261475 0.02818513 -7.705318e-08 +[8,] NA 0.12616029 -0.02661646 3.612420e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydeI_res/KEIO_ROBOT2_2_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydeI_res/KEIO_ROBOT2_2_res.txt new file mode 100644 index 0000000..3122921 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydeI_res/KEIO_ROBOT2_2_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0291993427561596 0.0288841434801561 0.027732507082685 0.00591827939354043 0.0201548639551344 0.0432887608910029 +Glc 14.4732250893598 14.4628843439165 14.4227740022594 0.448239629096527 13.6936400147215 15.3145879597357 +Ace 0.124696695598542 0.164644702381489 0.13444921673844 0.152910336827054 9.99999999903162e-07 0.476418009853547 +Lac 1e-06 0.0979348985369021 0.0702935172563742 0.0846640004625337 9.99999999986122e-07 0.288973678735273 +mu 0.508299139112642 0.514756039290279 0.520508469939653 0.0474493098590105 0.407814260663633 0.591934911045258 +qGlc -5.93300224659562 -5.97404137524174 -5.96671925213792 1.21100819473127 -8.48060613306343 -3.86347921261023 +qAce 3.04507468649018 2.96985959388596 2.99987798091653 0.487504462457662 1.93105215430049 3.82444187670715 +qLac -2.30544430448261e-06 -0.0371438472199528 -0.0101799808490799 0.224276334142747 -0.479722836269873 0.359673160969195 +res 2.18299009541177 21.5201528749033 20.7846961359731 6.85003954267017 11.4935379752834 38.6675988977682 + + +Goodness of fit (khi2 test) + +khi2 value 2.18299009541185 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.272873761926481 +p-value, i.e. P(X^2<=value) 0.0251184037444129 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydeN.txt b/validation/validation_results/Berges_2021/Berges_2021/ydeN.txt new file mode 100644 index 0000000..665e1bf --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydeN.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.063504 NA NA +1.61361111111111 0.078624 NA NA +2.36138888888889 0.123984 NA NA +3.28638888888889 0.216216 NA NA +3.81944444444444 0.276696 NA NA +4.41083333333333 0.44604 NA NA +0.283333333333333 NA 14.4166449029172 0.0490476175640166 +1.91666666666667 NA 14.2660549396086 0.443907349958386 +2.7 NA 13.3866585635387 0.716981415550494 +3.61666666666667 NA 11.9954863115715 1.1727220329069 +4.05 NA 11.5627603570146 1.55291085400683 +4.75 NA 10.2364977173744 2.19453087267614 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydeN_res/KEIO_ROBOT4_19.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydeN_res/KEIO_ROBOT4_19.pdf new file mode 100644 index 0000000..6faea67 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydeN_res/KEIO_ROBOT4_19.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydeN_res/KEIO_ROBOT4_19_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydeN_res/KEIO_ROBOT4_19_log.txt new file mode 100644 index 0000000..f6a8036 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydeN_res/KEIO_ROBOT4_19_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.063504 NA NA + [3,] 0.078624 NA NA + [4,] 0.123984 NA NA + [5,] 0.216216 NA NA + [6,] 0.276696 NA NA + [7,] 0.446040 NA NA + [8,] NA 14.41664 0.04904762 + [9,] NA 14.26605 0.44390735 +[10,] NA 13.38666 0.71698142 +[11,] NA 11.99549 1.17272203 +[12,] NA 11.56276 1.55291085 +[13,] NA 10.23650 2.19453087 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02908868 14.50158950 0.13832468 0.61101142 -5.46641000 2.59952226 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.425405e-09 -7.244404e-08 3.661569e-08 2.223780e-08 9.252655e-08 -5.036982e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006664814 0.382121769 0.166797434 0.057386245 0.900145239 0.394819484 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5780483 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.425405e-09 -7.244404e-08 3.661569e-08 2.223780e-08 9.252655e-08 -5.036982e-08 + +$result$normp +[1] 1.348612e-07 + +$result$res + [1] -0.28436606 -0.15665348 -0.03285696 -0.04304517 0.02264309 1.16956209 -0.76685328 0.07773187 -0.74706044 0.04448712 0.85754651 0.23522489 -0.46792994 0.56334062 -0.15077786 -0.29094416 -0.15111032 -0.34248576 0.37197749 + +$result$prevres + [1] -0.28436594 -0.15665331 -0.03285677 -0.04304498 0.02264320 1.16956207 -0.76685360 0.07773202 -0.74706038 0.04448713 0.85754645 0.23522481 -0.46793003 0.56334045 -0.15077794 -0.29094417 -0.15111026 -0.34248567 0.37197760 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 103.770490 0.000000 0 3.60716330 0.00000000 0.00000000 + [3,] 134.015812 0.000000 0 6.29040995 0.00000000 0.00000000 + [4,] 211.634036 0.000000 0 14.53707605 0.00000000 0.00000000 + [5,] 372.428131 0.000000 0 35.60290736 0.00000000 0.00000000 + [6,] 515.814448 0.000000 0 57.30832735 0.00000000 0.00000000 + [7,] 740.327353 0.000000 0 94.98794157 0.00000000 0.00000000 + [8,] -3.676011 2.173913 0 -0.01558532 0.01956134 0.00000000 + [9,] -43.284609 2.173913 0 -1.43693165 0.23033255 0.00000000 +[10,] -81.793874 2.173913 0 -4.05755482 0.43525383 0.00000000 +[11,] -157.810664 2.173913 0 -11.13546677 0.83976577 0.00000000 +[12,] -211.543943 2.173913 0 -17.14200971 1.12569936 0.00000000 +[13,] -334.833633 2.173913 0 -33.01108755 1.78176695 0.00000000 +[14,] 4.020647 0.000000 5 0.01704649 0.00000000 0.04499108 +[15,] 47.342661 0.000000 5 1.57164801 0.00000000 0.52976487 +[16,] 89.462278 0.000000 5 4.43796191 0.00000000 1.00108381 +[17,] 172.605854 0.000000 5 12.17944788 0.00000000 1.93146128 +[18,] 231.376779 0.000000 5 18.74912099 0.00000000 2.58910853 +[19,] 366.225221 0.000000 5 36.10596921 0.00000000 4.09806398 + +$result$retres +$result$retres$res + [1] -0.28436594 -0.15665331 -0.03285677 -0.04304498 0.02264320 1.16956207 -0.76685360 0.07773202 -0.74706038 0.04448713 0.85754645 0.23522481 -0.46793003 0.56334045 -0.15077794 -0.29094417 -0.15111026 -0.34248567 0.37197760 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02908868 14.50159 0.1383246 + [2,] 0.06037093 14.22172 0.2714137 + [3,] 0.07796686 14.06430 0.3462748 + [4,] 0.12312310 13.66031 0.5383901 + [5,] 0.21666886 12.82340 0.9363766 + [6,] 0.30008724 12.07710 1.2912766 + [7,] 0.43070293 10.90855 1.8469756 + [8,] 0.03458669 14.45240 0.1617157 + [9,] 0.09382716 13.92241 0.4137518 + [10,] 0.15142340 13.40712 0.6587926 + [11,] 0.26511765 12.38996 1.1425000 + [12,] 0.34548365 11.67096 1.4844137 + [13,] 0.52988144 10.02125 2.2689264 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0056873187 NA NA + [2,] 0.0031330661 NA NA + [3,] 0.0006571354 NA NA + [4,] 0.0008608997 NA NA + [5,] -0.0004528640 NA NA + [6,] -0.0233912414 NA NA + [7,] 0.0153370720 NA NA + [8,] NA -0.03575673 -0.11266809 + [9,] NA 0.34364777 0.03015559 +[10,] NA -0.02046408 0.05818883 +[11,] NA -0.39447137 0.03022205 +[12,] NA -0.10820341 0.06849713 +[13,] NA 0.21524781 -0.07439552 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydeN_res/KEIO_ROBOT4_19_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydeN_res/KEIO_ROBOT4_19_res.txt new file mode 100644 index 0000000..60da984 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydeN_res/KEIO_ROBOT4_19_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.029088678845559 0.029294382731905 0.0292756873845456 0.0031883730716229 0.0241544291240737 0.0352208083968778 +Glc 14.5015894959824 14.5187920210036 14.5231811669835 0.2325748560705 14.055989968023 14.8904491036409 +Ace 0.138324680442205 0.145887737025953 0.141584825163568 0.0814023315710668 0.0105995956472515 0.326283587064382 +mu 0.61101142253027 0.6105224275289 0.606825012480008 0.0257315707802551 0.56355090414162 0.656135449534971 +qGlc -5.46641000295335 -5.5009281142526 -5.5170614291019 0.583451052926897 -6.58340138801358 -4.34763369706428 +qAce 2.5995222581776 2.60204800198529 2.61421284276098 0.261290850805602 2.04623661310348 3.06783292302606 +res 4.34381803620314 32.0926124062284 30.9914146717662 7.05135203846472 19.9692719477951 46.4835864450292 + + +Goodness of fit (khi2 test) + +khi2 value 4.34381803620346 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.334139848938728 +p-value, i.e. P(X^2<=value) 0.0130459477850703 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfH.txt b/validation/validation_results/Berges_2021/Berges_2021/ydfH.txt new file mode 100644 index 0000000..bf4d401 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydfH.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.1992000000000005E-2 NA NA +2.2613888888888889 8.1647999999999998E-2 NA NA +2.7741666666666664 0.11037599999999999 NA NA +3.2088888888888891 0.13456799999999999 NA NA +3.7063888888888892 0.18446399999999999 NA NA +4.2258333333333331 0.270648 NA NA +4.6355555555555554 0.33566400000000002 NA NA +4.9675000000000002 0.41277600000000003 NA NA +2.8 NA 12.3869247468826 0.543951606055465 +3.73333333333333 NA 12.0535013257395 0.947805094908646 +4.28333333333333 NA 11.3813612885244 1.25470117323262 +4.75 NA 10.6525942250558 1.61341325009931 +5.11666666666667 NA 9.89804227656906 1.84643436651789 +5.43333333333333 NA 9.19972747751989 2.14713174293579 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfH_res/KEIO_ROBOT5_18.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydfH_res/KEIO_ROBOT5_18.pdf new file mode 100644 index 0000000..9005c46 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydfH_res/KEIO_ROBOT5_18.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfH_res/KEIO_ROBOT5_18_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydfH_res/KEIO_ROBOT5_18_log.txt new file mode 100644 index 0000000..c8f7eba --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydfH_res/KEIO_ROBOT5_18_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.061992 NA NA + [2,] 0.081648 NA NA + [3,] 0.110376 NA NA + [4,] 0.134568 NA NA + [5,] 0.184464 NA NA + [6,] 0.270648 NA NA + [7,] 0.335664 NA NA + [8,] 0.412776 NA NA + [9,] NA 12.386925 0.5439516 +[10,] NA 12.053501 0.9478051 +[11,] NA 11.381361 1.2547012 +[12,] NA 10.652594 1.6134133 +[13,] NA 9.898042 1.8464344 +[14,] NA 9.199727 2.1471317 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01982161 13.22356133 0.29868432 0.61127990 -4.62535546 2.20408252 + +$result$lastp + X Glc Ace mu qGlc qAce +-4.061793e-10 -1.494798e-08 2.115517e-09 4.592406e-09 8.119868e-09 6.226981e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.002490325 0.271153673 0.118635033 0.027925200 0.482552634 0.210493495 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.288039 + +$result$laststep + X Glc Ace mu qGlc qAce +-4.061793e-10 -1.494798e-08 2.115517e-09 4.592406e-09 8.119868e-09 6.226981e-09 + +$result$normp +[1] 1.88117e-08 + +$result$res + [1] -0.068263194 -0.133716349 -0.116455527 0.318374391 0.328142598 -0.411482918 0.072057754 0.008273885 0.339243280 -0.324779349 -0.140181481 -0.031845971 0.114364298 0.043199222 0.395230580 -0.101850455 -0.237203353 -0.413132645 0.059317423 0.297638451 + +$result$prevres + [1] -0.068263157 -0.133716309 -0.116455486 0.318374431 0.328142631 -0.411482904 0.072057740 0.008273837 0.339243292 -0.324779347 -0.140181484 -0.031845976 0.114364294 0.043199221 0.395230584 -0.101850447 -0.237203345 -0.413132643 0.059317417 0.297638433 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 152.93087 0.000000 0 5.543978 0.0000000 0.0000000 + [2,] 199.21100 0.000000 0 8.929509 0.0000000 0.0000000 + [3,] 272.54816 0.000000 0 14.987004 0.0000000 0.0000000 + [4,] 355.50961 0.000000 0 22.612316 0.0000000 0.0000000 + [5,] 481.86502 0.000000 0 35.400990 0.0000000 0.0000000 + [6,] 661.94997 0.000000 0 55.446809 0.0000000 0.0000000 + [7,] 850.34737 0.000000 0 78.133484 0.0000000 0.0000000 + [8,] 1041.64441 0.000000 0 102.564339 0.0000000 0.0000000 + [9,] -74.64235 2.173913 0 -2.635250 0.3198742 0.0000000 +[10,] -144.71011 2.173913 0 -7.233478 0.6201444 0.0000000 +[11,] -209.11335 2.173913 0 -12.370055 0.8961396 0.0000000 +[12,] -283.57453 2.173913 0 -19.052738 1.2152374 0.0000000 +[13,] -358.95285 2.173913 0 -26.433955 1.5382656 0.0000000 +[14,] -439.13001 2.173913 0 -34.825312 1.8818588 0.0000000 +[15,] 81.80802 0.000000 5 2.888234 0.0000000 0.7357107 +[16,] 158.60229 0.000000 5 7.927892 0.0000000 1.4263320 +[17,] 229.18824 0.000000 5 13.557581 0.0000000 2.0611211 +[18,] 310.79769 0.000000 5 20.881802 0.0000000 2.7950460 +[19,] 393.41234 0.000000 5 28.971615 0.0000000 3.5380108 +[20,] 481.28651 0.000000 5 38.168544 0.0000000 4.3282752 + +$result$retres +$result$retres$res + [1] -0.068263157 -0.133716309 -0.116455486 0.318374431 0.328142631 -0.411482904 0.072057740 0.008273837 0.339243292 -0.324779347 -0.140181484 -0.031845976 0.114364294 0.043199221 0.395230584 -0.101850447 -0.237203345 -0.413132643 0.059317417 0.297638433 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06062674 12.914802 0.4458147 + [2,] 0.07897367 12.775977 0.5119680 + [3,] 0.10804689 12.555989 0.6167968 + [4,] 0.14093549 12.307132 0.7353827 + [5,] 0.19102685 11.928107 0.9159964 + [6,] 0.26241834 11.387911 1.1734116 + [7,] 0.33710515 10.822780 1.4427087 + [8,] 0.41294148 10.248952 1.7161505 + [9,] 0.10976664 12.542977 0.6229977 + [10,] 0.19419923 11.904103 0.9274350 + [11,] 0.27180599 11.316878 1.2072605 + [12,] 0.36153270 10.637945 1.5307867 + [13,] 0.45236459 9.950650 1.8582978 + [14,] 0.54897913 9.219599 2.2066594 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0013652631 NA NA + [2,] 0.0026743262 NA NA + [3,] 0.0023291097 NA NA + [4,] -0.0063674886 NA NA + [5,] -0.0065628526 NA NA + [6,] 0.0082296581 NA NA + [7,] -0.0014411548 NA NA + [8,] -0.0001654767 NA NA + [9,] NA -0.15605191 -0.07904612 +[10,] NA 0.14939850 0.02037009 +[11,] NA 0.06448348 0.04744067 +[12,] NA 0.01464915 0.08262653 +[13,] NA -0.05260758 -0.01186348 +[14,] NA -0.01987164 -0.05952769 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfH_res/KEIO_ROBOT5_18_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydfH_res/KEIO_ROBOT5_18_res.txt new file mode 100644 index 0000000..ac7aa38 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydfH_res/KEIO_ROBOT5_18_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0198216140830896 0.0202173270636737 0.0202495332543727 0.00251753670732274 0.0162629667339795 0.0253080734133427 +Glc 13.2235613301044 13.2073078287601 13.2101957557174 0.224918336947497 12.7236033654501 13.6350333682921 +Ace 0.298684315442881 0.291037287601459 0.297981526155714 0.106672733579996 0.0923132464851825 0.466863010004324 +mu 0.61127990332729 0.609587258015786 0.608005128780355 0.0252347129450904 0.563128191953553 0.653142237805238 +qGlc -4.62535545796802 -4.59229843073473 -4.56519291223221 0.543472587874578 -5.66497680747706 -3.4713777645954 +qAce 2.20408252138294 2.20262567231272 2.20152183977016 0.229960072253511 1.75580455117218 2.61889722904887 +res 1.16153055269441 36.0283049029955 36.0076121381295 9.33937186142101 18.7622520387865 54.4055674809816 + + +Goodness of fit (khi2 test) + +khi2 value 1.16153055269442 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.0829664680496012 +p-value, i.e. P(X^2<=value) 2.66560158470916e-06 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfW.txt b/validation/validation_results/Berges_2021/Berges_2021/ydfW.txt new file mode 100644 index 0000000..e058b3c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydfW.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.033264 NA NA +1.195 0.063504 NA NA +1.61361111111111 0.080136 NA NA +2.36138888888889 0.127008 NA NA +3.28638888888889 0.21168 NA NA +3.81944444444444 0.322056 NA NA +4.41083333333333 0.43092 NA NA +0.283333333333333 NA 13.9723839412294 0.0447677648453156 +1.91666666666667 NA 13.8646166451015 0.430101741004181 +2.7 NA 13.4182190757922 0.790785748974942 +3.61666666666667 NA 12.1602599924059 1.42123774993354 +4.05 NA 11.5150516821812 1.79120213524801 +4.75 NA 9.55842794789116 2.32881777737842 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfW_res/KEIO_ROBOT4_35.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydfW_res/KEIO_ROBOT4_35.pdf new file mode 100644 index 0000000..661a923 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydfW_res/KEIO_ROBOT4_35.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfW_res/KEIO_ROBOT4_35_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydfW_res/KEIO_ROBOT4_35_log.txt new file mode 100644 index 0000000..4e1d79b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydfW_res/KEIO_ROBOT4_35_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.033264 NA NA + [2,] 0.063504 NA NA + [3,] 0.080136 NA NA + [4,] 0.127008 NA NA + [5,] 0.211680 NA NA + [6,] 0.322056 NA NA + [7,] 0.430920 NA NA + [8,] NA 13.972384 0.04476776 + [9,] NA 13.864617 0.43010174 +[10,] NA 13.418219 0.79078575 +[11,] NA 12.160260 1.42123775 +[12,] NA 11.515052 1.79120214 +[13,] NA 9.558428 2.32881778 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03190848 14.36495407 0.15070316 0.59214972 -5.50943592 2.77934937 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.109292e-09 2.264317e-08 9.001136e-10 -8.814780e-09 -4.974910e-09 -3.230282e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006942521 0.385632811 0.168831607 0.054696719 0.877639760 0.387611315 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5785582 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.109292e-09 2.264317e-08 9.001136e-10 -8.814780e-09 -4.974910e-09 -3.230282e-08 + +$result$normp +[1] 4.07514e-08 + +$result$res + [1] -0.06777585 0.06216116 0.14125269 0.10834737 0.58535517 -0.78795561 0.19094492 0.73551859 -0.27475246 -0.48931790 -0.05609637 -0.26069418 0.34534233 0.66646819 0.18382566 -0.24466518 -0.72656674 -0.71155369 0.83249177 + +$result$prevres + [1] -0.06777590 0.06216108 0.14125260 0.10834728 0.58535510 -0.78795563 0.19094501 0.73551855 -0.27475248 -0.48931790 -0.05609635 -0.26069416 0.34534234 0.66646818 0.18382563 -0.24466521 -0.72656675 -0.71155369 0.83249184 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.0000000 + [2,] 101.457697 0.000000 0 3.86864649 0.00000000 0.0000000 + [3,] 129.998431 0.000000 0 6.69334377 0.00000000 0.0000000 + [4,] 202.414746 0.000000 0 15.25161405 0.00000000 0.0000000 + [5,] 350.043450 0.000000 0 36.70684450 0.00000000 0.0000000 + [6,] 479.961548 0.000000 0 58.49419725 0.00000000 0.0000000 + [7,] 681.227802 0.000000 0 95.87804159 0.00000000 0.0000000 + [8,] -3.694777 2.173913 0 -0.01716856 0.02139869 0.0000000 + [9,] -42.698443 2.173913 0 -1.54750919 0.24729256 0.0000000 +[10,] -79.835744 2.173913 0 -4.31862508 0.46237717 0.0000000 +[11,] -151.963028 2.173913 0 -11.68240448 0.88010998 0.0000000 +[12,] -202.332850 2.173913 0 -17.85830831 1.17183214 0.0000000 +[13,] -316.643940 2.173913 0 -33.99522194 1.83387693 0.0000000 +[14,] 4.286986 0.000000 5 0.01992038 0.00000000 0.0492170 +[15,] 49.542268 0.000000 5 1.79554827 0.00000000 0.5687729 +[16,] 92.632040 0.000000 5 5.01082631 0.00000000 1.0634675 +[17,] 176.320084 0.000000 5 13.55489276 0.00000000 2.0242529 +[18,] 234.763322 0.000000 5 20.72068763 0.00000000 2.6952139 +[19,] 367.396512 0.000000 5 39.44407064 0.00000000 4.2179169 + +$result$retres +$result$retres$res + [1] -0.06777590 0.06216108 0.14125260 0.10834728 0.58535510 -0.78795563 0.19094501 0.73551855 -0.27475248 -0.48931790 -0.05609635 -0.26069416 0.34534234 0.66646818 0.18382563 -0.24466521 -0.72656675 -0.71155369 0.83249184 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03190848 14.364954 0.1507032 + [2,] 0.06474722 14.059418 0.3048370 + [3,] 0.08296105 13.889954 0.3903266 + [4,] 0.12917495 13.459975 0.6072389 + [5,] 0.22338710 12.583413 1.0494387 + [6,] 0.30629689 11.812010 1.4385890 + [7,] 0.43473890 10.616969 2.0414521 + [8,] 0.03773725 14.310722 0.1780614 + [9,] 0.09926822 13.738231 0.4668669 + [10,] 0.15785488 13.193133 0.7418527 + [11,] 0.27164065 12.134456 1.2759244 + [12,] 0.35110252 11.395132 1.6488914 + [13,] 0.53143616 9.717285 2.4953161 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.001355518 NA NA + [2,] -0.001243222 NA NA + [3,] -0.002825052 NA NA + [4,] -0.002166946 NA NA + [5,] -0.011707102 NA NA + [6,] 0.015759113 NA NA + [7,] -0.003818900 NA NA + [8,] NA -0.33833853 -0.13329364 + [9,] NA 0.12638614 -0.03676513 +[10,] NA 0.22508623 0.04893304 +[11,] NA 0.02580432 0.14531335 +[12,] NA 0.11991931 0.14231074 +[13,] NA -0.15885748 -0.16649837 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfW_res/KEIO_ROBOT4_35_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydfW_res/KEIO_ROBOT4_35_res.txt new file mode 100644 index 0000000..164e303 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydfW_res/KEIO_ROBOT4_35_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0319084830394165 0.0322396832908573 0.0321556476586694 0.00371367226058018 0.0252038507293104 0.039263088196733 +Glc 14.3649540733915 14.3884784576504 14.4009428142171 0.207844964849486 14.0154884067807 14.7658896364492 +Ace 0.150703155672323 0.144898861865627 0.140502509744541 0.0755528215471482 0.0196394262672753 0.313276559016218 +mu 0.592149718500474 0.591382500015207 0.590363455416934 0.0274771132918973 0.542033594772182 0.642590681776884 +qGlc -5.50943592242465 -5.57021075969012 -5.50317016507317 0.560237243817497 -6.70044608205194 -4.59492131898164 +qAce 2.7793493705833 2.78049693141808 2.81361738786305 0.251701472263273 2.28898981567243 3.19160566492022 +res 4.35148502742748 31.4689710938246 30.99801777212 8.01501989260603 19.7009184430822 46.7367904996458 + + +Goodness of fit (khi2 test) + +khi2 value 4.35148502742753 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.334729617494426 +p-value, i.e. P(X^2<=value) 0.0131543482934723 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfZ.txt b/validation/validation_results/Berges_2021/Berges_2021/ydfZ.txt new file mode 100644 index 0000000..888ca8f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydfZ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.03024 NA NA +1.18888888888889 0.058968 NA NA +2.27694444444444 0.10584 NA NA +3.12833333333333 0.148176 NA NA +3.77138888888889 0.225288 NA NA +4.41555555555556 0.326592 NA NA +4.82277777777778 0.439992 NA NA +0.0666666666666667 NA 15.1026327170455 0.0139344646573582 +1.71666666666667 NA 14.6563448866627 0.348435934306603 +2.8 NA 13.5615052701702 0.717520501374685 +3.63333333333333 NA 12.7076833377407 1.22361777188345 +4.26666666666667 NA 12.1843779508731 1.7829953873717 +4.88333333333333 NA 9.87672629544768 2.29287043754086 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfZ_res/KEIO_ROBOT1_41.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydfZ_res/KEIO_ROBOT1_41.pdf new file mode 100644 index 0000000..ae5194d Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydfZ_res/KEIO_ROBOT1_41.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfZ_res/KEIO_ROBOT1_41_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydfZ_res/KEIO_ROBOT1_41_log.txt new file mode 100644 index 0000000..0465765 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydfZ_res/KEIO_ROBOT1_41_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.030240 NA NA + [2,] 0.058968 NA NA + [3,] 0.105840 NA NA + [4,] 0.148176 NA NA + [5,] 0.225288 NA NA + [6,] 0.326592 NA NA + [7,] 0.439992 NA NA + [8,] NA 15.102633 0.01393446 + [9,] NA 14.656345 0.34843593 +[10,] NA 13.561505 0.71752050 +[11,] NA 12.707683 1.22361777 +[12,] NA 12.184378 1.78299539 +[13,] NA 9.876726 2.29287044 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02571184 15.09019712 0.10603474 0.58280703 -6.98221952 3.22039259 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.222969e-08 1.274441e-07 -1.677167e-07 -1.112063e-07 6.779757e-07 5.377203e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006364521 0.376583710 0.164181392 0.056116539 1.046693862 0.459813359 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5777439 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.222969e-08 1.274441e-07 -1.677167e-07 -1.112063e-07 6.779757e-07 5.377203e-08 + +$result$normp +[1] 7.207147e-07 + +$result$res + [1] -0.226408204 -0.377870392 -0.445589284 0.551238194 0.314808202 0.525207913 -0.630030499 -0.053564187 -0.208363844 0.568746242 0.283876282 -1.063053159 0.472358666 0.488645340 0.009554515 -0.135393575 -0.394651811 -0.555870876 0.587716408 + +$result$prevres + [1] -0.226408815 -0.377871275 -0.445590362 0.551237177 0.314807551 0.525208172 -0.630029203 -0.053564455 -0.208363813 0.568746467 0.283876544 -1.063053053 0.472358311 0.488646164 0.009554888 -0.135393601 -0.394652135 -0.555871334 0.587716018 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000e+00 0.000000000 0.000000000 + [2,] 99.974578 0.000000 0 3.056073e+00 0.000000000 0.000000000 + [3,] 188.489533 0.000000 0 1.103501e+01 0.000000000 0.000000000 + [4,] 309.586643 0.000000 0 2.490165e+01 0.000000000 0.000000000 + [5,] 450.345634 0.000000 0 4.366969e+01 0.000000000 0.000000000 + [6,] 655.527526 0.000000 0 7.442334e+01 0.000000000 0.000000000 + [7,] 831.118440 0.000000 0 1.030607e+02 0.000000000 0.000000000 + [8,] -1.031831 2.173913 0 -8.900686e-04 0.003799689 0.000000000 + [9,] -44.785643 2.173913 0 -1.150514e+00 0.164921834 0.000000000 +[10,] -107.129562 2.173913 0 -4.861335e+00 0.394501509 0.000000000 +[11,] -190.398823 2.173913 0 -1.182016e+01 0.701138152 0.000000000 +[12,] -287.029464 2.173913 0 -2.168242e+01 1.056977689 0.000000000 +[13,] -422.423309 2.173913 0 -3.767318e+01 1.555561603 0.000000000 +[14,] 1.094591 0.000000 5 9.442059e-04 0.000000000 0.008739286 +[15,] 47.509660 0.000000 5 1.220493e+00 0.000000000 0.379320219 +[16,] 113.645550 0.000000 5 5.157018e+00 0.000000000 0.907353471 +[17,] 201.979534 0.000000 5 1.253910e+01 0.000000000 1.612617749 +[18,] 304.487583 0.000000 5 2.300122e+01 0.000000000 2.431048685 +[19,] 448.116547 0.000000 5 3.996459e+01 0.000000000 3.577791686 + +$result$retres +$result$retres$res + [1] -0.226408815 -0.377871275 -0.445590362 0.551237177 0.314807551 0.525208172 -0.630029203 -0.053564455 -0.208363813 0.568746467 0.283876544 -1.063053053 0.472358311 0.488646164 0.009554888 -0.135393601 -0.394652135 -0.555871334 0.587716018 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02571182 15.09020 0.1060349 + [2,] 0.05141057 14.78232 0.2480374 + [3,] 0.09692819 14.23700 0.4995522 + [4,] 0.15920074 13.49096 0.8436489 + [5,] 0.23158415 12.62378 1.2436149 + [6,] 0.33709616 11.35971 1.8266381 + [7,] 0.42739142 10.27794 2.3255787 + [8,] 0.02673049 15.07799 0.1116637 + [9,] 0.06992593 14.56050 0.3503469 + [10,] 0.13147424 13.82313 0.6904418 + [11,] 0.21368085 12.83827 1.1446873 + [12,] 0.30907833 11.69537 1.6718211 + [13,] 0.44274433 10.09401 2.4104136 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.004528176 NA NA + [2,] 0.007557425 NA NA + [3,] 0.008911807 NA NA + [4,] -0.011024744 NA NA + [5,] -0.006296151 NA NA + [6,] -0.010504163 NA NA + [7,] 0.012600584 NA NA + [8,] NA 0.02463965 -0.097729233 + [9,] NA 0.09584735 -0.001910978 +[10,] NA -0.26162337 0.027078720 +[11,] NA -0.13058321 0.078930427 +[12,] NA 0.48900440 0.111174267 +[13,] NA -0.21728482 -0.117543204 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydfZ_res/KEIO_ROBOT1_41_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydfZ_res/KEIO_ROBOT1_41_res.txt new file mode 100644 index 0000000..c3015d9 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydfZ_res/KEIO_ROBOT1_41_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0257118359284264 0.0257352803830193 0.0257842548994151 0.00373570200535662 0.018759339722275 0.0333921345946065 +Glc 15.0901971189486 15.067983328316 15.0498523430585 0.21279314105469 14.6906266172285 15.502945763793 +Ace 0.106034743664178 0.116899454039911 0.119699113474766 0.0718727740757604 1.00000000000054e-06 0.239158096441678 +mu 0.582807025186828 0.584600389113796 0.583886692874852 0.0327715795346446 0.52596682119309 0.655244663590013 +qGlc -6.98221951781735 -6.98223563500238 -7.03778340135846 0.625737687834745 -8.05553563005406 -5.92710094580733 +qAce 3.22039259199783 3.21112231670624 3.23359179304205 0.243399925379705 2.7843526598374 3.66938844206118 +res 4.33924345787746 31.0693706726892 30.9595978250254 7.20978118323518 19.091303047625 43.9059864911672 + + +Goodness of fit (khi2 test) + +khi2 value 4.33924345788503 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.333787958298849 +p-value, i.e. P(X^2<=value) 0.0129815722021952 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydgJ.txt b/validation/validation_results/Berges_2021/Berges_2021/ydgJ.txt new file mode 100644 index 0000000..9d5614b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydgJ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.061992 NA NA +1.61361111111111 0.077112 NA NA +2.36138888888889 0.1134 NA NA +3.28638888888889 0.192024 NA NA +3.81944444444444 0.282744 NA NA +4.41083333333333 0.394632 NA NA +0.283333333333333 NA 13.9087195399652 0.0412057147221786 +1.91666666666667 NA 13.553122723813 0.38357431216198 +2.7 NA 13.6516764786761 0.674101204627893 +3.61666666666667 NA 12.4285351742037 1.13920039261254 +4.05 NA 11.9835842293579 1.31488259252049 +4.75 NA 10.1540205924178 1.94296564011312 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydgJ_res/KEIO_ROBOT4_15.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydgJ_res/KEIO_ROBOT4_15.pdf new file mode 100644 index 0000000..8a230de Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydgJ_res/KEIO_ROBOT4_15.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydgJ_res/KEIO_ROBOT4_15_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydgJ_res/KEIO_ROBOT4_15_log.txt new file mode 100644 index 0000000..2dc613b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydgJ_res/KEIO_ROBOT4_15_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.061992 NA NA + [3,] 0.077112 NA NA + [4,] 0.113400 NA NA + [5,] 0.192024 NA NA + [6,] 0.282744 NA NA + [7,] 0.394632 NA NA + [8,] NA 13.90872 0.04120571 + [9,] NA 13.55312 0.38357431 +[10,] NA 13.65168 0.67410120 +[11,] NA 12.42854 1.13920039 +[12,] NA 11.98358 1.31488259 +[13,] NA 10.15402 1.94296564 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02844535 14.21806768 0.13123706 0.59606643 -5.03164878 2.46050242 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.552705e-09 3.402130e-08 3.429712e-08 2.290404e-08 -2.430368e-07 -4.085679e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.005755338 0.318336649 0.139038127 0.050838581 0.799505659 0.351191247 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4798701 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.552705e-09 3.402130e-08 3.429712e-08 2.290404e-08 -2.430368e-07 -4.085679e-08 + +$result$normp +[1] 2.521924e-07 + +$result$res + [1] -0.31653239 -0.20006063 -0.13430429 0.14125845 0.48490361 -0.27875051 -0.01615810 0.57645632 0.33134176 -0.85655541 -0.09494350 -0.45603546 0.49973629 0.55817364 -0.00854261 -0.36610142 -0.55757909 0.05805098 0.31599849 + +$result$prevres + [1] -0.316532267 -0.200060448 -0.134304091 0.141258656 0.484903751 -0.278750482 -0.016158320 0.576456240 0.331341669 -0.856555487 -0.094943519 -0.456035414 0.499736510 0.558173483 -0.008542681 -0.366101429 -0.557579031 0.058051067 0.315998591 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 101.933676 0.000000 0 3.46494976 0.00000000 0.00000000 + [3,] 130.822623 0.000000 0 6.00472443 0.00000000 0.00000000 + [4,] 204.295525 0.000000 0 13.72264162 0.00000000 0.00000000 + [5,] 354.578239 0.000000 0 33.14685930 0.00000000 0.00000000 + [6,] 487.195526 0.000000 0 52.93157802 0.00000000 0.00000000 + [7,] 693.098818 0.000000 0 86.96152734 0.00000000 0.00000000 + [8,] -3.376285 2.173913 0 -0.01398840 0.01908711 0.00000000 + [9,] -39.169516 2.173913 0 -1.26678992 0.22143652 0.00000000 +[10,] -73.398298 2.173913 0 -3.54386735 0.41494167 0.00000000 +[11,] -140.101312 2.173913 0 -9.61526305 0.79203296 0.00000000 +[12,] -186.800556 2.173913 0 -14.71974965 1.05603720 0.00000000 +[13,] -293.023184 2.173913 0 -28.08785700 1.65654424 0.00000000 +[14,] 3.797349 0.000000 5 0.01573292 0.00000000 0.04390036 +[15,] 44.054426 0.000000 5 1.42477386 0.00000000 0.50930401 +[16,] 82.551949 0.000000 5 3.98583025 0.00000000 0.95436583 +[17,] 157.573631 0.000000 5 10.81440204 0.00000000 1.82167581 +[18,] 210.096832 0.000000 5 16.55547953 0.00000000 2.42888557 +[19,] 329.566700 0.000000 5 31.59075071 0.00000000 3.81005174 + +$result$retres +$result$retres$res + [1] -0.316532267 -0.200060448 -0.134304091 0.141258656 0.484903751 -0.278750482 -0.016158320 0.576456240 0.331341669 -0.856555487 -0.094943519 -0.456035414 0.499736510 0.558173483 -0.008542681 -0.366101429 -0.557579031 0.058051067 0.315998591 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02844535 14.21807 0.1312370 + [2,] 0.05799079 13.96866 0.2531976 + [3,] 0.07442592 13.82993 0.3210402 + [4,] 0.11622517 13.47708 0.4935833 + [5,] 0.20172208 12.75537 0.8465060 + [6,] 0.27716899 12.11849 1.1579433 + [7,] 0.39430883 11.12966 1.6414848 + [8,] 0.03367886 14.17389 0.1528404 + [9,] 0.08916116 13.70554 0.3818658 + [10,] 0.14221844 13.25766 0.6008809 + [11,] 0.24561331 12.38486 1.0276846 + [12,] 0.31800077 11.77381 1.3264928 + [13,] 0.48265413 10.38390 2.0061654 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0063306453 NA NA + [2,] 0.0040012090 NA NA + [3,] 0.0026860818 NA NA + [4,] -0.0028251731 NA NA + [5,] -0.0096980750 NA NA + [6,] 0.0055750096 NA NA + [7,] 0.0003231664 NA NA + [8,] NA -0.26516987 -0.111634697 + [9,] NA -0.15241717 0.001708536 +[10,] NA 0.39401552 0.073220286 +[11,] NA 0.04367402 0.111515806 +[12,] NA 0.20977629 -0.011610213 +[13,] NA -0.22987879 -0.063199718 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydgJ_res/KEIO_ROBOT4_15_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydgJ_res/KEIO_ROBOT4_15_res.txt new file mode 100644 index 0000000..acb6b77 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydgJ_res/KEIO_ROBOT4_15_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0284453521025303 0.0288013971809032 0.0285551343992527 0.00401242217162315 0.0212328467591572 0.0362681784717892 +Glc 14.2180676778706 14.2462681085178 14.2586011135922 0.204371508570213 13.8755726326889 14.6167793570103 +Ace 0.131237058408001 0.143923029128239 0.124695846289194 0.0852382902045924 9.99999999998268e-07 0.295024868034426 +mu 0.596066430081994 0.594587255794871 0.59230460170118 0.0350631076947776 0.534895442693823 0.655576323348729 +qGlc -5.03164878280011 -5.0423865397044 -5.07867941405701 0.55418148784625 -6.05395642238579 -4.07016754840508 +qAce 2.46050241572876 2.43262784225558 2.4672497490458 0.268253833430141 1.83680729564869 2.89427734701257 +res 2.99357885907585 32.1527936028327 30.8965144786703 8.81200948053384 17.4550858916196 51.67849017421 + + +Goodness of fit (khi2 test) + +khi2 value 2.99357885907619 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.230275296852015 +p-value, i.e. P(X^2<=value) 0.00204263833973246 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhR.txt b/validation/validation_results/Berges_2021/Berges_2021/ydhR.txt new file mode 100644 index 0000000..5c4710c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydhR.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.03024 NA NA +1.18888888888889 0.048384 NA NA +2.27694444444444 0.078624 NA NA +3.12833333333333 0.125496 NA NA +3.77138888888889 0.169344 NA NA +4.41555555555556 0.247968 NA NA +4.82277777777778 0.331128 NA NA +0.0666666666666667 NA 15.3793072853034 0.0148850213423291 +1.71666666666667 NA 14.6768519852581 0.300482385058974 +2.8 NA 14.0463653420712 0.711009763136968 +3.63333333333333 NA 12.887440269279 1.13588468955394 +4.26666666666667 NA 11.8140858713823 1.5743121948729 +4.88333333333333 NA 10.8576626936259 2.09946284862796 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhR_res/KEIO_ROBOT1_21.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydhR_res/KEIO_ROBOT1_21.pdf new file mode 100644 index 0000000..abc4ec2 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydhR_res/KEIO_ROBOT1_21.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhR_res/KEIO_ROBOT1_21_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydhR_res/KEIO_ROBOT1_21_log.txt new file mode 100644 index 0000000..1b5f80d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydhR_res/KEIO_ROBOT1_21_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.030240 NA NA + [2,] 0.048384 NA NA + [3,] 0.078624 NA NA + [4,] 0.125496 NA NA + [5,] 0.169344 NA NA + [6,] 0.247968 NA NA + [7,] 0.331128 NA NA + [8,] NA 15.37931 0.01488502 + [9,] NA 14.67685 0.30048239 +[10,] NA 14.04637 0.71100976 +[11,] NA 12.88744 1.13588469 +[12,] NA 11.81409 1.57431219 +[13,] NA 10.85766 2.09946285 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02381236 15.25022246 0.07793748 0.53741268 -8.14590834 3.69358032 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.611616e-09 4.813327e-08 -2.184609e-08 -1.650637e-08 -2.118891e-08 9.718029e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.005144712 0.281813225 0.122828599 0.049343864 0.995761626 0.436990544 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4216228 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.611616e-09 4.813327e-08 -2.184609e-08 -1.650637e-08 -2.118891e-08 9.718029e-09 + +$result$normp +[1] 6.010433e-08 + +$result$res + [1] -0.32138212 -0.16364431 0.11642878 0.12123592 0.56923395 0.37606120 -0.65679373 -0.30924091 0.05714853 -0.13159071 0.39171664 0.48316398 -0.49119754 0.34511141 0.12758642 -0.29881692 -0.34149670 -0.19556019 0.36317598 + +$result$prevres + [1] -0.32138220 -0.16364442 0.11642866 0.12123582 0.56923390 0.37606126 -0.65679354 -0.30924101 0.05714849 -0.13159070 0.39171668 0.48316404 -0.49119750 0.34511152 0.12758646 -0.29881693 -0.34149674 -0.19556024 0.36317594 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000e+00 0.000000000 0.000000000 + [2,] 94.722067 0.000000 0 2.681605e+00 0.000000000 0.000000000 + [3,] 169.980184 0.000000 0 9.216226e+00 0.000000000 0.000000000 + [4,] 268.601553 0.000000 0 2.000893e+01 0.000000000 0.000000000 + [5,] 379.485083 0.000000 0 3.407991e+01 0.000000000 0.000000000 + [6,] 536.463559 0.000000 0 5.640634e+01 0.000000000 0.000000000 + [7,] 667.704046 0.000000 0 7.668027e+01 0.000000000 0.000000000 + [8,] -1.201970 2.173913 0 -9.597544e-04 0.003513633 0.000000000 + [9,] -49.945035 2.173913 0 -1.175603e+00 0.146000780 0.000000000 +[10,] -115.430464 2.173913 0 -4.778663e+00 0.337429687 0.000000000 +[11,] -199.256480 2.173913 0 -1.126131e+01 0.582472336 0.000000000 +[12,] -293.406415 2.173913 0 -2.015713e+01 0.857694163 0.000000000 +[13,] -421.639941 2.173913 0 -3.417900e+01 1.232550133 0.000000000 +[14,] 1.253515 0.000000 5 1.000912e-03 0.000000000 0.008081355 +[15,] 52.086862 0.000000 5 1.226017e+00 0.000000000 0.335801794 +[16,] 120.380545 0.000000 5 4.983589e+00 0.000000000 0.776088280 +[17,] 207.801329 0.000000 5 1.174423e+01 0.000000000 1.339686374 +[18,] 305.988758 0.000000 5 2.102154e+01 0.000000000 1.972696576 +[19,] 439.721407 0.000000 5 3.564472e+01 0.000000000 2.834865307 + +$result$retres +$result$retres$res + [1] -0.32138220 -0.16364442 0.11642866 0.12123582 0.56923390 0.37606126 -0.65679354 -0.30924101 0.05714849 -0.13159070 0.39171668 0.48316404 -0.49119750 0.34511152 0.12758646 -0.29881693 -0.34149674 -0.19556024 0.36317594 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02381236 15.25022 0.07793750 + [2,] 0.04511111 14.92738 0.22432158 + [3,] 0.08095257 14.38411 0.47065613 + [4,] 0.12792072 13.67219 0.79346318 + [5,] 0.18072868 12.87174 1.15640669 + [6,] 0.25548923 11.73855 1.67022798 + [7,] 0.31799213 10.79115 2.09980378 + [8,] 0.02468096 15.23706 0.08390732 + [9,] 0.05990519 14.70314 0.32599968 + [10,] 0.10722830 13.98583 0.65124638 + [11,] 0.16780525 13.06763 1.06758534 + [12,] 0.23584279 12.03634 1.53520015 + [13,] 0.32851088 10.63171 2.17209804 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.006427644 NA NA + [2,] 0.003272888 NA NA + [3,] -0.002328573 NA NA + [4,] -0.002424716 NA NA + [5,] -0.011384678 NA NA + [6,] -0.007521225 NA NA + [7,] 0.013135871 NA NA + [8,] NA 0.14225086 -0.06902230 + [9,] NA -0.02628831 -0.02551729 +[10,] NA 0.06053172 0.05976339 +[11,] NA -0.18018967 0.06829935 +[12,] NA -0.22225546 0.03911205 +[13,] NA 0.22595085 -0.07263519 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhR_res/KEIO_ROBOT1_21_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydhR_res/KEIO_ROBOT1_21_res.txt new file mode 100644 index 0000000..2d4966b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydhR_res/KEIO_ROBOT1_21_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0238123576334832 0.0239623697566582 0.0236086576685178 0.0038461756451556 0.0170031634995056 0.0321887406819448 +Glc 15.2502224645974 15.2355478324231 15.2400865963229 0.235615931134914 14.7996947367495 15.7125651443812 +Ace 0.0779374761650635 0.115677030044682 0.1026589712393 0.0878018156272894 1.000000000001e-06 0.311855291699686 +mu 0.537412683050826 0.538813925394743 0.538383751063469 0.0349332834049877 0.469228560719097 0.606462787831753 +qGlc -8.14590833599141 -8.13802161470888 -8.23548037501294 0.833479673750638 -9.58141559356342 -6.45980940962494 +qAce 3.69358032450004 3.62303298562259 3.61408559644688 0.331778553822118 3.01262931072577 4.22813834038683 +res 2.31095574942027 31.1625306695245 30.5742757934855 8.14450839436251 18.6174191278784 52.235640480736 + + +Goodness of fit (khi2 test) + +khi2 value 2.31095574942039 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.177765826878492 +p-value, i.e. P(X^2<=value) 0.000507102632076382 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhS.txt b/validation/validation_results/Berges_2021/Berges_2021/ydhS.txt new file mode 100644 index 0000000..1331e93 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydhS.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.042336 NA NA +1.18888888888889 0.084672 NA NA +2.27694444444444 0.12852 NA NA +3.12833333333333 0.198072 NA NA +3.77138888888889 0.267624 NA NA +4.41555555555556 0.38556 NA NA +4.82277777777778 0.583632 NA NA +0.0666666666666667 NA 14.8601384033374 0.00614724117920393 +1.71666666666667 NA 14.6995674012756 0.362372602491705 +2.8 NA 13.3369377789629 0.866735048838875 +3.63333333333333 NA 12.3514624520271 1.50719502588268 +4.26666666666667 NA 11.1233997039422 2.21854753712641 +4.88333333333333 NA 9.27439532684473 3.0769944798112 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhS_res/KEIO_ROBOT1_24.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydhS_res/KEIO_ROBOT1_24.pdf new file mode 100644 index 0000000..7140505 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydhS_res/KEIO_ROBOT1_24.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhS_res/KEIO_ROBOT1_24_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydhS_res/KEIO_ROBOT1_24_log.txt new file mode 100644 index 0000000..06c6f12 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydhS_res/KEIO_ROBOT1_24_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.042336 NA NA + [2,] 0.084672 NA NA + [3,] 0.128520 NA NA + [4,] 0.198072 NA NA + [5,] 0.267624 NA NA + [6,] 0.385560 NA NA + [7,] 0.583632 NA NA + [8,] NA 14.860138 0.006147241 + [9,] NA 14.699567 0.362372602 +[10,] NA 13.336938 0.866735049 +[11,] NA 12.351462 1.507195026 +[12,] NA 11.123400 2.218547537 +[13,] NA 9.274395 3.076994480 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02957728 14.95510851 0.07325087 0.60464576 -6.44875059 3.47899293 + +$result$lastp + X Glc Ace mu qGlc qAce + 8.794795e-09 1.249277e-07 -8.415339e-08 -6.862967e-08 2.973202e-07 -1.143695e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01018782 0.63284808 0.27793130 0.07781399 1.41321998 0.63788197 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.982569 + +$result$laststep + X Glc Ace mu qGlc qAce + 8.794795e-09 1.249277e-07 -8.415339e-08 -6.862967e-08 2.973202e-07 -1.143695e-07 + +$result$normp +[1] 3.591041e-07 + +$result$res + [1] -0.63793605 -1.19884465 -0.56676537 -0.09943139 1.08230348 2.07348124 -1.86904998 0.17824908 -0.69496335 0.47584331 0.17611357 -0.03295004 -0.10229257 0.37051856 0.10601060 -0.19297270 -0.36512732 -0.34988494 0.43145581 + +$result$prevres + [1] -0.63793649 -1.19884530 -0.56676620 -0.09943220 1.08230293 2.07348136 -1.86904906 0.17824882 -0.69496340 0.47584344 0.17611376 -0.03294991 -0.10229271 0.37051897 0.10601071 -0.19297282 -0.36512756 -0.34988516 0.43145585 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000e+00 0.000000000 0.0000000 + [2,] 102.604286 0.000000 0 3.607986e+00 0.000000000 0.0000000 + [3,] 198.099208 0.000000 0 1.334115e+01 0.000000000 0.0000000 + [4,] 331.476425 0.000000 0 3.067070e+01 0.000000000 0.0000000 + [5,] 489.007364 0.000000 0 5.454749e+01 0.000000000 0.0000000 + [6,] 721.888166 0.000000 0 9.427865e+01 0.000000000 0.0000000 + [7,] 923.430416 0.000000 0 1.317224e+02 0.000000000 0.0000000 + [8,] -0.953694 2.173913 0 -9.465722e-04 0.004374129 0.0000000 + [9,] -42.278658 2.173913 0 -1.255767e+00 0.193911550 0.0000000 +[10,] -102.846501 2.173913 0 -5.406602e+00 0.471706661 0.0000000 +[11,] -185.412178 2.173913 0 -1.334701e+01 0.850395091 0.0000000 +[12,] -282.742502 2.173913 0 -2.477617e+01 1.296801743 0.0000000 +[13,] -420.987766 2.173913 0 -4.356114e+01 1.930865238 0.0000000 +[14,] 1.183354 0.000000 5 1.174518e-03 0.000000000 0.0100605 +[15,] 52.459843 0.000000 5 1.558169e+00 0.000000000 0.4459966 +[16,] 127.613117 0.000000 5 6.708574e+00 0.000000000 1.0849253 +[17,] 230.061555 0.000000 5 1.656112e+01 0.000000000 1.9559087 +[18,] 350.830136 0.000000 5 3.074256e+01 0.000000000 2.9826440 +[19,] 522.366444 0.000000 5 5.405116e+01 0.000000000 4.4409900 + +$result$retres +$result$retres$res + [1] -0.63793649 -1.19884530 -0.56676620 -0.09943220 1.08230293 2.07348136 -1.86904906 0.17824882 -0.69496340 0.47584344 0.17611376 -0.03294991 -0.10229271 0.37051897 0.10601071 -0.19297282 -0.36512756 -0.34988516 0.43145585 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02957727 14.955108 0.07325096 + [2,] 0.06069509 14.623226 0.25229576 + [3,] 0.11718468 14.020746 0.57732383 + [4,] 0.19608336 13.179265 1.03128869 + [5,] 0.28927006 12.185398 1.56746355 + [6,] 0.42702963 10.716145 2.36010043 + [7,] 0.54625102 9.444609 3.04607290 + [8,] 0.03079388 14.942133 0.08025104 + [9,] 0.08351126 14.379884 0.38357475 + [10,] 0.16077638 13.555826 0.82814049 + [11,] 0.26610368 12.432475 1.43416951 + [12,] 0.39026592 11.108243 2.14857051 + [13,] 0.56662249 9.227341 3.16328565 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.012758730 NA NA + [2,] 0.023976906 NA NA + [3,] 0.011335324 NA NA + [4,] 0.001988644 NA NA + [5,] -0.021646059 NA NA + [6,] -0.041469627 NA NA + [7,] 0.037380981 NA NA + [8,] NA -0.08199446 -0.07410379 + [9,] NA 0.31968316 -0.02120214 +[10,] NA -0.21888798 0.03859456 +[11,] NA -0.08101233 0.07302551 +[12,] NA 0.01515696 0.06997703 +[13,] NA 0.04705464 -0.08629117 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhS_res/KEIO_ROBOT1_24_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydhS_res/KEIO_ROBOT1_24_res.txt new file mode 100644 index 0000000..d4b2062 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydhS_res/KEIO_ROBOT1_24_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0295772790048795 0.0293286287178307 0.0289868999872646 0.00329944323233447 0.0240822203130686 0.037103220126677 +Glc 14.9551085105329 14.9633435611197 14.9589549645518 0.199136988197001 14.6354726842896 15.3711823188458 +Ace 0.0732508727000036 0.111979292004442 0.116346291042051 0.072106234165176 9.99999999995796e-07 0.261720646329493 +mu 0.604645755346303 0.60710481716774 0.608001833788258 0.0247953693564431 0.551919659089291 0.648510804794457 +qGlc -6.44875059147471 -6.48334328061937 -6.48292228625753 0.514111365989012 -7.51359451950615 -5.48727028858614 +qAce 3.47899292542984 3.43752351057888 3.44249142564994 0.206292131208411 3.01409177139305 3.77347825687719 +res 12.5507449716481 33.0177926748052 32.7126221168541 8.53433878740499 19.2388162438234 49.4402397735261 + + +Goodness of fit (khi2 test) + +khi2 value 12.5507449716522 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.96544192089632 +p-value, i.e. P(X^2<=value) 0.516919514859105 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhZ.txt b/validation/validation_results/Berges_2021/Berges_2021/ydhZ.txt new file mode 100644 index 0000000..313f89f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydhZ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.065016 NA NA +1.61361111111111 0.080136 NA NA +2.36138888888889 0.123984 NA NA +3.28638888888889 0.193536 NA NA +3.81944444444444 0.291816 NA NA +4.41083333333333 0.418824 NA NA +0.283333333333333 NA 14.2940537131501 0.0419441007863591 +1.91666666666667 NA 14.0793844561584 0.398442513501164 +2.7 NA 13.5729497044887 0.704031594743088 +3.61666666666667 NA 12.3643562393446 1.17486625971546 +4.05 NA 11.9079246425031 1.41989945337289 +4.75 NA 10.0867161176697 2.02434249983106 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhZ_res/KEIO_ROBOT4_25.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydhZ_res/KEIO_ROBOT4_25.pdf new file mode 100644 index 0000000..494395a Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydhZ_res/KEIO_ROBOT4_25.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhZ_res/KEIO_ROBOT4_25_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydhZ_res/KEIO_ROBOT4_25_log.txt new file mode 100644 index 0000000..9797a31 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydhZ_res/KEIO_ROBOT4_25_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.065016 NA NA + [3,] 0.080136 NA NA + [4,] 0.123984 NA NA + [5,] 0.193536 NA NA + [6,] 0.291816 NA NA + [7,] 0.418824 NA NA + [8,] NA 14.29405 0.0419441 + [9,] NA 14.07938 0.3984425 +[10,] NA 13.57295 0.7040316 +[11,] NA 12.36436 1.1748663 +[12,] NA 11.90792 1.4198995 +[13,] NA 10.08672 2.0243425 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02942589 14.54071908 0.13827852 0.59920334 -5.47857963 2.47103877 + +$result$lastp + X Glc Ace mu qGlc qAce + 9.022927e-10 1.366752e-09 -1.319633e-08 -7.952720e-09 4.452143e-08 1.772091e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.005117246 0.286436153 0.124729177 0.043662875 0.691601163 0.301737329 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4310438 + +$result$laststep + X Glc Ace mu qGlc qAce + 9.022927e-10 1.366752e-09 -1.319633e-08 -7.952720e-09 4.452143e-08 1.772091e-08 + +$result$normp +[1] 5.036129e-08 + +$result$res + [1] -0.267505401 -0.240045591 -0.137692513 -0.142925770 0.865100978 -0.081837621 -0.261992022 0.428004719 -0.256560658 -0.260368100 0.208309154 -0.313819097 0.194433983 0.593942256 0.005725384 -0.376167735 -0.490941040 -0.145123379 0.412564513 + +$result$prevres + [1] -0.267505446 -0.240045654 -0.137692582 -0.142925842 0.865100930 -0.081837625 -0.261991931 0.428004718 -0.256560644 -0.260368082 0.208309166 -0.313819097 0.194433940 0.593942318 0.005725413 -0.376167729 -0.490941062 -0.145123411 0.412564471 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.0000000 + [2,] 102.316505 0.000000 0 3.59785144 0.00000000 0.0000000 + [3,] 131.486500 0.000000 0 6.24323472 0.00000000 0.0000000 + [4,] 205.814469 0.000000 0 14.30121851 0.00000000 0.0000000 + [5,] 358.252564 0.000000 0 34.64478609 0.00000000 0.0000000 + [6,] 493.067902 0.000000 0 55.41617574 0.00000000 0.0000000 + [7,] 702.755543 0.000000 0 91.21254026 0.00000000 0.0000000 + [8,] -3.677861 2.173913 0 -0.01576540 0.01975409 0.0000000 + [9,] -42.801150 2.173913 0 -1.43309153 0.22988841 0.0000000 +[10,] -80.344705 2.173913 0 -4.01695444 0.43153786 0.0000000 +[11,] -153.705265 2.173913 0 -10.92497090 0.82556331 0.0000000 +[12,] -205.169157 2.173913 0 -16.74424266 1.10198000 0.0000000 +[13,] -322.443292 2.173913 0 -32.01237290 1.73186880 0.0000000 +[14,] 3.815353 0.000000 5 0.01635476 0.00000000 0.0454344 +[15,] 44.401215 0.000000 5 1.48666576 0.00000000 0.5287434 +[16,] 83.348286 0.000000 5 4.16712297 0.00000000 0.9925371 +[17,] 159.451333 0.000000 5 11.33338650 0.00000000 1.8987956 +[18,] 212.839135 0.000000 5 17.37020405 0.00000000 2.5345540 +[19,] 334.497408 0.000000 5 33.20911316 0.00000000 3.9832982 + +$result$retres +$result$retres$res + [1] -0.267505446 -0.240045654 -0.137692582 -0.142925842 0.865100930 -0.081837625 -0.261991931 0.428004718 -0.256560644 -0.260368082 0.208309166 -0.313819097 0.194433940 0.593942318 0.005725413 -0.376167729 -0.490941062 -0.145123411 0.412564471 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02942589 14.54072 0.1382785 + [2,] 0.06021509 14.25921 0.2652493 + [3,] 0.07738215 14.10225 0.3360441 + [4,] 0.12112548 13.70230 0.5164360 + [5,] 0.21083802 12.88205 0.8863992 + [6,] 0.29017925 12.15662 1.2135924 + [7,] 0.41358416 11.02832 1.7224986 + [8,] 0.03487078 14.49094 0.1607326 + [9,] 0.09279085 13.96137 0.3995876 + [10,] 0.14837220 13.45318 0.6287980 + [11,] 0.25697883 12.46018 1.0766780 + [12,] 0.33316854 11.76357 1.3908748 + [13,] 0.50678702 10.17616 2.1068554 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.005350109 NA NA + [2,] 0.004800913 NA NA + [3,] 0.002753852 NA NA + [4,] 0.002858517 NA NA + [5,] -0.017302019 NA NA + [6,] 0.001636752 NA NA + [7,] 0.005239839 NA NA + [8,] NA -0.19688217 -0.118788464 + [9,] NA 0.11801790 -0.001145083 +[10,] NA 0.11976932 0.075233546 +[11,] NA -0.09582222 0.098188212 +[12,] NA 0.14435678 0.029024682 +[13,] NA -0.08943961 -0.082512894 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydhZ_res/KEIO_ROBOT4_25_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydhZ_res/KEIO_ROBOT4_25_res.txt new file mode 100644 index 0000000..6d08615 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydhZ_res/KEIO_ROBOT4_25_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0294258919741539 0.0295773065354403 0.0296512584837785 0.00352420455174348 0.023658683541932 0.0363124635329529 +Glc 14.5407190771935 14.5261052212847 14.5339142586435 0.202805062283475 14.1090048258324 14.9046609678611 +Ace 0.138278520222065 0.153452546336584 0.149958175777187 0.0864489082630409 1.00000000000009e-06 0.332992616666859 +mu 0.599203338152408 0.599555819269295 0.598725098197202 0.0290489020149707 0.549450241073879 0.648733285967417 +qGlc -5.47857963440362 -5.45044489205698 -5.48671584918911 0.592206427378677 -6.53726385657483 -4.32086612853881 +qAce 2.47103877459226 2.44444939708198 2.4346987175417 0.216316284986643 2.04925588309484 2.84118901113186 +res 2.41538333414459 31.4763885689719 31.0631255542514 6.93265188524622 18.5563125210217 45.0549630532841 + + +Goodness of fit (khi2 test) + +khi2 value 2.41538333414464 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.185798718011126 +p-value, i.e. P(X^2<=value) 0.000646556722047758 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiH.txt b/validation/validation_results/Berges_2021/Berges_2021/ydiH.txt new file mode 100644 index 0000000..8d1fa9d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydiH.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.18888888888889 0.06048 NA NA +2.27694444444444 0.095256 NA NA +3.12833333333333 0.1512 NA NA +3.77138888888889 0.213192 NA NA +4.41555555555556 0.320544 NA NA +4.82277777777778 0.412776 NA NA +0.0666666666666667 NA 15.862285037 0.0160102371472471 +1.71666666666667 NA 15.2221858746599 0.368064433394518 +2.8 NA 13.6739464269398 0.82002859989278 +3.63333333333333 NA 12.702571780811 1.39926528120428 +4.26666666666667 NA 11.6134017136587 1.98273512840098 +4.88333333333333 NA 10.2360570652382 2.70723008461594 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiH_res/KEIO_ROBOT1_14.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydiH_res/KEIO_ROBOT1_14.pdf new file mode 100644 index 0000000..056f637 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydiH_res/KEIO_ROBOT1_14.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiH_res/KEIO_ROBOT1_14_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydiH_res/KEIO_ROBOT1_14_log.txt new file mode 100644 index 0000000..1b446aa --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydiH_res/KEIO_ROBOT1_14_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.060480 NA NA + [3,] 0.095256 NA NA + [4,] 0.151200 NA NA + [5,] 0.213192 NA NA + [6,] 0.320544 NA NA + [7,] 0.412776 NA NA + [8,] NA 15.86229 0.01601024 + [9,] NA 15.22219 0.36806443 +[10,] NA 13.67395 0.82002860 +[11,] NA 12.70257 1.39926528 +[12,] NA 11.61340 1.98273513 +[13,] NA 10.23606 2.70723008 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02848552 15.61832957 0.06725494 0.54887883 -8.02120005 3.83793770 + +$result$lastp + X Glc Ace mu qGlc qAce + 8.748185e-10 3.346096e-08 -1.008515e-08 -7.476452e-09 -3.330565e-08 -3.857392e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.006210453 0.349131484 0.152667994 0.049686757 0.992487476 0.440893514 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5252834 + +$result$laststep + X Glc Ace mu qGlc qAce + 8.748185e-10 3.346096e-08 -1.008515e-08 -7.476452e-09 -3.330565e-08 -3.857392e-09 + +$result$normp +[1] 4.901178e-08 + +$result$res + [1] -0.16332393 -0.28875884 0.20725183 0.37068654 0.62793691 0.04785410 -0.53750395 -0.56406550 -0.55573807 0.92384453 0.59503993 0.19901768 -0.59809857 0.29334034 0.05525995 -0.12886434 -0.33931252 -0.21514375 0.33472032 + +$result$prevres + [1] -0.16332397 -0.28875890 0.20725176 0.37068648 0.62793688 0.04785414 -0.53750384 -0.56406557 -0.55573811 0.92384453 0.59503996 0.19901772 -0.59809853 0.29334039 0.05525996 -0.12886435 -0.33931255 -0.21514377 0.33472031 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.000000000 + [2,] 96.022156 0.000000 0 3.251897752 0.000000000 0.000000000 + [3,] 174.476424 0.000000 0 11.316531750 0.000000000 0.000000000 + [4,] 278.411148 0.000000 0 24.809830881 0.000000000 0.000000000 + [5,] 396.255244 0.000000 0 42.569691181 0.000000000 0.000000000 + [6,] 564.323693 0.000000 0 70.980294620 0.000000000 0.000000000 + [7,] 705.667153 0.000000 0 96.944084427 0.000000000 0.000000000 + [8,] -1.184023 2.173913 0 -0.001131107 0.004204798 0.000000000 + [9,] -49.741762 2.173913 0 -1.404412832 0.176646883 0.000000000 +[10,] -115.956290 2.173913 0 -5.764638954 0.411793156 0.000000000 +[11,] -201.630995 2.173913 0 -13.692127526 0.716047954 0.000000000 +[12,] -298.655140 2.173913 0 -24.659676082 1.060607777 0.000000000 +[13,] -431.752365 2.173913 0 -42.070894282 1.533273181 0.000000000 +[14,] 1.303007 0.000000 5 0.001244773 0.000000000 0.009671035 +[15,] 54.740351 0.000000 5 1.545543384 0.000000000 0.406287831 +[16,] 127.608829 0.000000 5 6.343932063 0.000000000 0.947124260 +[17,] 221.893053 0.000000 5 15.068060204 0.000000000 1.646910294 +[18,] 328.667230 0.000000 5 27.137746353 0.000000000 2.439397886 +[19,] 475.139500 0.000000 5 46.298631582 0.000000000 3.526528316 + +$result$retres +$result$retres$res + [1] -0.16332397 -0.28875890 0.20725176 0.37068648 0.62793688 0.04785414 -0.53750384 -0.56406557 -0.55573811 0.92384453 0.59503996 0.19901772 -0.59809853 0.29334039 0.05525996 -0.12886435 -0.33931255 -0.21514377 0.33472031 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02848552 15.618330 0.06725495 + [2,] 0.05470482 15.235166 0.25058875 + [3,] 0.09940104 14.581985 0.56311908 + [4,] 0.15861373 13.716663 0.97715332 + [5,] 0.22575074 12.735537 1.44659691 + [6,] 0.32150108 11.336262 2.11611418 + [7,] 0.40202592 10.159489 2.67916981 + [8,] 0.02954717 15.602815 0.07467832 + [9,] 0.07308608 14.966546 0.37911643 + [10,] 0.13245681 14.098915 0.79425573 + [11,] 0.20927636 12.976290 1.33140277 + [12,] 0.29627230 11.704950 1.93970637 + [13,] 0.41561287 9.960932 2.77417415 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0032664795 NA NA + [2,] 0.0057751780 NA NA + [3,] -0.0041450353 NA NA + [4,] -0.0074137297 NA NA + [5,] -0.0125587376 NA NA + [6,] -0.0009570828 NA NA + [7,] 0.0107500768 NA NA + [8,] NA 0.25947016 -0.05866808 + [9,] NA 0.25563953 -0.01105199 +[10,] NA -0.42496848 0.02577287 +[11,] NA -0.27371838 0.06786251 +[12,] NA -0.09154815 0.04302875 +[13,] NA 0.27512532 -0.06694406 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiH_res/KEIO_ROBOT1_14_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydiH_res/KEIO_ROBOT1_14_res.txt new file mode 100644 index 0000000..500910b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydiH_res/KEIO_ROBOT1_14_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0284855213982659 0.0277762944995132 0.0275502760221195 0.00354809334438833 0.021668259034429 0.0355698843418592 +Glc 15.6183295702295 15.622066002929 15.6143455543704 0.201352743714949 15.2499425530871 16.0092728352464 +Ace 0.0672549387650649 0.0929878417128001 0.0916683857039435 0.0640443318404393 9.99999999995709e-07 0.195151583860687 +mu 0.548878831182607 0.556586171043906 0.557060202507269 0.0285790711363815 0.501620900645835 0.609993739952718 +qGlc -8.02120004876359 -8.1497613679001 -8.09526847115522 0.635655281689087 -9.35543535330869 -7.05577980668348 +qAce 3.83793770148359 3.80535974248314 3.80510840480656 0.25054842444489 3.31853585538387 4.26269391990323 +res 3.58699510006427 31.7390870392548 31.9871562060008 7.74926815976128 17.3118598728536 46.1937817321547 + + +Goodness of fit (khi2 test) + +khi2 value 3.58699510006431 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.275922700004947 +p-value, i.e. P(X^2<=value) 0.00515592232786233 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiJ.txt b/validation/validation_results/Berges_2021/Berges_2021/ydiJ.txt new file mode 100644 index 0000000..9185c8d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydiJ.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.114912 NA NA NA +3.34194444444444 0.16632 NA NA NA +3.9975 0.240408 NA NA NA +4.52333333333333 0.349272 NA NA NA +1.95 NA 13.6203699377907 0.400548690756581 0 +3.25 NA 12.9961618253129 0.95122231946938 0 +4.08333333333333 NA 12.1107980043963 1.48084182464673 0 +4.76666666666667 NA 10.8171742059366 2.04670329013705 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiJ_res/KEIO_ROBOT2_35.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydiJ_res/KEIO_ROBOT2_35.pdf new file mode 100644 index 0000000..1c10317 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydiJ_res/KEIO_ROBOT2_35.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiJ_res/KEIO_ROBOT2_35_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydiJ_res/KEIO_ROBOT2_35_log.txt new file mode 100644 index 0000000..65c7266 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydiJ_res/KEIO_ROBOT2_35_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.114912 NA NA NA +[2,] 0.166320 NA NA NA +[3,] 0.240408 NA NA NA +[4,] 0.349272 NA NA NA +[5,] NA 13.62037 0.4005487 0 +[6,] NA 12.99616 0.9512223 0 +[7,] NA 12.11080 1.4808418 0 +[8,] NA 10.81717 2.0467033 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.420960e-02 1.415490e+01 1.939622e-01 1.000000e-06 5.853682e-01 -5.178428e+00 3.003428e+00 -2.164503e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 1.933659e-09 1.250818e-08 -3.285656e-08 2.117582e-22 -1.953653e-08 9.016844e-08 2.265253e-08 -1.768512e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.006577981 0.404019304 0.180419537 0.169359582 0.065421871 1.006096002 0.445891534 0.426335990 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3749768 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 1.933659e-09 1.250818e-08 -3.285656e-08 2.117582e-22 -1.953653e-08 9.016844e-08 2.265253e-08 -1.768512e-13 + +$result$normp +[1] 1.013159e-07 + +$result$res + [1] -5.112091e-01 2.455821e-01 5.459975e-01 -3.678053e-01 1.696865e-01 -1.359003e-01 -1.731644e-01 1.393782e-01 2.908083e-01 -2.447477e-01 -2.756321e-01 2.295715e-01 4.046010e-06 2.447683e-06 5.615169e-07 -1.841589e-06 + +$result$prevres + [1] -5.112092e-01 2.455820e-01 5.459975e-01 -3.678052e-01 1.696865e-01 -1.359003e-01 -1.731643e-01 1.393782e-01 2.908084e-01 -2.447477e-01 -2.756321e-01 2.295714e-01 4.046010e-06 2.447683e-06 5.615174e-07 -1.841589e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.162114e+02 0.000000 0 0 1.309325e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.536441e+02 0.000000 0 0 2.861233e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.190668e+02 0.000000 0 0 5.023417e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.061578e+02 0.000000 0 0 7.732998e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.098908e+01 2.173913 0 0 -1.147710e+00 0.1916275 0.0000000 0.0000000 + [6,] -1.096627e+02 2.173913 0 0 -5.606124e+00 0.5126826 0.0000000 0.0000000 + [7,] -1.907036e+02 2.173913 0 0 -1.286621e+01 0.8915559 0.0000000 0.0000000 + [8,] -2.939554e+02 2.173913 0 0 -2.398409e+01 1.3742667 0.0000000 0.0000000 + [9,] 5.467834e+01 0.000000 5 0 1.531014e+00 0.0000000 0.4407432 0.0000000 +[10,] 1.462871e+02 0.000000 5 0 7.478420e+00 0.0000000 1.1791701 0.0000000 +[11,] 2.543936e+02 0.000000 5 0 1.716318e+01 0.0000000 2.0505786 0.0000000 +[12,] 3.921287e+02 0.000000 5 0 3.199414e+01 0.0000000 3.1608134 0.0000000 +[13,] -3.940544e-05 0.000000 0 5 -1.103367e-06 0.0000000 0.0000000 0.4407432 +[14,] -1.054258e-04 0.000000 0 5 -5.389527e-06 0.0000000 0.0000000 1.1791701 +[15,] -1.833357e-04 0.000000 0 5 -1.236911e-05 0.0000000 0.0000000 2.0505786 +[16,] -2.825982e-04 0.000000 0 5 -2.305745e-05 0.0000000 0.0000000 3.1608134 + +$result$retres +$result$retres$res + [1] -5.112092e-01 2.455820e-01 5.459975e-01 -3.678052e-01 1.696865e-01 -1.359003e-01 -1.731643e-01 1.393782e-01 2.908084e-01 -2.447477e-01 -2.756321e-01 2.295714e-01 4.046010e-06 2.447683e-06 5.615174e-07 -1.841589e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10468782 13.44295 0.6068828 7.024176e-07 + [2,] 0.17123164 12.85427 0.9483082 4.563600e-07 + [3,] 0.25132795 12.14571 1.3592692 1.601897e-07 + [4,] 0.34191590 11.34433 1.8240611 -1.747752e-07 + [5,] 0.07580901 13.69843 0.4587104 8.092020e-07 + [6,] 0.16225934 12.93365 0.9022728 4.895367e-07 + [7,] 0.26427831 12.03114 1.4257154 1.123035e-07 + [8,] 0.39425756 10.88129 2.0926176 -3.683178e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.010224185 NA NA NA +[2,] -0.004911639 NA NA NA +[3,] -0.010919949 NA NA NA +[4,] 0.007356104 NA NA NA +[5,] NA -0.07805578 -0.05816167 -8.092020e-07 +[6,] NA 0.06251415 0.04894954 -4.895367e-07 +[7,] NA 0.07965560 0.05512642 -1.123035e-07 +[8,] NA -0.06411396 -0.04591428 3.683178e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiJ_res/KEIO_ROBOT2_35_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydiJ_res/KEIO_ROBOT2_35_res.txt new file mode 100644 index 0000000..12009ab --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydiJ_res/KEIO_ROBOT2_35_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0242095989299895 0.0240604150694782 0.0237370637183754 0.00526618183483149 0.015320729831353 0.0352846211200721 +Glc 14.1548971315727 14.1580676644148 14.1749617767186 0.391444035679704 13.3742950517552 14.9107511260521 +Ace 0.193962194851266 0.186613627610068 0.185799410719706 0.133458345099989 9.99999999998689e-07 0.468584017264962 +Lac 1e-06 0.100963303561309 0.0744712891129002 0.0898229637080757 9.99999999986122e-07 0.313247259353248 +mu 0.585368218740699 0.592977771104262 0.59274224040489 0.0506937427689379 0.49275633570159 0.683722349674135 +qGlc -5.17842787778397 -5.20413101644457 -5.24574336118828 0.962652440175513 -6.71977739220705 -3.1368123184169 +qAce 3.00342837450129 3.08382873171802 3.07447093158498 0.401591045211733 2.20621878964381 3.88272695936172 +qLac -2.16450273058279e-06 -0.0429244956202549 -0.0157018904959832 0.252793131628888 -0.605991826618111 0.345285615130928 +res 1.12486086092002 20.0222894040748 19.9658624858022 6.62577835869087 8.5535034071881 33.1800739827302 + + +Goodness of fit (khi2 test) + +khi2 value 1.1248608609201 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.140607607615012 +p-value, i.e. P(X^2<=value) 0.00267022036494258 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiZ.txt b/validation/validation_results/Berges_2021/Berges_2021/ydiZ.txt new file mode 100644 index 0000000..962b591 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydiZ.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.116424 NA NA NA +3.34194444444444 0.182952 NA NA NA +3.9975 0.261576 NA NA NA +4.52333333333333 0.409752 NA NA NA +1.95 NA 13.6086699466233 0.375124438603109 0 +3.25 NA 12.7936220610784 0.872534949345456 0 +4.08333333333333 NA 12.1668923754695 1.41245189762293 0 +4.76666666666667 NA 10.5263213748603 1.92082851798455 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiZ_res/KEIO_ROBOT2_37.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydiZ_res/KEIO_ROBOT2_37.pdf new file mode 100644 index 0000000..e3c6820 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydiZ_res/KEIO_ROBOT2_37.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiZ_res/KEIO_ROBOT2_37_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydiZ_res/KEIO_ROBOT2_37_log.txt new file mode 100644 index 0000000..4f5a51e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydiZ_res/KEIO_ROBOT2_37_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.116424 NA NA NA +[2,] 0.182952 NA NA NA +[3,] 0.261576 NA NA NA +[4,] 0.409752 NA NA NA +[5,] NA 13.60867 0.3751244 0 +[6,] NA 12.79362 0.8725349 0 +[7,] NA 12.16689 1.4124519 0 +[8,] NA 10.52632 1.9208285 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 1.993472e-02 1.403802e+01 2.418539e-01 1.000000e-06 6.624355e-01 -5.019416e+00 2.570340e+00 -2.025405e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 1.054163e-08 9.656873e-08 -1.858851e-07 0.000000e+00 -1.277705e-07 4.889906e-07 1.377703e-07 -8.429707e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.007675458 0.569263188 0.250390109 0.239895484 0.091850933 1.356118765 0.594847246 0.575887902 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5584273 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 1.054163e-08 9.656873e-08 -1.858851e-07 0.000000e+00 -1.277705e-07 4.889906e-07 1.377703e-07 -8.429707e-13 + +$result$normp +[1] 5.642762e-07 + +$result$res + [1] -5.947127e-01 -2.683881e-02 1.002062e+00 -5.392343e-01 6.675235e-02 2.063479e-01 -5.142268e-01 2.411266e-01 3.543301e-01 -2.102887e-01 -4.565153e-01 3.124739e-01 4.195711e-06 2.680851e-06 7.476261e-07 -1.861312e-06 + +$result$prevres + [1] -5.947138e-01 -2.683974e-02 1.002061e+00 -5.392333e-01 6.675239e-02 2.063480e-01 -5.142268e-01 2.411263e-01 3.543306e-01 -2.102887e-01 -4.565155e-01 3.124736e-01 4.195712e-06 2.680852e-06 7.476286e-07 -1.861308e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.621802e+02 0.000000 0 0 1.307347e+01 0.0000000 0.000000 0.000000 + [2,] 4.575317e+02 0.000000 0 0 3.048107e+01 0.0000000 0.000000 0.000000 + [3,] 7.063490e+02 0.000000 0 0 5.628824e+01 0.0000000 0.000000 0.000000 + [4,] 1.000685e+03 0.000000 0 0 9.023311e+01 0.0000000 0.000000 0.000000 + [5,] -4.347258e+01 2.173913 0 0 -1.021992e+00 0.1726522 0.000000 0.000000 + [6,] -1.253523e+02 2.173913 0 0 -5.416263e+00 0.4978389 0.000000 0.000000 + [7,] -2.298449e+02 2.173913 0 0 -1.313349e+01 0.9128335 0.000000 0.000000 + [8,] -3.708606e+02 2.173913 0 0 -2.564485e+01 1.4728798 0.000000 0.000000 + [9,] 5.120126e+01 0.000000 5 0 1.203685e+00 0.0000000 0.397100 0.000000 +[10,] 1.476378e+02 0.000000 5 0 6.379183e+00 0.0000000 1.145030 0.000000 +[11,] 2.707074e+02 0.000000 5 0 1.546840e+01 0.0000000 2.099517 0.000000 +[12,] 4.367932e+02 0.000000 5 0 3.020407e+01 0.0000000 3.387624 0.000000 +[13,] -4.034612e-05 0.000000 0 5 -9.484924e-07 0.0000000 0.000000 0.397100 +[14,] -1.163372e-04 0.000000 0 5 -5.026737e-06 0.0000000 0.000000 1.145030 +[15,] -2.133150e-04 0.000000 0 5 -1.218896e-05 0.0000000 0.000000 2.099517 +[16,] -3.441891e-04 0.000000 0 5 -2.380053e-05 0.0000000 0.000000 3.387624 + +$result$retres +$result$retres$res + [1] -5.947138e-01 -2.683974e-02 1.002061e+00 -5.392333e-01 6.675239e-02 2.063480e-01 -5.142268e-01 2.411263e-01 3.543306e-01 -2.102887e-01 -4.565155e-01 3.124736e-01 4.195712e-06 2.680852e-06 7.476286e-07 -1.861308e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10452972 13.39702 0.5700943 7.413498e-07 + [2,] 0.18241521 12.80687 0.8723005 5.032140e-07 + [3,] 0.28161723 12.05519 1.2572179 1.999027e-07 + [4,] 0.39896733 11.16601 1.7125522 -1.588966e-07 + [5,] 0.07254535 13.63938 0.4459906 8.391424e-07 + [6,] 0.17163638 12.88854 0.8304772 5.361704e-07 + [7,] 0.29809370 11.93035 1.3211488 1.495257e-07 + [8,] 0.46875124 10.63724 1.9833232 -3.722617e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.0118942754 NA NA NA +[2,] 0.0005367948 NA NA NA +[3,] -0.0200412280 NA NA NA +[4,] 0.0107846662 NA NA NA +[5,] NA -0.03070610 -0.07086611 -8.391424e-07 +[6,] NA -0.09492009 0.04205773 -5.361704e-07 +[7,] NA 0.23654431 0.09130310 -1.495257e-07 +[8,] NA -0.11091812 -0.06249472 3.722617e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydiZ_res/KEIO_ROBOT2_37_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydiZ_res/KEIO_ROBOT2_37_res.txt new file mode 100644 index 0000000..c35bff4 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydiZ_res/KEIO_ROBOT2_37_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0199347183100999 0.0200385296800716 0.020278965256564 0.00350461429726868 0.013673189171134 0.0270906244267903 +Glc 14.0380181657261 14.0871388863174 14.1308022071208 0.358038057280613 13.4126192840497 14.6817338271748 +Ace 0.24185394257889 0.257592941523684 0.261963488718988 0.137093307866308 1.00000000000941e-06 0.515622436252692 +Lac 1e-06 0.0844021920686692 0.0734710854681151 0.0688648212921418 9.99999999998164e-07 0.228588165411173 +mu 0.662435514516829 0.664002913205217 0.657885149515278 0.0419411705932013 0.591843642290008 0.747020509216771 +qGlc -5.01941567036352 -5.18497969536774 -5.08792469062881 0.932431461116625 -7.01583033045568 -3.19415500056666 +qAce 2.57034042221779 2.55245534016882 2.53863099747538 0.324041585888331 1.97008594781866 3.24608416506309 +qLac -2.02540537407937e-06 -0.0184985589002135 0.00188798635337009 0.175056479027989 -0.342121708986843 0.343231313015565 +res 2.49472851379561 19.7452545516733 19.4514957374048 6.38049092940762 9.46102097073975 29.9269279864024 + + +Goodness of fit (khi2 test) + +khi2 value 2.49472851379941 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.311841064224927 +p-value, i.e. P(X^2<=value) 0.0380236897696997 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydjA.txt b/validation/validation_results/Berges_2021/Berges_2021/ydjA.txt new file mode 100644 index 0000000..ea86f0d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydjA.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.108864 NA NA NA +3.34194444444444 0.163296 NA NA NA +3.9975 0.229824 NA NA NA +4.52333333333333 0.314496 NA NA NA +1.95 NA 13.8185238368847 0.444433817037551 0 +3.25 NA 12.8697538083161 1.23054161002639 0 +4.08333333333333 NA 11.7950472793673 1.83533348962865 0 +4.76666666666667 NA 10.7011842327698 2.74771312384281 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydjA_res/KEIO_ROBOT2_3.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydjA_res/KEIO_ROBOT2_3.pdf new file mode 100644 index 0000000..3231beb Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydjA_res/KEIO_ROBOT2_3.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydjA_res/KEIO_ROBOT2_3_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydjA_res/KEIO_ROBOT2_3_log.txt new file mode 100644 index 0000000..5a8c151 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydjA_res/KEIO_ROBOT2_3_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.108864 NA NA NA +[2,] 0.163296 NA NA NA +[3,] 0.229824 NA NA NA +[4,] 0.314496 NA NA NA +[5,] NA 13.81852 0.4444338 0 +[6,] NA 12.86975 1.2305416 0 +[7,] NA 11.79505 1.8353335 0 +[8,] NA 10.70118 2.7477131 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.816062e-02 1.436330e+01 7.270957e-02 1.000000e-06 5.305144e-01 -6.064634e+00 4.376596e+00 -2.226408e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 2.297415e-09 7.064837e-08 -4.754572e-08 0.000000e+00 -2.061092e-08 -5.654523e-08 3.072566e-08 -4.322904e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.004965626 0.275511435 0.129611212 0.113811425 0.042756323 0.692994062 0.318782119 0.290871919 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.2423456 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 2.297415e-09 7.064837e-08 -4.754572e-08 0.000000e+00 -2.061092e-08 -5.654523e-08 3.072566e-08 -4.322904e-13 + +$result$normp +[1] 1.08735e-07 + +$result$res + [1] -1.352016e-01 1.259597e-01 2.478776e-01 -2.085887e-01 -8.498019e-02 2.212529e-02 1.765344e-01 -1.136795e-01 2.481565e-01 -4.367172e-01 1.608893e-01 2.767141e-02 3.928266e-06 2.277171e-06 4.348524e-07 -1.818051e-06 + +$result$prevres + [1] -1.352017e-01 1.259596e-01 2.478776e-01 -2.085885e-01 -8.498025e-02 2.212530e-02 1.765345e-01 -1.136795e-01 2.481566e-01 -4.367172e-01 1.608892e-01 2.767137e-02 3.928266e-06 2.277172e-06 4.348534e-07 -1.818050e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 1.884902e+02 0.000000 0 0 1.327737e+01 0.0000000 0.0000000 0.0000000 + [2,] 2.944098e+02 0.000000 0 0 2.770726e+01 0.0000000 0.0000000 0.0000000 + [3,] 4.168616e+02 0.000000 0 0 4.692696e+01 0.0000000 0.0000000 0.0000000 + [4,] 5.509898e+02 0.000000 0 0 7.018500e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.507305e+01 2.173913 0 0 -1.447216e+00 0.2092928 0.0000000 0.0000000 + [6,] -1.145118e+02 2.173913 0 0 -6.676309e+00 0.5317258 0.0000000 0.0000000 + [7,] -1.919927e+02 2.173913 0 0 -1.474341e+01 0.8915017 0.0000000 0.0000000 + [8,] -2.867412e+02 2.173913 0 0 -2.660506e+01 1.3314585 0.0000000 0.0000000 + [9,] 7.481292e+01 0.000000 5 0 2.402111e+00 0.0000000 0.4813735 0.0000000 +[10,] 1.900684e+02 0.000000 5 0 1.108144e+01 0.0000000 1.2229693 0.0000000 +[11,] 3.186723e+02 0.000000 5 0 2.447134e+01 0.0000000 2.0504539 0.0000000 +[12,] 4.759374e+02 0.000000 5 0 4.415947e+01 0.0000000 3.0623545 0.0000000 +[13,] -3.805790e-05 0.000000 0 5 -1.221972e-06 0.0000000 0.0000000 0.4813735 +[14,] -9.668925e-05 0.000000 0 5 -5.637212e-06 0.0000000 0.0000000 1.2229693 +[15,] -1.621111e-04 0.000000 0 5 -1.244876e-05 0.0000000 0.0000000 2.0504539 +[16,] -2.421130e-04 0.000000 0 5 -2.246426e-05 0.0000000 0.0000000 3.0623545 + +$result$retres +$result$retres$res + [1] -1.352017e-01 1.259596e-01 2.478776e-01 -2.085885e-01 -8.498025e-02 2.212530e-02 1.765345e-01 -1.136795e-01 2.481566e-01 -4.367172e-01 1.608892e-01 2.767137e-02 3.928266e-06 2.277172e-06 4.348534e-07 -1.818050e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10615997 13.47165 0.7161826 6.726604e-07 + [2,] 0.16581519 12.78969 1.2083216 4.223055e-07 + [3,] 0.23478155 12.00129 1.7772749 1.328746e-07 + [4,] 0.31032423 11.13772 2.4004810 -1.841551e-07 + [5,] 0.07923573 13.77943 0.4940651 7.856532e-07 + [6,] 0.15792118 12.87993 1.1431982 4.554343e-07 + [7,] 0.24571967 11.87625 1.8675113 8.697068e-08 + [8,] 0.35308523 10.64889 2.7532474 -3.636100e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.002704035 NA NA NA +[2,] -0.002519192 NA NA NA +[3,] -0.004957551 NA NA NA +[4,] 0.004171770 NA NA NA +[5,] NA 0.03909092 -0.049631313 -7.856532e-07 +[6,] NA -0.01017764 0.087343435 -4.554343e-07 +[7,] NA -0.08120586 -0.032177847 -8.697068e-08 +[8,] NA 0.05229258 -0.005534274 3.636100e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydjA_res/KEIO_ROBOT2_3_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydjA_res/KEIO_ROBOT2_3_res.txt new file mode 100644 index 0000000..cb841eb --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydjA_res/KEIO_ROBOT2_3_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0281606152890355 0.0272536258070205 0.0271977043188412 0.00482393020890188 0.0192278698910758 0.0364134980357354 +Glc 14.3633039034976 14.361201436315 14.3678534422454 0.310869291811588 13.8116358307249 14.9674027336285 +Ace 0.072709571996349 0.104044459080467 0.0541727892741807 0.13274472951177 9.99999999917039e-07 0.44632319604446 +Lac 1e-06 0.0883484010967289 0.075966426221709 0.0782011931123793 9.99999999979183e-07 0.254938849677695 +mu 0.530514354361507 0.54258170134892 0.54164506906208 0.0418038131407976 0.474075866604934 0.619942927889529 +qGlc -6.06463449975508 -6.130660345745 -6.19567733435412 0.86214961020209 -7.60265409249844 -4.37270514166522 +qAce 4.37659610264476 4.36991333381958 4.41438585141728 0.422349050444674 3.41675580870531 5.04956443493687 +qLac -2.22640823563035e-06 -0.00717292248186056 0.00349255379174455 0.211273260475054 -0.419761355142557 0.372602798719886 +res 0.469851019417017 21.3403201158766 20.8866275825399 7.39396414520895 9.57750097076236 37.1023151935271 + + +Goodness of fit (khi2 test) + +khi2 value 0.469851019417107 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.0587313774271383 +p-value, i.e. P(X^2<=value) 0.000105247523902134 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydjF.txt b/validation/validation_results/Berges_2021/Berges_2021/ydjF.txt new file mode 100644 index 0000000..b70b56f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydjF.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.110376 NA NA NA +3.34194444444444 0.167832 NA NA NA +3.9975 0.21924 NA NA NA +4.52333333333333 0.346248 NA NA NA +1.95 NA 13.6736936443904 0.387138806352232 0 +3.25 NA 12.9815197640083 0.943086638945607 0 +4.08333333333333 NA 11.864423958866 1.48231388462937 0 +4.76666666666667 NA 10.2190126504505 1.92929319355467 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydjF_res/KEIO_ROBOT2_29.pdf b/validation/validation_results/Berges_2021/Berges_2021/ydjF_res/KEIO_ROBOT2_29.pdf new file mode 100644 index 0000000..1107015 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ydjF_res/KEIO_ROBOT2_29.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydjF_res/KEIO_ROBOT2_29_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ydjF_res/KEIO_ROBOT2_29_log.txt new file mode 100644 index 0000000..55ac3b2 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydjF_res/KEIO_ROBOT2_29_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.110376 NA NA NA +[2,] 0.167832 NA NA NA +[3,] 0.219240 NA NA NA +[4,] 0.346248 NA NA NA +[5,] NA 13.67369 0.3871388 0 +[6,] NA 12.98152 0.9430866 0 +[7,] NA 11.86442 1.4823139 0 +[8,] NA 10.21901 1.9292932 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.234645e-02 1.435077e+01 2.326984e-01 1.000000e-06 5.974724e-01 -6.637961e+00 2.919702e+00 -2.252370e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 3.550266e-09 3.703717e-08 -6.305241e-08 4.235165e-22 -3.873578e-08 2.075037e-07 5.202806e-08 -2.128165e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.01054316 0.68492419 0.29817034 0.28123123 0.11341438 1.77095818 0.77069635 0.73885807 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6278128 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 3.550266e-09 3.703717e-08 -6.305241e-08 4.235165e-22 -3.873578e-08 2.075037e-07 5.202806e-08 -2.128165e-13 + +$result$normp +[1] 2.294017e-07 + +$result$res + [1] -5.387209e-01 -1.626824e-01 1.212344e+00 -6.442169e-01 2.811993e-01 -2.461343e-01 -2.454129e-01 2.103480e-01 4.323744e-01 -2.916252e-01 -5.317226e-01 3.909734e-01 4.070743e-06 2.484867e-06 5.901845e-07 -1.845704e-06 + +$result$prevres + [1] -5.387212e-01 -1.626826e-01 1.212344e+00 -6.442166e-01 2.811993e-01 -2.461343e-01 -2.454128e-01 2.103478e-01 4.323746e-01 -2.916252e-01 -5.317227e-01 3.909733e-01 4.070744e-06 2.484868e-06 5.901851e-07 -1.845703e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.228578e+02 0.000000 0 0 1.245711e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.682428e+02 0.000000 0 0 2.750058e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.448001e+02 0.000000 0 0 4.866694e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.458987e+02 0.000000 0 0 7.539575e+01 0.0000000 0.0000000 0.0000000 + [5,] -5.328369e+01 2.173913 0 0 -1.381421e+00 0.1793775 0.0000000 0.0000000 + [6,] -1.442180e+02 2.173913 0 0 -6.834066e+00 0.4855045 0.0000000 0.0000000 + [7,] -2.528594e+02 2.173913 0 0 -1.581940e+01 0.8512415 0.0000000 0.0000000 + [8,] -3.925335e+02 2.173913 0 0 -2.970317e+01 1.3214492 0.0000000 0.0000000 + [9,] 5.390461e+01 0.000000 5 0 1.397519e+00 0.0000000 0.4125683 0.0000000 +[10,] 1.458986e+02 0.000000 5 0 6.913705e+00 0.0000000 1.1166604 0.0000000 +[11,] 2.558060e+02 0.000000 5 0 1.600375e+01 0.0000000 1.9578554 0.0000000 +[12,] 3.971078e+02 0.000000 5 0 3.004931e+01 0.0000000 3.0393331 0.0000000 +[13,] -4.158408e-05 0.000000 0 5 -1.078100e-06 0.0000000 0.0000000 0.4125683 +[14,] -1.125518e-04 0.000000 0 5 -5.333497e-06 0.0000000 0.0000000 1.1166604 +[15,] -1.973386e-04 0.000000 0 5 -1.234591e-05 0.0000000 0.0000000 1.9578554 +[16,] -3.063442e-04 0.000000 0 5 -2.318119e-05 0.0000000 0.0000000 3.0393331 + +$result$retres +$result$retres$res + [1] -5.387212e-01 -1.626826e-01 1.212344e+00 -6.442166e-01 2.811993e-01 -2.461343e-01 -2.454128e-01 2.103478e-01 4.323746e-01 -2.916252e-01 -5.317227e-01 3.909733e-01 4.070744e-06 2.484868e-06 5.901851e-07 -1.845703e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09960158 13.49246 0.6102255 7.087612e-07 + [2,] 0.16457835 12.77056 0.9277511 4.638097e-07 + [3,] 0.24348689 11.89388 1.3133579 1.663379e-07 + [4,] 0.33336367 10.89534 1.7525638 -1.724824e-07 + [5,] 0.07164607 13.80305 0.4736137 8.141487e-07 + [6,] 0.15578120 12.86830 0.8847616 4.969735e-07 + [7,] 0.25629936 11.75153 1.3759693 1.180370e-07 + [8,] 0.38552997 10.31577 2.0074879 -3.691406e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.010774424 NA NA NA +[2,] 0.003253652 NA NA NA +[3,] -0.024246886 NA NA NA +[4,] 0.012884333 NA NA NA +[5,] NA -0.12935167 -0.08647492 -8.141487e-07 +[6,] NA 0.11322177 0.05832504 -4.969735e-07 +[7,] NA 0.11288991 0.10634454 -1.180370e-07 +[8,] NA -0.09676001 -0.07819466 3.691406e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ydjF_res/KEIO_ROBOT2_29_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ydjF_res/KEIO_ROBOT2_29_res.txt new file mode 100644 index 0000000..754d946 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ydjF_res/KEIO_ROBOT2_29_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0223464468251657 0.0213095720084569 0.0212068175688422 0.00418014186919936 0.014631723482752 0.0282579980959883 +Glc 14.3507677753491 14.3733382704001 14.3915658696514 0.325140527108985 13.7927778522407 14.9512130014598 +Ace 0.23269838544831 0.235449812012408 0.227253908126796 0.149238678679078 9.99999999987122e-07 0.50796145945642 +Lac 1e-06 0.0954558595794063 0.0853524811493586 0.0765651940285865 9.99999999996531e-07 0.262786235821551 +mu 0.597472360171256 0.61279594754113 0.610028580439636 0.0468754871619444 0.53838143366216 0.695786740598051 +qGlc -6.6379610330392 -6.81386548942062 -6.8291583727339 0.882307244792866 -8.61914354094912 -5.26126433026432 +qAce 2.91970207951461 2.95046594705959 2.97025730996416 0.465075697688743 2.15754528204387 3.83117104945916 +qLac -2.25237023965886e-06 -0.0411538433768322 -0.0392020178418277 0.195944278426561 -0.466923210218199 0.318507431927864 +res 3.15319097355126 19.2584940614591 19.2599558659247 5.27145705915841 9.35323454680745 30.509505384982 + + +Goodness of fit (khi2 test) + +khi2 value 3.15319097355157 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.394148871693946 +p-value, i.e. P(X^2<=value) 0.0756208379228134 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaC.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaC.txt new file mode 100644 index 0000000..d8f0d13 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaC.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.18888888888889 0.074088 NA NA +2.27694444444444 0.111888 NA NA +3.12833333333333 0.17388 NA NA +3.77138888888889 0.252504 NA NA +4.41555555555556 0.359856 NA NA +4.82277777777778 0.421848 NA NA +0.0666666666666667 NA 15.1237992100492 0.0198991820394443 +1.71666666666667 NA 14.8171086711194 0.341187900904207 +2.8 NA 13.6564280170534 0.727323765349295 +3.63333333333333 NA 12.8933311792329 1.1741835444884 +4.26666666666667 NA 11.5929834350248 1.73158278055854 +4.88333333333333 NA 10.1115734303306 2.21140576781665 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaC_res/KEIO_ROBOT1_17.pdf b/validation/validation_results/Berges_2021/Berges_2021/yeaC_res/KEIO_ROBOT1_17.pdf new file mode 100644 index 0000000..830af16 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yeaC_res/KEIO_ROBOT1_17.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaC_res/KEIO_ROBOT1_17_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaC_res/KEIO_ROBOT1_17_log.txt new file mode 100644 index 0000000..11c211f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaC_res/KEIO_ROBOT1_17_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.074088 NA NA + [3,] 0.111888 NA NA + [4,] 0.173880 NA NA + [5,] 0.252504 NA NA + [6,] 0.359856 NA NA + [7,] 0.421848 NA NA + [8,] NA 15.12380 0.01989918 + [9,] NA 14.81711 0.34118790 +[10,] NA 13.65643 0.72732377 +[11,] NA 12.89333 1.17418354 +[12,] NA 11.59298 1.73158278 +[13,] NA 10.11157 2.21140577 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03702464 15.27105870 0.06332650 0.50760842 -6.45211068 2.79854155 + +$result$lastp + X Glc Ace mu qGlc qAce + 3.489478e-10 3.603172e-09 -1.209498e-09 -2.200730e-09 1.162656e-08 -6.050656e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.004883081 0.241831119 0.105134506 0.030326244 0.584425158 0.254005378 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3607756 + +$result$laststep + X Glc Ace mu qGlc qAce + 3.489478e-10 3.603172e-09 -1.209498e-09 -2.200730e-09 1.162656e-08 -6.050656e-09 + +$result$normp +[1] 1.382744e-08 + +$result$res + [1] 0.11243188 -0.31944266 0.28613336 0.36555165 -0.06868009 -0.57967089 0.31922281 0.28491554 -0.43546865 0.29504720 -0.27759226 0.09612765 0.03697052 0.25226597 0.02960037 -0.11267293 -0.12077501 -0.46052810 0.41210969 + +$result$prevres + [1] 0.11243186 -0.31944268 0.28613333 0.36555163 -0.06868010 -0.57967088 0.31922284 0.28491553 -0.43546865 0.29504720 -0.27759226 0.09612766 0.03697052 0.25226598 0.02960037 -0.11267294 -0.12077502 -0.46052810 0.41210970 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 91.4244563 0.000000 0 4.024338148 0.000000000 0.00000000 + [3,] 158.8275748 0.000000 0 13.389647696 0.000000000 0.00000000 + [4,] 244.6898152 0.000000 0 28.341297336 0.000000000 0.00000000 + [5,] 339.1395800 0.000000 0 47.355519623 0.000000000 0.00000000 + [6,] 470.3119450 0.000000 0 76.888639017 0.000000000 0.00000000 + [7,] 578.3074320 0.000000 0 103.263498802 0.000000000 0.00000000 + [8,] -0.9510905 2.173913 0 -0.001180413 0.005457715 0.00000000 + [9,] -38.4154075 2.173913 0 -1.395920517 0.220442053 0.00000000 +[10,] -86.8345979 2.173913 0 -5.532993989 0.498289573 0.00000000 +[11,] -147.1065087 2.173913 0 -12.776490506 0.844152460 0.00000000 +[12,] -213.3630124 2.173913 0 -22.507877697 1.224357191 0.00000000 +[13,] -301.9422375 2.173913 0 -37.564780203 1.732658091 0.00000000 +[14,] 0.9488108 0.000000 5 0.001177583 0.000000000 0.01255274 +[15,] 38.3233293 0.000000 5 1.392574624 0.000000000 0.50701672 +[16,] 86.6264633 0.000000 5 5.519731909 0.000000000 1.14606602 +[17,] 146.7539079 0.000000 5 12.745866427 0.000000000 1.94155066 +[18,] 212.8516008 0.000000 5 22.453928375 0.000000000 2.81602154 +[19,] 301.2185096 0.000000 5 37.474740862 0.000000000 3.98511361 + +$result$retres +$result$retres$res + [1] 0.11243186 -0.31944268 0.28613333 0.36555163 -0.06868010 -0.57967088 0.31922284 0.28491553 -0.43546865 0.29504720 -0.27759226 0.09612766 0.03697052 0.25226598 0.02960037 -0.11267294 -0.12077502 -0.46052810 0.41210970 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03702464 15.27106 0.06332650 + [2,] 0.06769915 14.88116 0.23244089 + [3,] 0.11761067 14.24675 0.50761258 + [4,] 0.18119103 13.43859 0.85814320 + [5,] 0.25113040 12.54960 1.24373219 + [6,] 0.34826258 11.31497 1.77924036 + [7,] 0.42823246 10.29849 2.22012945 + [8,] 0.03829901 15.25486 0.07035238 + [9,] 0.08849783 14.61679 0.34710798 + [10,] 0.15337519 13.79215 0.70478918 + [11,] 0.23413413 12.76564 1.15002854 + [12,] 0.32291189 11.63720 1.63947716 + [13,] 0.44160008 10.12858 2.29382771 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.002248637 NA NA + [2,] 0.006388854 NA NA + [3,] -0.005722667 NA NA + [4,] -0.007311033 NA NA + [5,] 0.001373602 NA NA + [6,] 0.011593418 NA NA + [7,] -0.006384457 NA NA + [8,] NA -0.13106114 -0.050453196 + [9,] NA 0.20031558 -0.005920074 +[10,] NA -0.13572171 0.022534588 +[11,] NA 0.12769244 0.024155003 +[12,] NA -0.04421872 0.092105620 +[13,] NA -0.01700644 -0.082421940 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaC_res/KEIO_ROBOT1_17_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaC_res/KEIO_ROBOT1_17_res.txt new file mode 100644 index 0000000..d3b6f2c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaC_res/KEIO_ROBOT1_17_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0370246375100992 0.0367276853014493 0.0364712569173044 0.00454332825931046 0.0284016892194188 0.045353108914188 +Glc 15.2710586952827 15.2528453810921 15.2436246717043 0.224553774017229 14.8792136271488 15.6901222702541 +Ace 0.0633265018766684 0.106740896040075 0.0964964398603617 0.074465740005881 9.99999999999471e-07 0.260621733354089 +mu 0.507608418478546 0.51176809743747 0.512214225421958 0.0282486327752022 0.463217211226269 0.569134510399538 +qGlc -6.45211067623862 -6.39772078912019 -6.33052098171162 0.527003008386428 -7.438383631843 -5.55269046688062 +qAce 2.798541545687 2.70920818613715 2.71034764424956 0.186421647256178 2.33747130126798 3.04019679351903 +res 1.6920674320312 32.5554216559976 30.4919000548492 9.40449380487378 20.0163476738523 55.3490060478142 + + +Goodness of fit (khi2 test) + +khi2 value 1.6920674320312 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.130159033233169 +p-value, i.e. P(X^2<=value) 8.70277558366682e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaD.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaD.txt new file mode 100644 index 0000000..018460b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaD.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.033264 NA NA +1.195 0.06048 NA NA +1.61361111111111 0.0756 NA NA +2.36138888888889 0.116424 NA NA +3.28638888888889 0.20412 NA NA +3.81944444444444 0.285768 NA NA +4.41083333333333 0.43092 NA NA +0.283333333333333 NA 14.3260507829508 0.0387337285647629 +1.91666666666667 NA 14.078243412943 0.377213541869969 +2.7 NA 13.4628255017178 0.685933431659829 +3.61666666666667 NA 12.382761451358 1.19744301585333 +4.05 NA 11.9012792651976 1.44013490226223 +4.75 NA 10.288581677964 2.04738667531033 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaD_res/KEIO_ROBOT4_23.pdf b/validation/validation_results/Berges_2021/Berges_2021/yeaD_res/KEIO_ROBOT4_23.pdf new file mode 100644 index 0000000..dae8c27 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yeaD_res/KEIO_ROBOT4_23.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaD_res/KEIO_ROBOT4_23_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaD_res/KEIO_ROBOT4_23_log.txt new file mode 100644 index 0000000..e3a254c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaD_res/KEIO_ROBOT4_23_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.033264 NA NA + [2,] 0.060480 NA NA + [3,] 0.075600 NA NA + [4,] 0.116424 NA NA + [5,] 0.204120 NA NA + [6,] 0.285768 NA NA + [7,] 0.430920 NA NA + [8,] NA 14.32605 0.03873373 + [9,] NA 14.07824 0.37721354 +[10,] NA 13.46283 0.68593343 +[11,] NA 12.38276 1.19744302 +[12,] NA 11.90128 1.44013490 +[13,] NA 10.28858 2.04738668 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02734042 14.45876832 0.13788774 0.62103857 -5.23438435 2.51724624 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.625217e-09 -1.748175e-08 3.398356e-08 1.570541e-08 -3.006815e-08 -6.342466e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.004297483 0.250019924 0.109159911 0.039295965 0.606306468 0.266051028 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3804244 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.625217e-09 -1.748175e-08 3.398356e-08 1.570541e-08 -3.006815e-08 -6.342466e-08 + +$result$normp +[1] 8.146518e-08 + +$result$res + [1] -0.296178794 -0.152670498 -0.056184516 0.103604280 0.317473491 0.364765593 -0.389827550 0.192137866 -0.319018941 -0.013256174 0.279676313 -0.135622409 -0.003916654 0.602372766 0.071215942 -0.330792191 -0.615302119 -0.211668386 0.484173990 + +$result$prevres + [1] -0.296178713 -0.152670381 -0.056184389 0.103604412 0.317473573 0.364765585 -0.389827758 0.192137899 -0.319018944 -0.013256195 0.279676285 -0.135622427 -0.003916619 0.602372605 0.071215856 -0.330792222 -0.615302072 -0.211668300 0.484174133 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 105.021394 0.000000 0 3.43123889 0.00000000 0.00000000 + [3,] 136.201815 0.000000 0 6.00879025 0.00000000 0.00000000 + [4,] 216.704907 0.000000 0 13.99076731 0.00000000 0.00000000 + [5,] 384.905256 0.000000 0 34.58422662 0.00000000 0.00000000 + [6,] 535.952356 0.000000 0 55.96695188 0.00000000 0.00000000 + [7,] 773.805516 0.000000 0 93.31634973 0.00000000 0.00000000 + [8,] -3.525129 2.173913 0 -0.01405384 0.01841258 0.00000000 + [9,] -41.924989 2.173913 0 -1.31143405 0.21898412 0.00000000 +[10,] -79.675033 2.173913 0 -3.72651737 0.41616152 0.00000000 +[11,] -154.839658 2.173913 0 -10.30588446 0.80876411 0.00000000 +[12,] -208.313555 2.173913 0 -15.92440515 1.08807090 0.00000000 +[13,] -331.726356 2.173913 0 -30.85599983 1.73268511 0.00000000 +[14,] 3.899087 0.000000 5 0.01554472 0.00000000 0.04234894 +[15,] 46.372541 0.000000 5 1.45055565 0.00000000 0.50366348 +[16,] 88.127245 0.000000 5 4.12183964 0.00000000 0.95717149 +[17,] 171.265602 0.000000 5 11.39916950 0.00000000 1.86015745 +[18,] 230.412201 0.000000 5 17.61372292 0.00000000 2.50256308 +[19,] 366.917072 0.000000 5 34.12931450 0.00000000 3.98517576 + +$result$retres +$result$retres$res + [1] -0.296178713 -0.152670381 -0.056184389 0.103604412 0.317473573 0.364765585 -0.389827758 0.192137899 -0.319018944 -0.013256195 0.279676285 -0.135622427 -0.003916619 0.602372605 0.071215856 -0.330792222 -0.615302072 -0.211668300 0.484174133 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02734043 14.45877 0.1378877 + [2,] 0.05742659 14.20519 0.2598355 + [3,] 0.07447631 14.06149 0.3289429 + [4,] 0.11849609 13.69047 0.5073676 + [5,] 0.21046947 12.91528 0.8801619 + [6,] 0.29306331 12.21914 1.2149383 + [7,] 0.42312344 11.12294 1.7421091 + [8,] 0.03260049 14.41443 0.1592082 + [9,] 0.08989931 13.93149 0.3914567 + [10,] 0.14622851 13.45673 0.6197750 + [11,] 0.25838632 12.51141 1.0743826 + [12,] 0.33817806 11.83889 1.3978012 + [13,] 0.52232999 10.28678 2.1442215 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.005923574 NA NA + [2,] 0.003053408 NA NA + [3,] 0.001123688 NA NA + [4,] -0.002072088 NA NA + [5,] -0.006349471 NA NA + [6,] -0.007295312 NA NA + [7,] 0.007796555 NA NA + [8,] NA -0.088383433 -0.12047452 + [9,] NA 0.146748714 -0.01424317 +[10,] NA 0.006097850 0.06615844 +[11,] NA -0.128651091 0.12306041 +[12,] NA 0.062386316 0.04233366 +[13,] NA 0.001801645 -0.09683483 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaD_res/KEIO_ROBOT4_23_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaD_res/KEIO_ROBOT4_23_res.txt new file mode 100644 index 0000000..f627320 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaD_res/KEIO_ROBOT4_23_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0273404241174873 0.0279955804255347 0.027715287820735 0.00367241251114601 0.0221486677538099 0.0364879355573983 +Glc 14.4587683213248 14.4641696056035 14.4675092727609 0.186925454863748 14.1066077391946 14.7690791585905 +Ace 0.137887742396721 0.158313804063982 0.169189022638019 0.0740554765325372 0.0190940481894497 0.302997739283685 +mu 0.62103857188997 0.617711011041323 0.619887943377961 0.0306159292609226 0.55863817822941 0.668491620798044 +qGlc -5.23438435212893 -5.24251851194359 -5.24216838932332 0.501500506437329 -6.19791035593127 -4.06374046981917 +qAce 2.51724624318423 2.46382857628985 2.43776363034208 0.237746109752825 2.0741074993123 3.00867700079839 +res 1.88139575677197 30.6123578932332 29.823545871638 7.67936673228518 17.6756057426461 44.4941752559316 + + +Goodness of fit (khi2 test) + +khi2 value 1.88139575677215 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.144722750520934 +p-value, i.e. P(X^2<=value) 0.000159944357858504 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaG.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaG.txt new file mode 100644 index 0000000..005ba2d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaG.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.108864 NA NA NA +3.34194444444444 0.16632 NA NA NA +3.9975 0.2268 NA NA NA +4.52333333333333 0.353808 NA NA NA +1.95 NA 13.7371489713297 0.42309566479176 0 +3.25 NA 12.3750469420675 0.966108682071149 0 +4.08333333333333 NA 10.7826791746195 1.53472439857597 0 +4.76666666666667 NA 9.26805712506333 2.16926328647117 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaG_res/KEIO_ROBOT2_36.pdf b/validation/validation_results/Berges_2021/Berges_2021/yeaG_res/KEIO_ROBOT2_36.pdf new file mode 100644 index 0000000..ed54df9 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yeaG_res/KEIO_ROBOT2_36.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaG_res/KEIO_ROBOT2_36_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaG_res/KEIO_ROBOT2_36_log.txt new file mode 100644 index 0000000..c0a541b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaG_res/KEIO_ROBOT2_36_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.108864 NA NA NA +[2,] 0.166320 NA NA NA +[3,] 0.226800 NA NA NA +[4,] 0.353808 NA NA NA +[5,] NA 13.737149 0.4230957 0 +[6,] NA 12.375047 0.9661087 0 +[7,] NA 10.782679 1.5347244 0 +[8,] NA 9.268057 2.1692633 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.200721e-02 1.430415e+01 2.017569e-01 1.000000e-06 6.057802e-01 -8.397083e+00 3.256053e+00 -2.224389e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-1.882804e-09 -8.702447e-08 3.151061e-08 0.000000e+00 2.121162e-08 5.637475e-08 -1.506874e-08 1.779056e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.008597794 0.594078244 0.254095082 0.237062905 0.093794652 1.511059155 0.648870962 0.616325755 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5321666 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-1.882804e-09 -8.702447e-08 3.151061e-08 0.000000e+00 2.121162e-08 5.637475e-08 -1.506874e-08 1.779056e-13 + +$result$normp +[1] 1.114667e-07 + +$result$res + [1] -4.357347e-01 1.615241e-02 1.054396e+00 -6.466449e-01 -2.651622e-01 1.072975e-01 4.500161e-01 -2.921514e-01 2.290844e-01 -1.773144e-01 -2.387629e-01 1.869929e-01 4.087456e-06 2.510279e-06 6.099946e-07 -1.848305e-06 + +$result$prevres + [1] -4.357345e-01 1.615253e-02 1.054396e+00 -6.466451e-01 -2.651621e-01 1.072975e-01 4.500160e-01 -2.921514e-01 2.290843e-01 -1.773144e-01 -2.387629e-01 1.869929e-01 4.087456e-06 2.510279e-06 6.099941e-07 -1.848306e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.275375e+02 0.000000 0 0 1.252562e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.786101e+02 0.000000 0 0 2.784559e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.631970e+02 0.000000 0 0 4.954660e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.744622e+02 0.000000 0 0 7.709458e+01 0.0000000 0.0000000 0.0000000 + [5,] -6.805788e+01 2.173913 0 0 -1.741354e+00 0.1783672 0.0000000 0.0000000 + [6,] -1.856844e+02 2.173913 0 0 -8.690394e+00 0.4866447 0.0000000 0.0000000 + [7,] -3.274084e+02 2.173913 0 0 -2.023542e+01 0.8580774 0.0000000 0.0000000 + [8,] -5.107494e+02 2.173913 0 0 -3.818436e+01 1.3385804 0.0000000 0.0000000 + [9,] 6.069729e+01 0.000000 5 0 1.553023e+00 0.0000000 0.4102446 0.0000000 +[10,] 1.656023e+02 0.000000 5 0 7.750511e+00 0.0000000 1.1192829 0.0000000 +[11,] 2.919986e+02 0.000000 5 0 1.804692e+01 0.0000000 1.9735779 0.0000000 +[12,] 4.555109e+02 0.000000 5 0 3.405465e+01 0.0000000 3.0787350 0.0000000 +[13,] -4.146566e-05 0.000000 0 5 -1.060956e-06 0.0000000 0.0000000 0.4102446 +[14,] -1.131320e-04 0.000000 0 5 -5.294802e-06 0.0000000 0.0000000 1.1192829 +[15,] -1.994803e-04 0.000000 0 5 -1.232885e-05 0.0000000 0.0000000 1.9735779 +[16,] -3.111846e-04 0.000000 0 5 -2.326461e-05 0.0000000 0.0000000 3.0787350 + +$result$retres +$result$retres$res + [1] -4.357345e-01 1.615253e-02 1.054396e+00 -6.466451e-01 -2.651621e-01 1.072975e-01 4.500160e-01 -2.921514e-01 2.290843e-01 -1.773144e-01 -2.387629e-01 1.869929e-01 4.087456e-06 2.510279e-06 6.099941e-07 -1.848306e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10014931 13.220972 0.6217687 7.130668e-07 + [2,] 0.16664305 12.299262 0.9791708 4.689057e-07 + [3,] 0.24788792 11.173078 1.4158599 1.705793e-07 + [4,] 0.34087510 9.884127 1.9156636 -1.708642e-07 + [5,] 0.07171082 13.615174 0.4689125 8.174913e-07 + [6,] 0.15761510 12.424404 0.9306458 5.020558e-07 + [7,] 0.26111811 10.989687 1.4869718 1.219988e-07 + [8,] 0.39501457 9.133667 2.2066619 -3.696611e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.0087146901 NA NA NA +[2,] -0.0003230507 NA NA NA +[3,] -0.0210879167 NA NA NA +[4,] 0.0129329016 NA NA NA +[5,] NA 0.12197456 -0.04581687 -8.174913e-07 +[6,] NA -0.04935684 0.03546288 -5.020558e-07 +[7,] NA -0.20700737 0.04775257 -1.219988e-07 +[8,] NA 0.13438965 -0.03739858 3.696611e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaG_res/KEIO_ROBOT2_36_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaG_res/KEIO_ROBOT2_36_res.txt new file mode 100644 index 0000000..ce06d54 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaG_res/KEIO_ROBOT2_36_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0220072108069609 0.0218826623211437 0.0218752432985724 0.00442491828965073 0.0136921715039295 0.0292635170559909 +Glc 14.3041458494907 14.2570981927493 14.2418328400409 0.372996426360275 13.4605066469183 14.873312503262 +Ace 0.201756934866938 0.204345827623985 0.209184203518881 0.15975261729127 9.99999999990418e-07 0.524262333709969 +Lac 1e-06 0.0832110087582971 0.0601563260550519 0.0824119616879115 9.9999999999124e-07 0.289113542526276 +mu 0.605780245366064 0.611800542549701 0.60851699469414 0.0480602874658724 0.532905426888546 0.707753690087313 +qGlc -8.3970825665243 -8.33694195696251 -8.33550815823434 1.05143537557152 -10.4180949952759 -6.40493739033577 +qAce 3.25605312266047 3.26295999337416 3.23481572385344 0.402695332568759 2.49122000889963 3.9933667311298 +qLac -2.22438925283781e-06 0.000654956050985134 0.00992953576998597 0.21916792866967 -0.455117123602806 0.400267836000354 +res 2.26561050467637 21.641483218795 20.8460135699382 7.1478935459464 10.5891812996088 36.3223044687167 + + +Goodness of fit (khi2 test) + +khi2 value 2.26561050467647 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.283201313084559 +p-value, i.e. P(X^2<=value) 0.0282330575276523 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaO.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaO.txt new file mode 100644 index 0000000..8024b18 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaO.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 5.5944000000000001E-2 NA NA +2.2613888888888889 7.4088000000000001E-2 NA NA +2.7741666666666664 9.6768000000000007E-2 NA NA +3.2088888888888891 0.125496 NA NA +3.7063888888888892 0.17085600000000001 NA NA +4.2258333333333331 0.22075199999999998 NA NA +4.6355555555555554 0.33263999999999999 NA NA +4.9675000000000002 0.42184800000000006 NA NA +2.8 NA 12.2254836644733 0.623281028280121 +3.73333333333333 NA 11.464244558983 1.04836185011708 +4.28333333333333 NA 10.7574249393265 1.38111712691604 +4.75 NA 10.2073854564122 1.78175690593014 +5.11666666666667 NA 9.19077711405388 2.07082866650166 +5.43333333333333 NA 8.25805316906635 2.47929964570343 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaO_res/KEIO_ROBOT5_3.pdf b/validation/validation_results/Berges_2021/Berges_2021/yeaO_res/KEIO_ROBOT5_3.pdf new file mode 100644 index 0000000..e29e337 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yeaO_res/KEIO_ROBOT5_3.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaO_res/KEIO_ROBOT5_3_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaO_res/KEIO_ROBOT5_3_log.txt new file mode 100644 index 0000000..368db78 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaO_res/KEIO_ROBOT5_3_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.055944 NA NA + [2,] 0.074088 NA NA + [3,] 0.096768 NA NA + [4,] 0.125496 NA NA + [5,] 0.170856 NA NA + [6,] 0.220752 NA NA + [7,] 0.332640 NA NA + [8,] 0.421848 NA NA + [9,] NA 12.225484 0.623281 +[10,] NA 11.464245 1.048362 +[11,] NA 10.757425 1.381117 +[12,] NA 10.207385 1.781757 +[13,] NA 9.190777 2.070829 +[14,] NA 8.258053 2.479300 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01361306 12.85216433 0.39797915 0.68661143 -5.64559250 2.63170699 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.014620e-09 3.860920e-08 -2.858123e-08 -1.662264e-08 8.120642e-10 2.350757e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.003238253 0.430816168 0.188541524 0.052248723 0.840037319 0.366540014 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4797047 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.014620e-09 3.860920e-08 -2.858123e-08 -1.662264e-08 8.120642e-10 2.350757e-08 + +$result$normp +[1] 5.601932e-08 + +$result$res + [1] -0.40782070 -0.48886720 -0.26584491 -0.11183868 0.12960877 1.35132677 -0.21819037 -0.47696886 -0.05824197 0.10230825 0.18977068 -0.35470450 0.03810973 0.08275780 0.39657852 -0.12669211 -0.23681278 -0.37424085 0.12871682 0.21245040 + +$result$prevres + [1] -0.40782080 -0.48886732 -0.26584504 -0.11183881 0.12960866 1.35132672 -0.21819033 -0.47696869 -0.05824199 0.10230826 0.18977070 -0.35470449 0.03810973 0.08275778 0.39657858 -0.12669209 -0.23681279 -0.37424087 0.12871680 0.21245038 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 175.5211 0.000000 0 4.369909 0.0000000 0.0000000 + [2,] 236.2094 0.000000 0 7.271570 0.0000000 0.0000000 + [3,] 335.8947 0.000000 0 12.685030 0.0000000 0.0000000 + [4,] 452.7241 0.000000 0 19.776258 0.0000000 0.0000000 + [5,] 637.0652 0.000000 0 32.143319 0.0000000 0.0000000 + [6,] 910.0764 0.000000 0 52.353539 0.0000000 0.0000000 + [7,] 1205.7397 0.000000 0 76.087127 0.0000000 0.0000000 + [8,] 1514.3860 0.000000 0 102.407155 0.0000000 0.0000000 + [9,] -104.3550 2.173913 0 -2.589992 0.2516284 0.0000000 +[10,] -214.1258 2.173913 0 -7.545405 0.5163158 0.0000000 +[11,] -320.5752 2.173913 0 -13.378911 0.7729942 0.0000000 +[12,] -448.4093 2.173913 0 -21.260521 1.0812370 0.0000000 +[13,] -581.8990 2.173913 0 -30.239358 1.4031171 0.0000000 +[14,] -727.5689 2.173913 0 -40.711119 1.7543668 0.0000000 +[15,] 111.8843 0.000000 5 2.776862 0.0000000 0.5787452 +[16,] 229.5752 0.000000 5 8.089811 0.0000000 1.1875263 +[17,] 343.7049 0.000000 5 14.344209 0.0000000 1.7778868 +[18,] 480.7623 0.000000 5 22.794483 0.0000000 2.4868452 +[19,] 623.8834 0.000000 5 32.421149 0.0000000 3.2271694 +[20,] 780.0635 0.000000 5 43.648455 0.0000000 4.0350437 + +$result$retres +$result$retres$res + [1] -0.40782080 -0.48886732 -0.26584504 -0.11183881 0.12960866 1.35132672 -0.21819033 -0.47696869 -0.05824199 0.10230826 0.18977070 -0.35470449 0.03810973 0.08275778 0.39657858 -0.12669209 -0.23681279 -0.37424087 0.12871680 0.21245038 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.04778758 12.571168 0.5289664 + [2,] 0.06431065 12.435309 0.5922975 + [3,] 0.09145110 12.212149 0.6963239 + [4,] 0.12325922 11.950610 0.8182410 + [5,] 0.17344817 11.537936 1.0106098 + [6,] 0.24777853 10.926763 1.2955100 + [7,] 0.32827619 10.264879 1.6040487 + [8,] 0.41230863 9.573931 1.9261359 + [9,] 0.09308768 12.198692 0.7025967 + [10,] 0.17668689 11.511306 1.0230234 + [11,] 0.25775654 10.844719 1.3337546 + [12,] 0.35511233 10.044221 1.7069087 + [13,] 0.45677535 9.208308 2.0965720 + [14,] 0.56771450 8.296122 2.5217897 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.008156416 NA NA + [2,] 0.009777346 NA NA + [3,] 0.005316901 NA NA + [4,] 0.002236776 NA NA + [5,] -0.002592173 NA NA + [6,] -0.027026534 NA NA + [7,] 0.004363807 NA NA + [8,] 0.009539374 NA NA + [9,] NA 0.02679131 -0.07931572 +[10,] NA -0.04706180 0.02533842 +[11,] NA -0.08729452 0.04736256 +[12,] NA 0.16316406 0.07484817 +[13,] NA -0.01753048 -0.02574336 +[14,] NA -0.03806858 -0.04249008 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaO_res/KEIO_ROBOT5_3_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaO_res/KEIO_ROBOT5_3_res.txt new file mode 100644 index 0000000..7f6dcc0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaO_res/KEIO_ROBOT5_3_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.013613063580595 0.0138121685671921 0.0135062929605491 0.00205740192646472 0.0101725201560353 0.0180529386233553 +Glc 12.8521643271041 12.8707649157724 12.8550506553223 0.214344011202897 12.5381849266426 13.2969413128524 +Ace 0.397979148896268 0.4048305362115 0.414559211235392 0.101428417842322 0.199860784981958 0.597349238607069 +mu 0.686611427157274 0.685991280864177 0.687443066415926 0.0304062745494679 0.629534978953715 0.74965899841588 +qGlc -5.64559250447808 -5.69896140078426 -5.69054487781692 0.63118889332982 -6.8238814219012 -4.50171496972713 +qAce 2.63170698974648 2.60895303205386 2.59126091903383 0.259709765861773 2.12490191163988 3.09580331655807 +res 3.22163269268785 36.3777432949571 36.1503152727142 8.45137236504575 21.1204952918425 54.3936627103997 + + +Goodness of fit (khi2 test) + +khi2 value 3.22163269268797 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.230116620906284 +p-value, i.e. P(X^2<=value) 0.00138740907385389 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaY.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaY.txt new file mode 100644 index 0000000..12c0572 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaY.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.18888888888889 0.061992 NA NA +2.27694444444444 0.092232 NA NA +3.12833333333333 0.161784 NA NA +3.77138888888889 0.20412 NA NA +4.41555555555556 0.311472 NA NA +4.82277777777778 0.37044 NA NA +0.0666666666666667 NA 14.8651479167073 0.00876439553399119 +1.71666666666667 NA 15.2357846717099 0.354264417141582 +2.8 NA 13.6096372271884 0.76289232661733 +3.63333333333333 NA 12.4626855125767 1.18822001147116 +4.26666666666667 NA 11.7251102508248 1.73800625065914 +4.88333333333333 NA 10.5202212251419 2.3092549716879 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaY_res/KEIO_ROBOT1_4.pdf b/validation/validation_results/Berges_2021/Berges_2021/yeaY_res/KEIO_ROBOT1_4.pdf new file mode 100644 index 0000000..2f8d4fe Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yeaY_res/KEIO_ROBOT1_4.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaY_res/KEIO_ROBOT1_4_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaY_res/KEIO_ROBOT1_4_log.txt new file mode 100644 index 0000000..a28018c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaY_res/KEIO_ROBOT1_4_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.061992 NA NA + [3,] 0.092232 NA NA + [4,] 0.161784 NA NA + [5,] 0.204120 NA NA + [6,] 0.311472 NA NA + [7,] 0.370440 NA NA + [8,] NA 14.86515 0.008764396 + [9,] NA 15.23578 0.354264417 +[10,] NA 13.60964 0.762892327 +[11,] NA 12.46269 1.188220011 +[12,] NA 11.72511 1.738006251 +[13,] NA 10.52022 2.309254972 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03159782 15.15754603 0.05852551 0.51095332 -6.98692664 3.35229601 + +$result$lastp + X Glc Ace mu qGlc qAce + 5.848240e-10 1.240669e-08 -6.890130e-09 -4.493294e-09 1.847571e-09 2.266620e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.00799895 0.40519298 0.17698881 0.05814324 1.14610218 0.50752519 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6037248 + +$result$laststep + X Glc Ace mu qGlc qAce + 5.848240e-10 1.240669e-08 -6.890130e-09 -4.493294e-09 1.847571e-09 2.266620e-09 + +$result$normp +[1] 1.518166e-08 + +$result$res + [1] -0.007708886 -0.199275427 0.445373840 -0.276206140 0.646110717 -0.491649569 0.048424582 0.603101001 -1.488866739 0.376639406 0.785176548 0.091221347 -0.367271563 0.284722256 -0.023378638 -0.224068371 -0.050028252 -0.263732812 0.276485818 + +$result$prevres + [1] -0.007708915 -0.199275465 0.445373798 -0.276206175 0.646110700 -0.491649549 0.048424640 0.603100974 -1.488866748 0.376639411 0.785176560 0.091221360 -0.367271558 0.284722290 -0.023378625 -0.224068374 -0.050028266 -0.263732830 0.276485805 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 91.788749 0.000000 0 3.448163613 0.000000000 0.00000000 + [3,] 160.041849 0.000000 0 11.514448396 0.000000000 0.00000000 + [4,] 247.263685 0.000000 0 24.441649017 0.000000000 0.00000000 + [5,] 343.444900 0.000000 0 40.927529716 0.000000000 0.00000000 + [6,] 477.309816 0.000000 0 66.595190105 0.000000000 0.00000000 + [7,] 587.712179 0.000000 0 89.561031279 0.000000000 0.00000000 + [8,] -1.030042 2.173913 0 -0.001091062 0.004658283 0.00000000 + [9,] -41.736508 2.173913 0 -1.295351267 0.188750046 0.00000000 +[10,] -94.575498 2.173913 0 -5.148867421 0.427710188 0.00000000 +[11,] -160.555873 2.173913 0 -11.916551513 0.726101205 0.00000000 +[12,] -233.262774 2.173913 0 -21.030370095 1.054912398 0.00000000 +[13,] -330.668757 2.173913 0 -35.161136145 1.495423233 0.00000000 +[14,] 1.136682 0.000000 5 0.001204019 0.000000000 0.01071405 +[15,] 46.057474 0.000000 5 1.429458551 0.000000000 0.43412511 +[16,] 104.366867 0.000000 5 5.681927944 0.000000000 0.98373343 +[17,] 177.178169 0.000000 5 13.150268107 0.000000000 1.67003277 +[18,] 257.412391 0.000000 5 23.207637280 0.000000000 2.42629851 +[19,] 364.902783 0.000000 5 38.801356815 0.000000000 3.43947344 + +$result$retres +$result$retres$res + [1] -0.007708915 -0.199275465 0.445373798 -0.276206175 0.646110700 -0.491649549 0.048424640 0.603100974 -1.488866748 0.376639411 0.785176560 0.091221360 -0.367271558 0.284722290 -0.023378625 -0.224068374 -0.050028266 -0.263732830 0.276485805 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03159782 15.15755 0.05852552 + [2,] 0.05800649 14.79643 0.23178924 + [3,] 0.10113948 14.20661 0.51477896 + [4,] 0.15625988 13.45288 0.87641649 + [5,] 0.21704221 12.62172 1.27520123 + [6,] 0.30163901 11.46492 1.83022942 + [7,] 0.37140849 10.51087 2.28797761 + [8,] 0.03269270 15.14257 0.06570885 + [9,] 0.07596135 14.55091 0.34958869 + [10,] 0.13212619 13.78289 0.71807865 + [11,] 0.20225958 12.82387 1.17821436 + [12,] 0.27954288 11.76707 1.68525968 + [13,] 0.38307990 10.35128 2.36455213 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0001541783 NA NA + [2,] 0.0039855093 NA NA + [3,] -0.0089074760 NA NA + [4,] 0.0055241235 NA NA + [5,] -0.0129222140 NA NA + [6,] 0.0098329910 NA NA + [7,] -0.0009684928 NA NA + [8,] NA -0.27742645 -0.056944458 + [9,] NA 0.68487870 0.004675725 +[10,] NA -0.17325413 0.044813675 +[11,] NA -0.36118122 0.010005653 +[12,] NA -0.04196183 0.052746566 +[13,] NA 0.16894492 -0.055297161 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeaY_res/KEIO_ROBOT1_4_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yeaY_res/KEIO_ROBOT1_4_res.txt new file mode 100644 index 0000000..900bfee --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeaY_res/KEIO_ROBOT1_4_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.031597822275539 0.0316572161902043 0.0316058351338751 0.00427760247263745 0.023585537196435 0.0399294960394904 +Glc 15.1575460343678 15.1091771787063 15.1179330081042 0.176412207323781 14.7412803447951 15.4268246541989 +Ace 0.0585255128605896 0.0885932278893547 0.0672634446572806 0.077530522367269 9.99999999987599e-07 0.236894777182138 +mu 0.510953318431876 0.51410136665927 0.509367141338016 0.031636564427442 0.460202378923657 0.575384082540827 +qGlc -6.98692663677509 -6.85339656910397 -6.80580233832536 0.600003693417481 -7.96518943230013 -5.9024000988292 +qAce 3.35229600989106 3.2723112963394 3.27974596071671 0.207942789822305 2.83221979327115 3.65978035338293 +res 4.73828747177852 32.7596090735626 32.1387152115572 7.40826019498459 19.2252310013182 47.4713637356236 + + +Goodness of fit (khi2 test) + +khi2 value 4.73828747177853 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.364483651675271 +p-value, i.e. P(X^2<=value) 0.0194884562979672 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebG.txt b/validation/validation_results/Berges_2021/Berges_2021/yebG.txt new file mode 100644 index 0000000..f19c14b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebG.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.18888888888889 0.065016 NA NA +2.27694444444444 0.114912 NA NA +3.12833333333333 0.18144 NA NA +3.77138888888889 0.276696 NA NA +4.41555555555556 0.379512 NA NA +4.82277777777778 0.607824 NA NA +0.0666666666666667 NA 15.3502196491559 0.0152609845674903 +1.71666666666667 NA 14.9267352115362 0.417947793820344 +2.8 NA 13.2895893634044 0.962263749669751 +3.63333333333333 NA 12.287517157592 1.69428434500396 +4.26666666666667 NA 11.0145420863723 2.53531930035334 +4.88333333333333 NA 9.32690077793865 3.42927664180736 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebG_res/KEIO_ROBOT1_12.pdf b/validation/validation_results/Berges_2021/Berges_2021/yebG_res/KEIO_ROBOT1_12.pdf new file mode 100644 index 0000000..e440c4d Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yebG_res/KEIO_ROBOT1_12.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebG_res/KEIO_ROBOT1_12_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yebG_res/KEIO_ROBOT1_12_log.txt new file mode 100644 index 0000000..bd21f13 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebG_res/KEIO_ROBOT1_12_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.065016 NA NA + [3,] 0.114912 NA NA + [4,] 0.181440 NA NA + [5,] 0.276696 NA NA + [6,] 0.379512 NA NA + [7,] 0.607824 NA NA + [8,] NA 15.350220 0.01526098 + [9,] NA 14.926735 0.41794779 +[10,] NA 13.289589 0.96226375 +[11,] NA 12.287517 1.69428435 +[12,] NA 11.014542 2.53531930 +[13,] NA 9.326901 3.42927664 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02413529 15.11104829 0.14039289 0.65373051 -7.03420986 3.99182890 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.125620e-08 -3.433080e-07 1.695971e-07 1.085444e-07 -1.923027e-08 8.447482e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.01034476 0.73623232 0.32491766 0.09611366 1.73351246 0.79511913 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.161644 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.125620e-08 -3.433080e-07 1.695971e-07 1.085444e-07 -1.923027e-08 8.447482e-08 + +$result$normp +[1] 4.074776e-07 + +$result$res + [1] -0.6076356 -0.6256037 -0.3990538 0.2560843 0.3676531 2.6640246 -2.1511920 -0.5450865 -0.7689321 1.0032747 0.6317244 0.2852631 -0.6062436 0.6584842 0.1388299 -0.2505713 -0.5823994 -0.7233756 0.7590320 + +$result$prevres + [1] -0.6076350 -0.6256028 -0.3990527 0.2560855 0.3676539 2.6640243 -2.1511936 -0.5450858 -0.7689318 1.0032746 0.6317241 0.2852627 -0.6062438 0.6584834 0.1388296 -0.2505711 -0.5823990 -0.7233751 0.7590322 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000e+00 0.000000000 0.000000000 + [2,] 108.770028 0.000000 0 3.121068e+00 0.000000000 0.000000000 + [3,] 221.523972 0.000000 0 1.217379e+01 0.000000000 0.000000000 + [4,] 386.491396 0.000000 0 2.918136e+01 0.000000000 0.000000000 + [5,] 588.451537 0.000000 0 5.356298e+01 0.000000000 0.000000000 + [6,] 896.596480 0.000000 0 9.555096e+01 0.000000000 0.000000000 + [7,] 1170.070699 0.000000 0 1.361953e+02 0.000000000 0.000000000 + [8,] -1.041992 2.173913 0 -8.443816e-04 0.003575211 0.000000000 + [9,] -48.460686 2.173913 0 -1.187863e+00 0.166274988 0.000000000 +[10,] -122.493589 2.173913 0 -5.336364e+00 0.420291615 0.000000000 +[11,] -228.146657 2.173913 0 -1.363476e+01 0.782801189 0.000000000 +[12,] -357.160946 2.173913 0 -2.600211e+01 1.225466185 0.000000000 +[13,] -546.107931 2.173913 0 -4.695966e+01 1.873768143 0.000000000 +[14,] 1.360031 0.000000 5 1.102106e-03 0.000000000 0.008222985 +[15,] 63.251959 0.000000 5 1.550426e+00 0.000000000 0.382432472 +[16,] 159.881342 0.000000 5 6.965141e+00 0.000000000 0.966670715 +[17,] 297.782063 0.000000 5 1.779639e+01 0.000000000 1.800442736 +[18,] 466.174367 0.000000 5 3.393853e+01 0.000000000 2.818572226 +[19,] 712.792151 0.000000 5 6.129279e+01 0.000000000 4.309666730 + +$result$retres +$result$retres$res + [1] -0.6076350 -0.6256028 -0.3990527 0.2560855 0.3676539 2.6640243 -2.1511936 -0.5450858 -0.7689318 1.0032746 0.6317241 0.2852627 -0.6062438 0.6584834 0.1388296 -0.2505711 -0.5823990 -0.7233751 0.7590322 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02413530 15.111049 0.1403927 + [2,] 0.05250394 14.805799 0.3136182 + [3,] 0.10693095 14.220159 0.6459621 + [4,] 0.18656171 13.363323 1.1322059 + [5,] 0.28404908 12.314348 1.7274863 + [6,] 0.43279249 10.713853 2.6357479 + [7,] 0.56480013 9.293437 3.4418170 + [8,] 0.02521042 15.099480 0.1469577 + [9,] 0.07413685 14.573027 0.4457137 + [10,] 0.15052371 13.751096 0.9121495 + [11,] 0.25953613 12.578110 1.5778046 + [12,] 0.39265257 11.145763 2.3906443 + [13,] 0.58760733 9.048029 3.5810831 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.012152701 NA NA + [2,] 0.012512057 NA NA + [3,] 0.007981053 NA NA + [4,] -0.005121710 NA NA + [5,] -0.007353078 NA NA + [6,] -0.053280486 NA NA + [7,] 0.043023873 NA NA + [8,] NA 0.2507395 -0.13169668 + [9,] NA 0.3537086 -0.02776592 +[10,] NA -0.4615063 0.05011423 +[11,] NA -0.2905931 0.11647979 +[12,] NA -0.1312208 0.14467502 +[13,] NA 0.2788722 -0.15180644 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebG_res/KEIO_ROBOT1_12_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yebG_res/KEIO_ROBOT1_12_res.txt new file mode 100644 index 0000000..d2efd16 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebG_res/KEIO_ROBOT1_12_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0241352879226131 0.0241086614128982 0.0242105415708751 0.0029396313858723 0.0191675247140172 0.0301550492061153 +Glc 15.1110482882023 15.0891350606295 15.0883964529944 0.214340496561534 14.7029997498428 15.4579197046611 +Ace 0.140392887199244 0.144926848585403 0.145856891932262 0.0801607076131468 0.00241845941099397 0.290882889447501 +mu 0.65373050873627 0.655302934840658 0.651322769694929 0.0270824545437704 0.602200139464555 0.704888408198143 +qGlc -7.03420985796518 -7.01630788514997 -7.02169522843288 0.477077638184486 -7.79027203662477 -6.1538145886162 +qAce 3.9918288962542 3.99419092216923 4.00806160164137 0.208697813059016 3.56066367668917 4.34958395598302 +res 17.5424171629503 31.9085333733866 31.1137023137309 9.22206960524638 17.9025564774985 52.1011884831851 + + +Goodness of fit (khi2 test) + +khi2 value 17.5424171629607 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 1.34941670484313 +p-value, i.e. P(X^2<=value) 0.824321150677072 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebO.txt b/validation/validation_results/Berges_2021/Berges_2021/yebO.txt new file mode 100644 index 0000000..e6e374a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebO.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.18888888888889 0.066528 NA NA +2.27694444444444 0.114912 NA NA +3.12833333333333 0.16632 NA NA +3.77138888888889 0.229824 NA NA +4.41555555555556 0.337176 NA NA +4.82277777777778 0.424872 NA NA +0.0666666666666667 NA 15.479921145176 0.0120859705656403 +1.71666666666667 NA 15.5310114033064 0.329565594881471 +2.8 NA 13.747404329145 0.673982164280475 +3.63333333333333 NA 12.5188632649079 1.05941880912014 +4.26666666666667 NA 12.1553978323562 1.52375806423655 +4.88333333333333 NA 10.5827043636049 1.983750498898 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebO_res/KEIO_ROBOT1_15.pdf b/validation/validation_results/Berges_2021/Berges_2021/yebO_res/KEIO_ROBOT1_15.pdf new file mode 100644 index 0000000..917b32b Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yebO_res/KEIO_ROBOT1_15.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebO_res/KEIO_ROBOT1_15_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yebO_res/KEIO_ROBOT1_15_log.txt new file mode 100644 index 0000000..b466548 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebO_res/KEIO_ROBOT1_15_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.066528 NA NA + [3,] 0.114912 NA NA + [4,] 0.166320 NA NA + [5,] 0.229824 NA NA + [6,] 0.337176 NA NA + [7,] 0.424872 NA NA + [8,] NA 15.47992 0.01208597 + [9,] NA 15.53101 0.32956559 +[10,] NA 13.74740 0.67398216 +[11,] NA 12.51886 1.05941881 +[12,] NA 12.15540 1.52375806 +[13,] NA 10.58270 1.98375050 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03420909 15.54933441 0.07589012 0.51832710 -6.70502449 2.58857797 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.405720e-08 4.931306e-07 -1.627842e-07 -1.009187e-07 -5.994278e-07 1.478182e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.008427933 0.426914327 0.184812580 0.056528910 1.085701101 0.463893917 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6387404 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.405720e-08 4.931306e-07 -1.627842e-07 -1.009187e-07 -5.994278e-07 1.478182e-07 + +$result$normp +[1] 8.131559e-07 + +$result$res + [1] -0.103945342 -0.158741890 -0.178015873 0.340055772 0.589054827 0.009925212 -0.410654700 0.117074938 -1.340297826 0.772686000 1.224890634 -0.442706426 -0.331647321 0.349054323 -0.042889942 -0.198252769 -0.155485296 -0.294830918 0.342404602 + +$result$prevres + [1] -0.103946045 -0.158742811 -0.178016881 0.340054948 0.589054461 0.009925797 -0.410653121 0.117073883 -1.340298345 0.772685954 1.224890971 -0.442705844 -0.331646617 0.349055123 -0.042889580 -0.198252775 -0.155485579 -0.294831348 0.342404158 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 92.5969734 0.000000 0 3.765992435 0.000000000 0.00000000 + [3,] 162.7516222 0.000000 0 12.677077451 0.000000000 0.00000000 + [4,] 253.0338488 0.000000 0 27.079025228 0.000000000 0.00000000 + [5,] 353.1300690 0.000000 0 45.559337450 0.000000000 0.00000000 + [6,] 493.1066910 0.000000 0 74.484795909 0.000000000 0.00000000 + [7,] 608.9888249 0.000000 0 100.472673255 0.000000000 0.00000000 + [8,] -0.9887270 2.173913 0 -0.001133941 0.005044492 0.00000000 + [9,] -40.3439650 2.173913 0 -1.358013083 0.205835194 0.00000000 +[10,] -91.9215705 2.173913 0 -5.431644087 0.468984500 0.00000000 +[11,] -156.7738402 2.173913 0 -12.634276993 0.799861237 0.00000000 +[12,] -228.6184828 2.173913 0 -22.384851717 1.166413110 0.00000000 +[13,] -325.3132698 2.173913 0 -37.572459231 1.659750594 0.00000000 +[14,] 0.8779406 0.000000 5 0.001006883 0.000000000 0.01160233 +[15,] 35.8234419 0.000000 5 1.205848329 0.000000000 0.47342095 +[16,] 81.6217999 0.000000 5 4.823030816 0.000000000 1.07866435 +[17,] 139.2074021 0.000000 5 11.218611953 0.000000000 1.83968085 +[18,] 203.0018849 0.000000 5 19.876639176 0.000000000 2.68275015 +[19,] 288.8620646 0.000000 5 33.362482116 0.000000000 3.81742637 + +$result$retres +$result$retres$res + [1] -0.103946045 -0.158742811 -0.178016881 0.340054948 0.589054461 0.009925797 -0.410653121 0.117073883 -1.340298345 0.772685954 1.224890971 -0.442705844 -0.331646617 0.349055123 -0.042889580 -0.198252775 -0.155485579 -0.294831348 0.342404158 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03420908 15.54933 0.07589029 + [2,] 0.06335314 15.17233 0.22143866 + [3,] 0.11135166 14.55143 0.46114805 + [4,] 0.17312110 13.75238 0.76963079 + [5,] 0.24160509 12.86648 1.11164668 + [6,] 0.33737452 11.62762 1.58992876 + [7,] 0.41665894 10.60200 1.98588308 + [8,] 0.03541184 15.53378 0.08189700 + [9,] 0.08328647 14.91447 0.32098768 + [10,] 0.14602929 14.10284 0.63433161 + [11,] 0.22492040 13.08231 1.02832169 + [12,] 0.31231756 11.95175 1.46479179 + [13,] 0.42994426 10.43015 2.05223133 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0020789209 NA NA + [2,] 0.0031748562 NA NA + [3,] 0.0035603376 NA NA + [4,] -0.0068010990 NA NA + [5,] -0.0117810892 NA NA + [6,] -0.0001985159 NA NA + [7,] 0.0082130624 NA NA + [8,] NA -0.05385399 -0.069811025 + [9,] NA 0.61653724 0.008577916 +[10,] NA -0.35543554 0.039650555 +[11,] NA -0.56344985 0.031097116 +[12,] NA 0.20364469 0.058966270 +[13,] NA 0.15255744 -0.068480832 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebO_res/KEIO_ROBOT1_15_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yebO_res/KEIO_ROBOT1_15_res.txt new file mode 100644 index 0000000..67b0078 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebO_res/KEIO_ROBOT1_15_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0342090931549279 0.0349167302948826 0.0346101878532025 0.00492462221690387 0.0265973276795729 0.0446323249128083 +Glc 15.5493344072062 15.5353198094375 15.5494604159866 0.207167215841507 15.1654380774949 15.9528727291752 +Ace 0.0758901244356171 0.0966559675833004 0.0839045440163206 0.070384437702983 9.99999999996533e-07 0.231663961533301 +mu 0.518327101224662 0.515781264887252 0.514952005932662 0.0316930224004211 0.453035025497836 0.573225888373747 +qGlc -6.70502448504809 -6.64580063618243 -6.62021103546192 0.576433937334553 -7.79689992940504 -5.54667696489425 +qAce 2.58857796633334 2.56048863449669 2.57613126156683 0.212337056146673 2.18290781539215 2.91518129473268 +res 5.30386152017918 31.8538835512503 30.8153150360815 7.88306548322184 17.7314520455511 47.8388898665634 + + +Goodness of fit (khi2 test) + +khi2 value 5.3038615201891 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.407989347706854 +p-value, i.e. P(X^2<=value) 0.0321192796765509 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebT.txt b/validation/validation_results/Berges_2021/Berges_2021/yebT.txt new file mode 100644 index 0000000..2a76163 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebT.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.117936 NA NA NA +3.34194444444444 0.184464 NA NA NA +3.9975 0.2646 NA NA NA +4.52333333333333 0.379512 NA NA NA +1.95 NA 13.8480957702151 0.413319263541811 0 +3.25 NA 12.9788949118182 0.98590406443239 0 +4.08333333333333 NA 11.500262794436 1.48645478485938 0 +4.76666666666667 NA 9.80909773494247 2.0233904066653 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebT_res/KEIO_ROBOT2_26.pdf b/validation/validation_results/Berges_2021/Berges_2021/yebT_res/KEIO_ROBOT2_26.pdf new file mode 100644 index 0000000..7255a17 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yebT_res/KEIO_ROBOT2_26.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebT_res/KEIO_ROBOT2_26_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yebT_res/KEIO_ROBOT2_26_log.txt new file mode 100644 index 0000000..acba654 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebT_res/KEIO_ROBOT2_26_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.117936 NA NA NA +[2,] 0.184464 NA NA NA +[3,] 0.264600 NA NA NA +[4,] 0.379512 NA NA NA +[5,] NA 13.848096 0.4133193 0 +[6,] NA 12.978895 0.9859041 0 +[7,] NA 11.500263 1.4864548 0 +[8,] NA 9.809098 2.0233904 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.553198e-02 1.459510e+01 2.367023e-01 1.000000e-06 5.933984e-01 -6.949173e+00 2.687847e+00 -1.998321e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 8.483766e-09 9.749136e-08 -1.783610e-07 0.000000e+00 -8.140788e-08 4.336282e-07 2.138949e-07 -1.036813e-12 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.005806472 0.375105983 0.161068545 0.153158578 0.054697298 0.858152509 0.369735596 0.356643866 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.340967 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 8.483766e-09 9.749136e-08 -1.783610e-07 0.000000e+00 -8.140788e-08 4.336282e-07 2.138949e-07 -1.036813e-12 + +$result$normp +[1] 5.308492e-07 + +$result$res + [1] -2.644902e-01 5.162647e-02 4.551251e-01 -2.790667e-01 2.064127e-01 -3.081823e-01 4.581525e-02 5.595435e-02 3.779432e-01 -3.462163e-01 -3.043143e-01 2.725874e-01 4.062469e-06 2.472372e-06 5.805093e-07 -1.844362e-06 + +$result$prevres + [1] -2.644910e-01 5.162591e-02 4.551250e-01 -2.790660e-01 2.064128e-01 -3.081822e-01 4.581532e-02 5.595408e-02 3.779437e-01 -3.462162e-01 -3.043145e-01 2.725870e-01 4.062470e-06 2.472374e-06 5.805121e-07 -1.844358e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.205983e+02 0.000000 0 0 1.408860e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.632632e+02 0.000000 0 0 3.099595e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.359995e+02 0.000000 0 0 5.470629e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.322792e+02 0.000000 0 0 8.457066e+01 0.0000000 0.0000000 0.0000000 + [5,] -5.551893e+01 2.173913 0 0 -1.642844e+00 0.2039822 0.0000000 0.0000000 + [6,] -1.496817e+02 2.173913 0 0 -8.092617e+00 0.5499459 0.0000000 0.0000000 + [7,] -2.617146e+02 2.173913 0 0 -1.867865e+01 0.9615661 0.0000000 0.0000000 + [8,] -4.053113e+02 2.173913 0 0 -3.498649e+01 1.4891550 0.0000000 0.0000000 + [9,] 4.939014e+01 0.000000 5 0 1.461489e+00 0.0000000 0.4691591 0.0000000 +[10,] 1.331582e+02 0.000000 5 0 7.199265e+00 0.0000000 1.2648757 0.0000000 +[11,] 2.328237e+02 0.000000 5 0 1.661670e+01 0.0000000 2.2116021 0.0000000 +[12,] 3.605686e+02 0.000000 5 0 3.112429e+01 0.0000000 3.4250566 0.0000000 +[13,] -3.671984e-05 0.000000 0 5 -1.086566e-06 0.0000000 0.0000000 0.4691591 +[14,] -9.899846e-05 0.000000 0 5 -5.352401e-06 0.0000000 0.0000000 1.2648757 +[15,] -1.730962e-04 0.000000 0 5 -1.235393e-05 0.0000000 0.0000000 2.2116021 +[16,] -2.680701e-04 0.000000 0 5 -2.313982e-05 0.0000000 0.0000000 3.4250566 + +$result$retres +$result$retres$res + [1] -2.644910e-01 5.162591e-02 4.551250e-01 -2.790660e-01 2.064128e-01 -3.081822e-01 4.581532e-02 5.595408e-02 3.779437e-01 -3.462162e-01 -3.043145e-01 2.725870e-01 4.062470e-06 2.472374e-06 5.805121e-07 -1.844358e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.11264618 13.574922 0.6312934 7.066355e-07 + [2,] 0.18549652 12.721786 0.9612749 4.613058e-07 + [3,] 0.27370250 11.688822 1.3608111 1.642647e-07 + [4,] 0.37393068 10.515070 1.8148028 -1.732623e-07 + [5,] 0.08121163 13.943046 0.4889080 8.124940e-07 + [6,] 0.17564702 12.837131 0.9166608 4.944748e-07 + [7,] 0.28800422 11.521338 1.4255919 1.161024e-07 + [8,] 0.43201662 9.834837 2.0779078 -3.688716e-07 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.005289819 NA NA NA +[2,] -0.001032518 NA NA NA +[3,] -0.009102501 NA NA NA +[4,] 0.005581321 NA NA NA +[5,] NA -0.09494987 -0.07558874 -8.124940e-07 +[6,] NA 0.14176380 0.06924325 -4.944748e-07 +[7,] NA -0.02107505 0.06086289 -1.161024e-07 +[8,] NA -0.02573888 -0.05451740 3.688716e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebT_res/KEIO_ROBOT2_26_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yebT_res/KEIO_ROBOT2_26_res.txt new file mode 100644 index 0000000..8c46fe7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebT_res/KEIO_ROBOT2_26_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0255319814460694 0.0263911838847815 0.0269191746656244 0.0045360725652629 0.0178037027598461 0.0345759550197093 +Glc 14.5950993788025 14.6071651342783 14.5920519252331 0.36172117814969 13.8136698303526 15.3827817063128 +Ace 0.236702279176504 0.238302115364834 0.222117512485118 0.147436896150549 0.00743499594810751 0.521380311702565 +Lac 1e-06 0.0829861088163006 0.0639596923604979 0.074045757404003 9.99999999994709e-07 0.252211734317656 +mu 0.59339835387531 0.588227576725979 0.583723636402163 0.041571278630675 0.522823215306799 0.679703072496167 +qGlc -6.94917333952205 -6.92608865144928 -6.83663568398116 0.875704539133757 -8.81848414503858 -4.98065671808572 +qAce 2.68784683215764 2.66539136757851 2.66403768538179 0.354352262447231 2.04332049141188 3.45092601130354 +qLac -1.9983207062641e-06 -0.0135773677801267 -0.00571851330861117 0.166983400310558 -0.367654504392033 0.272120267909279 +res 0.930067836558154 21.4258419702533 21.1826277543585 6.89718501115864 11.0817027876062 34.2347630433867 + + +Goodness of fit (khi2 test) + +khi2 value 0.93006783656004 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.116258479570005 +p-value, i.e. P(X^2<=value) 0.00134723662520212 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebV.txt b/validation/validation_results/Berges_2021/Berges_2021/yebV.txt new file mode 100644 index 0000000..add74bf --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebV.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.063504 NA NA +1.61361111111111 0.080136 NA NA +2.36138888888889 0.127008 NA NA +3.28638888888889 0.220752 NA NA +3.81944444444444 0.312984 NA NA +4.41083333333333 0.43092 NA NA +0.283333333333333 NA 14.1329971614314 0.0337579631172278 +1.91666666666667 NA 14.1852919300862 0.369989917886613 +2.7 NA 13.2965346110073 0.660531674461426 +3.61666666666667 NA 12.9587896544632 1.18780403426208 +4.05 NA 12.0489883459884 1.44527088718652 +4.75 NA 10.2244902484088 1.78828682349687 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebV_res/KEIO_ROBOT4_20.pdf b/validation/validation_results/Berges_2021/Berges_2021/yebV_res/KEIO_ROBOT4_20.pdf new file mode 100644 index 0000000..66a19b4 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yebV_res/KEIO_ROBOT4_20.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebV_res/KEIO_ROBOT4_20_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yebV_res/KEIO_ROBOT4_20_log.txt new file mode 100644 index 0000000..5ef799b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebV_res/KEIO_ROBOT4_20_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.063504 NA NA + [3,] 0.080136 NA NA + [4,] 0.127008 NA NA + [5,] 0.220752 NA NA + [6,] 0.312984 NA NA + [7,] 0.430920 NA NA + [8,] NA 14.13300 0.03375796 + [9,] NA 14.18529 0.36998992 +[10,] NA 13.29653 0.66053167 +[11,] NA 12.95879 1.18780403 +[12,] NA 12.04899 1.44527089 +[13,] NA 10.22449 1.78828682 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03223574 14.49892143 0.15612990 0.58903480 -4.76939939 2.13822251 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.377208e-09 8.906737e-08 3.119211e-08 -1.862764e-08 -1.415423e-07 -1.371396e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.007363304 0.398870563 0.173593824 0.057492331 0.900943648 0.392595073 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6003614 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.377208e-09 8.906737e-08 3.119211e-08 -1.862764e-08 -1.415423e-07 -1.371396e-07 + +$result$normp +[1] 2.193173e-07 + +$result$res + [1] -0.12701280 0.08321284 0.16278593 0.12677119 0.13138861 -0.36026539 0.11423253 0.69242864 -0.50552374 0.39773314 -0.86084726 -0.27190394 0.54811317 0.71812768 0.15499860 -0.23684979 -0.81834977 -0.67355048 0.85562377 + +$result$prevres + [1] -0.12701291 0.08321268 0.16278575 0.12677100 0.13138847 -0.36026543 0.11423272 0.69242846 -0.50552384 0.39773310 -0.86084721 -0.27190384 0.54811333 0.71812753 0.15499846 -0.23684990 -0.81834977 -0.67355040 0.85562409 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 101.080742 0.000000 0 3.89380315 0.00000000 0.00000000 + [3,] 129.346667 0.000000 0 6.72808989 0.00000000 0.00000000 + [4,] 200.931347 0.000000 0 15.29511962 0.00000000 0.00000000 + [5,] 346.478408 0.000000 0 36.70563962 0.00000000 0.00000000 + [6,] 474.285180 0.000000 0 58.39523622 0.00000000 0.00000000 + [7,] 671.932196 0.000000 0 95.53967648 0.00000000 0.00000000 + [8,] -3.197038 2.173913 0 -0.01500593 0.02160836 0.00000000 + [9,] -36.832623 2.173913 0 -1.34754368 0.24894685 0.00000000 +[10,] -68.748258 2.173913 0 -3.75329149 0.46466043 0.00000000 +[11,] -130.568101 2.173913 0 -10.12904382 0.88249261 0.00000000 +[12,] -173.653369 2.173913 0 -15.46589305 1.17370026 0.00000000 +[13,] -271.255685 2.173913 0 -29.38500006 1.83338146 0.00000000 +[14,] 3.296590 0.000000 5 0.01547319 0.00000000 0.04969923 +[15,] 37.979542 0.000000 5 1.38950442 0.00000000 0.57257775 +[16,] 70.888989 0.000000 5 3.87016406 0.00000000 1.06871899 +[17,] 134.633821 0.000000 5 10.44444897 0.00000000 2.02973300 +[18,] 179.060707 0.000000 5 15.94748069 0.00000000 2.69951060 +[19,] 279.702231 0.000000 5 30.30001045 0.00000000 4.21677737 + +$result$retres +$result$retres$res + [1] -0.12701291 0.08321268 0.16278575 0.12677100 0.13138847 -0.36026543 0.11423272 0.69242846 -0.50552384 0.39773310 -0.86084721 -0.27190384 0.54811333 0.71812753 0.15499846 -0.23684990 -0.81834977 -0.67355040 0.85562409 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03223574 14.49892 0.1561299 + [2,] 0.06516825 14.23227 0.2756764 + [3,] 0.08339171 14.08471 0.3418283 + [4,] 0.12954342 13.71102 0.5093611 + [5,] 0.22337977 12.95123 0.8499912 + [6,] 0.30577869 12.28405 1.1491030 + [7,] 0.43320465 11.25229 1.6116649 + [8,] 0.03809066 14.45151 0.1773835 + [9,] 0.09968939 13.95275 0.4009896 + [10,] 0.15813828 13.47949 0.6131617 + [11,] 0.27135243 12.56280 1.0241341 + [12,] 0.35025689 11.92391 1.3105608 + [13,] 0.52900148 10.47662 1.9594116 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.002540258 NA NA + [2,] -0.001664254 NA NA + [3,] -0.003255715 NA NA + [4,] -0.002535420 NA NA + [5,] -0.002627769 NA NA + [6,] 0.007205309 NA NA + [7,] -0.002284654 NA NA + [8,] NA -0.3185171 -0.14362551 + [9,] NA 0.2325410 -0.03099969 +[10,] NA -0.1829572 0.04736998 +[11,] NA 0.3959897 0.16366995 +[12,] NA 0.1250758 0.13471008 +[13,] NA -0.2521321 -0.17112482 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebV_res/KEIO_ROBOT4_20_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yebV_res/KEIO_ROBOT4_20_res.txt new file mode 100644 index 0000000..ec48a07 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebV_res/KEIO_ROBOT4_20_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0322357440887887 0.0320105104103245 0.0315501367171161 0.00354231367495996 0.0255790668486648 0.0398068635259021 +Glc 14.498921434795 14.5248384618349 14.5064713404279 0.205723484945693 14.1675351717727 14.9722117922701 +Ace 0.156129896712086 0.160143394139355 0.157222138235623 0.0898850040440809 0.00598566170157972 0.344024970123393 +mu 0.58903480422989 0.590970207527767 0.591418259702339 0.0264469942624451 0.535591488380095 0.642774484389306 +qGlc -4.7693993947236 -4.87860281946043 -4.81141780793175 0.604858167390181 -6.08907305055539 -3.85957006592149 +qAce 2.13822251310082 2.15434836842388 2.18086211403905 0.234725625574788 1.7273025055417 2.57855577184745 +res 4.68563954129392 31.9813699250315 31.8924459033229 7.96151566586498 19.1590935827481 47.7219249767398 + + +Goodness of fit (khi2 test) + +khi2 value 4.6856395412943 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.360433810868793 +p-value, i.e. P(X^2<=value) 0.0185226334891616 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebY.txt b/validation/validation_results/Berges_2021/Berges_2021/yebY.txt new file mode 100644 index 0000000..655046d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebY.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.18888888888889 0.06804 NA NA +2.27694444444444 0.107352 NA NA +3.12833333333333 0.17388 NA NA +3.77138888888889 0.235872 NA NA +4.41555555555556 0.337176 NA NA +4.82277777777778 0.424872 NA NA +0.0666666666666667 NA 14.9046021015743 0.0102253172380167 +1.71666666666667 NA 15.1405295656903 0.364570662980585 +2.8 NA 13.289232406063 0.762785165027064 +3.63333333333333 NA 12.3752280591833 1.25937689399425 +4.26666666666667 NA 11.0972617587888 1.66619151377461 +4.88333333333333 NA 9.85401200622047 2.37310298902367 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebY_res/KEIO_ROBOT1_19.pdf b/validation/validation_results/Berges_2021/Berges_2021/yebY_res/KEIO_ROBOT1_19.pdf new file mode 100644 index 0000000..5487f69 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yebY_res/KEIO_ROBOT1_19.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebY_res/KEIO_ROBOT1_19_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yebY_res/KEIO_ROBOT1_19_log.txt new file mode 100644 index 0000000..dc63179 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebY_res/KEIO_ROBOT1_19_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.068040 NA NA + [3,] 0.107352 NA NA + [4,] 0.173880 NA NA + [5,] 0.235872 NA NA + [6,] 0.337176 NA NA + [7,] 0.424872 NA NA + [8,] NA 14.904602 0.01022532 + [9,] NA 15.140530 0.36457066 +[10,] NA 13.289232 0.76278517 +[11,] NA 12.375228 1.25937689 +[12,] NA 11.097262 1.66619151 +[13,] NA 9.854012 2.37310299 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03411747 15.15457012 0.06735489 0.52012069 -7.18654740 3.03858501 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.231425e-09 3.798114e-08 -1.804937e-08 -8.907126e-09 -3.159913e-08 1.937606e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.007116133 0.366546192 0.159170282 0.047824821 0.937314306 0.405535320 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5474395 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.231425e-09 3.798114e-08 -1.804937e-08 -8.907126e-09 -3.159913e-08 1.937606e-08 + +$result$normp +[1] 5.677268e-08 + +$result$res + [1] -0.03292663 -0.23608244 0.20779475 -0.01255408 0.33607089 0.09850983 -0.28595072 0.50725116 -1.44736638 0.68329597 0.28491957 0.41715929 -0.44525960 0.32081021 -0.04886686 -0.19817012 -0.36144034 0.17760761 0.11005951 + +$result$prevres + [1] -0.03292670 -0.23608252 0.20779467 -0.01255416 0.33607086 0.09850988 -0.28595058 0.50725107 -1.44736642 0.68329597 0.28491960 0.41715934 -0.44525956 0.32081030 -0.04886682 -0.19817012 -0.36144037 0.17760756 0.11005945 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 92.794625 0.000000 0 3.763924112 0.000000000 0.00000000 + [3,] 163.417607 0.000000 0 12.694863908 0.000000000 0.00000000 + [4,] 254.457521 0.000000 0 27.158456414 0.000000000 0.00000000 + [5,] 355.526721 0.000000 0 45.745705923 0.000000000 0.00000000 + [6,] 497.027236 0.000000 0 74.875943860 0.000000000 0.00000000 + [7,] 614.279190 0.000000 0 101.074085908 0.000000000 0.00000000 + [8,] -1.059796 2.173913 0 -0.001212218 0.005031285 0.00000000 + [9,] -43.317674 2.173913 0 -1.454831717 0.205646633 0.00000000 +[10,] -98.828732 2.173913 0 -5.827714984 0.469180228 0.00000000 +[11,] -168.744310 2.173913 0 -13.572140175 0.801097937 0.00000000 +[12,] -246.298366 2.173913 0 -24.069552448 1.169278614 0.00000000 +[13,] -350.794278 2.173913 0 -40.438710453 1.665363252 0.00000000 +[14,] 1.030627 0.000000 5 0.001178853 0.000000000 0.01157196 +[15,] 42.125402 0.000000 5 1.414789057 0.000000000 0.47298726 +[16,] 96.108579 0.000000 5 5.667313471 0.000000000 1.07911452 +[17,] 164.099806 0.000000 5 13.198581786 0.000000000 1.84252526 +[18,] 239.519271 0.000000 5 23.407064208 0.000000000 2.68934081 +[19,] 341.139047 0.000000 5 39.325678952 0.000000000 3.83033548 + +$result$retres +$result$retres$res + [1] -0.03292670 -0.23608252 0.20779467 -0.01255416 0.33607086 0.09850988 -0.28595058 0.50725107 -1.44736642 0.68329597 0.28491960 0.41715934 -0.44525956 0.32081030 -0.04886682 -0.19817012 -0.36144037 0.17760756 0.11005945 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03411747 15.154570 0.06735490 + [2,] 0.06331835 14.751099 0.23794870 + [3,] 0.11150789 14.085261 0.51947571 + [4,] 0.17362892 13.226930 0.88239150 + [5,] 0.24259342 12.274042 1.28528740 + [6,] 0.33914620 10.939965 1.84935615 + [7,] 0.41915299 9.834505 2.31676196 + [8,] 0.03532123 15.137938 0.07438738 + [9,] 0.08331956 14.474741 0.35479730 + [10,] 0.14637143 13.603549 0.72315114 + [11,] 0.22578457 12.506291 1.18708882 + [12,] 0.31387383 11.289155 1.70171303 + [13,] 0.43256482 9.649193 2.39511488 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0006585339 NA NA + [2,] 0.0047216504 NA NA + [3,] -0.0041558933 NA NA + [4,] 0.0002510831 NA NA + [5,] -0.0067214173 NA NA + [6,] -0.0019701977 NA NA + [7,] 0.0057190116 NA NA + [8,] NA -0.2333355 -0.064162061 + [9,] NA 0.6657886 0.009773364 +[10,] NA -0.3143161 0.039634024 +[11,] NA -0.1310630 0.072288075 +[12,] NA -0.1918933 -0.035521512 +[13,] NA 0.2048194 -0.022011890 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yebY_res/KEIO_ROBOT1_19_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yebY_res/KEIO_ROBOT1_19_res.txt new file mode 100644 index 0000000..c904099 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yebY_res/KEIO_ROBOT1_19_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0341174673262826 0.0334055701303748 0.0333777093458549 0.0040718429389124 0.0262591534223504 0.0407822087450523 +Glc 15.1545701163674 15.1477882987481 15.1598528419063 0.228907915997051 14.7245887859398 15.5367477249292 +Ace 0.0673548851519583 0.107957907183177 0.107203128599278 0.0714547159956394 9.99999999999626e-07 0.246460300361656 +mu 0.520120685236345 0.526387720971836 0.526539122927 0.0266683776370856 0.4799792546979 0.580115582192038 +qGlc -7.18654739512102 -7.25223012580488 -7.14769286896597 0.661793886112287 -8.5850489596523 -6.15147088579608 +qAce 3.03858500523349 2.98758246020831 3.00726839299087 0.243586121786517 2.534097611607 3.51123648665229 +res 3.89596994044747 32.1537227809012 32.2196273306749 8.04934562189564 18.5416003974552 48.4477436753191 + + +Goodness of fit (khi2 test) + +khi2 value 3.89596994044755 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.299689995419042 +p-value, i.e. P(X^2<=value) 0.00775154619098704 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecA.txt b/validation/validation_results/Berges_2021/Berges_2021/yecA.txt new file mode 100644 index 0000000..21f243d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecA.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.110376 NA NA NA +3.34194444444444 0.15876 NA NA NA +3.9975 0.237384 NA NA NA +4.52333333333333 0.356832 NA NA NA +1.95 NA 13.983428740538 0.364265287381051 0 +3.25 NA 13.112089963965 0.969715965027672 0 +4.08333333333333 NA 12.0861899626969 1.60257388109013 0 +4.76666666666667 NA 11.1956696147441 2.36175176765571 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecA_res/KEIO_ROBOT2_18.pdf b/validation/validation_results/Berges_2021/Berges_2021/yecA_res/KEIO_ROBOT2_18.pdf new file mode 100644 index 0000000..fcb4a50 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yecA_res/KEIO_ROBOT2_18.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecA_res/KEIO_ROBOT2_18_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yecA_res/KEIO_ROBOT2_18_log.txt new file mode 100644 index 0000000..1b3f629 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecA_res/KEIO_ROBOT2_18_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.110376 NA NA NA +[2,] 0.158760 NA NA NA +[3,] 0.237384 NA NA NA +[4,] 0.356832 NA NA NA +[5,] NA 13.98343 0.3642653 0 +[6,] NA 13.11209 0.9697160 0 +[7,] NA 12.08619 1.6025739 0 +[8,] NA 11.19567 2.3617518 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.067283e-02 1.429178e+01 1.200871e-01 1.000000e-06 6.237870e-01 -5.213500e+00 3.699476e+00 -2.228623e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-6.933611e-09 -2.298114e-07 1.278983e-07 0.000000e+00 8.240605e-08 1.995163e-07 -3.353194e-08 6.827868e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.006775585 0.461841222 0.211661841 0.193979513 0.078525441 1.197476990 0.541788211 0.507507747 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4406411 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-6.933611e-09 -2.298114e-07 1.278983e-07 0.000000e+00 8.240605e-08 1.995163e-07 -3.353194e-08 6.827868e-13 + +$result$normp +[1] 3.419667e-07 + +$result$res + [1] -5.982426e-01 3.744089e-01 6.426534e-01 -4.726443e-01 -2.217359e-01 8.791862e-02 3.736915e-01 -2.398742e-01 2.350069e-01 -2.061343e-01 -1.969554e-01 1.680828e-01 4.122944e-06 2.565029e-06 6.532817e-07 -1.853327e-06 + +$result$prevres + [1] -5.982419e-01 3.744094e-01 6.426535e-01 -4.726450e-01 -2.217357e-01 8.791863e-02 3.736914e-01 -2.398743e-01 2.350066e-01 -2.061342e-01 -1.969552e-01 1.680829e-01 4.122944e-06 2.565028e-06 6.532799e-07 -1.853329e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.380205e+02 0.000000 0 0 1.230823e+01 0.0000000 0.0000000 0.0000000 + [2,] 4.020933e+02 0.000000 0 0 2.777961e+01 0.0000000 0.0000000 0.0000000 + [3,] 6.052316e+02 0.000000 0 0 5.001613e+01 0.0000000 0.0000000 0.0000000 + [4,] 8.401825e+02 0.000000 0 0 7.856557e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.315114e+01 2.173913 0 0 -1.041881e+00 0.1711051 0.0000000 0.0000000 + [6,] -1.198005e+02 2.173913 0 0 -5.299439e+00 0.4750392 0.0000000 0.0000000 + [7,] -2.138585e+02 2.173913 0 0 -1.249895e+01 0.8480025 0.0000000 0.0000000 + [8,] -3.371836e+02 2.173913 0 0 -2.384209e+01 1.3370175 0.0000000 0.0000000 + [9,] 7.042565e+01 0.000000 5 0 1.700421e+00 0.0000000 0.3935417 0.0000000 +[10,] 1.955228e+02 0.000000 5 0 8.649052e+00 0.0000000 1.0925901 0.0000000 +[11,] 3.490319e+02 0.000000 5 0 2.039915e+01 0.0000000 1.9504058 0.0000000 +[12,] 5.503070e+02 0.000000 5 0 3.891195e+01 0.0000000 3.0751402 0.0000000 +[13,] -4.242554e-05 0.000000 0 5 -1.024361e-06 0.0000000 0.0000000 0.3935417 +[14,] -1.177861e-04 0.000000 0 5 -5.210328e-06 0.0000000 0.0000000 1.0925901 +[15,] -2.102624e-04 0.000000 0 5 -1.228877e-05 0.0000000 0.0000000 1.9504058 +[16,] -3.315137e-04 0.000000 0 5 -2.344118e-05 0.0000000 0.0000000 3.0751402 + +$result$retres +$result$retres$res + [1] -5.982419e-01 3.744094e-01 6.426535e-01 -4.726450e-01 -2.217357e-01 8.791863e-02 3.736914e-01 -2.398743e-01 2.350066e-01 -2.061342e-01 -1.969552e-01 1.680829e-01 4.122944e-06 2.565028e-06 6.532799e-07 -1.853329e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09841116 13.64205 0.5811276 7.222618e-07 + [2,] 0.16624819 13.07508 0.9834467 4.798983e-07 + [3,] 0.25023707 12.37312 1.4815573 1.798285e-07 + [4,] 0.34737910 11.56122 2.0576749 -1.672339e-07 + [5,] 0.06977007 13.88143 0.4112666 8.245888e-07 + [6,] 0.15698151 13.15253 0.9284891 5.130056e-07 + [7,] 0.26400036 12.25809 1.5631828 1.306560e-07 + [8,] 0.40431927 11.08533 2.3953683 -3.706659e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.011964838 NA NA NA +[2,] -0.007488187 NA NA NA +[3,] -0.012853069 NA NA NA +[4,] 0.009452899 NA NA NA +[5,] NA 0.10199842 -0.04700132 -8.245888e-07 +[6,] NA -0.04044257 0.04122685 -5.130056e-07 +[7,] NA -0.17189804 0.03939105 -1.306560e-07 +[8,] NA 0.11034220 -0.03361658 3.706659e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecA_res/KEIO_ROBOT2_18_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yecA_res/KEIO_ROBOT2_18_res.txt new file mode 100644 index 0000000..08b8cef --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecA_res/KEIO_ROBOT2_18_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.020672829710484 0.0202604435827189 0.0200043885542702 0.00405863146861743 0.0129657444052255 0.0289560321816924 +Glc 14.2917760257369 14.2896673116951 14.2746630911057 0.380666585540747 13.4887137529414 15.0284118509424 +Ace 0.120087148445444 0.15978455532438 0.147389372850277 0.135377740177228 9.99999999976541e-07 0.444066361365093 +Lac 1e-06 0.0846986775672793 0.0579918625400753 0.0826087227459262 9.9999999999124e-07 0.280958079366381 +mu 0.623786986064071 0.632484406398329 0.630290442530906 0.0473378110182424 0.544806669561166 0.734092119353473 +qGlc -5.21350008180558 -5.3229208875368 -5.40181104312708 1.06327606952953 -7.17277813934437 -3.21770932878652 +qAce 3.69947575083769 3.64665061996082 3.64891010246592 0.407220762004245 2.8952452294878 4.32928778070642 +qLac -2.22862275263037e-06 -0.0184542063623069 0.0273009100325964 0.228310587340563 -0.541245418389949 0.361580994412314 +res 1.55331650786799 20.4237647467381 19.7965794499031 6.19690930778966 10.6492613900133 33.8157537734304 + + +Goodness of fit (khi2 test) + +khi2 value 1.55331650786935 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.194164563483668 +p-value, i.e. P(X^2<=value) 0.00821335928054805 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecF.txt b/validation/validation_results/Berges_2021/Berges_2021/yecF.txt new file mode 100644 index 0000000..db24f89 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecF.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.18888888888889 0.063504 NA NA +2.27694444444444 0.114912 NA NA +3.12833333333333 0.179928 NA NA +3.77138888888889 0.25704 NA NA +4.41555555555556 0.356832 NA NA +4.82277777777778 0.4914 NA NA +0.0666666666666667 NA 15.7490480873133 0.0174671314255406 +1.71666666666667 NA 15.5310292363534 0.371047379962693 +2.8 NA 12.9092756829437 0.738236669482093 +3.63333333333333 NA 12.4026153378477 1.17806785029944 +4.26666666666667 NA 11.6774033762684 1.7557070577395 +4.88333333333333 NA 9.65247365705832 2.23365675753451 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecF_res/KEIO_ROBOT1_13.pdf b/validation/validation_results/Berges_2021/Berges_2021/yecF_res/KEIO_ROBOT1_13.pdf new file mode 100644 index 0000000..7931315 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yecF_res/KEIO_ROBOT1_13.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecF_res/KEIO_ROBOT1_13_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yecF_res/KEIO_ROBOT1_13_log.txt new file mode 100644 index 0000000..c9874eb --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecF_res/KEIO_ROBOT1_13_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.063504 NA NA + [3,] 0.114912 NA NA + [4,] 0.179928 NA NA + [5,] 0.257040 NA NA + [6,] 0.356832 NA NA + [7,] 0.491400 NA NA + [8,] NA 15.749048 0.01746713 + [9,] NA 15.531029 0.37104738 +[10,] NA 12.909276 0.73823667 +[11,] NA 12.402615 1.17806785 +[12,] NA 11.677403 1.75570706 +[13,] NA 9.652474 2.23365676 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0325876 15.5344894 0.1045651 0.5539034 -7.3386496 2.7207297 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.529921e-09 5.604006e-08 -1.610330e-08 -1.133712e-08 -5.037071e-08 5.219366e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.01120525 0.61931836 0.26748256 0.07835159 1.49775498 0.63462262 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.9367423 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.529921e-09 5.604006e-08 -1.610330e-08 -1.133712e-08 -5.037071e-08 5.219366e-09 + +$result$normp +[1] 7.807128e-08 + +$result$res + [1] -0.185019909 -0.027320106 0.005590069 0.220087187 0.308035150 0.960915727 -1.009951151 -0.501739190 -1.482918095 2.219319139 0.724362021 -0.650085713 -0.308938163 0.465596540 -0.061510506 -0.194418256 -0.179625957 -0.551503388 0.521461567 + +$result$prevres + [1] -0.185019986 -0.027320211 0.005589947 0.220087082 0.308035095 0.960915786 -1.009950969 -0.501739310 -1.482918153 2.219319136 0.724362062 -0.650085646 -0.308938089 0.465596619 -0.061510473 -0.194418262 -0.179625989 -0.551503431 0.521461536 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 96.5974715 0.000000 0 3.742479305 0.000000000 0.00000000 + [3,] 176.4839969 0.000000 0 13.095140000 0.000000000 0.00000000 + [4,] 282.8219016 0.000000 0 28.832243754 0.000000000 0.00000000 + [5,] 403.8356609 0.000000 0 49.631610135 0.000000000 0.00000000 + [6,] 576.9837491 0.000000 0 83.023553035 0.000000000 0.00000000 + [7,] 722.9758813 0.000000 0 113.624880911 0.000000000 0.00000000 + [8,] -1.0834536 2.173913 0 -0.001184148 0.004811124 0.00000000 + [9,] -45.7364153 2.173913 0 -1.479043440 0.203094589 0.00000000 +[10,] -107.0243573 2.173913 0 -6.096998173 0.475246425 0.00000000 +[11,] -186.6986072 2.173913 0 -14.531659985 0.829043479 0.00000000 +[12,] -277.2543838 2.173913 0 -26.242617170 1.231160437 0.00000000 +[13,] -401.8684559 2.173913 0 -44.892256433 1.784514773 0.00000000 +[14,] 0.9238626 0.000000 5 0.001009725 0.000000000 0.01106558 +[15,] 38.9995153 0.000000 5 1.261182735 0.000000000 0.46711755 +[16,] 91.2598427 0.000000 5 5.198920208 0.000000000 1.09306678 +[17,] 159.1982044 0.000000 5 12.391169983 0.000000000 1.90680000 +[18,] 236.4152617 0.000000 5 22.377122125 0.000000000 2.83166901 +[19,] 342.6738826 0.000000 5 38.279699703 0.000000000 4.10438398 + +$result$retres +$result$retres$res + [1] -0.185019986 -0.027320211 0.005589947 0.220087082 0.308035095 0.960915786 -1.009950969 -0.501739310 -1.482918153 2.219319136 0.724362062 -0.650085646 -0.308938089 0.465596619 -0.061510473 -0.194418262 -0.179625989 -0.551503431 0.521461536 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03258760 15.534489 0.1045652 + [2,] 0.06295760 15.132118 0.2537402 + [3,] 0.11502380 14.442295 0.5094853 + [4,] 0.18432974 13.524062 0.8499106 + [5,] 0.26320070 12.479103 1.2373186 + [6,] 0.37605032 10.983962 1.7916270 + [7,] 0.47120098 9.723313 2.2589995 + [8,] 0.03381345 15.518248 0.1105865 + [9,] 0.08433520 14.848887 0.3587453 + [10,] 0.15367827 13.930162 0.6993530 + [11,] 0.24382419 12.735822 1.1421427 + [12,] 0.34628180 11.378364 1.6454064 + [13,] 0.48727402 9.510362 2.3379491 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0037003997 NA NA + [2,] 0.0005464042 NA NA + [3,] -0.0001117989 NA NA + [4,] -0.0044017416 NA NA + [5,] -0.0061607019 NA NA + [6,] -0.0192183157 NA NA + [7,] 0.0201990194 NA NA + [8,] NA 0.2308001 -0.09311932 + [9,] NA 0.6821424 0.01230209 +[10,] NA -1.0208868 0.03888365 +[11,] NA -0.3332065 0.03592520 +[12,] NA 0.2990394 0.11030069 +[13,] NA 0.1421115 -0.10429231 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecF_res/KEIO_ROBOT1_13_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yecF_res/KEIO_ROBOT1_13_res.txt new file mode 100644 index 0000000..58db633 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecF_res/KEIO_ROBOT1_13_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0325876018108784 0.0331470349940494 0.0329306593348849 0.00411724816691809 0.0253776940496148 0.0418531096005281 +Glc 15.5344893508942 15.5309703632516 15.5313296033741 0.214354370927978 15.094395892226 15.9373669924019 +Ace 0.104565145971206 0.125177435265092 0.129493426051854 0.079056935435963 9.99999999998355e-07 0.269438183253425 +mu 0.553903357221997 0.551333333363551 0.550057873572682 0.0281626152546046 0.498870178500377 0.609378872744576 +qGlc -7.33864963756179 -7.33448496199472 -7.2920080748015 0.565043286510092 -8.40185025373328 -6.38418464598555 +qAce 2.72072973477798 2.67661257179404 2.67266815302773 0.190544095194658 2.27832721675935 3.10190546135014 +res 11.4073204548114 31.1535129599988 30.4430578309984 8.7816112331457 17.4291948602976 51.8274185425686 + + +Goodness of fit (khi2 test) + +khi2 value 11.4073204548115 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.877486188831655 +p-value, i.e. P(X^2<=value) 0.42326446823805 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecJ.txt b/validation/validation_results/Berges_2021/Berges_2021/yecJ.txt new file mode 100644 index 0000000..271514d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecJ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.18888888888889 0.072576 NA NA +2.27694444444444 0.119448 NA NA +3.12833333333333 0.189 NA NA +3.77138888888889 0.276696 NA NA +4.41555555555556 0.412776 NA NA +4.82277777777778 0.644112 NA NA +0.0666666666666667 NA 15.3330531010271 0.0136380037467362 +1.71666666666667 NA 14.694491476636 0.352269036196835 +2.8 NA 13.483979712142 0.767678478417788 +3.63333333333333 NA 12.2913939350736 1.19653508109911 +4.26666666666667 NA 11.0492016913524 1.64973989344492 +4.88333333333333 NA 9.6919196868613 2.18925331966878 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecJ_res/KEIO_ROBOT1_22.pdf b/validation/validation_results/Berges_2021/Berges_2021/yecJ_res/KEIO_ROBOT1_22.pdf new file mode 100644 index 0000000..be70c4b Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yecJ_res/KEIO_ROBOT1_22.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecJ_res/KEIO_ROBOT1_22_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yecJ_res/KEIO_ROBOT1_22_log.txt new file mode 100644 index 0000000..e9ef965 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecJ_res/KEIO_ROBOT1_22_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.072576 NA NA + [3,] 0.119448 NA NA + [4,] 0.189000 NA NA + [5,] 0.276696 NA NA + [6,] 0.412776 NA NA + [7,] 0.644112 NA NA + [8,] NA 15.33305 0.0136380 + [9,] NA 14.69449 0.3522690 +[10,] NA 13.48398 0.7676785 +[11,] NA 12.29139 1.1965351 +[12,] NA 11.04920 1.6497399 +[13,] NA 9.69192 2.1892533 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02290083 14.97524900 0.19461270 0.67853620 -6.33183808 2.37974087 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.129899e-08 -6.175789e-07 2.371472e-07 2.133842e-07 -7.643350e-08 1.434418e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.00987955 0.72295818 0.31284585 0.09648792 1.63675564 0.69921176 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.154787 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.129899e-08 -6.175789e-07 2.371472e-07 2.133842e-07 -7.643350e-08 1.434418e-08 + +$result$normp +[1] 6.997691e-07 + +$result$res + [1] -0.74495866 -1.06332181 -0.60453649 0.11516787 0.96279438 2.27077687 -2.00475072 -0.79933270 -0.41419332 0.60070654 0.83218555 0.59768489 -0.81705096 0.92345664 0.09735344 -0.58222205 -0.68551046 -0.41451527 0.66143769 + +$result$prevres + [1] -0.74495759 -1.06332007 -0.60453411 0.11517038 0.96279623 2.27077659 -2.00475372 -0.79933137 -0.41419270 0.60070648 0.83218497 0.59768410 -0.81705148 0.92345547 0.09735288 -0.58222202 -0.68550995 -0.41451457 0.66143818 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.000000000 0.000000000 + [2,] 112.0255421 0.000000 0 3.050071e+00 0.000000000 0.000000000 + [3,] 234.3959426 0.000000 0 1.222233e+01 0.000000000 0.000000000 + [4,] 417.6775598 0.000000 0 2.992304e+01 0.000000000 0.000000000 + [5,] 646.1593091 0.000000 0 5.580749e+01 0.000000000 0.000000000 + [6,] 1000.3811396 0.000000 0 1.011585e+02 0.000000000 0.000000000 + [7,] 1318.7654039 0.000000 0 1.456520e+02 0.000000000 0.000000000 + [8,] -0.9387297 2.173913 0 -7.219925e-04 0.003395176 0.000000000 + [9,] -44.7379271 2.173913 0 -1.046376e+00 0.161807121 0.000000000 +[10,] -115.3313010 2.173913 0 -4.803636e+00 0.417127635 0.000000000 +[11,] -218.4322546 2.173913 0 -1.249073e+01 0.790020827 0.000000000 +[12,] -346.5899004 2.173913 0 -2.415002e+01 1.253538496 0.000000000 +[13,] -537.2094182 2.173913 0 -4.421508e+01 1.942966847 0.000000000 +[14,] 0.8114621 0.000000 5 6.241090e-04 0.000000000 0.007808905 +[15,] 38.6726173 0.000000 5 9.045147e-01 0.000000000 0.372156377 +[16,] 99.6953492 0.000000 5 4.152387e+00 0.000000000 0.959393561 +[17,] 188.8184709 0.000000 5 1.079731e+01 0.000000000 1.817047903 +[18,] 299.6012431 0.000000 5 2.087590e+01 0.000000000 2.883138540 +[19,] 464.3776675 0.000000 5 3.822066e+01 0.000000000 4.468823749 + +$result$retres +$result$retres$res + [1] -0.74495759 -1.06332007 -0.60453411 0.11517038 0.96279623 2.27077659 -2.00475372 -0.79933137 -0.41419270 0.60070648 0.83218497 0.59768410 -0.81705148 0.92345547 0.09735288 -0.58222202 -0.68550995 -0.41451457 0.66143818 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02290085 14.975250 0.1946125 + [2,] 0.05130960 14.710150 0.2942468 + [3,] 0.10735732 14.187134 0.4908156 + [4,] 0.19130341 13.403781 0.7852288 + [5,] 0.29595192 12.427242 1.1522489 + [6,] 0.45819153 10.913284 1.7212508 + [7,] 0.60401693 9.552497 2.2326852 + [8,] 0.02396057 14.965361 0.1983291 + [9,] 0.07340515 14.503963 0.3717396 + [10,] 0.15309746 13.760305 0.6512341 + [11,] 0.26948733 12.674199 1.0594331 + [12,] 0.41416350 11.324136 1.5668370 + [13,] 0.62935239 9.316076 2.3215410 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.014899152 NA NA + [2,] 0.021266401 NA NA + [3,] 0.012090682 NA NA + [4,] -0.002303408 NA NA + [5,] -0.019255925 NA NA + [6,] -0.045415532 NA NA + [7,] 0.040095074 NA NA + [8,] NA 0.3676924 -0.18469109 + [9,] NA 0.1905286 -0.01947058 +[10,] NA -0.2763250 0.11644440 +[11,] NA -0.3828051 0.13710199 +[12,] NA -0.2749347 0.08290291 +[13,] NA 0.3758437 -0.13228764 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecJ_res/KEIO_ROBOT1_22_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yecJ_res/KEIO_ROBOT1_22_res.txt new file mode 100644 index 0000000..5faf248 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecJ_res/KEIO_ROBOT1_22_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0229008268697419 0.0228407843210101 0.0228767181320221 0.00259622645812441 0.0178199608841557 0.0275690491296163 +Glc 14.9752489966706 14.9561225870802 14.9481963621062 0.188899686439034 14.5421971855226 15.29412911653 +Ace 0.194612701518155 0.212453458519692 0.211635633345861 0.0788155741654709 0.0564769626782036 0.364418063002447 +mu 0.6785361989043 0.680646178894234 0.678718593252678 0.0259027443497092 0.633946051869313 0.735417227881849 +qGlc -6.3318380793659 -6.3713938060793 -6.35682932222311 0.464919968530962 -7.19326509613404 -5.59218310785272 +qAce 2.37974087095862 2.35375710443762 2.34343770920732 0.180813851275479 2.05754326314827 2.68565025312722 +res 17.3359199338367 32.3694904346293 32.0590858669473 8.22314886796468 16.7763047241214 50.2621286209137 + + +Goodness of fit (khi2 test) + +khi2 value 17.3359199338757 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 1.33353230260582 +p-value, i.e. P(X^2<=value) 0.815600747338158 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecR.txt b/validation/validation_results/Berges_2021/Berges_2021/yecR.txt new file mode 100644 index 0000000..2b011c3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecR.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.18888888888889 0.065016 NA NA +2.27694444444444 0.086184 NA NA +3.12833333333333 0.130032 NA NA +3.77138888888889 0.16632 NA NA +4.41555555555556 0.24192 NA NA +4.82277777777778 0.276696 NA NA +0.0666666666666667 NA 14.9167468258044 0.0114305108349673 +1.71666666666667 NA 14.984826655799 0.328390966242866 +2.8 NA 13.5743574729863 0.688534091987589 +3.63333333333333 NA 13.1874065561996 1.0914266276744 +4.26666666666667 NA 12.5554515578383 1.52969595740389 +4.88333333333333 NA 11.1173517625731 2.00104528817886 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecR_res/KEIO_ROBOT1_25.pdf b/validation/validation_results/Berges_2021/Berges_2021/yecR_res/KEIO_ROBOT1_25.pdf new file mode 100644 index 0000000..3cb5a91 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yecR_res/KEIO_ROBOT1_25.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecR_res/KEIO_ROBOT1_25_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yecR_res/KEIO_ROBOT1_25_log.txt new file mode 100644 index 0000000..cd40025 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecR_res/KEIO_ROBOT1_25_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.065016 NA NA + [3,] 0.086184 NA NA + [4,] 0.130032 NA NA + [5,] 0.166320 NA NA + [6,] 0.241920 NA NA + [7,] 0.276696 NA NA + [8,] NA 14.91675 0.01143051 + [9,] NA 14.98483 0.32839097 +[10,] NA 13.57436 0.68853409 +[11,] NA 13.18741 1.09142663 +[12,] NA 12.55545 1.52969596 +[13,] NA 11.11735 2.00104529 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03302464 15.14664852 0.03116621 0.44225767 -6.76524140 3.50559077 + +$result$lastp + X Glc Ace mu qGlc qAce + 6.048706e-09 -3.499292e-08 -5.763195e-08 -4.359204e-08 5.991592e-07 -1.881469e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.007136337 0.315559375 0.138297874 0.050404643 1.044105516 0.469534725 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4573503 + +$result$laststep + X Glc Ace mu qGlc qAce + 6.048706e-09 -3.499292e-08 -5.763195e-08 -4.359204e-08 5.991592e-07 -1.881469e-08 + +$result$normp +[1] 6.048376e-07 + +$result$res + [1] -0.087568068 -0.457239727 0.210826162 0.085090679 0.437444689 -0.457309319 0.100596348 0.466924563 -0.896430889 0.727592204 -0.119561313 -0.516227604 0.337703038 0.137843292 0.001510003 -0.080365274 -0.082640037 -0.163915294 0.187567310 + +$result$prevres + [1] -0.087568371 -0.457240094 0.210825783 0.085090371 0.437444525 -0.457309210 0.100596726 0.466924642 -0.896430748 0.727592338 -0.119561258 -0.516227688 0.337702714 0.137843574 0.001510089 -0.080365321 -0.082640158 -0.163915424 0.187567240 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.0000000 + [2,] 84.590189 0.000000 0 3.321232333 0.000000000 0.0000000 + [3,] 136.868314 0.000000 0 10.291847596 0.000000000 0.0000000 + [4,] 199.447802 0.000000 0 20.605363043 0.000000000 0.0000000 + [5,] 265.058044 0.000000 0 33.012643422 0.000000000 0.0000000 + [6,] 352.424535 0.000000 0 51.391285776 0.000000000 0.0000000 + [7,] 421.969773 0.000000 0 67.207321654 0.000000000 0.0000000 + [8,] -0.995067 2.173913 0 -0.001100773 0.004857435 0.0000000 + [9,] -37.796559 2.173913 0 -1.205669687 0.184504484 0.0000000 +[10,] -81.467424 2.173913 0 -4.524813287 0.397684481 0.0000000 +[11,] -132.591422 2.173913 0 -9.998789957 0.647247060 0.0000000 +[12,] -186.202363 2.173913 0 -17.018331096 0.908949693 0.0000000 +[13,] -255.010805 2.173913 0 -27.446247914 1.244839156 0.0000000 +[14,] 1.185927 0.000000 5 0.001311909 0.000000000 0.0111721 +[15,] 45.046182 0.000000 5 1.436924869 0.000000000 0.4243603 +[16,] 97.093399 0.000000 5 5.392701508 0.000000000 0.9146743 +[17,] 158.023307 0.000000 5 11.916622025 0.000000000 1.4886682 +[18,] 221.917171 0.000000 5 20.282556192 0.000000000 2.0905843 +[19,] 303.923513 0.000000 5 32.710614363 0.000000000 2.8631301 + +$result$retres +$result$retres$res + [1] -0.087568371 -0.457240094 0.210825783 0.085090371 0.437444525 -0.457309210 0.100596726 0.466924642 -0.896430748 0.727592338 -0.119561258 -0.516227688 0.337702714 0.137843574 0.001510089 -0.080365321 -0.082640158 -0.163915424 0.187567240 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03302463 15.14665 0.03116626 + [2,] 0.05587120 14.79716 0.21226137 + [3,] 0.09040052 14.26897 0.48596074 + [4,] 0.13173381 13.63669 0.81359235 + [5,] 0.17506889 12.97379 1.15709132 + [6,] 0.23277382 12.09107 1.61449398 + [7,] 0.27870793 11.38842 1.97859441 + [8,] 0.03401282 15.13153 0.03899923 + [9,] 0.07055996 14.57247 0.32869298 + [10,] 0.11392899 13.90905 0.67246103 + [11,] 0.16469964 13.13241 1.07489860 + [12,] 0.21794004 12.31799 1.49691287 + [13,] 0.28627290 11.27270 2.03855874 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.001751367 NA NA + [2,] 0.009144802 NA NA + [3,] -0.004216516 NA NA + [4,] -0.001701807 NA NA + [5,] -0.008748891 NA NA + [6,] 0.009146184 NA NA + [7,] -0.002011935 NA NA + [8,] NA -0.21478534 -0.0275687147 + [9,] NA 0.41235814 -0.0003020178 +[10,] NA -0.33469248 0.0160730642 +[11,] NA 0.05499818 0.0165280315 +[12,] NA 0.23746474 0.0327830848 +[13,] NA -0.15534325 -0.0375134480 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yecR_res/KEIO_ROBOT1_25_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yecR_res/KEIO_ROBOT1_25_res.txt new file mode 100644 index 0000000..7befab2 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yecR_res/KEIO_ROBOT1_25_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0330246386322267 0.0330642862762178 0.0327766124554999 0.00470740529512687 0.024534027441204 0.041049575031372 +Glc 15.1466485180724 15.1305100651458 15.1312698776335 0.201928037996026 14.7703323239569 15.5799417565084 +Ace 0.0311662058902883 0.0667151140853381 0.0667857645678972 0.057747585902291 9.99999999990418e-07 0.203559917764972 +mu 0.442257671185 0.444269475943023 0.444652011636132 0.0330921678627501 0.387589313209789 0.510331701038565 +qGlc -6.76524139605841 -6.75857673389642 -6.78878764889991 0.706783580827609 -8.10108147323859 -5.32796105972233 +qAce 3.50559077103041 3.43454953136099 3.43133277014729 0.342651492792896 2.84521791417668 4.09093094634914 +res 2.71920094046714 31.9025229219743 31.764601640048 7.33765135395978 18.7248105514044 46.6429139323555 + + +Goodness of fit (khi2 test) + +khi2 value 2.71920094046809 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.20916930311293 +p-value, i.e. P(X^2<=value) 0.00122789826791147 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yedD.txt b/validation/validation_results/Berges_2021/Berges_2021/yedD.txt new file mode 100644 index 0000000..3e9443d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yedD.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 8.769600000000001E-2 NA NA +2.2613888888888889 7.4088000000000001E-2 NA NA +2.7741666666666664 0.104328 NA NA +3.2088888888888891 0.12852000000000002 NA NA +3.7063888888888892 0.17236800000000002 NA NA +4.2258333333333331 0.22075199999999998 NA NA +4.6355555555555554 0.314496 NA NA +4.9675000000000002 0.41277600000000003 NA NA +2.8 NA 12.4679665195911 0.638086972391896 +3.73333333333333 NA 11.7047979733294 1.17769832420858 +4.28333333333333 NA 11.0623363223335 1.62448654572132 +4.75 NA 10.2654694741708 2.14902490214313 +5.11666666666667 NA 9.55880185287743 2.6032239867547 +5.43333333333333 NA 8.60550303333731 3.06749352788246 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yedD_res/KEIO_ROBOT5_8.pdf b/validation/validation_results/Berges_2021/Berges_2021/yedD_res/KEIO_ROBOT5_8.pdf new file mode 100644 index 0000000..ab92ae2 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yedD_res/KEIO_ROBOT5_8.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yedD_res/KEIO_ROBOT5_8_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yedD_res/KEIO_ROBOT5_8_log.txt new file mode 100644 index 0000000..78fc055 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yedD_res/KEIO_ROBOT5_8_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.087696 NA NA + [2,] 0.074088 NA NA + [3,] 0.104328 NA NA + [4,] 0.128520 NA NA + [5,] 0.172368 NA NA + [6,] 0.220752 NA NA + [7,] 0.314496 NA NA + [8,] 0.412776 NA NA + [9,] NA 12.467967 0.638087 +[10,] NA 11.704798 1.177698 +[11,] NA 11.062336 1.624487 +[12,] NA 10.265469 2.149025 +[13,] NA 9.558802 2.603224 +[14,] NA 8.605503 3.067494 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01770664 13.20711714 0.22312573 0.62426635 -5.60225734 3.56798472 + +$result$lastp + X Glc Ace mu qGlc qAce +-3.307005e-09 -1.136052e-07 8.926205e-08 4.211296e-08 1.213100e-08 -4.421184e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.005357563 0.616208790 0.281004285 0.067089273 1.164180398 0.519667540 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6530645 + +$result$laststep + X Glc Ace mu qGlc qAce +-3.307005e-09 -1.136052e-07 8.926205e-08 4.211296e-08 1.213100e-08 -4.421184e-08 + +$result$normp +[1] 1.573536e-07 + +$result$res + [1] -1.6118244421 -0.0719180507 -0.2134584111 0.1367420479 0.3345314790 1.3445101849 0.2662389335 -0.9657388752 -0.0314965744 0.0588377490 0.0001815231 0.0388621171 -0.1486098275 0.0822250126 0.3250947674 -0.0750396777 -0.1771934639 -0.3189894593 -0.0650456119 0.3111734456 + +$result$prevres + [1] -1.611824138 -0.071917718 -0.213458061 0.136742387 0.334531754 1.344510294 0.266238798 -0.965739316 -0.031496514 0.058837732 0.000181478 0.038862075 -0.148609837 0.082225065 0.325094618 -0.075039690 -0.177193413 -0.318989387 -0.065045562 0.311173433 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 156.60657 0.000000 0 5.071465 0.0000000 0.0000000 + [2,] 205.14805 0.000000 0 8.214455 0.0000000 0.0000000 + [3,] 282.54612 0.000000 0 13.878995 0.0000000 0.0000000 + [4,] 370.63740 0.000000 0 21.059111 0.0000000 0.0000000 + [5,] 505.62571 0.000000 0 33.183047 0.0000000 0.0000000 + [6,] 699.29198 0.000000 0 52.324734 0.0000000 0.0000000 + [7,] 903.10980 0.000000 0 74.127349 0.0000000 0.0000000 + [8,] 1111.05564 0.000000 0 97.725929 0.0000000 0.0000000 + [9,] -92.52721 2.173913 0 -2.930164 0.2924439 0.0000000 +[10,] -181.12268 2.173913 0 -8.125366 0.5724610 0.0000000 +[11,] -263.31287 2.173913 0 -13.981598 0.8322334 0.0000000 +[12,] -358.96279 2.173913 0 -21.650360 1.1345470 0.0000000 +[13,] -456.31079 2.173913 0 -30.166021 1.4422276 0.0000000 +[14,] -560.31438 2.173913 0 -39.889818 1.7709440 0.0000000 +[15,] 135.53681 0.000000 5 4.292197 0.0000000 0.6726209 +[16,] 265.31426 0.000000 5 11.902294 0.0000000 1.3166603 +[17,] 385.70907 0.000000 5 20.480690 0.0000000 1.9141369 +[18,] 525.82013 0.000000 5 31.714137 0.0000000 2.6094582 +[19,] 668.41858 0.000000 5 44.188148 0.0000000 3.3171235 +[20,] 820.76634 0.000000 5 58.431876 0.0000000 4.0731712 + +$result$retres +$result$retres$res + [1] -1.611824138 -0.071917718 -0.213458061 0.136742387 0.334531754 1.344510294 0.266238798 -0.965739316 -0.031496514 0.058837732 0.000181478 0.038862075 -0.148609837 0.082225065 0.325094618 -0.075039690 -0.177193413 -0.318989387 -0.065045562 0.311173433 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05545952 12.868317 0.4389017 + [2,] 0.07264965 12.714051 0.5371516 + [3,] 0.10005884 12.468077 0.6938084 + [4,] 0.13125485 12.188119 0.8721087 + [5,] 0.17905864 11.759121 1.1453306 + [6,] 0.24764221 11.143642 1.5373189 + [7,] 0.31982078 10.495901 1.9498545 + [8,] 0.39346121 9.835041 2.3707453 + [9,] 0.10168556 12.453478 0.7031059 + [10,] 0.18209597 11.731863 1.1626904 + [11,] 0.25669287 11.062420 1.5890479 + [12,] 0.34350600 10.283346 2.0852270 + [13,] 0.43186033 9.490441 2.5902149 + [14,] 0.52625535 8.643327 3.1297282 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.032236483 NA NA + [2,] 0.001438354 NA NA + [3,] 0.004269161 NA NA + [4,] -0.002734848 NA NA + [5,] -0.006690635 NA NA + [6,] -0.026890206 NA NA + [7,] -0.005324776 NA NA + [8,] 0.019314786 NA NA + [9,] NA 1.448840e-02 -0.06501892 +[10,] NA -2.706536e-02 0.01500794 +[11,] NA -8.347986e-05 0.03543868 +[12,] NA -1.787655e-02 0.06379788 +[13,] NA 6.836052e-02 0.01300911 +[14,] NA -3.782353e-02 -0.06223469 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yedD_res/KEIO_ROBOT5_8_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yedD_res/KEIO_ROBOT5_8_res.txt new file mode 100644 index 0000000..f91127e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yedD_res/KEIO_ROBOT5_8_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0177066352217958 0.0181605719184631 0.0181830115156461 0.00269213983855281 0.0135669845424096 0.0233930052120269 +Glc 13.2071171399629 13.2209752504578 13.2075236528009 0.233542316172903 12.7511482562346 13.6047439939494 +Ace 0.223125726118771 0.215631759632107 0.202106661021119 0.115881816296139 0.0100119109927319 0.446742494439899 +mu 0.624266346706192 0.620735869070736 0.61699070329002 0.031386253442649 0.56325944240018 0.68023955598121 +qGlc -5.60225733594837 -5.64626185541038 -5.71159186556213 0.563144871363267 -6.66850732297544 -4.62913543844314 +qAce 3.56798471958737 3.57699959838679 3.57562123505361 0.287063597945143 3.04604890110673 4.14774377671788 +res 5.97090606192203 35.2584467852323 35.4609263258875 7.6775146862873 22.1820328278725 47.7122736908045 + + +Goodness of fit (khi2 test) + +khi2 value 5.97090606192288 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.426493290137349 +p-value, i.e. P(X^2<=value) 0.032780556232721 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yedV.txt b/validation/validation_results/Berges_2021/Berges_2021/yedV.txt new file mode 100644 index 0000000..1bb9bda --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yedV.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.18888888888889 0.05292 NA NA +2.27694444444444 0.084672 NA NA +3.12833333333333 0.134568 NA NA +3.77138888888889 0.175392 NA NA +4.41555555555556 0.244944 NA NA +4.82277777777778 0.337176 NA NA +0.0666666666666667 NA 14.0042771787617 0.0130592124021829 +1.71666666666667 NA 15.3032563161238 0.325073443768164 +2.8 NA 13.6751055268759 0.722570137805818 +3.63333333333333 NA 12.8110643342243 1.16940283499877 +4.26666666666667 NA 12.1520761714542 1.62777664140305 +4.88333333333333 NA 10.9297935900362 2.13639255382759 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yedV_res/KEIO_ROBOT1_1.pdf b/validation/validation_results/Berges_2021/Berges_2021/yedV_res/KEIO_ROBOT1_1.pdf new file mode 100644 index 0000000..a25fbf7 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yedV_res/KEIO_ROBOT1_1.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yedV_res/KEIO_ROBOT1_1_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yedV_res/KEIO_ROBOT1_1_log.txt new file mode 100644 index 0000000..fa4cc36 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yedV_res/KEIO_ROBOT1_1_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 1 1 1 1 1 1 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.002 0.5 0.5 + [2,] 0.002 0.5 0.5 + [3,] 0.002 0.5 0.5 + [4,] 0.002 0.5 0.5 + [5,] 0.002 0.5 0.5 + [6,] 0.002 0.5 0.5 + [7,] 0.002 0.5 0.5 + [8,] 0.002 0.5 0.5 + [9,] 0.002 0.5 0.5 + [10,] 0.002 0.5 0.5 + [11,] 0.002 0.5 0.5 + [12,] 0.002 0.5 0.5 + [13,] 0.002 0.5 0.5 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.052920 NA NA + [3,] 0.084672 NA NA + [4,] 0.134568 NA NA + [5,] 0.175392 NA NA + [6,] 0.244944 NA NA + [7,] 0.337176 NA NA + [8,] NA 14.00428 0.01305921 + [9,] NA 15.30326 0.32507344 +[10,] NA 13.67511 0.72257014 +[11,] NA 12.81106 1.16940283 +[12,] NA 12.15208 1.62777664 +[13,] NA 10.92979 2.13639255 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02439604 14.76981201 0.08605372 0.53602614 -6.56847002 3.69297576 + +$result$lastp + X Glc Ace mu qGlc qAce +-3.569116e-10 1.833069e-09 4.396917e-09 3.396215e-09 -4.154324e-08 1.400588e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.004619698 2.475988141 2.475665768 0.043356414 7.827668924 7.823292673 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 3.505242 + +$result$laststep + X Glc Ace mu qGlc qAce +-3.569116e-10 1.833069e-09 4.396917e-09 3.396215e-09 -4.154324e-08 1.400588e-09 + +$result$normp +[1] 4.197806e-08 + +$result$res + [1] -3.67798169 -3.38963197 -0.99828651 -2.03948761 4.40046200 7.60501507 -6.78032252 1.50931736 -1.96955859 0.10537518 0.32318617 -0.05341899 0.08509887 0.15821876 0.02946661 -0.10132908 -0.14587806 -0.10988504 0.16940680 + +$result$prevres + [1] -3.67798152 -3.38963172 -0.99828622 -2.03948735 4.40046216 7.60501502 -6.78032280 1.50931736 -1.96955860 0.10537517 0.32318616 -0.05341898 0.08509889 0.15821875 0.02946661 -0.10132907 -0.14587806 -0.10988503 0.16940681 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 500.0000000 0 0 0.000000e+00 0.000000000 0.000000000 + [2,] 945.6604901 0 0 2.742810e+01 0.000000000 0.000000000 + [3,] 1694.4438078 0 0 9.412368e+01 0.000000000 0.000000000 + [4,] 2674.3898092 0 0 2.041066e+02 0.000000000 0.000000000 + [5,] 3775.0583131 0 0 3.473316e+02 0.000000000 0.000000000 + [6,] 5331.8912079 0 0 5.743623e+02 0.000000000 0.000000000 + [7,] 6632.5394329 0 0 7.803625e+02 0.000000000 0.000000000 + [8,] -0.8916324 2 0 -7.293949e-04 0.003311623 0.000000000 + [9,] -37.0006809 2 0 -8.919724e-01 0.137424694 0.000000000 +[10,] -85.4252595 2 0 -3.621481e+00 0.317279031 0.000000000 +[11,] -147.3316829 2 0 -8.526215e+00 0.547206456 0.000000000 +[12,] -216.7930251 2 0 -1.525012e+01 0.805193701 0.000000000 +[13,] -311.3185128 2 0 -2.583938e+01 1.156272004 0.000000000 +[14,] 0.5013004 0 2 4.100860e-04 0.000000000 0.003311623 +[15,] 20.8028077 0 2 5.014916e-01 0.000000000 0.137424694 +[16,] 48.0284471 0 2 2.036097e+00 0.000000000 0.317279031 +[17,] 82.8339531 0 2 4.793674e+00 0.000000000 0.547206456 +[18,] 121.8870436 0 2 8.574037e+00 0.000000000 0.805193701 +[19,] 175.0318911 0 2 1.452762e+01 0.000000000 1.156272004 + +$result$retres +$result$retres$res + [1] -3.67798152 -3.38963172 -0.99828622 -2.03948735 4.40046216 7.60501502 -6.78032280 1.50931736 -1.96955860 0.10537517 0.32318616 -0.05341898 0.08509889 0.15821875 0.02946661 -0.10132907 -0.14587806 -0.10988503 0.16940681 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02439604 14.76981 0.08605372 + [2,] 0.04614074 14.50335 0.23586478 + [3,] 0.08267543 14.05566 0.48757215 + [4,] 0.13048903 13.46975 0.81698605 + [5,] 0.18419292 12.81166 1.18698144 + [6,] 0.26015403 11.88083 1.71031883 + [7,] 0.32361535 11.10318 2.14753843 + [8,] 0.02528360 14.75894 0.09216859 + [9,] 0.06122765 14.31848 0.33980675 + [10,] 0.10943096 13.72779 0.67190560 + [11,] 0.17105452 12.97266 1.09646381 + [12,] 0.24019847 12.12537 1.57283413 + [13,] 0.33429204 10.97234 2.22109596 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.007355963 NA NA + [2,] 0.006779263 NA NA + [3,] 0.001996572 NA NA + [4,] 0.004078975 NA NA + [5,] -0.008800924 NA NA + [6,] -0.015210030 NA NA + [7,] 0.013560646 NA NA + [8,] NA -0.75465868 -0.07910937 + [9,] NA 0.98477930 -0.01473330 +[10,] NA -0.05268759 0.05066454 +[11,] NA -0.16159308 0.07293903 +[12,] NA 0.02670949 0.05494252 +[13,] NA -0.04254944 -0.08470340 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yedV_res/KEIO_ROBOT1_1_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yedV_res/KEIO_ROBOT1_1_res.txt new file mode 100644 index 0000000..a76379e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yedV_res/KEIO_ROBOT1_1_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0243960366115019 0.0243806196695427 0.0243793652731369 0.000430787552793218 0.0235436616702449 0.0252456958163593 +Glc 14.7698120087311 14.77255408614 14.7739255458344 0.215744450763922 14.3575571526084 15.2006317137785 +Ace 0.0860537194159208 0.184684381001253 0.154208623001349 0.174671911884784 9.99999999979837e-07 0.574514358995984 +mu 0.536026138560439 0.536143654239499 0.53594032901361 0.00397949323324097 0.528191213642527 0.544572055994257 +qGlc -6.56847002230933 -6.65298780154708 -6.68753513656023 0.688408974323449 -7.80317953514636 -5.30055222987325 +qAce 3.69297576425338 3.44713757345606 3.48574537056487 0.630267955767687 2.37410159086577 4.48972715592508 +res 159.727404674356 31.4106271439666 30.4156939773608 7.93027851680287 17.6263878148188 47.293432170921 + + +Goodness of fit (khi2 test) + +khi2 value 159.727404674355 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 12.2867234364889 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yegD.txt b/validation/validation_results/Berges_2021/Berges_2021/yegD.txt new file mode 100644 index 0000000..ce47e61 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yegD.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.039312 NA NA +1.195 0.074088 NA NA +1.61361111111111 0.092232 NA NA +2.36138888888889 0.130032 NA NA +3.28638888888889 0.229824 NA NA +3.81944444444444 0.322056 NA NA +4.41083333333333 0.464184 NA NA +0.283333333333333 NA 13.8811493145498 0.0312228068307768 +1.91666666666667 NA 14.0657012202199 0.392389755498907 +2.7 NA 13.2213123664081 0.585353147248096 +3.61666666666667 NA 12.1995139382106 1.21214801217509 +4.05 NA 11.5911939293129 1.21024868095068 +4.75 NA 9.69033189904698 2.18014071818986 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yegD_res/KEIO_ROBOT4_24.pdf b/validation/validation_results/Berges_2021/Berges_2021/yegD_res/KEIO_ROBOT4_24.pdf new file mode 100644 index 0000000..12f99d6 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yegD_res/KEIO_ROBOT4_24.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yegD_res/KEIO_ROBOT4_24_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yegD_res/KEIO_ROBOT4_24_log.txt new file mode 100644 index 0000000..c8c7c7b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yegD_res/KEIO_ROBOT4_24_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.039312 NA NA + [2,] 0.074088 NA NA + [3,] 0.092232 NA NA + [4,] 0.130032 NA NA + [5,] 0.229824 NA NA + [6,] 0.322056 NA NA + [7,] 0.464184 NA NA + [8,] NA 13.881149 0.03122281 + [9,] NA 14.065701 0.39238976 +[10,] NA 13.221312 0.58535315 +[11,] NA 12.199514 1.21214801 +[12,] NA 11.591194 1.21024868 +[13,] NA 9.690332 2.18014072 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03263293 14.31231267 0.06793635 0.60070837 -5.04834488 2.34046956 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.459435e-09 1.989311e-08 1.630726e-08 1.896213e-08 -1.717050e-07 1.071238e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006158169 0.343014121 0.149492999 0.047374383 0.740484951 0.323678124 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5180142 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.459435e-09 1.989311e-08 1.630726e-08 1.896213e-08 -1.717050e-07 1.071238e-08 + +$result$normp +[1] 1.749989e-07 + +$result$res + [1] -0.333953332 -0.359501906 -0.310376898 0.238641746 0.257599090 0.080210577 -0.123480675 0.826693163 -0.753136146 -0.050433550 -0.045753722 -0.279827254 0.302457509 0.301520850 -0.247534274 -0.004306237 -0.774684374 0.894526321 -0.169522286 + +$result$prevres + [1] -0.333953209 -0.359501730 -0.310376706 0.238641952 0.257599244 0.080210624 -0.123480866 0.826693115 -0.753136215 -0.050433615 -0.045753745 -0.279827227 0.302457687 0.301520777 -0.247534288 -0.004306219 -0.774684332 0.894526359 -0.169522298 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 102.500685 0.000000 0 3.99715343 0.00000000 0.00000000 + [3,] 131.806201 0.000000 0 6.94050170 0.00000000 0.00000000 + [4,] 206.547213 0.000000 0 15.91633245 0.00000000 0.00000000 + [5,] 360.028877 0.000000 0 38.61112329 0.00000000 0.00000000 + [6,] 495.910350 0.000000 0 61.81011002 0.00000000 0.00000000 + [7,] 707.436170 0.000000 0 101.82725948 0.00000000 0.00000000 + [8,] -3.389780 2.173913 0 -0.01611527 0.02191183 0.00000000 + [9,] -39.507570 2.173913 0 -1.46754055 0.25538034 0.00000000 +[10,] -74.224807 2.173913 0 -4.11738194 0.47979556 0.00000000 +[11,] -142.150692 2.173913 0 -11.21098113 0.91887434 0.00000000 +[12,] -189.848156 2.173913 0 -17.19221086 1.22719487 0.00000000 +[13,] -298.634686 2.173913 0 -32.89913851 1.93040038 0.00000000 +[14,] 3.614543 0.000000 5 0.01718381 0.00000000 0.05039721 +[15,] 42.127157 0.000000 5 1.56484721 0.00000000 0.58737479 +[16,] 79.146353 0.000000 5 4.39038884 0.00000000 1.10352978 +[17,] 151.576128 0.000000 5 11.95433581 0.00000000 2.11341099 +[18,] 202.436218 0.000000 5 18.33215662 0.00000000 2.82254819 +[19,] 318.435941 0.000000 5 35.08054694 0.00000000 4.43992088 + +$result$retres +$result$retres$res + [1] -0.333953209 -0.359501730 -0.310376706 0.238641952 0.257599244 0.080210624 -0.123480866 0.826693115 -0.753136215 -0.050433615 -0.045753745 -0.279827227 0.302457687 0.301520777 -0.247534288 -0.004306219 -0.774684332 0.894526359 -0.169522298 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03263294 14.312313 0.06793633 + [2,] 0.06689797 14.024350 0.20143915 + [3,] 0.08602447 13.863611 0.27595950 + [4,] 0.13480484 13.453661 0.46601675 + [5,] 0.23497598 12.611824 0.85630185 + [6,] 0.32366021 11.866523 1.20183181 + [7,] 0.46171438 10.706318 1.73971610 + [8,] 0.03868774 14.261428 0.09152696 + [9,] 0.10320112 13.719259 0.34288290 + [10,] 0.16521285 13.198113 0.58449190 + [11,] 0.28654166 12.178467 1.05721115 + [12,] 0.37173859 11.462473 1.38915395 + [13,] 0.56605244 9.829462 2.14623626 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.006679064 NA NA + [2,] 0.007190035 NA NA + [3,] 0.006207534 NA NA + [4,] -0.004772839 NA NA + [5,] -0.005151985 NA NA + [6,] -0.001604212 NA NA + [7,] 0.002469617 NA NA + [8,] NA -0.38027883 -0.0603041554 + [9,] NA 0.34644266 0.0495068576 +[10,] NA 0.02319946 0.0008612438 +[11,] NA 0.02104672 0.1549368664 +[12,] NA 0.12872052 -0.1789052719 +[13,] NA -0.13913054 0.0339044595 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yegD_res/KEIO_ROBOT4_24_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yegD_res/KEIO_ROBOT4_24_res.txt new file mode 100644 index 0000000..4dfb23e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yegD_res/KEIO_ROBOT4_24_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0326329333521056 0.0332053297017342 0.0330017190517166 0.00339863505068409 0.0268057247809532 0.0399806243598278 +Glc 14.3123126664393 14.2952226870035 14.2669447004512 0.196628436076105 13.9322081499879 14.6859018835276 +Ace 0.0679363507866065 0.0946048949717603 0.0946375451462371 0.0619056396254383 9.99999999992066e-07 0.210356713963928 +mu 0.600708366119292 0.597265706711662 0.597803091201496 0.0240498448135465 0.552977666044323 0.638720431763497 +qGlc -5.04834487588246 -5.00148479840678 -4.97993989754255 0.498490812925587 -5.99268036921886 -4.21615764144214 +qAce 2.34046956037334 2.26846290833457 2.263376255291 0.185596641974861 1.90692271686278 2.62542704359378 +res 3.4884026852182 30.6065521378983 30.4986481843738 7.8069491386795 16.8061718782655 47.1588075968697 + + +Goodness of fit (khi2 test) + +khi2 value 3.48840268521845 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.268338668093727 +p-value, i.e. P(X^2<=value) 0.00448323906533334 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yegQ.txt b/validation/validation_results/Berges_2021/Berges_2021/yegQ.txt new file mode 100644 index 0000000..7e487dd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yegQ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.18888888888889 0.055944 NA NA +2.27694444444444 0.099792 NA NA +3.12833333333333 0.157248 NA NA +3.77138888888889 0.21168 NA NA +4.41555555555556 0.320544 NA NA +4.82277777777778 0.37044 NA NA +0.0666666666666667 NA 15.4860993695238 0.0105977294024324 +1.71666666666667 NA 15.0009987151592 0.315410252906521 +2.8 NA 13.4041657711752 0.688527188173931 +3.63333333333333 NA 12.804085265974 1.10820135827963 +4.26666666666667 NA 11.8901486256479 1.51335373468779 +4.88333333333333 NA 10.2655736005935 1.82589513438566 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yegQ_res/KEIO_ROBOT1_10.pdf b/validation/validation_results/Berges_2021/Berges_2021/yegQ_res/KEIO_ROBOT1_10.pdf new file mode 100644 index 0000000..a2d78cb Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yegQ_res/KEIO_ROBOT1_10.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yegQ_res/KEIO_ROBOT1_10_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yegQ_res/KEIO_ROBOT1_10_log.txt new file mode 100644 index 0000000..a34d1e4 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yegQ_res/KEIO_ROBOT1_10_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.055944 NA NA + [3,] 0.099792 NA NA + [4,] 0.157248 NA NA + [5,] 0.211680 NA NA + [6,] 0.320544 NA NA + [7,] 0.370440 NA NA + [8,] NA 15.48610 0.01059773 + [9,] NA 15.00100 0.31541025 +[10,] NA 13.40417 0.68852719 +[11,] NA 12.80409 1.10820136 +[12,] NA 11.89015 1.51335373 +[13,] NA 10.26557 1.82589513 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0330976 15.3958326 0.1002261 0.5031048 -7.3573856 2.6443154 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.798732e-09 1.375546e-07 -1.176322e-07 1.526886e-08 -7.652197e-07 4.976209e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.007426254 0.367881203 0.158733158 0.051633438 1.025021737 0.432143622 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.544847 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.798732e-09 1.375546e-07 -1.176322e-07 1.526886e-08 -7.652197e-07 4.976209e-07 + +$result$normp +[1] 9.306918e-07 + +$result$res + [1] 0.06727999 0.21257143 0.21358044 0.12294396 0.45166348 -0.76749836 0.20733309 -0.23212209 -0.58512644 1.07773323 0.14051938 -0.32899835 -0.07200573 0.47780993 0.11730489 -0.25328389 -0.49854059 -0.49379106 0.65050072 + +$result$prevres + [1] 0.06728013 0.21257163 0.21358070 0.12294426 0.45166378 -0.76749809 0.20733330 -0.23212239 -0.58512669 1.07773308 0.14051938 -0.32899815 -0.07200523 0.47781052 0.11730534 -0.25328365 -0.49854064 -0.49379144 0.65049987 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 90.9362432 0.000000 0 3.578284053 0.000000000 0.00000000 + [3,] 157.2071781 0.000000 0 11.847353377 0.000000000 0.00000000 + [4,] 241.2665465 0.000000 0 24.980818619 0.000000000 0.00000000 + [5,] 333.4278901 0.000000 0 41.619779751 0.000000000 0.00000000 + [6,] 461.0515790 0.000000 0 67.380061525 0.000000000 0.00000000 + [7,] 565.8818726 0.000000 0 90.327412411 0.000000000 0.00000000 + [8,] -1.0843711 2.173913 0 -0.001203024 0.004878103 0.00000000 + [9,] -43.6122532 2.173913 0 -1.415134455 0.196192132 0.00000000 +[10,] -98.2541627 2.173913 0 -5.587915824 0.442001783 0.00000000 +[11,] -165.9852478 2.173913 0 -12.863912439 0.746693813 0.00000000 +[12,] -240.2001796 2.173913 0 -22.607678725 1.080553787 0.00000000 +[13,] -339.1406366 2.173913 0 -37.641520072 1.525642903 0.00000000 +[14,] 0.8963868 0.000000 5 0.000994470 0.000000000 0.01121964 +[15,] 36.0517259 0.000000 5 1.169809761 0.000000000 0.45124190 +[16,] 81.2210303 0.000000 5 4.619206641 0.000000000 1.01660410 +[17,] 137.2103988 0.000000 5 10.633851984 0.000000000 1.71739577 +[18,] 198.5595882 0.000000 5 18.688459705 0.000000000 2.48527371 +[19,] 280.3479383 0.000000 5 31.116066345 0.000000000 3.50897868 + +$result$retres +$result$retres$res + [1] 0.06728013 0.21257163 0.21358070 0.12294426 0.45166378 -0.76749809 0.20733330 -0.23212239 -0.58512669 1.07773308 0.14051938 -0.32899815 -0.07200523 0.47781052 0.11730534 -0.25328365 -0.49854064 -0.49379144 0.65049987 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03309760 15.39583 0.1002262 + [2,] 0.06019543 14.99955 0.2426522 + [3,] 0.10406361 14.35803 0.4732230 + [4,] 0.15970689 13.54430 0.7656837 + [5,] 0.22071328 12.65215 1.0863328 + [6,] 0.30519404 11.41670 1.5303631 + [7,] 0.37458667 10.40191 1.8950903 + [8,] 0.03422653 15.37932 0.1061598 + [9,] 0.07850199 14.73184 0.3388713 + [10,] 0.13538927 13.89992 0.6378705 + [11,] 0.20590359 12.86872 1.0084932 + [12,] 0.28316820 11.73881 1.4145954 + [13,] 0.38617436 10.23245 1.9559951 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.001345603 NA NA + [2,] -0.004251433 NA NA + [3,] -0.004271614 NA NA + [4,] -0.002458885 NA NA + [5,] -0.009033276 NA NA + [6,] 0.015349962 NA NA + [7,] -0.004146666 NA NA + [8,] NA 0.10677630 -0.09556210 + [9,] NA 0.26915828 -0.02346107 +[10,] NA -0.49575722 0.05065673 +[11,] NA -0.06463892 0.09970813 +[12,] NA 0.15133915 0.09875829 +[13,] NA 0.03312241 -0.13009997 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yegQ_res/KEIO_ROBOT1_10_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yegQ_res/KEIO_ROBOT1_10_res.txt new file mode 100644 index 0000000..0b904eb --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yegQ_res/KEIO_ROBOT1_10_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0330975997256718 0.0326624647877178 0.0325352365050914 0.00410622819987078 0.0261000139499385 0.0407183263002782 +Glc 15.3958326466743 15.4101008451739 15.4195142937595 0.200094249438057 14.9791415023358 15.7611237520411 +Ace 0.100226064277254 0.126201636898616 0.129993129981262 0.0727879608397512 0.00152197875651946 0.259002407002282 +mu 0.50310475224275 0.50733401785063 0.504842456586544 0.0297616953324604 0.45500770748226 0.561291654258996 +qGlc -7.3573856224388 -7.38584330527454 -7.39012668103916 0.541153737845472 -8.31596709760401 -6.48787408991342 +qAce 2.64431540753241 2.59792256718112 2.58690431280386 0.247489664716939 2.09599789223527 3.06945416404171 +res 3.85915764454038 32.6940616459589 33.4955761654878 8.52483760559543 17.7838488128043 49.2204074529919 + + +Goodness of fit (khi2 test) + +khi2 value 3.85915764454268 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.296858280349437 +p-value, i.e. P(X^2<=value) 0.00740066333936628 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yehS.txt b/validation/validation_results/Berges_2021/Berges_2021/yehS.txt new file mode 100644 index 0000000..c1ba25d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yehS.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.18888888888889 0.071064 NA NA +2.27694444444444 0.117936 NA NA +3.12833333333333 0.184464 NA NA +3.77138888888889 0.2646 NA NA +4.41555555555556 0.379512 NA NA +4.82277777777778 0.571536 NA NA +0.0666666666666667 NA 14.1958193865896 0.0145452209242924 +1.71666666666667 NA 15.2360191060715 0.340996262207858 +2.8 NA 13.6981143071046 0.755016872171432 +3.63333333333333 NA 12.2019224551393 1.16571823122566 +4.26666666666667 NA 11.3968755024808 1.65940649790006 +4.88333333333333 NA 9.72653169012383 2.22883589266411 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yehS_res/KEIO_ROBOT1_26.pdf b/validation/validation_results/Berges_2021/Berges_2021/yehS_res/KEIO_ROBOT1_26.pdf new file mode 100644 index 0000000..9a129ad Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yehS_res/KEIO_ROBOT1_26.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yehS_res/KEIO_ROBOT1_26_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yehS_res/KEIO_ROBOT1_26_log.txt new file mode 100644 index 0000000..139928a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yehS_res/KEIO_ROBOT1_26_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.071064 NA NA + [3,] 0.117936 NA NA + [4,] 0.184464 NA NA + [5,] 0.264600 NA NA + [6,] 0.379512 NA NA + [7,] 0.571536 NA NA + [8,] NA 14.195819 0.01454522 + [9,] NA 15.236019 0.34099626 +[10,] NA 13.698114 0.75501687 +[11,] NA 12.201922 1.16571823 +[12,] NA 11.396876 1.65940650 +[13,] NA 9.726532 2.22883589 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02507698 14.82627485 0.15031848 0.63680045 -6.14842516 2.58805015 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.134832e-08 1.240937e-07 -1.115157e-07 -1.035193e-07 5.483872e-07 -5.592276e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.01053965 0.69492902 0.30180730 0.09453195 1.64312679 0.71142068 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.093801 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.134832e-08 1.240937e-07 -1.115157e-07 -1.035193e-07 5.483872e-07 -5.592276e-08 + +$result$normp +[1] 5.852657e-07 + +$result$res + [1] -0.63615113 -0.87992879 -0.55171654 -0.03112238 0.61383560 1.88882743 -1.53550978 1.34772875 -1.93489237 -0.15183332 0.90905409 0.01516062 -0.18521777 0.70096559 0.05748510 -0.50211939 -0.43375776 -0.34245028 0.51987674 + +$result$prevres + [1] -0.63615170 -0.87992967 -0.55171770 -0.03112356 0.61383474 1.88882753 -1.53550851 1.34772848 -1.93489237 -0.15183313 0.90905434 0.01516075 -0.18521807 0.70096613 0.05748533 -0.50211945 -0.43375802 -0.34245059 0.51987660 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.000000000 0.00000000 + [2,] 106.6026217 0.000000 0 3.178221e+00 0.000000000 0.00000000 + [3,] 213.1470882 0.000000 0 1.217046e+01 0.000000000 0.00000000 + [4,] 366.5545667 0.000000 0 2.875588e+01 0.000000000 0.00000000 + [5,] 552.0538128 0.000000 0 5.221048e+01 0.000000000 0.00000000 + [6,] 832.0156217 0.000000 0 9.212804e+01 0.000000000 0.00000000 + [7,] 1078.3318604 0.000000 0 1.304141e+02 0.000000000 0.00000000 + [8,] -0.9102613 2.173913 0 -7.662702e-04 0.003712591 0.00000000 + [9,] -41.6375611 2.173913 0 -1.056349e+00 0.169822937 0.00000000 +[10,] -103.8544997 2.173913 0 -4.676235e+00 0.423580912 0.00000000 +[11,] -191.2535697 2.173913 0 -1.180661e+01 0.780046716 0.00000000 +[12,] -296.6887989 2.173913 0 -2.230652e+01 1.210074791 0.00000000 +[13,] -449.4808475 2.173913 0 -3.991303e+01 1.833252365 0.00000000 +[14,] 0.8812572 0.000000 5 7.418539e-04 0.000000000 0.00853896 +[15,] 40.3108436 0.000000 5 1.022690e+00 0.000000000 0.39059275 +[16,] 100.5453341 0.000000 5 4.527234e+00 0.000000000 0.97423610 +[17,] 185.1595658 0.000000 5 1.143041e+01 0.000000000 1.79410745 +[18,] 287.2352619 0.000000 5 2.159575e+01 0.000000000 2.78317202 +[19,] 435.1588244 0.000000 5 3.864126e+01 0.000000000 4.21648044 + +$result$retres +$result$retres$res + [1] -0.63615170 -0.87992967 -0.55171770 -0.03112356 0.61383474 1.88882753 -1.53550851 1.34772848 -1.93489237 -0.15183313 0.90905434 0.01516075 -0.18521807 0.70096613 0.05748533 -0.50211945 -0.43375802 -0.34245059 0.51987660 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02507697 14.826275 0.1503186 + [2,] 0.05346541 14.552179 0.2656934 + [3,] 0.10690165 14.036242 0.4828660 + [4,] 0.18384153 13.293374 0.7955609 + [5,] 0.27687669 12.395102 1.1736694 + [6,] 0.41728855 11.039400 1.7443236 + [7,] 0.54082583 9.846625 2.2463971 + [8,] 0.02616449 14.815774 0.1547384 + [9,] 0.07482290 14.345969 0.3524933 + [10,] 0.14915578 13.628271 0.6545930 + [11,] 0.25357469 12.620087 1.0789666 + [12,] 0.37954206 11.403849 1.5909164 + [13,] 0.56208838 9.641331 2.3328112 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0127230339 NA NA + [2,] 0.0175985934 NA NA + [3,] 0.0110343540 NA NA + [4,] 0.0006224713 NA NA + [5,] -0.0122766948 NA NA + [6,] -0.0377765505 NA NA + [7,] 0.0307101703 NA NA + [8,] NA -0.619955102 -0.14019323 + [9,] NA 0.890050490 -0.01149707 +[10,] NA 0.069843238 0.10042389 +[11,] NA -0.418164997 0.08675160 +[12,] NA -0.006973943 0.06849012 +[13,] NA 0.085200314 -0.10397532 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yehS_res/KEIO_ROBOT1_26_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yehS_res/KEIO_ROBOT1_26_res.txt new file mode 100644 index 0000000..9cc7af5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yehS_res/KEIO_ROBOT1_26_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0250769774298105 0.0250622808596032 0.0250463679620882 0.00334256880629186 0.0189294920049902 0.0314602731161393 +Glc 14.8262748453938 14.8351179869089 14.8376315397478 0.234777765964298 14.3965939569401 15.281309188195 +Ace 0.150318484654602 0.160266681213298 0.159274964926369 0.0800886280861579 1.00000000000009e-06 0.327118253230341 +mu 0.63680044761039 0.638293227055181 0.635629775820017 0.0309744605513344 0.588031359723817 0.701977350991447 +qGlc -6.14842515685091 -6.16514914626661 -6.18869103531404 0.545117981735207 -7.25510116706014 -5.09781303640839 +qAce 2.58805015194329 2.57023798699515 2.56987923011954 0.202445121512842 2.21063976856022 2.95751448424929 +res 15.5531965569055 31.9466985941318 30.2803635504945 7.56830925410255 20.6153232962106 47.045566859545 + + +Goodness of fit (khi2 test) + +khi2 value 15.5531965569132 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 1.19639973514717 +p-value, i.e. P(X^2<=value) 0.725899274684101 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeiR.txt b/validation/validation_results/Berges_2021/Berges_2021/yeiR.txt new file mode 100644 index 0000000..1024677 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeiR.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.114912 NA NA NA +3.34194444444444 0.175392 NA NA NA +3.9975 0.243432 NA NA NA +4.52333333333333 0.356832 NA NA NA +1.95 NA 13.7599492416692 0.390911056811081 0 +3.25 NA 12.9947819447841 0.930674832522745 0 +4.08333333333333 NA 12.0099231257721 1.45392780040442 0 +4.76666666666667 NA 10.6681172899903 1.92377678867137 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeiR_res/KEIO_ROBOT2_9.pdf b/validation/validation_results/Berges_2021/Berges_2021/yeiR_res/KEIO_ROBOT2_9.pdf new file mode 100644 index 0000000..da23937 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yeiR_res/KEIO_ROBOT2_9.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeiR_res/KEIO_ROBOT2_9_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yeiR_res/KEIO_ROBOT2_9_log.txt new file mode 100644 index 0000000..8285780 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeiR_res/KEIO_ROBOT2_9_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.114912 NA NA NA +[2,] 0.175392 NA NA NA +[3,] 0.243432 NA NA NA +[4,] 0.356832 NA NA NA +[5,] NA 13.75995 0.3909111 0 +[6,] NA 12.99478 0.9306748 0 +[7,] NA 12.00992 1.4539278 0 +[8,] NA 10.66812 1.9237768 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.539986e-02 1.431566e+01 2.114262e-01 1.000000e-06 5.790429e-01 -5.561001e+00 2.736922e+00 -2.106757e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 2.986181e-09 3.445287e-08 -5.648071e-08 -4.235165e-22 -2.893009e-08 1.013151e-07 6.241908e-08 -2.830365e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.007129292 0.432916218 0.190363559 0.180416812 0.067639670 1.045681179 0.458306795 0.441380340 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3977236 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 2.986181e-09 3.445287e-08 -5.648071e-08 -4.235165e-22 -2.893009e-08 1.013151e-07 6.241908e-08 -2.830365e-13 + +$result$normp +[1] 1.392259e-07 + +$result$res + [1] -3.400670e-01 2.502540e-02 6.834352e-01 -4.112029e-01 9.818710e-02 -8.007208e-02 -9.843947e-02 8.032444e-02 3.589451e-01 -2.551512e-01 -4.270662e-01 3.232723e-01 4.032904e-06 2.428180e-06 5.466319e-07 -1.839285e-06 + +$result$prevres + [1] -3.400673e-01 2.502522e-02 6.834352e-01 -4.112026e-01 9.818710e-02 -8.007204e-02 -9.843945e-02 8.032438e-02 3.589452e-01 -2.551511e-01 -4.270663e-01 3.232722e-01 4.032905e-06 2.428181e-06 5.466327e-07 -1.839284e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.128174e+02 0.000000 0 0 1.352134e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.462470e+02 0.000000 0 0 2.939115e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.061065e+02 0.000000 0 0 5.138800e+01 0.0000000 0.0000000 0.0000000 + [4,] 6.862399e+02 0.000000 0 0 7.884350e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.369670e+01 2.173913 0 0 -1.281590e+00 0.1995846 0.0000000 0.0000000 + [6,] -1.162036e+02 2.173913 0 0 -6.218708e+00 0.5307599 0.0000000 0.0000000 + [7,] -2.012185e+02 2.173913 0 0 -1.420846e+01 0.9190650 0.0000000 0.0000000 + [8,] -3.090224e+02 2.173913 0 0 -2.638655e+01 1.4114594 0.0000000 0.0000000 + [9,] 4.946362e+01 0.000000 5 0 1.450729e+00 0.0000000 0.4590445 0.0000000 +[10,] 1.315398e+02 0.000000 5 0 7.039430e+00 0.0000000 1.2207478 0.0000000 +[11,] 2.277745e+02 0.000000 5 0 1.608364e+01 0.0000000 2.1138495 0.0000000 +[12,] 3.498060e+02 0.000000 5 0 2.986895e+01 0.0000000 3.2463565 0.0000000 +[13,] -3.807483e-05 0.000000 0 5 -1.116705e-06 0.0000000 0.0000000 0.4590445 +[14,] -1.012533e-04 0.000000 0 5 -5.418630e-06 0.0000000 0.0000000 1.2207478 +[15,] -1.753304e-04 0.000000 0 5 -1.238045e-05 0.0000000 0.0000000 2.1138495 +[16,] -2.692646e-04 0.000000 0 5 -2.299175e-05 0.0000000 0.0000000 3.2463565 + +$result$retres +$result$retres$res + [1] -3.400673e-01 2.502522e-02 6.834352e-01 -4.112026e-01 9.818710e-02 -8.007204e-02 -9.843945e-02 8.032438e-02 3.589452e-01 -2.551511e-01 -4.270663e-01 3.232722e-01 4.032905e-06 2.428181e-06 5.466327e-07 -1.839284e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10811065 13.52133 0.6023696 6.990697e-07 + [2,] 0.17589250 12.87037 0.9227494 4.524561e-07 + [3,] 0.25710070 12.09046 1.3065906 1.569928e-07 + [4,] 0.34860795 11.21165 1.7391115 -1.759420e-07 + [5,] 0.07856116 13.80512 0.4627001 8.065809e-07 + [6,] 0.16677294 12.95795 0.8796446 4.856362e-07 + [7,] 0.27020179 11.96464 1.3685145 1.093265e-07 + [8,] 0.40135583 10.70507 1.9884312 -3.678569e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.0068013458 NA NA NA +[2,] -0.0005005043 NA NA NA +[3,] -0.0136687040 NA NA NA +[4,] 0.0082240527 NA NA NA +[5,] NA -0.04516607 -0.07178905 -8.065809e-07 +[6,] NA 0.03683314 0.05103023 -4.856362e-07 +[7,] NA 0.04528214 0.08541326 -1.093265e-07 +[8,] NA -0.03694922 -0.06465444 3.678569e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yeiR_res/KEIO_ROBOT2_9_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yeiR_res/KEIO_ROBOT2_9_res.txt new file mode 100644 index 0000000..45734ec --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yeiR_res/KEIO_ROBOT2_9_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0253998641352519 0.0259307662410229 0.0256889527218927 0.00523911069412674 0.0177129568667443 0.0371292593336334 +Glc 14.3156647410535 14.4242504858694 14.3756010827122 0.389416164318847 13.7583031166499 15.3256540488458 +Ace 0.211426223188872 0.217457657827903 0.204125964904124 0.14316121150767 9.99999999990418e-07 0.537530073619913 +Lac 1e-06 0.0863322511054338 0.0707536186872995 0.0768911316653726 9.99999999989418e-07 0.244673649320963 +mu 0.579042909151731 0.578493897618866 0.577592377836727 0.0454912023854683 0.492448120029332 0.66004915535739 +qGlc -5.56100062444278 -5.80629837331929 -5.763067426896 0.891178138301432 -7.6728396943696 -3.97341589413654 +qAce 2.73692211106106 2.70528320059065 2.76204991543931 0.389344795375838 1.95317598592001 3.30477963097899 +qLac -2.10675731006388e-06 -0.00996914073333711 -0.00590625172986522 0.210061008767572 -0.412916851579423 0.432131019063129 +res 1.26547218765627 19.3667128199918 18.7445971901559 5.86562984986204 8.90854609791625 31.2177724720842 + + +Goodness of fit (khi2 test) + +khi2 value 1.26547218765646 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.158184023457058 +p-value, i.e. P(X^2<=value) 0.00404806643874257 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yejF.txt b/validation/validation_results/Berges_2021/Berges_2021/yejF.txt new file mode 100644 index 0000000..0f9d10b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yejF.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.1992000000000005E-2 NA NA +2.2613888888888889 8.0135999999999999E-2 NA NA +2.7741666666666664 0.11037599999999999 NA NA +3.2088888888888891 0.13608000000000001 NA NA +3.7063888888888892 0.19656000000000001 NA NA +4.2258333333333331 0.24343200000000001 NA NA +4.6355555555555554 0.32659199999999999 NA NA +4.9675000000000002 0.43545599999999995 NA NA +2.8 NA 12.3825925964304 0.651208677922795 +3.73333333333333 NA 11.622902984891 1.12319506596587 +4.28333333333333 NA 10.8718626736131 1.49036452152206 +4.75 NA 9.91093510241133 1.85685202643494 +5.11666666666667 NA 9.23872147364089 2.24851975069804 +5.43333333333333 NA 9.03199736201217 2.52794838236177 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yejF_res/KEIO_ROBOT5_16.pdf b/validation/validation_results/Berges_2021/Berges_2021/yejF_res/KEIO_ROBOT5_16.pdf new file mode 100644 index 0000000..0fe21e5 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yejF_res/KEIO_ROBOT5_16.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yejF_res/KEIO_ROBOT5_16_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yejF_res/KEIO_ROBOT5_16_log.txt new file mode 100644 index 0000000..22c7790 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yejF_res/KEIO_ROBOT5_16_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.061992 NA NA + [2,] 0.080136 NA NA + [3,] 0.110376 NA NA + [4,] 0.136080 NA NA + [5,] 0.196560 NA NA + [6,] 0.243432 NA NA + [7,] 0.326592 NA NA + [8,] 0.435456 NA NA + [9,] NA 12.382593 0.6512087 +[10,] NA 11.622903 1.1231951 +[11,] NA 10.871863 1.4903645 +[12,] NA 9.910935 1.8568520 +[13,] NA 9.238721 2.2485198 +[14,] NA 9.031997 2.5279484 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01860322 12.92058838 0.37398177 0.62636020 -4.91554398 2.60116138 + +$result$lastp + X Glc Ace mu qGlc qAce +-5.315533e-09 -3.590840e-07 1.575293e-07 6.543482e-08 4.374896e-07 -1.652627e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.004612106 0.523611865 0.231444303 0.054962255 0.938240780 0.411520695 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5612529 + +$result$laststep + X Glc Ace mu qGlc qAce +-5.315533e-09 -3.590840e-07 1.575293e-07 6.543482e-08 4.374896e-07 -1.652627e-07 + +$result$normp +[1] 6.138206e-07 + +$result$res + [1] -0.1750349 -0.1722711 -0.2319099 0.1375346 -0.3484478 0.9531060 0.6350217 -0.8874723 -0.3464228 -0.1511197 0.1286443 0.6414620 0.4972737 -0.7698375 0.4589518 -0.1286550 -0.3178586 -0.2319696 -0.2362392 0.4557706 + +$result$prevres + [1] -0.1750344 -0.1722706 -0.2319094 0.1375352 -0.3484474 0.9531061 0.6350214 -0.8874731 -0.3464224 -0.1511196 0.1286443 0.6414619 0.4972735 -0.7698377 0.4589515 -0.1286551 -0.3178586 -0.2319695 -0.2362391 0.4557708 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 157.20742 0.000000 0 5.348706 0.0000000 0.0000000 + [2,] 206.12172 0.000000 0 8.671362 0.0000000 0.0000000 + [3,] 284.19210 0.000000 0 14.666716 0.0000000 0.0000000 + [4,] 373.13604 0.000000 0 22.274615 0.0000000 0.0000000 + [5,] 509.56491 0.000000 0 35.134908 0.0000000 0.0000000 + [6,] 705.50690 0.000000 0 55.462821 0.0000000 0.0000000 + [7,] 911.91813 0.000000 0 78.640445 0.0000000 0.0000000 + [8,] 1122.67216 0.000000 0 103.747861 0.0000000 0.0000000 + [9,] -81.49012 2.173913 0 -2.713103 0.3084052 0.0000000 +[10,] -159.76665 2.173913 0 -7.535849 0.6046483 0.0000000 +[11,] -232.49233 2.173913 0 -12.980173 0.8798838 0.0000000 +[12,] -317.21716 2.173913 0 -20.117033 1.2005310 0.0000000 +[13,] -403.52059 2.173913 0 -28.048867 1.5271525 0.0000000 +[14,] -495.79013 2.173913 0 -37.112443 1.8763531 0.0000000 +[15,] 99.18100 0.000000 5 3.302097 0.0000000 0.7093319 +[16,] 194.45077 0.000000 5 9.171824 0.0000000 1.3906911 +[17,] 282.96464 0.000000 5 15.798070 0.0000000 2.0237328 +[18,] 386.08258 0.000000 5 24.484287 0.0000000 2.7612213 +[19,] 491.12183 0.000000 5 34.138061 0.0000000 3.5124507 +[20,] 603.42238 0.000000 5 45.169271 0.0000000 4.3156122 + +$result$retres +$result$retres$res + [1] -0.1750344 -0.1722706 -0.2319094 0.1375352 -0.3484474 0.9531061 0.6350214 -0.8874731 -0.3464224 -0.1511196 0.1286443 0.6414619 0.4972735 -0.7698377 0.4589515 -0.1286551 -0.3178586 -0.2319695 -0.2362391 0.4557708 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05849131 12.607555 0.5396297 + [2,] 0.07669059 12.464731 0.6152080 + [3,] 0.10573781 12.236775 0.7358359 + [4,] 0.13883070 11.977068 0.8732648 + [5,] 0.18959105 11.578712 1.0840634 + [6,] 0.26249412 11.006584 1.3868168 + [7,] 0.33929243 10.403886 1.7057465 + [8,] 0.41770654 9.788509 2.0313862 + [9,] 0.10746267 12.223238 0.7429990 + [10,] 0.19281792 11.553388 1.0974640 + [11,] 0.27212034 10.931039 1.4267928 + [12,] 0.36450701 10.206008 1.8104581 + [13,] 0.45861505 9.467467 2.2012719 + [14,] 0.55922872 8.677872 2.6191025 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.003500687 NA NA + [2,] 0.003445411 NA NA + [3,] 0.004638188 NA NA + [4,] -0.002750703 NA NA + [5,] 0.006968948 NA NA + [6,] -0.019062122 NA NA + [7,] -0.012700428 NA NA + [8,] 0.017749462 NA NA + [9,] NA 0.15935431 -0.09179029 +[10,] NA 0.06951500 0.02573102 +[11,] NA -0.05917636 0.06357171 +[12,] NA -0.29507249 0.04639390 +[13,] NA -0.22874581 0.04724781 +[14,] NA 0.35412535 -0.09115415 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yejF_res/KEIO_ROBOT5_16_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yejF_res/KEIO_ROBOT5_16_res.txt new file mode 100644 index 0000000..adb03ac --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yejF_res/KEIO_ROBOT5_16_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0186032233493763 0.019227416557623 0.0187627339294858 0.00283208092051872 0.0145038557127292 0.0259833202243335 +Glc 12.9205883836268 12.9450363503314 12.940783877506 0.238382209581158 12.5543174381664 13.4389073000362 +Ace 0.37398177185785 0.350759574412019 0.352484348633893 0.0926376788895518 0.197963624064373 0.519564880619453 +mu 0.626360200924325 0.621882796269109 0.624219415313839 0.0298661132782315 0.562160387244527 0.680084693974785 +qGlc -4.91554397579415 -4.9311187920984 -4.89763922951827 0.516205216111001 -5.98044550748481 -4.05666408272866 +qAce 2.60116137791334 2.6179161777885 2.62699551983008 0.208334948967277 2.21883279097018 3.00169877902368 +res 4.41006737216672 35.7482026699066 35.4120784813323 8.52352010976518 20.7604134635421 54.0290038026377 + + +Goodness of fit (khi2 test) + +khi2 value 4.41006737216938 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.315004812297813 +p-value, i.e. P(X^2<=value) 0.00754955776127364 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfaT.txt b/validation/validation_results/Berges_2021/Berges_2021/yfaT.txt new file mode 100644 index 0000000..6218030 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfaT.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.18888888888889 0.066528 NA NA +2.27694444444444 0.114912 NA NA +3.12833333333333 0.175392 NA NA +3.77138888888889 0.243432 NA NA +4.41555555555556 0.356832 NA NA +4.82277777777778 0.43092 NA NA +0.0666666666666667 NA 15.9807681836697 0.0155104630204021 +1.71666666666667 NA 15.235089937916 0.351452145442628 +2.8 NA 13.4668089342453 0.689175502001487 +3.63333333333333 NA 12.8628100213301 1.10461357708151 +4.26666666666667 NA 11.7588071670754 1.57621860060176 +4.88333333333333 NA 10.0644136198538 2.03946322885838 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfaT_res/KEIO_ROBOT1_9.pdf b/validation/validation_results/Berges_2021/Berges_2021/yfaT_res/KEIO_ROBOT1_9.pdf new file mode 100644 index 0000000..ed39dce Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yfaT_res/KEIO_ROBOT1_9.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfaT_res/KEIO_ROBOT1_9_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yfaT_res/KEIO_ROBOT1_9_log.txt new file mode 100644 index 0000000..792ab80 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfaT_res/KEIO_ROBOT1_9_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.066528 NA NA + [3,] 0.114912 NA NA + [4,] 0.175392 NA NA + [5,] 0.243432 NA NA + [6,] 0.356832 NA NA + [7,] 0.430920 NA NA + [8,] NA 15.98077 0.01551046 + [9,] NA 15.23509 0.35145215 +[10,] NA 13.46681 0.68917550 +[11,] NA 12.86281 1.10461358 +[12,] NA 11.75881 1.57621860 +[13,] NA 10.06441 2.03946323 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03652103 15.74297923 0.08039951 0.51119068 -7.27691564 2.55310514 + +$result$lastp + X Glc Ace mu qGlc qAce + 3.304135e-09 2.884296e-07 -8.011500e-08 -2.470669e-08 -6.686526e-07 1.736161e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.006747915 0.339136403 0.146232157 0.042451141 0.834319061 0.350839652 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5041791 + +$result$laststep + X Glc Ace mu qGlc qAce + 3.304135e-09 2.884296e-07 -8.011500e-08 -2.470669e-08 -6.686526e-07 1.736161e-07 + +$result$normp +[1] 7.533062e-07 + +$result$res + [1] 0.08725148 0.02676575 0.10245287 0.26743227 0.38259460 -0.39147452 -0.05756151 -0.55611233 -0.48378692 1.34937384 0.15079699 -0.21734122 -0.24293036 0.35606158 -0.07390446 -0.13979299 -0.19022126 -0.31447903 0.36233616 + +$result$prevres + [1] 0.08725132 0.02676554 0.10245267 0.26743215 0.38259463 -0.39147419 -0.05756089 -0.55611294 -0.48378730 1.34937372 0.15079712 -0.21734086 -0.24292974 0.35606198 -0.07390424 -0.13979293 -0.19022135 -0.31447925 0.36233579 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 91.8146581 0.000000 0 3.986541259 0.000000000 0.00000000 + [3,] 160.1283770 0.000000 0 13.315691037 0.000000000 0.00000000 + [4,] 247.4473765 0.000000 0 28.270848904 0.000000000 0.00000000 + [5,] 343.7525146 0.000000 0 47.346750149 0.000000000 0.00000000 + [6,] 477.8103894 0.000000 0 77.051999960 0.000000000 0.00000000 + [7,] 588.3854117 0.000000 0 103.633966612 0.000000000 0.00000000 + [8,] -1.0728017 2.173913 0 -0.001313412 0.005384125 0.00000000 + [9,] -43.4788941 2.173913 0 -1.559770061 0.218209756 0.00000000 +[10,] -98.5410960 2.173913 0 -6.201142118 0.494553252 0.00000000 +[11,] -167.3129233 2.173913 0 -14.354256013 0.839701948 0.00000000 +[12,] -243.1088266 2.173913 0 -25.335642448 1.220102735 0.00000000 +[13,] -344.6682155 2.173913 0 -42.364546123 1.729804048 0.00000000 +[14,] 0.8657025 0.000000 5 0.001059864 0.000000000 0.01238349 +[15,] 35.0855020 0.000000 5 1.258663927 0.000000000 0.50188244 +[16,] 79.5182098 0.000000 5 5.004041356 0.000000000 1.13747248 +[17,] 135.0139654 0.000000 5 11.583235694 0.000000000 1.93131448 +[18,] 196.1778329 0.000000 5 20.444718114 0.000000000 2.80623629 +[19,] 278.1316686 0.000000 5 34.186273560 0.000000000 3.97854931 + +$result$retres +$result$retres$res + [1] 0.08725132 0.02676554 0.10245267 0.26743215 0.38259463 -0.39147419 -0.05756089 -0.55611294 -0.48378730 1.34937372 0.15079712 -0.21734086 -0.24292974 0.35606198 -0.07390424 -0.13979293 -0.19022135 -0.31447925 0.36233579 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03652103 15.742979 0.08039959 + [2,] 0.06706331 15.308203 0.23294082 + [3,] 0.11696105 14.597897 0.48215148 + [4,] 0.18074064 13.689980 0.80069402 + [5,] 0.25108389 12.688628 1.15201828 + [6,] 0.34900252 11.294735 1.64106575 + [7,] 0.42976878 10.145008 2.04444702 + [8,] 0.03778709 15.724956 0.08672286 + [9,] 0.08783255 15.012548 0.33667130 + [10,] 0.15281410 14.087521 0.66121692 + [11,] 0.23397503 12.932177 1.06656931 + [12,] 0.32342541 11.658830 1.51332275 + [13,] 0.44328051 9.952666 2.11193039 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0017450263 NA NA + [2,] -0.0005353109 NA NA + [3,] -0.0020490534 NA NA + [4,] -0.0053486430 NA NA + [5,] -0.0076518927 NA NA + [6,] 0.0078294838 NA NA + [7,] 0.0011512178 NA NA + [8,] NA 0.25581195 -0.07121240 + [9,] NA 0.22254216 0.01478085 +[10,] NA -0.62071191 0.02795859 +[11,] NA -0.06936668 0.03804427 +[12,] NA 0.09997679 0.06289585 +[13,] NA 0.11174768 -0.07246716 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfaT_res/KEIO_ROBOT1_9_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yfaT_res/KEIO_ROBOT1_9_res.txt new file mode 100644 index 0000000..31b70cf --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfaT_res/KEIO_ROBOT1_9_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.036521029624787 0.0371860676799604 0.0369366195505405 0.00432521410470838 0.0291536202549547 0.0462511412413223 +Glc 15.742979234891 15.7361115096094 15.7238585085504 0.19702954539677 15.4137574515638 16.1752577034418 +Ace 0.0803995096434231 0.0906498070476535 0.0775244576186213 0.0721237315248692 9.99999999997531e-07 0.268693899158366 +mu 0.511190683943795 0.508633933088738 0.5125990525686 0.0259699596645693 0.456398344812492 0.558556120417426 +qGlc -7.27691563696831 -7.21752374214203 -7.13276601915036 0.536247956424873 -8.22304963736695 -6.380756036445 +qAce 2.55310513623904 2.52915838511419 2.53187205707962 0.202593119057912 2.18421285103263 2.94771686101428 +res 3.30455512959934 30.6692063789287 29.0949976299977 8.25111589592318 19.0319908603101 47.7613742766238 + + +Goodness of fit (khi2 test) + +khi2 value 3.3045551296015 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.254196548430884 +p-value, i.e. P(X^2<=value) 0.00340642471396051 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfcD.txt b/validation/validation_results/Berges_2021/Berges_2021/yfcD.txt new file mode 100644 index 0000000..6427e3d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfcD.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.18888888888889 0.063504 NA NA +2.27694444444444 0.1134 NA NA +3.12833333333333 0.178416 NA NA +3.77138888888889 0.240408 NA NA +4.41555555555556 0.403704 NA NA +4.82277777777778 0.563976 NA NA +0.0666666666666667 NA 14.8194318046645 0.0163890457989502 +1.71666666666667 NA 15.0742718760501 0.345402674152249 +2.8 NA 13.4274836570535 0.720777156174933 +3.63333333333333 NA 12.5366612786145 1.14134785357372 +4.26666666666667 NA 11.7061401982306 1.61033105724427 +4.88333333333333 NA 10.0475074457405 2.07756675525876 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfcD_res/KEIO_ROBOT1_6.pdf b/validation/validation_results/Berges_2021/Berges_2021/yfcD_res/KEIO_ROBOT1_6.pdf new file mode 100644 index 0000000..2cef294 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yfcD_res/KEIO_ROBOT1_6.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfcD_res/KEIO_ROBOT1_6_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yfcD_res/KEIO_ROBOT1_6_log.txt new file mode 100644 index 0000000..ce8455f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfcD_res/KEIO_ROBOT1_6_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.063504 NA NA + [3,] 0.113400 NA NA + [4,] 0.178416 NA NA + [5,] 0.240408 NA NA + [6,] 0.403704 NA NA + [7,] 0.563976 NA NA + [8,] NA 14.81943 0.01638905 + [9,] NA 15.07427 0.34540267 +[10,] NA 13.42748 0.72077716 +[11,] NA 12.53666 1.14134785 +[12,] NA 11.70614 1.61033106 +[13,] NA 10.04751 2.07756676 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0227261 14.9175719 0.1777326 0.6581540 -6.0601471 2.4688172 + +$result$lastp + X Glc Ace mu qGlc qAce +-4.929269e-09 -1.037143e-07 6.133622e-08 4.987808e-08 -1.006155e-07 -1.736169e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008035019 0.557155185 0.241731335 0.079290278 1.353877984 0.584012177 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.8845172 + +$result$laststep + X Glc Ace mu qGlc qAce +-4.929269e-09 -1.037143e-07 6.133622e-08 4.987808e-08 -1.006155e-07 -1.736169e-08 + +$result$normp +[1] 1.65698e-07 + +$result$res + [1] -0.75369486 -0.69024674 -0.58465972 -0.01496274 1.57778744 0.59285462 -1.03426424 0.19294371 -1.29374337 0.82176810 0.65975065 -0.10552629 -0.27519280 0.82583641 0.05468385 -0.45000574 -0.58650956 -0.52265899 0.67865403 + +$result$prevres + [1] -0.7536946 -0.6902463 -0.5846592 -0.0149622 1.5777878 0.5928546 -1.0342649 0.1929439 -1.2937433 0.8217681 0.6597505 -0.1055264 -0.2751928 0.8258361 0.0546837 -0.4500057 -0.5865094 -0.5226588 0.6786542 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000e+00 0.000000000 0.000000000 + [2,] 109.3435654 0.000000 0 2.954334e+00 0.000000000 0.000000000 + [3,] 223.7664654 0.000000 0 1.157904e+01 0.000000000 0.000000000 + [4,] 391.8769500 0.000000 0 2.786043e+01 0.000000000 0.000000000 + [5,] 598.3509348 0.000000 0 5.128405e+01 0.000000000 0.000000000 + [6,] 914.2812646 0.000000 0 9.174665e+01 0.000000000 0.000000000 + [7,] 1195.3008141 0.000000 0 1.310085e+02 0.000000000 0.000000000 + [8,] -0.8978353 2.173913 0 -6.851170e-04 0.003366965 0.000000000 + [9,] -41.9381694 2.173913 0 -9.689360e-01 0.157271986 0.000000000 +[10,] -106.3778465 2.173913 0 -4.369657e+00 0.398926692 0.000000000 +[11,] -198.7204480 2.173913 0 -1.119965e+01 0.745219928 0.000000000 +[12,] -311.8395789 2.173913 0 -2.141053e+01 1.169427056 0.000000000 +[13,] -477.9652444 2.173913 0 -3.876147e+01 1.792413556 0.000000000 +[14,] 0.8412601 0.000000 5 6.419458e-04 0.000000000 0.007744019 +[15,] 39.2955234 0.000000 5 9.078806e-01 0.000000000 0.361725569 +[16,] 99.6746690 0.000000 5 4.094312e+00 0.000000000 0.917531393 +[17,] 186.1984947 0.000000 5 1.049393e+01 0.000000000 1.714005834 +[18,] 292.1896602 0.000000 5 2.006139e+01 0.000000000 2.689682228 +[19,] 447.8472643 0.000000 5 3.631899e+01 0.000000000 4.122551178 + +$result$retres +$result$retres$res + [1] -0.7536946 -0.6902463 -0.5846592 -0.0149622 1.5777878 0.5928546 -1.0342649 0.1929439 -1.2937433 0.8217681 0.6597505 -0.1055264 -0.2751928 0.8258361 0.0546837 -0.4500057 -0.5865094 -0.5226588 0.6786542 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02272611 14.917572 0.1777326 + [2,] 0.04969907 14.669210 0.2789115 + [3,] 0.10170682 14.190334 0.4739990 + [4,] 0.17811676 13.486767 0.7606222 + [5,] 0.27196376 12.622643 1.1126539 + [6,] 0.41556109 11.300428 1.6513054 + [7,] 0.54329070 10.124319 2.1304350 + [8,] 0.02374546 14.908186 0.1815563 + [9,] 0.07034033 14.479150 0.3563394 + [10,] 0.14350149 13.805497 0.6307760 + [11,] 0.24834204 12.840147 1.0240460 + [12,] 0.37677109 11.657598 1.5057993 + [13,] 0.56538076 9.920919 2.2132976 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.015073892 NA NA + [2,] 0.013804927 NA NA + [3,] 0.011693184 NA NA + [4,] 0.000299244 NA NA + [5,] -0.031555757 NA NA + [6,] -0.011857091 NA NA + [7,] 0.020685298 NA NA + [8,] NA -0.08875421 -0.16516722 + [9,] NA 0.59512191 -0.01093674 +[10,] NA -0.37801331 0.09000115 +[11,] NA -0.30348525 0.11730189 +[12,] NA 0.04854215 0.10453176 +[13,] NA 0.12658870 -0.13573084 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfcD_res/KEIO_ROBOT1_6_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yfcD_res/KEIO_ROBOT1_6_res.txt new file mode 100644 index 0000000..4b000b7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfcD_res/KEIO_ROBOT1_6_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0227261028416437 0.0231184759170629 0.0230838661778941 0.00324580739576116 0.0173432936137286 0.0298352984345253 +Glc 14.9175718864592 14.933146793761 14.9208130415893 0.173985273686625 14.611340220504 15.2708079083259 +Ace 0.17773261530004 0.176932622779295 0.183663514477747 0.0825210311817044 0.0104959831060294 0.325393884430934 +mu 0.658153981234686 0.657496799485487 0.656331174923459 0.031255560981066 0.599692749732158 0.717974639135386 +qGlc -6.06014711296003 -6.07706542549924 -6.02149275649725 0.503214102655667 -7.00328564919216 -5.20246108828023 +qAce 2.4688171671622 2.45164480255266 2.44148628506528 0.179419549034042 2.16781832807402 2.79536836727742 +res 10.170817902834 31.6541774567999 31.3999045974079 7.09450370141403 18.6143620079279 48.5283273366477 + + +Goodness of fit (khi2 test) + +khi2 value 10.1708179028358 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.782370607910445 +p-value, i.e. P(X^2<=value) 0.320090122344808 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfcL.txt b/validation/validation_results/Berges_2021/Berges_2021/yfcL.txt new file mode 100644 index 0000000..b1605cc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfcL.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.18888888888889 0.072576 NA NA +2.27694444444444 0.1134 NA NA +3.12833333333333 0.15876 NA NA +3.77138888888889 0.21924 NA NA +4.41555555555556 0.343224 NA NA +4.82277777777778 0.406728 NA NA +0.0666666666666667 NA 15.5410543619979 0.016953009173844 +1.71666666666667 NA 15.5702251042236 0.337751874695501 +2.8 NA 13.7170489770929 0.725391316327317 +3.63333333333333 NA 12.4153896539183 1.13407896403018 +4.26666666666667 NA 11.7393813289846 1.64057309310509 +4.88333333333333 NA 10.25083039065 2.15744259824785 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfcL_res/KEIO_ROBOT1_8.pdf b/validation/validation_results/Berges_2021/Berges_2021/yfcL_res/KEIO_ROBOT1_8.pdf new file mode 100644 index 0000000..f82c246 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yfcL_res/KEIO_ROBOT1_8.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfcL_res/KEIO_ROBOT1_8_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yfcL_res/KEIO_ROBOT1_8_log.txt new file mode 100644 index 0000000..14f2d59 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfcL_res/KEIO_ROBOT1_8_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.072576 NA NA + [3,] 0.113400 NA NA + [4,] 0.158760 NA NA + [5,] 0.219240 NA NA + [6,] 0.343224 NA NA + [7,] 0.406728 NA NA + [8,] NA 15.54105 0.01695301 + [9,] NA 15.57023 0.33775187 +[10,] NA 13.71705 0.72539132 +[11,] NA 12.41539 1.13407896 +[12,] NA 11.73938 1.64057309 +[13,] NA 10.25083 2.15744260 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03462683 15.64415659 0.06671144 0.50994351 -7.46739035 2.86421883 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.273712e-08 4.849937e-07 -1.461330e-07 -9.135212e-08 -6.051938e-07 1.099824e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.00909203 0.45895957 0.19846189 0.06032967 1.19936004 0.51023513 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6813212 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.273712e-08 4.849937e-07 -1.461330e-07 -9.135212e-08 -6.051938e-07 1.099824e-07 + +$result$normp +[1] 8.021451e-07 + +$result$res + [1] -0.007458422 -0.454259941 -0.140985297 0.596953125 0.885203767 -0.707004650 -0.084658090 0.186016797 -1.382332291 0.695399185 1.091283751 -0.119111304 -0.471256139 0.282420159 0.006073251 -0.211036578 -0.107377249 -0.275581189 0.305501607 + +$result$prevres + [1] -0.007459059 -0.454260764 -0.140986181 0.596952425 0.885203491 -0.707004066 -0.084656617 0.186015760 -1.382332791 0.695399149 1.091284086 -0.119110737 -0.471255466 0.282420876 0.006073551 -0.211036615 -0.107377521 -0.275581565 0.305501273 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 91.6786278 0.000000 0 3.774174425 0.000000000 0.00000000 + [3,] 159.6743220 0.000000 0 12.589257299 0.000000000 0.00000000 + [4,] 246.4838733 0.000000 0 26.700176170 0.000000000 0.00000000 + [5,] 342.1395292 0.000000 0 44.680411610 0.000000000 0.00000000 + [6,] 475.1864737 0.000000 0 72.654416270 0.000000000 0.00000000 + [7,] 584.8571734 0.000000 0 97.669657950 0.000000000 0.00000000 + [8,] -1.1008365 2.173913 0 -0.001277815 0.005104657 0.00000000 + [9,] -44.5623483 2.173913 0 -1.515267822 0.206638787 0.00000000 +[10,] -100.9034123 2.173913 0 -6.017883409 0.467896319 0.00000000 +[11,] -171.1902398 2.173913 0 -13.918244464 0.793821352 0.00000000 +[12,] -248.5862649 2.173913 0 -24.549760024 1.152712240 0.00000000 +[13,] -352.2089814 2.173913 0 -41.023320860 1.633218167 0.00000000 +[14,] 0.9711538 0.000000 5 0.001127283 0.000000000 0.01174071 +[15,] 39.3127355 0.000000 5 1.336763555 0.000000000 0.47526921 +[16,] 89.0166096 0.000000 5 5.308954038 0.000000000 1.07616153 +[17,] 151.0233837 0.000000 5 12.278622751 0.000000000 1.82578911 +[18,] 219.3018650 0.000000 5 21.657705665 0.000000000 2.65123815 +[19,] 310.7174345 0.000000 5 36.190618880 0.000000000 3.75640178 + +$result$retres +$result$retres$res + [1] -0.007459059 -0.454260764 -0.140986181 0.596952425 0.885203491 -0.707004066 -0.084656617 0.186015760 -1.382332791 0.695399149 1.091284086 -0.119110737 -0.471255466 0.282420876 0.006073551 -0.211036615 -0.107377521 -0.275581565 0.305501273 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03462682 15.64416 0.06671159 + [2,] 0.06349078 15.22148 0.22883288 + [3,] 0.11058028 14.53193 0.49332213 + [4,] 0.17069905 13.65157 0.83099342 + [5,] 0.23694407 12.68151 1.20307423 + [6,] 0.32908392 11.33226 1.72059947 + [7,] 0.40503487 10.22006 2.14719592 + [8,] 0.03582424 15.62662 0.07343718 + [9,] 0.08309892 14.93435 0.33896658 + [10,] 0.14438316 14.03693 0.68318399 + [11,] 0.22083671 12.91738 1.11260346 + [12,] 0.30502320 11.68459 1.58545678 + [13,] 0.41773743 10.03405 2.21854285 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0001491812 NA NA + [2,] 0.0090852153 NA NA + [3,] 0.0028197236 NA NA + [4,] -0.0119390485 NA NA + [5,] -0.0177040698 NA NA + [6,] 0.0141400813 NA NA + [7,] 0.0016931323 NA NA + [8,] NA -0.08556725 -0.05648418 + [9,] NA 0.63587308 -0.00121471 +[10,] NA -0.31988361 0.04220732 +[11,] NA -0.50199068 0.02147550 +[12,] NA 0.05479094 0.05511631 +[13,] NA 0.21677751 -0.06110025 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfcL_res/KEIO_ROBOT1_8_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yfcL_res/KEIO_ROBOT1_8_res.txt new file mode 100644 index 0000000..cd0584f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfcL_res/KEIO_ROBOT1_8_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0346268315619983 0.0348051794997108 0.0345363857330585 0.00461178907532031 0.0269894534650066 0.043048707342186 +Glc 15.6441565914363 15.6655027506045 15.6639137691516 0.227912200114991 15.2357778262245 16.0366652994604 +Ace 0.0667114446933437 0.0905618865658445 0.083928222470899 0.0782246889478739 9.9999999999662e-07 0.253090476540251 +mu 0.509943509069324 0.510926333141286 0.51168915561634 0.0302559897007221 0.461573230301906 0.568182398666806 +qGlc -7.46739034950585 -7.53539349531699 -7.44980913138226 0.596175144128347 -8.92546060815005 -6.60470366598995 +qAce 2.86421883061105 2.84205361122283 2.85582936280567 0.211604020889277 2.36575763963403 3.26068655120219 +res 6.0345813655402 31.4457119236482 30.3038984777025 8.04355480641811 19.178332993456 52.0660592569599 + + +Goodness of fit (khi2 test) + +khi2 value 6.03458136554854 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.464198566580657 +p-value, i.e. P(X^2<=value) 0.0551146794859632 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfdI.txt b/validation/validation_results/Berges_2021/Berges_2021/yfdI.txt new file mode 100644 index 0000000..adbc561 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfdI.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.195 0.066528 NA NA +1.61361111111111 0.077112 NA NA +2.36138888888889 0.116424 NA NA +3.28638888888889 0.195048 NA NA +3.81944444444444 0.291816 NA NA +4.41083333333333 0.361368 NA NA +0.283333333333333 NA 14.3172814086383 0.0463144984740883 +1.91666666666667 NA 13.8078715181341 0.411548054997461 +2.7 NA 13.6931600885217 0.696410362701486 +3.61666666666667 NA 12.3455263191061 1.12253765593359 +4.05 NA 11.9464626878832 1.43110893749102 +4.75 NA 10.6670537834667 1.90572860835267 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfdI_res/KEIO_ROBOT4_2.pdf b/validation/validation_results/Berges_2021/Berges_2021/yfdI_res/KEIO_ROBOT4_2.pdf new file mode 100644 index 0000000..9c03aba Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yfdI_res/KEIO_ROBOT4_2.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfdI_res/KEIO_ROBOT4_2_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yfdI_res/KEIO_ROBOT4_2_log.txt new file mode 100644 index 0000000..4713167 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfdI_res/KEIO_ROBOT4_2_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.066528 NA NA + [3,] 0.077112 NA NA + [4,] 0.116424 NA NA + [5,] 0.195048 NA NA + [6,] 0.291816 NA NA + [7,] 0.361368 NA NA + [8,] NA 14.31728 0.0463145 + [9,] NA 13.80787 0.4115481 +[10,] NA 13.69316 0.6964104 +[11,] NA 12.34553 1.1225377 +[12,] NA 11.94646 1.4311089 +[13,] NA 10.66705 1.9057286 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03520933 14.45075027 0.11742670 0.53300056 -4.96521533 2.45535616 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.383357e-11 -2.670487e-09 -6.742028e-09 2.421069e-11 4.969990e-09 2.173606e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006775596 0.335028760 0.146349197 0.049050416 0.820298687 0.360695849 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4913063 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.383357e-11 -2.670487e-09 -6.742028e-09 2.421069e-11 4.969990e-09 2.173606e-08 + +$result$normp +[1] 2.344664e-08 + +$result$res + [1] -0.129533476 0.002075924 0.304896745 0.376637583 0.395085857 -1.108942568 0.409131843 0.173913555 0.130078535 -0.646828302 0.388508997 -0.017352917 -0.028319867 0.487765257 -0.029000319 -0.286045673 -0.262148347 -0.356679150 0.446108232 + +$result$prevres + [1] -0.129533474 0.002075926 0.304896747 0.376637587 0.395085863 -1.108942560 0.409131854 0.173913560 0.130078539 -0.646828300 0.388508996 -0.017352920 -0.028319875 0.487765290 -0.029000297 -0.286045660 -0.262148353 -0.356679168 0.446108188 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 94.533917 0.000000 0 3.97752873 0.00000000 0.00000000 + [3,] 118.164608 0.000000 0 6.71342378 0.00000000 0.00000000 + [4,] 176.028271 0.000000 0 14.63550481 0.00000000 0.00000000 + [5,] 288.204454 0.000000 0 33.34858479 0.00000000 0.00000000 + [6,] 382.905816 0.000000 0 51.49320550 0.00000000 0.00000000 + [7,] 524.790775 0.000000 0 81.50131342 0.00000000 0.00000000 + [8,] -3.301288 2.173913 0 -0.01688109 0.02341009 0.00000000 + [9,] -35.998525 2.173913 0 -1.41797695 0.25527271 0.00000000 +[10,] -65.146467 2.173913 0 -3.81486206 0.46196657 0.00000000 +[11,] -118.947584 2.173913 0 -9.86811723 0.84348100 0.00000000 +[12,] -155.113894 2.173913 0 -14.76006276 1.09994351 0.00000000 +[13,] -234.419312 2.173913 0 -27.10677308 1.66231401 0.00000000 +[14,] 3.754807 0.000000 5 0.01920015 0.00000000 0.05384321 +[15,] 40.943876 0.000000 5 1.61277363 0.00000000 0.58712723 +[16,] 74.096059 0.000000 5 4.33893436 0.00000000 1.06252310 +[17,] 135.288184 0.000000 5 11.22376440 0.00000000 1.94000631 +[18,] 176.422894 0.000000 5 16.78774817 0.00000000 2.52987006 +[19,] 266.623011 0.000000 5 30.83060604 0.00000000 3.82332223 + +$result$retres +$result$retres$res + [1] -0.129533474 0.002075926 0.304896747 0.376637587 0.395085863 -1.108942560 0.409131854 0.173913560 0.130078539 -0.646828300 0.388508996 -0.017352920 -0.028319875 0.487765290 -0.029000297 -0.286045660 -0.262148353 -0.356679168 0.446108188 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03520933 14.45075 0.1174267 + [2,] 0.06656952 14.15861 0.2618927 + [3,] 0.08320993 14.00360 0.3385495 + [4,] 0.12395675 13.62402 0.5262565 + [5,] 0.20294972 12.88815 0.8901508 + [6,] 0.26963715 12.26692 1.1973576 + [7,] 0.36955064 11.33616 1.6576258 + [8,] 0.04094902 14.39728 0.1438676 + [9,] 0.09779716 13.86771 0.4057480 + [10,] 0.14847441 13.39562 0.6392012 + [11,] 0.24201422 12.52424 1.0701080 + [12,] 0.30489376 11.93848 1.3597731 + [13,] 0.44277591 10.65403 1.9949502 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 2.590669e-03 NA NA + [2,] -4.151851e-05 NA NA + [3,] -6.097935e-03 NA NA + [4,] -7.532752e-03 NA NA + [5,] -7.901717e-03 NA NA + [6,] 2.217885e-02 NA NA + [7,] -8.182637e-03 NA NA + [8,] NA -0.080000238 -0.097553058 + [9,] NA -0.059836128 0.005800059 +[10,] NA 0.297541018 0.057209132 +[11,] NA -0.178714138 0.052429671 +[12,] NA 0.007982343 0.071335834 +[13,] NA 0.013027142 -0.089221638 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfdI_res/KEIO_ROBOT4_2_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yfdI_res/KEIO_ROBOT4_2_res.txt new file mode 100644 index 0000000..d9f0db0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfdI_res/KEIO_ROBOT4_2_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0352093304880174 0.0358253462341558 0.0354109703731499 0.00489063905261385 0.0267036951214398 0.0451513538508075 +Glc 14.4507502698194 14.4595196986364 14.4629091209424 0.1999052745604 14.0300551529017 14.8893815490788 +Ace 0.117426698585978 0.134142893526 0.134083761185507 0.0722154161130043 1.00000000000054e-06 0.255619231871243 +mu 0.533000564011214 0.530786023571697 0.531628315185141 0.0328874197297233 0.470051667796462 0.602357631292387 +qGlc -4.9652153336144 -4.98046772377266 -4.97199101074593 0.55720904097485 -5.82679714604519 -3.84108075432764 +qAce 2.45535616229845 2.43296859989161 2.39959721242759 0.231453701336685 2.07583260715089 2.90998336595795 +res 3.13796444234877 30.9423739781007 29.7072853167358 7.33878751166647 18.9576311238193 49.574268498166 + + +Goodness of fit (khi2 test) + +khi2 value 3.13796444234878 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.241381880180676 +p-value, i.e. P(X^2<=value) 0.00261052955553399 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfeC.txt b/validation/validation_results/Berges_2021/Berges_2021/yfeC.txt new file mode 100644 index 0000000..7f773a0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfeC.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.3504000000000005E-2 NA NA +2.2613888888888889 7.8623999999999999E-2 NA NA +2.7741666666666664 0.11037599999999999 NA NA +3.2088888888888891 0.119448 NA NA +3.7063888888888892 0.16480800000000001 NA NA +4.2258333333333331 0.20563200000000001 NA NA +4.6355555555555554 0.26611199999999996 NA NA +4.9675000000000002 0.320544 NA NA +2.8 NA 12.5405570743837 0.590945104678636 +3.73333333333333 NA 11.7414868561002 1.05232568296418 +4.28333333333333 NA 10.9361526216317 1.3899423720575 +4.75 NA 10.2728740637473 1.79916260832131 +5.11666666666667 NA 9.79853474040638 2.17415276248813 +5.43333333333333 NA 8.9894527853244 2.51451810916875 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfeC_res/KEIO_ROBOT5_7.pdf b/validation/validation_results/Berges_2021/Berges_2021/yfeC_res/KEIO_ROBOT5_7.pdf new file mode 100644 index 0000000..4254b5e Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yfeC_res/KEIO_ROBOT5_7.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfeC_res/KEIO_ROBOT5_7_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yfeC_res/KEIO_ROBOT5_7_log.txt new file mode 100644 index 0000000..dc6002a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfeC_res/KEIO_ROBOT5_7_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.063504 NA NA + [2,] 0.078624 NA NA + [3,] 0.110376 NA NA + [4,] 0.119448 NA NA + [5,] 0.164808 NA NA + [6,] 0.205632 NA NA + [7,] 0.266112 NA NA + [8,] 0.320544 NA NA + [9,] NA 12.540557 0.5909451 +[10,] NA 11.741487 1.0523257 +[11,] NA 10.936153 1.3899424 +[12,] NA 10.272874 1.7991626 +[13,] NA 9.798535 2.1741528 +[14,] NA 8.989453 2.5145181 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02416395 13.38026350 0.11329151 0.51709136 -6.04340455 3.33894466 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.313426e-09 1.247958e-07 -5.783365e-08 -2.251926e-08 -1.485813e-07 5.690405e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.002990388 0.272644223 0.122224503 0.028000141 0.550101055 0.243136005 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.2600106 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.313426e-09 1.247958e-07 -5.783365e-08 -2.251926e-08 -1.485813e-07 5.690405e-08 + +$result$normp +[1] 2.115318e-07 + +$result$res + [1] -0.06454827 -0.04094667 -0.44734765 0.37736840 -0.02778578 0.46158420 -0.02724393 -0.26237882 -0.17229524 -0.05524322 0.30339043 0.21047396 -0.25283947 -0.03348647 0.15033753 -0.09790016 -0.01700074 -0.11274254 -0.08859606 0.16590198 + +$result$prevres + [1] -0.06454844 -0.04094685 -0.44734782 0.37736826 -0.02778588 0.46158419 -0.02724382 -0.26237856 -0.17229535 -0.05524325 0.30339044 0.21047400 -0.25283942 -0.03348642 0.15033763 -0.09790013 -0.01700076 -0.11274258 -0.08859610 0.16590195 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 128.73109 0.000000 0 5.689036 0.0000000 0.0000000 + [2,] 160.99410 0.000000 0 8.797375 0.0000000 0.0000000 + [3,] 209.87680 0.000000 0 14.069054 0.0000000 0.0000000 + [4,] 262.77858 0.000000 0 20.375701 0.0000000 0.0000000 + [5,] 339.87053 0.000000 0 30.439142 0.0000000 0.0000000 + [6,] 444.59555 0.000000 0 45.398906 0.0000000 0.0000000 + [7,] 549.51102 0.000000 0 61.552558 0.0000000 0.0000000 + [8,] 652.41081 0.000000 0 78.311750 0.0000000 0.0000000 + [9,] -82.67456 2.173913 0 -3.449284 0.3305660 0.0000000 +[10,] -149.71894 2.173913 0 -8.802047 0.5986362 0.0000000 +[11,] -207.32927 2.173913 0 -14.400141 0.8289854 0.0000000 +[12,] -270.84647 2.173913 0 -21.346830 1.0829525 0.0000000 +[13,] -332.69422 2.173913 0 -28.728279 1.3302446 0.0000000 +[14,] -396.40569 2.173913 0 -36.855901 1.5849886 0.0000000 +[15,] 105.05755 0.000000 5 4.383130 0.0000000 0.7603017 +[16,] 190.25328 0.000000 5 11.185080 0.0000000 1.3768634 +[17,] 263.46080 0.000000 5 18.298781 0.0000000 1.9066663 +[18,] 344.17440 0.000000 5 27.126189 0.0000000 2.4907908 +[19,] 422.76658 0.000000 5 36.506064 0.0000000 3.0595626 +[20,] 503.72705 0.000000 5 46.834127 0.0000000 3.6454737 + +$result$retres +$result$retres$res + [1] -0.06454844 -0.04094685 -0.44734782 0.37736826 -0.02778588 0.46158419 -0.02724382 -0.26237856 -0.17229535 -0.05524325 0.30339044 0.21047400 -0.25283942 -0.03348642 0.15033763 -0.09790013 -0.01700076 -0.11274258 -0.08859610 0.16590195 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06221303 12.935572 0.3589808 + [2,] 0.07780506 12.753343 0.4596611 + [3,] 0.10142904 12.477243 0.6122051 + [4,] 0.12699537 12.178441 0.7772910 + [5,] 0.16425228 11.743008 1.0178651 + [6,] 0.21486368 11.151498 1.3446713 + [7,] 0.26556712 10.558911 1.6720718 + [8,] 0.31529643 9.977709 1.9931822 + [9,] 0.10279304 12.461301 0.6210126 + [10,] 0.16655678 11.716075 1.0327457 + [11,] 0.22134810 11.075712 1.3865422 + [12,] 0.28175724 10.369692 1.7766141 + [13,] 0.34057863 9.682229 2.1564335 + [14,] 0.40117255 8.974049 2.5476985 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0012909687 NA NA + [2,] 0.0008189370 NA NA + [3,] 0.0089469564 NA NA + [4,] -0.0075473651 NA NA + [5,] 0.0005557176 NA NA + [6,] -0.0092316839 NA NA + [7,] 0.0005448763 NA NA + [8,] 0.0052475712 NA NA + [9,] NA 0.07925586 -0.030067526 +[10,] NA 0.02541189 0.019580027 +[11,] NA -0.13955960 0.003400152 +[12,] NA -0.09681804 0.022548516 +[13,] NA 0.11630613 0.017719221 +[14,] NA 0.01540375 -0.033180390 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfeC_res/KEIO_ROBOT5_7_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yfeC_res/KEIO_ROBOT5_7_res.txt new file mode 100644 index 0000000..22c6688 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfeC_res/KEIO_ROBOT5_7_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0241639510598606 0.0247910755487202 0.024861995441228 0.00383789181602104 0.0178914110073037 0.0316723411129085 +Glc 13.3802634951431 13.4153679101382 13.4039104034626 0.273586632306827 12.8610136535039 13.879498435343 +Ace 0.113291505650555 0.114668586176522 0.0990780648557726 0.105187908563536 9.99999999987122e-07 0.337447999467289 +mu 0.517091359232198 0.514214563922797 0.514327336325248 0.0345949031485824 0.453534049407611 0.58551607146518 +qGlc -6.04340454982558 -6.11637832294414 -6.0800041545835 0.69648195907569 -7.52311746113682 -4.79278649326915 +qAce 3.33894466186166 3.33422837471611 3.32494823960399 0.263542794062175 2.85994958453131 3.87548740791047 +res 0.946476934311006 36.6468869925707 35.5068455761217 8.45182086643761 23.5280109128615 54.1903355129763 + + +Goodness of fit (khi2 test) + +khi2 value 0.946476934311242 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.0676054953079459 +p-value, i.e. P(X^2<=value) 6.98072844120486e-07 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfeY.txt b/validation/validation_results/Berges_2021/Berges_2021/yfeY.txt new file mode 100644 index 0000000..8088d5c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfeY.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.18888888888889 0.061992 NA NA +2.27694444444444 0.107352 NA NA +3.12833333333333 0.157248 NA NA +3.77138888888889 0.246456 NA NA +4.41555555555556 0.374976 NA NA +4.82277777777778 0.563976 NA NA +0.0666666666666667 NA 15.6780752294661 0.0125339835931122 +1.71666666666667 NA 14.5318538174204 0.323736754166788 +2.8 NA 13.4938150015177 0.729389676764353 +3.63333333333333 NA 12.6934572309558 1.18934838301768 +4.26666666666667 NA 11.4979342424855 1.62304913631216 +4.88333333333333 NA 9.61395152844894 2.09229134767477 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfeY_res/KEIO_ROBOT1_7.pdf b/validation/validation_results/Berges_2021/Berges_2021/yfeY_res/KEIO_ROBOT1_7.pdf new file mode 100644 index 0000000..f0f7600 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yfeY_res/KEIO_ROBOT1_7.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfeY_res/KEIO_ROBOT1_7_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yfeY_res/KEIO_ROBOT1_7_log.txt new file mode 100644 index 0000000..e2c1cb6 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfeY_res/KEIO_ROBOT1_7_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.061992 NA NA + [3,] 0.107352 NA NA + [4,] 0.157248 NA NA + [5,] 0.246456 NA NA + [6,] 0.374976 NA NA + [7,] 0.563976 NA NA + [8,] NA 15.678075 0.01253398 + [9,] NA 14.531854 0.32373675 +[10,] NA 13.493815 0.72938968 +[11,] NA 12.693457 1.18934838 +[12,] NA 11.497934 1.62304914 +[13,] NA 9.613952 2.09229135 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02030857 15.14486649 0.18845485 0.67786396 -7.18276357 2.60191292 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.271029e-08 -3.741288e-07 1.692306e-07 1.440457e-07 -1.886220e-07 -4.040781e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.00824862 0.61092500 0.26371822 0.09083474 1.58428571 0.67088920 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.97083 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.271029e-08 -3.741288e-07 1.692306e-07 1.440457e-07 -1.886220e-07 -4.040781e-08 + +$result$normp +[1] 4.76165e-07 + +$result$res + [1] -0.72337139 -0.82633818 -0.61463151 0.60222071 0.76655614 1.50731568 -1.50321960 -1.18077522 0.30267955 0.93550710 0.30538639 -0.04025021 -0.32254760 0.89762208 0.18171039 -0.49368497 -0.81886244 -0.53404014 0.76725508 + +$result$prevres + [1] -0.72337076 -0.82633715 -0.61463010 0.60222220 0.76655722 1.50731547 -1.50322144 -1.18077442 0.30267989 0.93550702 0.30538599 -0.04025068 -0.32254780 0.89762125 0.18170997 -0.49368497 -0.81886211 -0.53403964 0.76725550 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.00000 0.000000 0 0.000000e+00 0.000000000 0.000000000 + [2,] 111.93605 0.000000 0 2.702657e+00 0.000000000 0.000000000 + [3,] 234.03747 0.000000 0 1.082225e+01 0.000000000 0.000000000 + [4,] 416.80020 0.000000 0 2.648016e+01 0.000000000 0.000000000 + [5,] 644.52335 0.000000 0 4.936506e+01 0.000000000 0.000000000 + [6,] 997.41639 0.000000 0 8.944200e+01 0.000000000 0.000000000 + [7,] 1314.49723 0.000000 0 1.287468e+02 0.000000000 0.000000000 + [8,] -1.06486 2.173913 0 -7.262892e-04 0.003010791 0.000000000 + [9,] -50.71536 2.173913 0 -1.051754e+00 0.143392885 0.000000000 +[10,] -130.67066 2.173913 0 -4.825482e+00 0.369458943 0.000000000 +[11,] -247.37151 2.173913 0 -1.254156e+01 0.699419585 0.000000000 +[12,] -392.36437 2.173913 0 -2.423924e+01 1.109373183 0.000000000 +[13,] -607.93388 2.173913 0 -4.436196e+01 1.718875610 0.000000000 +[14,] 0.88720 0.000000 5 6.051160e-04 0.000000000 0.006924819 +[15,] 42.25407 0.000000 5 8.762803e-01 0.000000000 0.329803636 +[16,] 108.86972 0.000000 5 4.020404e+00 0.000000000 0.849755568 +[17,] 206.10035 0.000000 5 1.044914e+01 0.000000000 1.608665045 +[18,] 326.90277 0.000000 5 2.019520e+01 0.000000000 2.551558321 +[19,] 506.50692 0.000000 5 3.696066e+01 0.000000000 3.953413903 + +$result$retres +$result$retres$res + [1] -0.72337076 -0.82633715 -0.61463010 0.60222220 0.76655722 1.50731547 -1.50322144 -1.18077442 0.30267989 0.93550702 0.30538599 -0.04025068 -0.32254780 0.89762125 0.18170997 -0.49368497 -0.81886211 -0.53403964 0.76725550 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02030858 15.14487 0.1884547 + [2,] 0.04546526 14.87830 0.2850161 + [3,] 0.09505940 14.35279 0.4753783 + [4,] 0.16929244 13.56621 0.7603144 + [5,] 0.26178714 12.58612 1.1153462 + [6,] 0.40512231 11.06731 1.6655240 + [7,] 0.53391157 9.70264 2.1598688 + [8,] 0.02124740 15.13492 0.1920582 + [9,] 0.06502097 14.67109 0.3600787 + [10,] 0.13551229 13.92415 0.6306527 + [11,] 0.23839975 12.83393 1.0255760 + [12,] 0.36623040 11.47942 1.5162412 + [13,] 0.55628383 9.46558 2.2457424 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.01446742 NA NA + [2,] 0.01652674 NA NA + [3,] 0.01229260 NA NA + [4,] -0.01204444 NA NA + [5,] -0.01533114 NA NA + [6,] -0.03014631 NA NA + [7,] 0.03006443 NA NA + [8,] NA 0.54315623 -0.17952425 + [9,] NA -0.13923275 -0.03634199 +[10,] NA -0.43033323 0.09873699 +[11,] NA -0.14047756 0.16377242 +[12,] NA 0.01851531 0.10680793 +[13,] NA 0.14837199 -0.15345110 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfeY_res/KEIO_ROBOT1_7_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yfeY_res/KEIO_ROBOT1_7_res.txt new file mode 100644 index 0000000..ef5a6e3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfeY_res/KEIO_ROBOT1_7_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0203085721608342 0.0208414693139972 0.0204261697378756 0.00293558947535425 0.0154792657632309 0.026397026580914 +Glc 15.1448664901791 15.1486646684542 15.1780196142973 0.199439504617593 14.7257054971385 15.4479223604169 +Ace 0.188454846801141 0.199600403085642 0.198640466558109 0.0887823032942497 0.0478302620705902 0.365066704335058 +mu 0.677863956607332 0.674542850333911 0.674378762965449 0.032113319350675 0.619419410563258 0.741475209533622 +qGlc -7.182763571296 -7.20065326656937 -7.15540579281847 0.50543890227563 -8.11326695384253 -6.19623729478103 +qAce 2.60191291516418 2.56095398510705 2.57599702013273 0.210326613071267 2.19856422670195 2.8651261977862 +res 12.2526409639966 32.3101585537217 31.4415587024545 7.57817984521135 20.3664510482564 47.5751571187139 + + +Goodness of fit (khi2 test) + +khi2 value 12.2526409640111 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.942510843385469 +p-value, i.e. P(X^2<=value) 0.492955864906685 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfgD.txt b/validation/validation_results/Berges_2021/Berges_2021/yfgD.txt new file mode 100644 index 0000000..f6912b0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfgD.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.149688 NA NA +3.67805555555556 0.228312 NA NA +4.09222222222222 0.27972 NA NA +4.565 0.373464 NA NA +0.05 NA 14.0487794878788 0.0117684297487982 +1.95 NA 14.0382822212269 0.41995337560936 +2.83333333333333 NA 13.5280374045763 0.724420671218976 +3.98333333333333 NA 12.067119465913 1.30364619207534 +4.88333333333333 NA 9.96542601301856 2.09873141117474 +5.16666666666667 NA 9.38170640986481 2.60554405242448 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfgD_res/KEIO_ROBOT3_33.pdf b/validation/validation_results/Berges_2021/Berges_2021/yfgD_res/KEIO_ROBOT3_33.pdf new file mode 100644 index 0000000..b726574 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yfgD_res/KEIO_ROBOT3_33.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfgD_res/KEIO_ROBOT3_33_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yfgD_res/KEIO_ROBOT3_33_log.txt new file mode 100644 index 0000000..f98c3ac --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfgD_res/KEIO_ROBOT3_33_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.149688 NA NA + [2,] 0.228312 NA NA + [3,] 0.279720 NA NA + [4,] 0.373464 NA NA + [5,] NA 14.048779 0.01176843 + [6,] NA 14.038282 0.41995338 + [7,] NA 13.528037 0.72442067 + [8,] NA 12.067119 1.30364619 + [9,] NA 9.965426 2.09873141 +[10,] NA 9.381706 2.60554405 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02874594 14.43852276 0.09171007 0.56103047 -5.78443741 2.81265525 + +$result$lastp + X Glc Ace mu qGlc qAce +-6.639665e-09 1.131256e-07 7.240553e-08 5.403795e-08 -6.403275e-07 -1.377014e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008055164 0.313638212 0.138021638 0.066801209 0.639331733 0.283574796 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4546671 + +$result$laststep + X Glc Ace mu qGlc qAce +-6.639665e-09 1.131256e-07 7.240553e-08 5.403795e-08 -6.403275e-07 -1.377014e-08 + +$result$normp +[1] 6.566682e-07 + +$result$res + [1] -0.26466884 -0.09905896 0.29065357 -0.06004988 0.82893829 -0.40965077 -0.53459288 -0.22110157 0.39305195 -0.05664501 0.42020748 -0.21000250 -0.35208760 -0.04699053 0.40042849 -0.21155534 + +$result$prevres + [1] -0.26466829 -0.09905860 0.29065371 -0.06005018 0.82893804 -0.40965109 -0.53459319 -0.22110169 0.39305231 -0.05664439 0.42020712 -0.21000262 -0.35208757 -0.04699034 0.40042865 -0.21155525 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 251.1565264 0.000000 0 2.077077e+01 0.000000000 0.000000000 + [2,] 393.6743558 0.000000 0 4.162287e+01 0.000000000 0.000000000 + [3,] 496.6493075 0.000000 0 5.842324e+01 0.000000000 0.000000000 + [4,] 647.5052319 0.000000 0 8.496903e+01 0.000000000 0.000000000 + [5,] -0.6376448 2.173913 0 -4.603847e-04 0.003168796 0.000000000 + [6,] -44.5189389 2.173913 0 -1.470840e+00 0.221238302 0.000000000 + [7,] -87.4526453 2.173913 0 -4.467403e+00 0.434598741 0.000000000 + [8,] -187.0290223 2.173913 0 -1.439924e+01 0.929446758 0.000000000 + [9,] -324.6047674 2.173913 0 -3.208108e+01 1.613133860 0.000000000 +[10,] -384.3924124 2.173913 0 -4.072375e+01 1.910250489 0.000000000 +[11,] 0.7131191 0.000000 5 5.148780e-04 0.000000000 0.007288231 +[12,] 49.7883883 0.000000 5 1.644935e+00 0.000000000 0.508848096 +[13,] 97.8039094 0.000000 5 4.996183e+00 0.000000000 0.999577104 +[14,] 209.1665665 0.000000 5 1.610360e+01 0.000000000 2.137727542 +[15,] 363.0263574 0.000000 5 3.587833e+01 0.000000000 3.710207877 +[16,] 429.8907203 0.000000 5 4.554399e+01 0.000000000 4.393576125 + +$result$retres +$result$retres$res + [1] -0.26466829 -0.09905860 0.29065371 -0.06005018 0.82893804 -0.40965109 -0.53459319 -0.22110169 0.39305231 -0.05664439 0.42020712 -0.21000262 -0.35208757 -0.04699034 0.40042865 -0.21155525 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.14439463 13.24614 0.67150012 + [2,] 0.22633083 12.40135 1.08227689 + [3,] 0.28553307 11.79095 1.37907989 + [4,] 0.37226300 10.89673 1.81388942 + [5,] 0.02956373 14.43009 0.09580985 + [6,] 0.08584180 13.84984 0.37795285 + [7,] 0.14090458 13.28212 0.65400316 + [8,] 0.26861198 11.96541 1.29424812 + [9,] 0.44505384 10.14623 2.17881714 + [10,] 0.52173192 9.35565 2.56323300 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.005293366 NA NA + [2,] 0.001981172 NA NA + [3,] -0.005813074 NA NA + [4,] 0.001201004 NA NA + [5,] NA -0.38131150 -0.084041424 + [6,] NA 0.18843950 0.042000523 + [7,] NA 0.24591287 0.070417513 + [8,] NA 0.10170678 0.009398069 + [9,] NA -0.18080406 -0.080085731 +[10,] NA 0.02605642 0.042311050 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfgD_res/KEIO_ROBOT3_33_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yfgD_res/KEIO_ROBOT3_33_res.txt new file mode 100644 index 0000000..5d96c6e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfgD_res/KEIO_ROBOT3_33_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0287459384191828 0.028649507097241 0.0282166752443301 0.00447442015157285 0.0220959980622002 0.0364135733341925 +Glc 14.4385227619649 14.3915795953054 14.408236517168 0.263678396441313 13.8214275757127 14.899169206791 +Ace 0.0917100696008848 0.11451735888234 0.0992932391270561 0.0889873003891732 9.99999999990418e-07 0.30704860296938 +mu 0.561030474263499 0.563916934599302 0.566404597999713 0.032540662367377 0.509554314606557 0.614150908371539 +qGlc -5.7844374093687 -5.7421865748401 -5.74365149799046 0.571423920334101 -6.85060378474145 -4.73115471510662 +qAce 2.81265525252373 2.77130694349385 2.7809256013786 0.23781561179543 2.31460902779 3.19883159741795 +res 2.06722193443385 23.2845852918766 23.2785826521042 5.55750328929686 13.3583111908121 34.0940260829645 + + +Goodness of fit (khi2 test) + +khi2 value 2.06722193443544 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.206722193443544 +p-value, i.e. P(X^2<=value) 0.00420150479471291 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfhG.txt b/validation/validation_results/Berges_2021/Berges_2021/yfhG.txt new file mode 100644 index 0000000..21d0c23 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfhG.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.05292 NA NA +1.18888888888889 0.080136 NA NA +2.27694444444444 0.114912 NA NA +3.12833333333333 0.170856 NA NA +3.77138888888889 0.240408 NA NA +4.41555555555556 0.349272 NA NA +4.82277777777778 0.452088 NA NA +0.0666666666666667 NA 15.9964482752953 0.00970317565270478 +1.71666666666667 NA 14.864218589467 0.356200811699361 +2.8 NA 13.6898486991947 0.803413612494241 +3.63333333333333 NA 12.7332571306407 1.34820615815309 +4.26666666666667 NA 11.175429677542 1.85759009157641 +4.88333333333333 NA 10.2419109693048 2.63426020675281 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfhG_res/KEIO_ROBOT1_23.pdf b/validation/validation_results/Berges_2021/Berges_2021/yfhG_res/KEIO_ROBOT1_23.pdf new file mode 100644 index 0000000..a76c2e7 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yfhG_res/KEIO_ROBOT1_23.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfhG_res/KEIO_ROBOT1_23_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yfhG_res/KEIO_ROBOT1_23_log.txt new file mode 100644 index 0000000..c229f40 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfhG_res/KEIO_ROBOT1_23_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.052920 NA NA + [2,] 0.080136 NA NA + [3,] 0.114912 NA NA + [4,] 0.170856 NA NA + [5,] 0.240408 NA NA + [6,] 0.349272 NA NA + [7,] 0.452088 NA NA + [8,] NA 15.99645 0.009703176 + [9,] NA 14.86422 0.356200812 +[10,] NA 13.68985 0.803413612 +[11,] NA 12.73326 1.348206158 +[12,] NA 11.17543 1.857590092 +[13,] NA 10.24191 2.634260207 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03721566 15.62708502 0.03091458 0.51033572 -7.14464675 3.23703436 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.091082e-08 5.798903e-07 -1.324532e-07 -1.351605e-07 -2.789626e-07 -2.444018e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.008462741 0.428180886 0.186522415 0.052236869 1.033307378 0.452687850 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6371644 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.091082e-08 5.798903e-07 -1.324532e-07 -1.351605e-07 -2.789626e-07 -2.444018e-07 + +$result$normp +[1] 7.14195e-07 + +$result$res + [1] -0.78521713 -0.59332866 0.20209276 0.64151862 0.73139123 0.25142249 -0.79735566 -0.84216180 0.07105439 0.61606937 0.18971260 0.81614929 -0.85082385 0.14690407 0.02769005 -0.11594799 -0.22859878 0.10072896 0.06922370 + +$result$prevres + [1] -0.78521817 -0.59333003 0.20209125 0.64151735 0.73139056 0.25142311 -0.79735369 -0.84216304 0.07105387 0.61606943 0.18971307 0.81614994 -0.85082328 0.14690471 0.02769012 -0.11594828 -0.22859919 0.10072869 0.06922395 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 91.721392 0.000000 0 4.058236519 0.000000000 0.00000000 + [3,] 159.816996 0.000000 0 13.542562553 0.000000000 0.00000000 + [4,] 246.786518 0.000000 0 28.731606102 0.000000000 0.00000000 + [5,] 342.646042 0.000000 0 48.091961250 0.000000000 0.00000000 + [6,] 476.010214 0.000000 0 78.221668713 0.000000000 0.00000000 + [7,] 585.964620 0.000000 0 105.170538327 0.000000000 0.00000000 + [8,] -1.053272 2.173913 0 -0.001314015 0.005486371 0.00000000 + [9,] -42.652775 2.173913 0 -1.558915197 0.222173366 0.00000000 +[10,] -96.607581 2.173913 0 -6.193276954 0.503217708 0.00000000 +[11,] -163.942268 2.173913 0 -14.327717946 0.853956301 0.00000000 +[12,] -238.108528 2.173913 0 -25.277290912 1.240279761 0.00000000 +[13,] -337.431341 2.173913 0 -42.247826513 1.757640799 0.00000000 +[14,] 1.097577 0.000000 5 0.001369288 0.000000000 0.01261865 +[15,] 44.446925 0.000000 5 1.624489562 0.000000000 0.51099874 +[16,] 100.671292 0.000000 5 6.453791578 0.000000000 1.15740073 +[17,] 170.838352 0.000000 5 14.930400512 0.000000000 1.96409949 +[18,] 248.124349 0.000000 5 26.340557414 0.000000000 2.85264345 +[19,] 351.625087 0.000000 5 44.024943327 0.000000000 4.04257384 + +$result$retres +$result$retres$res + [1] -0.78521817 -0.59333003 0.20209125 0.64151735 0.73139056 0.25142311 -0.79735369 -0.84216304 0.07105387 0.61606943 0.18971307 0.81614994 -0.85082328 0.14690471 0.02769012 -0.11594828 -0.22859919 0.10072869 0.06922395 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03721564 15.627084 0.03091471 + [2,] 0.06826940 15.192335 0.22788717 + [3,] 0.11895383 14.482759 0.54937593 + [4,] 0.18368635 13.576510 0.95997105 + [5,] 0.25503581 12.577626 1.41253711 + [6,] 0.35430046 11.187931 2.04216779 + [7,] 0.43614093 10.042174 2.56127774 + [8,] 0.03850359 15.609053 0.03908412 + [9,] 0.08937183 14.896903 0.36173884 + [10,] 0.15534825 13.973241 0.78022396 + [11,] 0.23768571 12.820525 1.30248632 + [12,] 0.32837688 11.550859 1.87773583 + [13,] 0.44982971 9.850532 2.64810500 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.015704363 NA NA + [2,] 0.011866601 NA NA + [3,] -0.004041825 NA NA + [4,] -0.012830347 NA NA + [5,] -0.014627811 NA NA + [6,] -0.005028462 NA NA + [7,] 0.015947074 NA NA + [8,] NA 0.38739500 -0.029380942 + [9,] NA -0.03268478 -0.005538025 +[10,] NA -0.28339194 0.023189656 +[11,] NA -0.08726801 0.045719838 +[12,] NA -0.37542897 -0.020145737 +[13,] NA 0.39137871 -0.013844790 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfhG_res/KEIO_ROBOT1_23_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yfhG_res/KEIO_ROBOT1_23_res.txt new file mode 100644 index 0000000..2e6068c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfhG_res/KEIO_ROBOT1_23_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0372156574403534 0.0374666797888562 0.036806240330148 0.00469393377076566 0.0295407414384617 0.0460830431356414 +Glc 15.6270850224239 15.6488789990266 15.6433310119889 0.189866598514058 15.3398138638018 15.9782765810228 +Ace 0.0309145817406786 0.0835886304420664 0.0667003116262327 0.079574827634971 9.99999999983306e-07 0.256036490030358 +mu 0.510335716878257 0.510626721890158 0.513274438514812 0.0285000422255625 0.458623424409481 0.562384972037125 +qGlc -7.14464674999742 -7.20036382836098 -7.18588735478685 0.497199294098665 -8.14950571960609 -6.35119555078219 +qAce 3.23703436308016 3.15304937264658 3.15080295109778 0.196532143741877 2.79829697309983 3.52642148121467 +res 5.27772048274493 30.6697486113821 29.9091551016969 7.29467014805039 18.4970283199157 45.3656653477827 + + +Goodness of fit (khi2 test) + +khi2 value 5.27772048276124 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.405978498673942 +p-value, i.e. P(X^2<=value) 0.0314402445718197 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfhm.txt b/validation/validation_results/Berges_2021/Berges_2021/yfhm.txt new file mode 100644 index 0000000..231d5e7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfhm.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 5.8968E-2 NA NA +2.2613888888888889 7.8623999999999999E-2 NA NA +2.7741666666666664 0.1134 NA NA +3.2088888888888891 0.14061599999999999 NA NA +3.7063888888888892 0.17690400000000001 NA NA +4.2258333333333331 0.24192 NA NA +4.6355555555555554 0.32659199999999999 NA NA +4.9675000000000002 0.40068000000000004 NA NA +2.8 NA 12.4391185753183 0.592995327234633 +3.73333333333333 NA 11.8773612362043 1.02952274753423 +4.28333333333333 NA 11.3079674709324 1.37236566459683 +4.75 NA 10.651405353804 1.76519195723761 +5.11666666666667 NA 9.80748290848681 2.06068435491446 +5.43333333333333 NA 9.02207954282273 2.3812108970302 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfhm_res/KEIO_ROBOT5_46.pdf b/validation/validation_results/Berges_2021/Berges_2021/yfhm_res/KEIO_ROBOT5_46.pdf new file mode 100644 index 0000000..a683603 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yfhm_res/KEIO_ROBOT5_46.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfhm_res/KEIO_ROBOT5_46_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yfhm_res/KEIO_ROBOT5_46_log.txt new file mode 100644 index 0000000..6739ae7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfhm_res/KEIO_ROBOT5_46_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.058968 NA NA + [2,] 0.078624 NA NA + [3,] 0.113400 NA NA + [4,] 0.140616 NA NA + [5,] 0.176904 NA NA + [6,] 0.241920 NA NA + [7,] 0.326592 NA NA + [8,] 0.400680 NA NA + [9,] NA 12.439119 0.5929953 +[10,] NA 11.877361 1.0295227 +[11,] NA 11.307967 1.3723657 +[12,] NA 10.651405 1.7651920 +[13,] NA 9.807483 2.0606844 +[14,] NA 9.022080 2.3812109 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01959246 13.24356536 0.29755544 0.60523450 -4.98081644 2.57320792 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.032785e-10 -3.159154e-09 1.443995e-09 1.185772e-09 4.961148e-10 1.327121e-10 + +$result$hci + X Glc Ace mu qGlc qAce +0.002689614 0.290969197 0.128365198 0.030542492 0.534289706 0.234094508 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3060076 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.032785e-10 -3.159154e-09 1.443995e-09 1.185772e-09 4.961148e-10 1.327121e-10 + +$result$normp +[1] 3.707538e-09 + +$result$res + [1] 0.01494602 -0.08116220 -0.41892000 -0.19931101 0.38653332 0.54610011 -0.12961123 -0.22938919 0.19083196 -0.03696413 -0.12528751 -0.22655390 0.06451067 0.13346290 0.37402891 -0.08684718 -0.22530124 -0.37312667 -0.01648987 0.32773604 + +$result$prevres + [1] 0.01494603 -0.08116219 -0.41891999 -0.19931100 0.38653333 0.54610012 -0.12961124 -0.22938920 0.19083196 -0.03696413 -0.12528751 -0.22655390 0.06451067 0.13346290 0.37402891 -0.08684717 -0.22530124 -0.37312667 -0.01648987 0.32773604 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 151.24933 0.000000 0 5.419631 0.0000000 0.0000000 + [2,] 196.50612 0.000000 0 8.706433 0.0000000 0.0000000 + [3,] 268.01539 0.000000 0 14.567371 0.0000000 0.0000000 + [4,] 348.67954 0.000000 0 21.921489 0.0000000 0.0000000 + [5,] 471.18813 0.000000 0 34.216394 0.0000000 0.0000000 + [6,] 645.25342 0.000000 0 53.423408 0.0000000 0.0000000 + [7,] 826.84823 0.000000 0 75.095948 0.0000000 0.0000000 + [8,] 1010.82832 0.000000 0 98.379404 0.0000000 0.0000000 + [9,] -79.51863 2.173913 0 -2.769596 0.3127932 0.0000000 +[10,] -153.47606 2.173913 0 -7.566349 0.6037109 0.0000000 +[11,] -221.16210 2.173913 0 -12.902139 0.8699596 0.0000000 +[12,] -299.18066 2.173913 0 -19.822972 1.1768521 0.0000000 +[13,] -377.96350 2.173913 0 -27.448273 1.4867510 0.0000000 +[14,] -461.58989 2.173913 0 -36.099360 1.8157024 0.0000000 +[15,] 94.48679 0.000000 5 3.290930 0.0000000 0.7194243 +[16,] 182.36555 0.000000 5 8.990597 0.0000000 1.3885350 +[17,] 262.79245 0.000000 5 15.330767 0.0000000 2.0009071 +[18,] 355.49680 0.000000 5 23.554340 0.0000000 2.7067599 +[19,] 449.10929 0.000000 5 32.614987 0.0000000 3.4195273 +[20,] 548.47705 0.000000 5 42.894507 0.0000000 4.1761154 + +$result$retres +$result$retres$res + [1] 0.01494603 -0.08116219 -0.41891999 -0.19931100 0.38653333 0.54610012 -0.12961124 -0.22938920 0.19083196 -0.03696413 -0.12528751 -0.22655390 0.06451067 0.13346290 0.37402891 -0.08684717 -0.22530124 -0.37312667 -0.01648987 0.32773604 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05926692 12.917062 0.4662349 + [2,] 0.07700076 12.771120 0.5416319 + [3,] 0.10502160 12.540521 0.6607650 + [4,] 0.13662978 12.280399 0.7951500 + [5,] 0.18463467 11.885340 0.9992470 + [6,] 0.25284200 11.324023 1.2892365 + [7,] 0.32399978 10.738426 1.5917700 + [8,] 0.39609222 10.145136 1.8982774 + [9,] 0.10667654 12.526901 0.6678011 + [10,] 0.18767032 11.860358 1.0121533 + [11,] 0.26179605 11.250335 1.3273054 + [12,] 0.34723735 10.547191 1.6905666 + [13,] 0.43351564 9.837158 2.0573864 + [14,] 0.52509829 9.083472 2.4467581 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0002989207 NA NA + [2,] 0.0016232438 NA NA + [3,] 0.0083783998 NA NA + [4,] 0.0039862199 NA NA + [5,] -0.0077306666 NA NA + [6,] -0.0109220024 NA NA + [7,] 0.0025922247 NA NA + [8,] 0.0045877841 NA NA + [9,] NA -0.08778270 -0.074805782 +[10,] NA 0.01700350 0.017369435 +[11,] NA 0.05763225 0.045060248 +[12,] NA 0.10421479 0.074625333 +[13,] NA -0.02967491 0.003297974 +[14,] NA -0.06139294 -0.065547208 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfhm_res/KEIO_ROBOT5_46_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yfhm_res/KEIO_ROBOT5_46_res.txt new file mode 100644 index 0000000..1f0cd23 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfhm_res/KEIO_ROBOT5_46_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0195924572650678 0.0198963267898792 0.0198744149810259 0.00286642093699248 0.0154896692520202 0.0258952197321023 +Glc 13.2435653625718 13.2249846217448 13.207788678899 0.245446008698939 12.7621241400571 13.6633614750924 +Ace 0.297555443639973 0.28551623058288 0.285059606404764 0.10432286841371 0.0646598105269446 0.4490209947082 +mu 0.605234503181024 0.604259252730646 0.603526773463064 0.0296923792031673 0.548608196987671 0.652611128182424 +qGlc -4.98081644105261 -4.92526168706889 -4.90923915732321 0.565709014875031 -6.06316764301419 -3.86229970815983 +qAce 2.57320791818478 2.60244770767564 2.58213045298042 0.235998571701373 2.0846372762173 3.03277885650697 +res 1.31096917901313 35.0741954423784 34.5842002526118 8.32712923824751 20.6675548893494 49.6570520700495 + + +Goodness of fit (khi2 test) + +khi2 value 1.31096917901314 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.0936406556437955 +p-value, i.e. P(X^2<=value) 5.82894140183674e-06 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfiF.txt b/validation/validation_results/Berges_2021/Berges_2021/yfiF.txt new file mode 100644 index 0000000..9a67372 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfiF.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.114912 NA NA NA +3.34194444444444 0.170856 NA NA NA +3.9975 0.240408 NA NA NA +4.52333333333333 0.349272 NA NA NA +1.95 NA 13.3513950228131 0.366080204605129 0 +3.25 NA 12.7848651443071 0.906583734428254 0 +4.08333333333333 NA 11.7250413977365 1.38525511856318 0 +4.76666666666667 NA 10.613157623291 1.93166974892704 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfiF_res/KEIO_ROBOT2_23.pdf b/validation/validation_results/Berges_2021/Berges_2021/yfiF_res/KEIO_ROBOT2_23.pdf new file mode 100644 index 0000000..4d40050 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yfiF_res/KEIO_ROBOT2_23.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfiF_res/KEIO_ROBOT2_23_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yfiF_res/KEIO_ROBOT2_23_log.txt new file mode 100644 index 0000000..0819ea0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfiF_res/KEIO_ROBOT2_23_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.114912 NA NA NA +[2,] 0.170856 NA NA NA +[3,] 0.240408 NA NA NA +[4,] 0.349272 NA NA NA +[5,] NA 13.35140 0.3660802 0 +[6,] NA 12.78487 0.9065837 0 +[7,] NA 11.72504 1.3852551 0 +[8,] NA 10.61316 1.9316697 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.529560e-02 1.389335e+01 1.673591e-01 1.000000e-06 5.755523e-01 -5.112789e+00 2.823361e+00 -2.139982e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 2.372365e-09 2.200537e-08 -3.933347e-08 0.000000e+00 -2.301373e-08 8.424608e-08 3.178246e-08 -2.394984e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.006561503 0.392268965 0.174171383 0.164477452 0.062538878 0.963246735 0.425062494 0.408388142 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.36171 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 2.372365e-09 2.200537e-08 -3.933347e-08 0.000000e+00 -2.301373e-08 8.424608e-08 3.178246e-08 -2.394984e-13 + +$result$normp +[1] 1.033157e-07 + +$result$res + [1] -4.090571e-01 1.141433e-01 6.044636e-01 -3.766890e-01 1.660120e-01 -2.729755e-01 7.918852e-02 2.777496e-02 2.919329e-01 -2.887962e-01 -2.031801e-01 2.000435e-01 4.025619e-06 2.417398e-06 5.384467e-07 -1.837969e-06 + +$result$prevres + [1] -4.090573e-01 1.141432e-01 6.044636e-01 -3.766889e-01 1.660120e-01 -2.729755e-01 7.918854e-02 2.777492e-02 2.919330e-01 -2.887962e-01 -2.031802e-01 2.000434e-01 4.025619e-06 2.417398e-06 5.384474e-07 -1.837968e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.109673e+02 0.000000 0 0 1.334877e+01 0.0000000 0.000000 0.000000 + [2,] 3.422313e+02 0.000000 0 0 2.893102e+01 0.0000000 0.000000 0.000000 + [3,] 4.990934e+02 0.000000 0 0 5.046789e+01 0.0000000 0.000000 0.000000 + [4,] 6.754896e+02 0.000000 0 0 7.728979e+01 0.0000000 0.000000 0.000000 + [5,] -4.001325e+01 2.173913 0 0 -1.167688e+00 0.1979661 0.000000 0.000000 + [6,] -1.060553e+02 2.173913 0 0 -5.645346e+00 0.5247103 0.000000 0.000000 + [7,] -1.832151e+02 2.173913 0 0 -1.286671e+01 0.9064590 0.000000 0.000000 + [8,] -2.808033e+02 2.173913 0 0 -2.384520e+01 1.3892781 0.000000 0.000000 + [9,] 5.082064e+01 0.000000 5 0 1.483075e+00 0.0000000 0.455322 0.000000 +[10,] 1.347004e+02 0.000000 5 0 7.170127e+00 0.0000000 1.206834 0.000000 +[11,] 2.327006e+02 0.000000 5 0 1.634195e+01 0.0000000 2.084856 0.000000 +[12,] 3.566470e+02 0.000000 5 0 3.028567e+01 0.0000000 3.195340 0.000000 +[13,] -3.851978e-05 0.000000 0 5 -1.124105e-06 0.0000000 0.000000 0.455322 +[14,] -1.020969e-04 0.000000 0 5 -5.434636e-06 0.0000000 0.000000 1.206834 +[15,] -1.763767e-04 0.000000 0 5 -1.238647e-05 0.0000000 0.000000 2.084856 +[16,] -2.703225e-04 0.000000 0 5 -2.295519e-05 0.0000000 0.000000 3.195340 + +$result$retres +$result$retres$res + [1] -4.090573e-01 1.141432e-01 6.044636e-01 -3.766889e-01 1.660120e-01 -2.729755e-01 7.918854e-02 2.777492e-02 2.919330e-01 -2.887962e-01 -2.031802e-01 2.000434e-01 4.025619e-06 2.417398e-06 5.384474e-07 -1.837968e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10673085 13.16994 0.5668383 6.972126e-07 + [2,] 0.17313886 12.58002 0.8926015 4.502987e-07 + [3,] 0.25249727 11.87506 1.2818926 1.552333e-07 + [4,] 0.34173822 11.08231 1.7196624 -1.765767e-07 + [5,] 0.07770792 13.42776 0.4244668 8.051239e-07 + [6,] 0.16421477 12.65930 0.8488245 4.834797e-07 + [7,] 0.26528428 11.76147 1.3446191 1.076895e-07 + [8,] 0.39311259 10.62593 1.9716784 -3.675935e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.008181145 NA NA NA +[2,] -0.002282863 NA NA NA +[3,] -0.012089271 NA NA NA +[4,] 0.007533777 NA NA NA +[5,] NA -0.07636552 -0.05838660 -8.051239e-07 +[6,] NA 0.12556871 0.05775924 -4.834797e-07 +[7,] NA -0.03642673 0.04063604 -1.076895e-07 +[8,] NA -0.01277646 -0.04000868 3.675935e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yfiF_res/KEIO_ROBOT2_23_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yfiF_res/KEIO_ROBOT2_23_res.txt new file mode 100644 index 0000000..561cdb4 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yfiF_res/KEIO_ROBOT2_23_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0252955961187436 0.025566792299117 0.0250552935155731 0.00439218435323094 0.0177628114368965 0.0344345211756013 +Glc 13.8933536564708 13.9303366895627 13.991214073947 0.396730488917893 12.9787515786464 14.5342240270465 +Ace 0.167359103645873 0.173045296010325 0.153335534584466 0.137095291536267 9.99999999945489e-07 0.432840415631173 +Lac 1e-06 0.086541465573469 0.0723750942985056 0.0807503722158222 9.99999999994709e-07 0.298569987347592 +mu 0.575552252660472 0.57613232493539 0.576373775202697 0.0418672265991196 0.503300778174422 0.66572297469078 +qGlc -5.1127890465395 -5.14435132154132 -5.24007098718146 0.996334312779209 -6.89919901970844 -3.11599151224475 +qAce 2.8233607586457 2.80974344490021 2.8451672433261 0.397163924570344 2.1058567855511 3.5824665181608 +qLac -2.13998174414108e-06 -0.0251813269823274 -0.0253008532080925 0.201913652537915 -0.483261571814537 0.406420900217132 +res 1.04667273621826 20.5190210777817 20.1115568878873 6.18901303262198 11.3681649491155 34.576935762495 + + +Goodness of fit (khi2 test) + +khi2 value 1.04667273621837 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.130834092027296 +p-value, i.e. P(X^2<=value) 0.00206405254163526 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygaM.txt b/validation/validation_results/Berges_2021/Berges_2021/ygaM.txt new file mode 100644 index 0000000..6713448 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygaM.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.3504000000000005E-2 NA NA +2.2613888888888889 8.1647999999999998E-2 NA NA +2.7741666666666664 0.104328 NA NA +3.2088888888888891 0.13759199999999999 NA NA +3.7063888888888892 0.16783200000000001 NA NA +4.2258333333333331 0.232848 NA NA +4.6355555555555554 0.30542400000000003 NA NA +4.9675000000000002 0.38858399999999998 NA NA +2.8 NA 12.3768570683639 0.587559497591229 +3.73333333333333 NA 11.7149225598339 1.1123183290557 +4.28333333333333 NA 11.3363064425742 1.60224475374827 +4.75 NA 10.492995686707 2.12267370832773 +5.11666666666667 NA 10.1120374123064 2.67572167809902 +5.43333333333333 NA 9.36009794057296 3.25551502998283 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygaM_res/KEIO_ROBOT5_9.pdf b/validation/validation_results/Berges_2021/Berges_2021/ygaM_res/KEIO_ROBOT5_9.pdf new file mode 100644 index 0000000..7f40f4f Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ygaM_res/KEIO_ROBOT5_9.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygaM_res/KEIO_ROBOT5_9_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ygaM_res/KEIO_ROBOT5_9_log.txt new file mode 100644 index 0000000..55e061c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygaM_res/KEIO_ROBOT5_9_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.063504 NA NA + [2,] 0.081648 NA NA + [3,] 0.104328 NA NA + [4,] 0.137592 NA NA + [5,] 0.167832 NA NA + [6,] 0.232848 NA NA + [7,] 0.305424 NA NA + [8,] 0.388584 NA NA + [9,] NA 12.376857 0.5875595 +[10,] NA 11.714923 1.1123183 +[11,] NA 11.336306 1.6022448 +[12,] NA 10.492996 2.1226737 +[13,] NA 10.112037 2.6757217 +[14,] NA 9.360098 3.2555150 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01925894 12.97995967 0.03172549 0.59960194 -4.49273901 4.01748465 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.845689e-09 8.142245e-08 -6.898591e-08 -3.335657e-08 -2.248883e-08 1.185624e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.002703083 0.289290177 0.137093374 0.031250587 0.553594896 0.252400120 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3049717 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.845689e-09 8.142245e-08 -6.898591e-08 -3.335657e-08 -2.248883e-08 1.185624e-08 + +$result$normp +[1] 1.146985e-07 + +$result$res + [1] -0.292150949 -0.345799389 -0.134735729 -0.284683616 0.495502531 0.492201111 0.242619485 -0.498863544 -0.056533142 0.121418833 -0.204978727 0.307114424 -0.195752946 0.028731559 0.033625351 0.003403655 -0.082101444 0.033047039 0.005351594 0.006673804 + +$result$prevres + [1] -0.292151200 -0.345799659 -0.134736010 -0.284683884 0.495502316 0.492201029 0.242619592 -0.498863204 -0.056533191 0.121418837 -0.204978701 0.307114452 -0.195752934 0.028731538 0.033625439 0.003403638 -0.082101500 0.033046984 0.005351578 0.006673861 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 149.69927 0.000000 0 5.272776 0.0000000 0.0000000 + [2,] 194.01903 0.000000 0 8.449906 0.0000000 0.0000000 + [3,] 263.86004 0.000000 0 14.097383 0.0000000 0.0000000 + [4,] 342.43406 0.000000 0 21.162353 0.0000000 0.0000000 + [5,] 461.45341 0.000000 0 32.939057 0.0000000 0.0000000 + [6,] 630.07635 0.000000 0 51.278802 0.0000000 0.0000000 + [7,] 805.53871 0.000000 0 71.915173 0.0000000 0.0000000 + [8,] 982.93776 0.000000 0 94.036448 0.0000000 0.0000000 + [9,] -71.01252 2.173913 0 -2.426839 0.3044080 0.0000000 +[10,] -136.49048 2.173913 0 -6.600828 0.5850911 0.0000000 +[11,] -196.17581 2.173913 0 -11.225654 0.8409431 0.0000000 +[12,] -264.77727 2.173913 0 -17.207392 1.1350156 0.0000000 +[13,] -333.88999 2.173913 0 -23.782778 1.4312798 0.0000000 +[14,] -407.11140 2.173913 0 -31.228468 1.7451566 0.0000000 +[15,] 146.05142 0.000000 5 4.991279 0.0000000 0.7001384 +[16,] 280.71993 0.000000 5 13.575920 0.0000000 1.3457096 +[17,] 403.47472 0.000000 5 23.087798 0.0000000 1.9341691 +[18,] 544.56731 0.000000 5 35.390436 0.0000000 2.6105359 +[19,] 686.71141 0.000000 5 48.914031 0.0000000 3.2919434 +[20,] 837.30586 0.000000 5 64.227579 0.0000000 4.0138601 + +$result$retres +$result$retres$res + [1] -0.292151200 -0.345799659 -0.134736010 -0.284683884 0.495502316 0.492201029 0.242619592 -0.498863204 -0.056533191 0.121418837 -0.204978701 0.307114452 -0.195752934 0.028731538 0.033625439 0.003403638 -0.082101500 0.033046984 0.005351578 0.006673861 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05766098 12.692218 0.2890289 + [2,] 0.07473201 12.564307 0.4034091 + [3,] 0.10163328 12.362739 0.5836545 + [4,] 0.13189832 12.135967 0.7864379 + [5,] 0.17774205 11.792466 1.0936024 + [6,] 0.24269202 11.305805 1.5287836 + [7,] 0.31027639 10.799404 1.9816160 + [8,] 0.37860674 10.287414 2.4394466 + [9,] 0.10321981 12.350852 0.5942846 + [10,] 0.18063696 11.770775 1.1129991 + [11,] 0.25120525 11.242016 1.5858245 + [12,] 0.33231543 10.634268 2.1292831 + [13,] 0.41403009 10.021991 2.6767920 + [14,] 0.50060262 9.373314 3.2568498 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.005843024 NA NA + [2,] 0.006915993 NA NA + [3,] 0.002694720 NA NA + [4,] 0.005693678 NA NA + [5,] -0.009910046 NA NA + [6,] -0.009844021 NA NA + [7,] -0.004852392 NA NA + [8,] 0.009977264 NA NA + [9,] NA 0.02600527 -0.0067250878 +[10,] NA -0.05585267 -0.0006807275 +[11,] NA 0.09429020 0.0164202999 +[12,] NA -0.14127265 -0.0066093967 +[13,] NA 0.09004635 -0.0010703155 +[14,] NA -0.01321651 -0.0013347723 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygaM_res/KEIO_ROBOT5_9_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ygaM_res/KEIO_ROBOT5_9_res.txt new file mode 100644 index 0000000..e821ac7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygaM_res/KEIO_ROBOT5_9_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0192589402722418 0.0195219793511811 0.0192936492340559 0.00265400753456096 0.0142703850626054 0.0243867546852788 +Glc 12.979959668503 12.9904657584766 13.0181619722284 0.221148473004948 12.5929205268121 13.3535922039363 +Ace 0.0317254912983395 0.0534145744326849 0.0270485653808272 0.0662080000665088 9.99999999889284e-07 0.221326186647398 +mu 0.599601938537842 0.599290497505213 0.600018538592805 0.0288762879620682 0.550815389254956 0.658403771500777 +qGlc -4.49273901405305 -4.49908750393685 -4.51570000917262 0.502049525755187 -5.59546258038901 -3.49179916195964 +qAce 4.01748464796846 3.96860467818366 3.97729177478288 0.200917370108565 3.62755349051681 4.39525537493383 +res 1.30210859104228 36.3084862404693 36.1767861523081 7.4698835476569 23.7588816958367 51.6439406479442 + + +Goodness of fit (khi2 test) + +khi2 value 1.30210859104279 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.0930077565030562 +p-value, i.e. P(X^2<=value) 5.58007767665911e-06 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygaU.txt b/validation/validation_results/Berges_2021/Berges_2021/ygaU.txt new file mode 100644 index 0000000..781ed64 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygaU.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.101304 NA NA NA +3.34194444444444 0.15876 NA NA NA +3.9975 0.216216 NA NA NA +4.52333333333333 0.3402 NA NA NA +1.95 NA 13.7903862493265 0.415898294077704 0 +3.25 NA 13.1644674208747 1.15092414134877 0 +4.08333333333333 NA 11.4984592954263 1.88849248292632 0 +4.76666666666667 NA 10.1107641842259 2.67715372558353 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygaU_res/KEIO_ROBOT2_27.pdf b/validation/validation_results/Berges_2021/Berges_2021/ygaU_res/KEIO_ROBOT2_27.pdf new file mode 100644 index 0000000..a5d845f Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ygaU_res/KEIO_ROBOT2_27.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygaU_res/KEIO_ROBOT2_27_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ygaU_res/KEIO_ROBOT2_27_log.txt new file mode 100644 index 0000000..f9d1819 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygaU_res/KEIO_ROBOT2_27_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.101304 NA NA NA +[2,] 0.158760 NA NA NA +[3,] 0.216216 NA NA NA +[4,] 0.340200 NA NA NA +[5,] NA 13.79039 0.4158983 0 +[6,] NA 13.16447 1.1509241 0 +[7,] NA 11.49846 1.8884925 0 +[8,] NA 10.11076 2.6771537 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 1.972280e-02 1.447201e+01 1.684151e-01 1.000000e-06 6.216751e-01 -7.550233e+00 4.420354e+00 -2.352714e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-4.496878e-09 -9.505971e-08 1.190419e-07 0.000000e+00 5.621013e-08 -1.877142e-07 -9.542404e-08 4.970343e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.00879271 0.62803386 0.28675607 0.25520817 0.10680159 1.70628399 0.77090324 0.70451249 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5789312 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-4.496878e-09 -9.505971e-08 1.190419e-07 0.000000e+00 5.621013e-08 -1.877142e-07 -9.542404e-08 4.970343e-13 + +$result$normp +[1] 2.659502e-07 + +$result$res + [1] -3.955016e-01 -6.336396e-02 1.025719e+00 -5.967809e-01 2.523196e-01 -5.639161e-01 3.922137e-01 -8.061716e-02 4.181459e-01 -3.256261e-01 -4.240509e-01 3.315311e-01 4.118834e-06 2.558632e-06 6.481812e-07 -1.852781e-06 + +$result$prevres + [1] -3.955012e-01 -6.336365e-02 1.025719e+00 -5.967813e-01 2.523196e-01 -5.639162e-01 3.922136e-01 -8.061706e-02 4.181456e-01 -3.256261e-01 -4.240508e-01 3.315312e-01 4.118834e-06 2.558632e-06 6.481799e-07 -1.852783e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.367664e+02 0.000000 0 0 1.168073e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.992655e+02 0.000000 0 0 2.631660e+01 0.0000000 0.0000000 0.0000000 + [3,] 6.001437e+02 0.000000 0 0 4.731648e+01 0.0000000 0.0000000 0.0000000 + [4,] 8.321948e+02 0.000000 0 0 7.424246e+01 0.0000000 0.0000000 0.0000000 + [5,] -6.233791e+01 2.173913 0 0 -1.435209e+00 0.1628398 0.0000000 0.0000000 + [6,] -1.727141e+02 2.173913 0 0 -7.283777e+00 0.4511659 0.0000000 0.0000000 + [7,] -3.078687e+02 2.173913 0 0 -1.715322e+01 0.8042182 0.0000000 0.0000000 + [8,] -4.847988e+02 2.173913 0 0 -3.267868e+01 1.2663972 0.0000000 0.0000000 + [9,] 8.394151e+01 0.000000 5 0 1.932590e+00 0.0000000 0.3745316 0.0000000 +[10,] 2.325693e+02 0.000000 5 0 9.808016e+00 0.0000000 1.0376816 0.0000000 +[11,] 4.145625e+02 0.000000 5 0 2.309777e+01 0.0000000 1.8497018 0.0000000 +[12,] 6.528089e+02 0.000000 5 0 4.400368e+01 0.0000000 2.9127136 0.0000000 +[13,] -4.467751e-05 0.000000 0 5 -1.028612e-06 0.0000000 0.0000000 0.3745316 +[14,] -1.237840e-04 0.000000 0 5 -5.220274e-06 0.0000000 0.0000000 1.0376816 +[15,] -2.206491e-04 0.000000 0 5 -1.229369e-05 0.0000000 0.0000000 1.8497018 +[16,] -3.474547e-04 0.000000 0 5 -2.342077e-05 0.0000000 0.0000000 2.9127136 + +$result$retres +$result$retres$res + [1] -3.955012e-01 -6.336365e-02 1.025719e+00 -5.967813e-01 2.523196e-01 -5.639162e-01 3.922136e-01 -8.061706e-02 4.181456e-01 -3.256261e-01 -4.240508e-01 3.315312e-01 4.118834e-06 2.558632e-06 6.481799e-07 -1.852783e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09339398 13.57728 0.6922459 7.211932e-07 + [2,] 0.15749273 12.79880 1.1480132 4.786131e-07 + [3,] 0.23673037 11.83646 1.7114240 1.787401e-07 + [4,] 0.32826437 10.72478 2.3622667 -1.676681e-07 + [5,] 0.06629020 13.90645 0.4995274 8.237668e-07 + [6,] 0.14874296 12.90507 1.0857989 5.117263e-07 + [7,] 0.24970551 11.67888 1.8036823 1.296360e-07 + [8,] 0.38187509 10.07368 2.7434600 -3.705566e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.007910024 NA NA NA +[2,] 0.001267273 NA NA NA +[3,] -0.020514373 NA NA NA +[4,] 0.011935627 NA NA NA +[5,] NA -0.11606702 -0.08362913 -8.237668e-07 +[6,] NA 0.25940143 0.06512522 -5.117263e-07 +[7,] NA -0.18041826 0.08481015 -1.296360e-07 +[8,] NA 0.03708385 -0.06630624 3.705566e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygaU_res/KEIO_ROBOT2_27_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ygaU_res/KEIO_ROBOT2_27_res.txt new file mode 100644 index 0000000..010800d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygaU_res/KEIO_ROBOT2_27_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0197228035770298 0.0194941338244563 0.0190234373505077 0.00418619645436559 0.0125929589525639 0.029132062981468 +Glc 14.4720133707724 14.4595094514186 14.4670593467965 0.402954650239673 13.6129845568065 15.2174966916061 +Ace 0.168415066688336 0.194685980655363 0.192263733186119 0.13735753983091 9.99999999995709e-07 0.476407731485118 +Lac 9.99999999999999e-07 0.0799994952931605 0.0673935123015535 0.0769564471171164 9.99999999978836e-07 0.272094682162562 +mu 0.6216751253604 0.630810801383115 0.634442323479948 0.0494554667230886 0.533732544054405 0.719935570446969 +qGlc -7.55023302506846 -7.63334227581321 -7.60922107874018 1.07062296515216 -9.47765454087032 -5.69739423705425 +qAce 4.42035391488983 4.37641742614177 4.38324482069605 0.473881621658114 3.40458066586172 5.20069376665979 +qLac -2.35271386084534e-06 -0.0148834141994813 0.0200489538095376 0.228608587451643 -0.492419586176154 0.418677788252001 +res 2.6812902345601 19.0923506051514 19.0230070890496 5.50699745018998 9.48183318177975 29.6233585171464 + + +Goodness of fit (khi2 test) + +khi2 value 2.68129023456073 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.335161279320092 +p-value, i.e. P(X^2<=value) 0.04725920989457 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygdI.txt b/validation/validation_results/Berges_2021/Berges_2021/ygdI.txt new file mode 100644 index 0000000..4ebe652 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygdI.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.061992 NA NA +1.61361111111111 0.077112 NA NA +2.36138888888889 0.1134 NA NA +3.28638888888889 0.198072 NA NA +3.81944444444444 0.288792 NA NA +4.41083333333333 0.40068 NA NA +0.283333333333333 NA 14.2338709270593 0.0377650163153612 +1.91666666666667 NA 13.7186640531812 0.378113295198293 +2.7 NA 13.428512521451 0.565351300173037 +3.61666666666667 NA 12.6240766360425 1.22506340762229 +4.05 NA 11.7545275686641 1.33176071667687 +4.75 NA 10.4786883043363 2.15662192110782 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygdI_res/KEIO_ROBOT4_32.pdf b/validation/validation_results/Berges_2021/Berges_2021/ygdI_res/KEIO_ROBOT4_32.pdf new file mode 100644 index 0000000..cc240f0 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ygdI_res/KEIO_ROBOT4_32.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygdI_res/KEIO_ROBOT4_32_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ygdI_res/KEIO_ROBOT4_32_log.txt new file mode 100644 index 0000000..773ef35 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygdI_res/KEIO_ROBOT4_32_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.061992 NA NA + [3,] 0.077112 NA NA + [4,] 0.113400 NA NA + [5,] 0.198072 NA NA + [6,] 0.288792 NA NA + [7,] 0.400680 NA NA + [8,] NA 14.23387 0.03776502 + [9,] NA 13.71866 0.37811330 +[10,] NA 13.42851 0.56535130 +[11,] NA 12.62408 1.22506341 +[12,] NA 11.75453 1.33176072 +[13,] NA 10.47869 2.15662192 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02916068 14.30805805 0.06599816 0.59423249 -4.92328732 2.71456134 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.552805e-09 1.456393e-09 -2.306613e-08 -1.388447e-08 7.090469e-08 2.934140e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.004051516 0.223947939 0.098334723 0.034918943 0.551228803 0.245067624 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3376069 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.552805e-09 1.456393e-09 -2.306613e-08 -1.388447e-08 7.090469e-08 2.934140e-08 + +$result$normp +[1] 8.134955e-08 + +$result$res + [1] -0.28076608 -0.13365196 -0.05199596 0.26165286 0.37401220 -0.33181338 0.01440061 0.06496762 0.16600754 -0.17568729 -0.31899342 0.24823312 0.01547243 0.26330011 -0.14622308 0.15081562 -0.74829460 0.39611149 0.08429046 + +$result$prevres + [1] -0.28076616 -0.13365206 -0.05199607 0.26165274 0.37401212 -0.33181338 0.01440077 0.06496762 0.16600756 -0.17568727 -0.31899341 0.24823312 0.01547236 0.26330022 -0.14622303 0.15081562 -0.74829464 0.39611143 0.08429040 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 101.710531 0.000000 0 3.54430778 0.00000000 0.00000000 + [3,] 130.436064 0.000000 0 6.13753756 0.00000000 0.00000000 + [4,] 203.412725 0.000000 0 14.00693886 0.00000000 0.00000000 + [5,] 352.447653 0.000000 0 33.77623028 0.00000000 0.00000000 + [6,] 483.794895 0.000000 0 53.88390723 0.00000000 0.00000000 + [7,] 687.514932 0.000000 0 88.43015442 0.00000000 0.00000000 + [8,] -3.302692 2.173913 0 -0.01402641 0.01956187 0.00000000 + [9,] -38.246154 2.173913 0 -1.26744515 0.22653232 0.00000000 +[10,] -71.594455 2.173913 0 -3.54164738 0.42405462 0.00000000 +[11,] -136.479087 2.173913 0 -9.59580898 0.80836690 0.00000000 +[12,] -181.851749 2.173913 0 -14.67997229 1.07710960 0.00000000 +[13,] -284.946900 2.173913 0 -27.98053698 1.68774313 0.00000000 +[14,] 4.188325 0.000000 5 0.01778766 0.00000000 0.04499231 +[15,] 48.502047 0.000000 5 1.60731678 0.00000000 0.52102434 +[16,] 90.792858 0.000000 5 4.49135747 0.00000000 0.97532562 +[17,] 173.076623 0.000000 5 12.16897218 0.00000000 1.85924387 +[18,] 230.616187 0.000000 5 18.61647879 0.00000000 2.47735207 +[19,] 361.356807 0.000000 5 35.48365506 0.00000000 3.88180920 + +$result$retres +$result$retres$res + [1] -0.28076616 -0.13365206 -0.05199607 0.26165274 0.37401212 -0.33181338 0.01440077 0.06496762 0.16600756 -0.17568727 -0.31899341 0.24823312 0.01547236 0.26330022 -0.14622303 0.15081562 -0.74829464 0.39611143 0.08429040 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02916068 14.30806 0.06599818 + [2,] 0.05931896 14.05819 0.20376666 + [3,] 0.07607208 13.91939 0.28029793 + [4,] 0.11863305 13.56677 0.47472415 + [5,] 0.20555224 12.84663 0.87178668 + [6,] 0.28215573 12.21196 1.22172525 + [7,] 0.40096802 11.22759 1.76448120 + [8,] 0.03450786 14.26376 0.09042506 + [9,] 0.09108260 13.79503 0.34886869 + [10,] 0.14507471 13.34770 0.59551443 + [11,] 0.25012531 12.47734 1.07540448 + [12,] 0.32358530 11.86871 1.41098300 + [13,] 0.49050012 10.48581 2.17348000 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0056153231 NA NA + [2,] 0.0026730413 NA NA + [3,] 0.0010399214 NA NA + [4,] -0.0052330547 NA NA + [5,] -0.0074802425 NA NA + [6,] 0.0066362676 NA NA + [7,] -0.0002880155 NA NA + [8,] NA -0.029885106 -0.05266004 + [9,] NA -0.076363480 0.02924461 +[10,] NA 0.080816142 -0.03016312 +[11,] NA 0.146736966 0.14965893 +[12,] NA -0.114187236 -0.07922229 +[13,] NA -0.007117288 -0.01685808 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygdI_res/KEIO_ROBOT4_32_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ygdI_res/KEIO_ROBOT4_32_res.txt new file mode 100644 index 0000000..88d5e0d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygdI_res/KEIO_ROBOT4_32_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0291606784310061 0.0291147801379183 0.0288085221415007 0.00416233060197706 0.0225348020390324 0.0378133791204471 +Glc 14.3080580497003 14.3261856394213 14.3372000968662 0.207587078035304 13.8787555157415 14.7556066570717 +Ace 0.0659981601146967 0.0947762884236066 0.0864294563814445 0.0657283180667172 9.99999999995709e-07 0.233244222904248 +mu 0.59423249157929 0.596623571345668 0.598452900273448 0.034624587467676 0.529158268042511 0.660178439608453 +qGlc -4.92328731609308 -4.97287125988641 -4.93577621315853 0.524111181322662 -5.87655439164848 -3.9475795039161 +qAce 2.71456134314506 2.67920314370298 2.66612409832666 0.240500158440135 2.18554959460635 3.19236466062057 +res 1.48171955269251 31.1179613037376 31.77037468268 7.83577465777862 16.9729942325597 49.0865261870533 + + +Goodness of fit (khi2 test) + +khi2 value 1.48171955269261 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.113978427130201 +p-value, i.e. P(X^2<=value) 4.01776084399455e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygeA.txt b/validation/validation_results/Berges_2021/Berges_2021/ygeA.txt new file mode 100644 index 0000000..180d1af --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygeA.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.092232 NA NA NA +3.34194444444444 0.161784 NA NA NA +3.9975 0.20412 NA NA NA +4.52333333333333 0.311472 NA NA NA +1.95 NA 13.6535646245786 0.365865115402857 0 +3.25 NA 12.9230128844916 0.873755475665086 0 +4.08333333333333 NA 12.1175596065268 1.31874129166162 0 +4.76666666666667 NA 10.7200471513699 1.74211946389674 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygeA_res/KEIO_ROBOT2_4.pdf b/validation/validation_results/Berges_2021/Berges_2021/ygeA_res/KEIO_ROBOT2_4.pdf new file mode 100644 index 0000000..b29d62d Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ygeA_res/KEIO_ROBOT2_4.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygeA_res/KEIO_ROBOT2_4_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ygeA_res/KEIO_ROBOT2_4_log.txt new file mode 100644 index 0000000..ceec4ee --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygeA_res/KEIO_ROBOT2_4_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.092232 NA NA NA +[2,] 0.161784 NA NA NA +[3,] 0.204120 NA NA NA +[4,] 0.311472 NA NA NA +[5,] NA 13.65356 0.3658651 0 +[6,] NA 12.92301 0.8737555 0 +[7,] NA 12.11756 1.3187413 0 +[8,] NA 10.72005 1.7421195 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.123997e-02 1.417757e+01 2.227202e-01 1.000000e-06 5.876630e-01 -6.047340e+00 2.826027e+00 -2.448403e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 1.114779e-09 7.916594e-09 -2.416221e-08 0.000000e+00 -1.289316e-08 6.983307e-08 3.520810e-08 -1.556949e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.008436138 0.528381110 0.231386460 0.218767859 0.095602134 1.484143077 0.648626576 0.623291799 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.485132 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 1.114779e-09 7.916594e-09 -2.416221e-08 0.000000e+00 -1.289316e-08 6.983307e-08 3.520810e-08 -1.556949e-13 + +$result$normp +[1] 8.324799e-08 + +$result$res + [1] 7.159856e-03 -5.199827e-01 9.205643e-01 -4.183314e-01 1.197584e-01 -5.976154e-03 -2.822656e-01 1.684833e-01 3.799494e-01 -3.173612e-01 -3.633143e-01 3.007261e-01 4.050734e-06 2.454747e-06 5.669337e-07 -1.842399e-06 + +$result$prevres + [1] 7.159762e-03 -5.199828e-01 9.205642e-01 -4.183313e-01 1.197584e-01 -5.976134e-03 -2.822656e-01 1.684833e-01 3.799495e-01 -3.173612e-01 -3.633143e-01 3.007261e-01 4.050734e-06 2.454747e-06 5.669340e-07 -1.842399e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.174561e+02 0.000000 0 0 1.155331e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.563667e+02 0.000000 0 0 2.529590e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.238503e+02 0.000000 0 0 4.447844e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.135260e+02 0.000000 0 0 6.855233e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.799408e+01 2.173913 0 0 -1.179706e+00 0.1685688 0.0000000 0.0000000 + [6,] -1.286858e+02 2.173913 0 0 -5.776306e+00 0.4519811 0.0000000 0.0000000 + [7,] -2.241321e+02 2.173913 0 0 -1.327832e+01 0.7872152 0.0000000 0.0000000 + [8,] -3.459459e+02 2.173913 0 0 -2.478622e+01 1.2150598 0.0000000 0.0000000 + [9,] 5.158548e+01 0.000000 5 0 1.267983e+00 0.0000000 0.3877082 0.0000000 +[10,] 1.383154e+02 0.000000 5 0 6.208548e+00 0.0000000 1.0395564 0.0000000 +[11,] 2.409039e+02 0.000000 5 0 1.427194e+01 0.0000000 1.8105950 0.0000000 +[12,] 3.718331e+02 0.000000 5 0 2.664098e+01 0.0000000 2.7946375 0.0000000 +[13,] -4.469243e-05 0.000000 0 5 -1.098551e-06 0.0000000 0.0000000 0.3877082 +[14,] -1.198332e-04 0.000000 0 5 -5.378938e-06 0.0000000 0.0000000 1.0395564 +[15,] -2.087134e-04 0.000000 0 5 -1.236487e-05 0.0000000 0.0000000 1.8105950 +[16,] -3.221473e-04 0.000000 0 5 -2.308111e-05 0.0000000 0.0000000 2.7946375 + +$result$retres +$result$retres$res + [1] 7.159762e-03 -5.199828e-01 9.205642e-01 -4.183313e-01 1.197584e-01 -5.976134e-03 -2.822656e-01 1.684833e-01 3.799495e-01 -3.173612e-01 -3.633143e-01 3.007261e-01 4.050734e-06 2.454747e-06 5.669340e-07 -1.842399e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09237520 13.44556 0.5648042 7.036266e-07 + [2,] 0.15138434 12.83832 0.8485748 4.577745e-07 + [3,] 0.22253128 12.10619 1.1907150 1.613523e-07 + [4,] 0.30310537 11.27704 1.5781898 -1.743466e-07 + [5,] 0.06680832 13.70865 0.4418550 8.101468e-07 + [6,] 0.14342175 12.92026 0.8102832 4.909494e-07 + [7,] 0.23404392 11.98772 1.2460784 1.133868e-07 + [8,] 0.34970101 10.79755 1.8022647 -3.684797e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] -0.0001431952 NA NA NA +[2,] 0.0103996561 NA NA NA +[3,] -0.0184112849 NA NA NA +[4,] 0.0083666262 NA NA NA +[5,] NA -0.055088860 -0.07598990 -8.101468e-07 +[6,] NA 0.002749022 0.06347225 -4.909494e-07 +[7,] NA 0.129842157 0.07266286 -1.133868e-07 +[8,] NA -0.077502319 -0.06014521 3.684797e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygeA_res/KEIO_ROBOT2_4_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ygeA_res/KEIO_ROBOT2_4_res.txt new file mode 100644 index 0000000..fc7deca --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygeA_res/KEIO_ROBOT2_4_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0212399691661844 0.0220371982188674 0.0211764456979644 0.00522069517676335 0.0143719796791161 0.0338235851261972 +Glc 14.1775741061544 14.2141315854167 14.2088689510965 0.372240971762005 13.5276643013199 15.001407579369 +Ace 0.222720211844331 0.227091620636816 0.219430280832293 0.149295116205485 9.99999999996739e-07 0.554881480985938 +Lac 1e-06 0.0794101299092057 0.0656756150185733 0.0689958119625427 9.99999999998265e-07 0.218257631153853 +mu 0.587663027928844 0.584709326937979 0.585071844609055 0.0551207477631241 0.477954617491812 0.677811205245121 +qGlc -6.047339867457 -6.13845240891482 -6.07262838661535 1.10063849948712 -8.56252977529039 -4.3474985617811 +qAce 2.82602742196031 2.79351067874156 2.82023416915288 0.450613529573552 1.92262675622448 3.53190017785601 +qLac -2.44840305774115e-06 0.00569176730048895 -0.0160651696234355 0.228904084221094 -0.375545315721657 0.491814138524109 +res 1.88282446856577 21.2904521039752 20.9142800290046 6.77642992415422 10.4838209925658 34.4040869734523 + + +Goodness of fit (khi2 test) + +khi2 value 1.8828244685658 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.235353058570725 +p-value, i.e. P(X^2<=value) 0.0156042346721642 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygeV.txt b/validation/validation_results/Berges_2021/Berges_2021/ygeV.txt new file mode 100644 index 0000000..ca69c85 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygeV.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.154224 NA NA +3.67805555555556 0.2646 NA NA +4.09222222222222 0.338688 NA NA +4.565 0.449064 NA NA +0.05 NA 14.0454801624688 0.0144986884884332 +1.95 NA 13.9420664915931 0.440966559349163 +2.83333333333333 NA 13.0933265647112 0.764262298546003 +3.98333333333333 NA 11.679387251573 1.44564455274809 +4.88333333333333 NA 9.28260821014881 2.07308756007992 +5.16666666666667 NA 8.45363504229892 2.26202567413835 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygeV_res/KEIO_ROBOT3_23.pdf b/validation/validation_results/Berges_2021/Berges_2021/ygeV_res/KEIO_ROBOT3_23.pdf new file mode 100644 index 0000000..cc53a87 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ygeV_res/KEIO_ROBOT3_23.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygeV_res/KEIO_ROBOT3_23_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ygeV_res/KEIO_ROBOT3_23_log.txt new file mode 100644 index 0000000..ccfb522 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygeV_res/KEIO_ROBOT3_23_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.154224 NA NA + [2,] 0.264600 NA NA + [3,] 0.338688 NA NA + [4,] 0.449064 NA NA + [5,] NA 14.045480 0.01449869 + [6,] NA 13.942066 0.44096656 + [7,] NA 13.093327 0.76426230 + [8,] NA 11.679387 1.44564455 + [9,] NA 9.282608 2.07308756 +[10,] NA 8.453635 2.26202567 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0293358 14.3250214 0.2043055 0.5968408 -5.7463363 2.1472693 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.221015e-08 2.341944e-07 4.667627e-08 -9.805988e-08 5.855704e-08 -3.212504e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.009902352 0.416075768 0.178570453 0.080230155 0.731191853 0.311402266 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6111472 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.221015e-08 2.341944e-07 4.667627e-08 -9.805988e-08 5.855704e-08 -3.212504e-07 + +$result$normp +[1] 4.164388e-07 + +$result$res + [1] 0.45622928 -0.05540925 -0.06533263 -0.08467815 0.58909905 -0.51965628 -0.03948259 -0.25176934 0.25293170 -0.03112256 0.96501940 -0.02117812 -0.46457496 -1.04725769 -0.14014393 0.70813530 + +$result$prevres + [1] 0.45622818 -0.05540998 -0.06533289 -0.08467745 0.58909855 -0.51965639 -0.03948247 -0.25176901 0.25293188 -0.03112256 0.96501916 -0.02117853 -0.46457541 -1.04725792 -0.14014347 0.70813616 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 278.4117735 0.000000 0 2.349724e+01 0.000000000 0.000000000 + [2,] 449.0962014 0.000000 0 4.845687e+01 0.000000000 0.000000000 + [3,] 575.0337544 0.000000 0 6.903197e+01 0.000000000 0.000000000 + [4,] 762.4995157 0.000000 0 1.021123e+02 0.000000000 0.000000000 + [5,] -0.6340149 2.173913 0 -4.672956e-04 0.003236727 0.000000000 + [6,] -46.0927346 2.173913 0 -1.568496e+00 0.235309335 0.000000000 + [7,] -92.6199654 2.173913 0 -4.885640e+00 0.472836829 0.000000000 + [8,] -204.6356333 2.173913 0 -1.630012e+01 1.044691213 0.000000000 + [9,] -365.0434145 2.173913 0 -3.735068e+01 1.863593556 0.000000000 +[10,] -436.1569013 2.173913 0 -4.784201e+01 2.226637047 0.000000000 +[11,] 0.5449075 0.000000 5 4.016199e-04 0.000000000 0.007444473 +[12,] 39.6146521 0.000000 5 1.348053e+00 0.000000000 0.541211471 +[13,] 79.6027342 0.000000 5 4.198990e+00 0.000000000 1.087524707 +[14,] 175.8752106 0.000000 5 1.400923e+01 0.000000000 2.402789789 +[15,] 313.7385527 0.000000 5 3.210124e+01 0.000000000 4.286265178 +[16,] 374.8574266 0.000000 5 4.111808e+01 0.000000000 5.121265208 + +$result$retres +$result$retres$res + [1] 0.45622818 -0.05540998 -0.06533289 -0.08467745 0.58909855 -0.51965639 -0.03948247 -0.25176901 0.25293188 -0.03112256 0.96501916 -0.02117853 -0.46457541 -1.04725792 -0.14014347 0.70813616 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.16334856 13.034757 0.6864466 + [2,] 0.26349180 12.070586 1.0467344 + [3,] 0.33738134 11.359183 1.3125687 + [4,] 0.44737045 10.300217 1.7082793 + [5,] 0.03022442 14.316465 0.2075025 + [6,] 0.09393922 13.703025 0.4367309 + [7,] 0.15915164 13.075165 0.6713472 + [8,] 0.31615245 11.563574 1.2361930 + [9,] 0.54097949 9.398957 2.0450589 + [10,] 0.64065193 8.439319 2.4036529 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.009124564 NA NA + [2,] 0.001108200 NA NA + [3,] 0.001306658 NA NA + [4,] 0.001693549 NA NA + [5,] NA -0.27098533 -0.193003833 + [6,] NA 0.23904194 0.004235706 + [7,] NA 0.01816194 0.092915082 + [8,] NA 0.11581374 0.209451584 + [9,] NA -0.11634867 0.028028694 +[10,] NA 0.01431638 -0.141627232 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygeV_res/KEIO_ROBOT3_23_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ygeV_res/KEIO_ROBOT3_23_res.txt new file mode 100644 index 0000000..ec69c99 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygeV_res/KEIO_ROBOT3_23_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0293357981254432 0.0290300652013839 0.0287738240001857 0.00375184384722597 0.0226202323599295 0.0358491619871336 +Glc 14.3250214204015 14.3428308899989 14.3490535653526 0.260390439573346 13.8935864279206 14.7921698741551 +Ace 0.20430550987948 0.229616817136459 0.230770922297575 0.110552965231541 1.000000000001e-06 0.415132620110895 +mu 0.596840836845522 0.599743871995364 0.597200201525897 0.0283811616491064 0.554600312055332 0.655806309940137 +qGlc -5.74633632808827 -5.84134050993795 -5.82828014324001 0.494041561611712 -6.76363419093215 -4.99572787746393 +qAce 2.14726930250589 2.11436704322991 2.09043338242462 0.195799874129009 1.77984027313253 2.52550977504977 +res 3.73500959297403 23.7877935822187 22.7311290839764 7.11151086952964 12.1955500850578 41.7369027167223 + + +Goodness of fit (khi2 test) + +khi2 value 3.73500959297795 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.373500959297795 +p-value, i.e. P(X^2<=value) 0.0414895966075159 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggE.txt b/validation/validation_results/Berges_2021/Berges_2021/yggE.txt new file mode 100644 index 0000000..3ce59aa --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yggE.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.10584 NA NA NA +3.34194444444444 0.160272 NA NA NA +3.9975 0.208656 NA NA NA +4.52333333333333 0.303912 NA NA NA +1.95 NA 13.6701275114696 0.358161324696786 0 +3.25 NA 12.8038640691561 0.861437437261192 0 +4.08333333333333 NA 12.0594443022253 1.34562291442891 0 +4.76666666666667 NA 10.9749423750066 1.90507043960789 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggE_res/KEIO_ROBOT2_39.pdf b/validation/validation_results/Berges_2021/Berges_2021/yggE_res/KEIO_ROBOT2_39.pdf new file mode 100644 index 0000000..ea09f57 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yggE_res/KEIO_ROBOT2_39.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggE_res/KEIO_ROBOT2_39_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yggE_res/KEIO_ROBOT2_39_log.txt new file mode 100644 index 0000000..0a549ea --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yggE_res/KEIO_ROBOT2_39_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.105840 NA NA NA +[2,] 0.160272 NA NA NA +[3,] 0.208656 NA NA NA +[4,] 0.303912 NA NA NA +[5,] NA 13.67013 0.3581613 0 +[6,] NA 12.80386 0.8614374 0 +[7,] NA 12.05944 1.3456229 0 +[8,] NA 10.97494 1.9050704 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.670267e-02 1.413014e+01 1.027088e-01 1.000000e-06 5.315586e-01 -5.408293e+00 3.130935e+00 -2.340082e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 8.989966e-09 1.663907e-07 -1.240150e-07 4.235165e-22 -8.339979e-08 6.519117e-08 4.767679e-08 -1.034765e-12 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.007008092 0.379586704 0.170159159 0.158165472 0.063652409 1.005665945 0.446501525 0.424972000 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3370508 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 8.989966e-09 1.663907e-07 -1.240150e-07 4.235165e-22 -8.339979e-08 6.519117e-08 4.767679e-08 -1.034765e-12 + +$result$normp +[1] 2.379599e-07 + +$result$res + [1] -2.456466e-01 -1.245920e-01 7.450772e-01 -4.130446e-01 -7.455774e-02 1.504694e-01 -8.339973e-02 7.488046e-03 1.535603e-01 -1.549857e-01 -1.097422e-01 1.111677e-01 3.930593e-06 2.280442e-06 4.372092e-07 -1.818575e-06 + +$result$prevres + [1] -2.456473e-01 -1.245925e-01 7.450772e-01 -4.130440e-01 -7.455786e-02 1.504695e-01 -8.339965e-02 7.488025e-03 1.535605e-01 -1.549857e-01 -1.097424e-01 1.111676e-01 3.930594e-06 2.280444e-06 4.372117e-07 -1.818572e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 1.889832e+02 0.000000 0 0 1.262289e+01 0.0000000 0.0000000 0.0000000 + [2,] 2.954390e+02 0.000000 0 0 2.636462e+01 0.0000000 0.0000000 0.0000000 + [3,] 4.186054e+02 0.000000 0 0 4.468356e+01 0.0000000 0.0000000 0.0000000 + [4,] 5.535987e+02 0.000000 0 0 6.686643e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.024294e+01 2.173913 0 0 -1.225570e+00 0.1986936 0.0000000 0.0000000 + [6,] -1.023399e+02 2.173913 0 0 -5.659925e+00 0.5052883 0.0000000 0.0000000 + [7,] -1.717028e+02 2.173913 0 0 -1.250802e+01 0.8477573 0.0000000 0.0000000 + [8,] -2.565904e+02 2.173913 0 0 -2.258506e+01 1.2668776 0.0000000 0.0000000 + [9,] 5.358353e+01 0.000000 5 0 1.631848e+00 0.0000000 0.4569953 0.0000000 +[10,] 1.362657e+02 0.000000 5 0 7.536198e+00 0.0000000 1.1621631 0.0000000 +[11,] 2.286225e+02 0.000000 5 0 1.665444e+01 0.0000000 1.9498419 0.0000000 +[12,] 3.416505e+02 0.000000 5 0 3.007203e+01 0.0000000 2.9138184 0.0000000 +[13,] -4.004868e-05 0.000000 0 5 -1.219654e-06 0.0000000 0.0000000 0.4569953 +[14,] -1.018459e-04 0.000000 0 5 -5.632604e-06 0.0000000 0.0000000 1.1621631 +[15,] -1.708739e-04 0.000000 0 5 -1.244764e-05 0.0000000 0.0000000 1.9498419 +[16,] -2.553518e-04 0.000000 0 5 -2.247604e-05 0.0000000 0.0000000 2.9138184 + +$result$retres +$result$retres$res + [1] -2.456473e-01 -1.245925e-01 7.450772e-01 -4.130440e-01 -7.455786e-02 1.504695e-01 -8.339965e-02 7.488025e-03 1.535605e-01 -1.549857e-01 -1.097424e-01 1.111676e-01 3.930594e-06 2.280444e-06 4.372117e-07 -1.818572e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10092705 13.37495 0.5398982 6.732419e-07 + [2,] 0.15778015 12.79651 0.8747687 4.229574e-07 + [3,] 0.22355754 12.12726 1.2622043 1.333856e-07 + [4,] 0.29565112 11.39375 1.6868428 -1.839921e-07 + [5,] 0.07528662 13.63583 0.3888734 7.861188e-07 + [6,] 0.15025423 12.87308 0.8304403 4.560888e-07 + [7,] 0.23399373 12.02108 1.3236744 8.744234e-08 + [8,] 0.33647574 10.97839 1.9273040 -3.637143e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.004912945 NA NA NA +[2,] 0.002491849 NA NA NA +[3,] -0.014901544 NA NA NA +[4,] 0.008260880 NA NA NA +[5,] NA 0.034296615 -0.03071211 -7.861188e-07 +[6,] NA -0.069215960 0.03099715 -4.560888e-07 +[7,] NA 0.038363837 0.02194848 -8.744234e-08 +[8,] NA -0.003444492 -0.02223351 3.637143e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggE_res/KEIO_ROBOT2_39_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yggE_res/KEIO_ROBOT2_39_res.txt new file mode 100644 index 0000000..3f5d064 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yggE_res/KEIO_ROBOT2_39_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0267026664816497 0.0269449766368109 0.0266787044190442 0.00632916491522331 0.0170573351438986 0.0405081558689016 +Glc 14.1301440502259 14.1964322145345 14.1455279716857 0.341570391810498 13.6315803048344 14.8609074747089 +Ace 0.102708792577151 0.123303563996782 0.0992738236310497 0.122730072195119 9.99999999944101e-07 0.383151139557355 +Lac 1e-06 0.0950009711334603 0.0741274666305339 0.0791004756224482 9.99999999989418e-07 0.280417856677885 +mu 0.531558579550592 0.536117461453027 0.532716949140957 0.0553482475830371 0.434306216649772 0.6388530139762 +qGlc -5.40829342281796 -5.56033417411794 -5.64410414373841 0.977015718876804 -7.68523806730949 -3.65041621540025 +qAce 3.13093476223819 3.08960537307122 3.11427853614606 0.425142080596322 2.26670734984675 3.86225169621912 +qLac -2.34008222157682e-06 -0.0352946745646934 -0.0355831470351027 0.187999854359653 -0.377849535175853 0.30624256320813 +res 0.908825761412961 19.0102587471832 18.3421368042212 6.52629251458714 8.24640505777858 31.1772220220492 + + +Goodness of fit (khi2 test) + +khi2 value 0.908825761414105 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.113603220176763 +p-value, i.e. P(X^2<=value) 0.00123862319309735 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggL.txt b/validation/validation_results/Berges_2021/Berges_2021/yggL.txt new file mode 100644 index 0000000..43c0bc9 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yggL.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.16632 NA NA +3.67805555555556 0.269136 NA NA +4.09222222222222 0.35532 NA NA +4.565 0.464184 NA NA +0.05 NA 14.7878401817743 0.016257679675552 +1.95 NA 13.505500171676 0.47057132255511 +2.83333333333333 NA 13.6525003211222 0.842016541772457 +3.98333333333333 NA 11.81567689001 1.60791760781478 +4.88333333333333 NA 8.81615952687584 2.09102580166301 +5.16666666666667 NA 8.07834859627695 2.51793786842694 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggL_res/KEIO_ROBOT3_30.pdf b/validation/validation_results/Berges_2021/Berges_2021/yggL_res/KEIO_ROBOT3_30.pdf new file mode 100644 index 0000000..96acf1b Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yggL_res/KEIO_ROBOT3_30.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggL_res/KEIO_ROBOT3_30_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yggL_res/KEIO_ROBOT3_30_log.txt new file mode 100644 index 0000000..8ab986b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yggL_res/KEIO_ROBOT3_30_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.166320 NA NA + [2,] 0.269136 NA NA + [3,] 0.355320 NA NA + [4,] 0.464184 NA NA + [5,] NA 14.787840 0.01625768 + [6,] NA 13.505500 0.47057132 + [7,] NA 13.652500 0.84201654 + [8,] NA 11.815677 1.60791761 + [9,] NA 8.816160 2.09102580 +[10,] NA 8.078349 2.51793787 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03205155 14.74298196 0.21839703 0.58452340 -6.30240358 2.20750218 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.008096e-08 1.084296e-07 -1.092146e-07 -7.640456e-08 2.150259e-07 7.599432e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.01332072 0.55185743 0.23507303 0.09887684 0.93332246 0.39256625 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7995667 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.008096e-08 1.084296e-07 -1.092146e-07 -7.640456e-08 2.150259e-07 7.599432e-08 + +$result$normp +[1] 2.85719e-07 + +$result$res + [1] 0.29684446 0.29985654 -0.24127177 -0.10619727 -0.11979859 1.09282378 -0.81409216 -0.59380591 0.59032266 -0.15544978 1.02864626 0.02596677 -0.55248010 -1.34258801 0.54103761 0.29941746 + +$result$prevres + [1] 0.29684365 0.29985607 -0.24127180 -0.10619648 -0.11979882 1.09282385 -0.81409194 -0.59380563 0.59032261 -0.15545007 1.02864680 0.02596698 -0.55248010 -1.34258826 0.54103733 0.29941725 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 268.7185533 0.000000 0 2.477867e+01 0.000000000 0.000000000 + [2,] 429.2042059 0.000000 0 5.059775e+01 0.000000000 0.000000000 + [3,] 546.7671074 0.000000 0 7.171508e+01 0.000000000 0.000000000 + [4,] 720.8078930 0.000000 0 1.054652e+02 0.000000000 0.000000000 + [5,] -0.6951527 2.173913 0 -5.597309e-04 0.003535273 0.000000000 + [6,] -49.8370340 2.173913 0 -1.847069e+00 0.253451504 0.000000000 + [7,] -99.3619621 2.173913 0 -5.703546e+00 0.505315761 0.000000000 + [8,] -217.0726253 2.173913 0 -1.880376e+01 1.103945781 0.000000000 + [9,] -383.5720060 2.173913 0 -4.267211e+01 1.950695982 0.000000000 +[10,] -456.8823503 2.173913 0 -5.448859e+01 2.323523487 0.000000000 +[11,] 0.5600193 0.000000 5 4.509228e-04 0.000000000 0.008131127 +[12,] 40.1490178 0.000000 5 1.488010e+00 0.000000000 0.582938460 +[13,] 80.0466012 0.000000 5 4.594812e+00 0.000000000 1.162226251 +[14,] 174.8750276 0.000000 5 1.514843e+01 0.000000000 2.539075297 +[15,] 309.0079417 0.000000 5 3.437691e+01 0.000000000 4.486600758 +[16,] 368.0672010 0.000000 5 4.389634e+01 0.000000000 5.344104019 + +$result$retres +$result$retres$res + [1] 0.29684365 0.29985607 -0.24127180 -0.10619648 -0.11979882 1.09282385 -0.81409194 -0.59380563 0.59032261 -0.15545007 1.02864680 0.02596698 -0.55248010 -1.34258826 0.54103733 0.29941725 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.17225687 13.231271 0.7478944 + [2,] 0.27513312 12.122046 1.1364152 + [3,] 0.35049456 11.309490 1.4210240 + [4,] 0.46206007 10.106577 1.8423606 + [5,] 0.03300211 14.732733 0.2219870 + [6,] 0.10019978 14.008199 0.4757647 + [7,] 0.16792125 13.278018 0.7315205 + [8,] 0.32888136 11.542526 1.3394000 + [9,] 0.55655623 9.087708 2.1992333 + [10,] 0.65680239 8.006842 2.5778213 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.005936873 NA NA + [2,] -0.005997121 NA NA + [3,] 0.004825436 NA NA + [4,] 0.002123930 NA NA + [5,] NA 0.05510746 -0.205729360 + [6,] NA -0.50269897 -0.005193396 + [7,] NA 0.37448229 0.110496019 + [8,] NA 0.27315059 0.268517652 + [9,] NA -0.27154840 -0.108207465 +[10,] NA 0.07150703 -0.059883450 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggL_res/KEIO_ROBOT3_30_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yggL_res/KEIO_ROBOT3_30_res.txt new file mode 100644 index 0000000..78edb30 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yggL_res/KEIO_ROBOT3_30_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0320515507803656 0.0313190782601683 0.03100670733295 0.00361008757703715 0.0253840119462531 0.0383220017272009 +Glc 14.7429819646367 14.7446729448051 14.7941960657236 0.278499624481247 14.271546890692 15.255133287185 +Ace 0.218397034183877 0.25605307883299 0.255849480554035 0.116340216793051 0.0266101501760457 0.470653482155923 +mu 0.584523395916658 0.590495750930976 0.591763070182961 0.0240639689826323 0.545189180921772 0.632424457053928 +qGlc -6.30240358216438 -6.32095552502018 -6.28093970626874 0.521393461633332 -7.17968538658972 -5.40854659001043 +qAce 2.20750218139997 2.17555804123064 2.20476188001783 0.211755292357538 1.78389419129347 2.55099881823334 +res 6.39306973452499 23.1146422773036 22.4614534719634 6.90450815776572 10.8874781213702 36.319397138565 + + +Goodness of fit (khi2 test) + +khi2 value 6.3930697345274 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.63930697345274 +p-value, i.e. P(X^2<=value) 0.218770641490959 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggN.txt b/validation/validation_results/Berges_2021/Berges_2021/yggN.txt new file mode 100644 index 0000000..9a625c4 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yggN.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.167832 NA NA +3.67805555555556 0.263088 NA NA +4.09222222222222 0.344736 NA NA +4.565 0.479304 NA NA +0.05 NA 14.2899950644664 0.0137057049190505 +1.95 NA 13.9768922388986 0.424205365060642 +2.83333333333333 NA 13.7476033518268 0.762328239344529 +3.98333333333333 NA 11.8082734106525 1.30615035742605 +4.88333333333333 NA 9.17737095296122 1.9711598731154 +5.16666666666667 NA 8.54446077264878 2.51071184453254 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggN_res/KEIO_ROBOT3_37.pdf b/validation/validation_results/Berges_2021/Berges_2021/yggN_res/KEIO_ROBOT3_37.pdf new file mode 100644 index 0000000..aa9bd8c Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yggN_res/KEIO_ROBOT3_37.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggN_res/KEIO_ROBOT3_37_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yggN_res/KEIO_ROBOT3_37_log.txt new file mode 100644 index 0000000..fee3c0f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yggN_res/KEIO_ROBOT3_37_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.167832 NA NA + [2,] 0.263088 NA NA + [3,] 0.344736 NA NA + [4,] 0.479304 NA NA + [5,] NA 14.289995 0.0137057 + [6,] NA 13.976892 0.4242054 + [7,] NA 13.747603 0.7623282 + [8,] NA 11.808273 1.3061504 + [9,] NA 9.177371 1.9711599 +[10,] NA 8.544461 2.5107118 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02576721 14.56773873 0.17584403 0.63783787 -5.87764979 2.19856351 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.022216e-09 1.815684e-09 -1.657356e-08 -9.557861e-09 4.466380e-08 1.863088e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008444403 0.402537820 0.172801793 0.077590932 0.696703397 0.296861162 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6003864 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.022216e-09 1.815684e-09 -1.657356e-08 -9.557861e-09 4.466380e-08 1.863088e-08 + +$result$normp +[1] 5.208015e-08 + +$result$res + [1] -0.31965351 0.30090779 0.28673517 -0.27407712 0.58706324 0.01014289 -0.84622264 -0.03471987 0.60563565 -0.32189928 0.82508261 -0.14548782 -0.67051538 -0.46070403 0.58384311 -0.13221848 + +$result$prevres + [1] -0.31965361 0.30090773 0.28673516 -0.27407703 0.58706323 0.01014292 -0.84622260 -0.03471984 0.60563563 -0.32189934 0.82508269 -0.14548778 -0.67051536 -0.46070406 0.58384305 -0.13221854 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 313.2642718 0.000000 0 2.322254e+01 0.000000000 0.000000000 + [2,] 522.1872116 0.000000 0 4.948937e+01 0.000000000 0.000000000 + [3,] 680.0711027 0.000000 0 7.171020e+01 0.000000000 0.000000000 + [4,] 919.4290977 0.000000 0 1.081500e+02 0.000000000 0.000000000 + [5,] -0.6491716 2.173913 0 -4.204064e-04 0.002845923 0.000000000 + [6,] -49.4545572 2.173913 0 -1.493599e+00 0.216805358 0.000000000 + [7,] -102.0337693 2.173913 0 -4.789771e+00 0.447308987 0.000000000 + [8,] -234.1564107 2.173913 0 -1.663041e+01 1.026525509 0.000000000 + [9,] -431.2672980 2.173913 0 -3.936478e+01 1.890646006 0.000000000 +[10,] -520.6610132 2.173913 0 -5.094932e+01 2.282541870 0.000000000 +[11,] 0.5584993 0.000000 5 3.616865e-04 0.000000000 0.006545624 +[12,] 42.5470503 0.000000 5 1.284983e+00 0.000000000 0.498652324 +[13,] 87.7823231 0.000000 5 4.120766e+00 0.000000000 1.028810671 +[14,] 201.4508907 0.000000 5 1.430757e+01 0.000000000 2.361008671 +[15,] 371.0305477 0.000000 5 3.386655e+01 0.000000000 4.348485813 +[16,] 447.9383013 0.000000 5 4.383303e+01 0.000000000 5.249846301 + +$result$retres +$result$retres$res + [1] -0.31965361 0.30090773 0.28673516 -0.27407703 0.58706323 0.01014292 -0.84622260 -0.03471984 0.60563563 -0.32189934 0.82508269 -0.14548778 -0.67051536 -0.46070406 0.58384305 -0.13221854 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.16143893 13.317529 0.6434909 + [2,] 0.26910615 12.325380 1.0146091 + [3,] 0.35047070 11.575609 1.2950646 + [4,] 0.47382246 10.438928 1.7202458 + [5,] 0.02660222 14.560044 0.1787222 + [6,] 0.08937908 13.981558 0.3951078 + [7,] 0.15701009 13.358341 0.6282252 + [8,] 0.32695536 11.792302 1.2140095 + [9,] 0.58049301 9.455963 2.0879285 + [10,] 0.69547738 8.396387 2.4842681 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.006393072 NA NA + [2,] -0.006018155 NA NA + [3,] -0.005734703 NA NA + [4,] 0.005481541 NA NA + [5,] NA -0.270049088 -0.16501654 + [6,] NA -0.004665741 0.02909756 + [7,] NA 0.389262397 0.13410307 + [8,] NA 0.015971127 0.09214081 + [9,] NA -0.278592390 -0.11676861 +[10,] NA 0.148073695 0.02644371 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yggN_res/KEIO_ROBOT3_37_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yggN_res/KEIO_ROBOT3_37_res.txt new file mode 100644 index 0000000..58ec334 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yggN_res/KEIO_ROBOT3_37_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0257672113825424 0.0266147110475575 0.0265099716078671 0.00363406720698906 0.0205336201207244 0.03370482086315 +Glc 14.567738731393 14.5726667389258 14.5741955340476 0.269729079627153 14.0648351078625 15.0264467104947 +Ace 0.175844032887691 0.169117271214646 0.135340084127831 0.0950599185730293 0.022620923318656 0.340776664017189 +mu 0.637837871274848 0.633337304824194 0.631494167296591 0.0290934004330753 0.582554799735109 0.689403562918134 +qGlc -5.87764979264714 -5.81097042106213 -5.77487899242973 0.471018619497991 -6.63056409993473 -4.90670493843488 +qAce 2.19856351458499 2.20003582468493 2.21416457212051 0.206611514557032 1.7572006325712 2.58867214536004 +res 3.60463882826433 23.8095708678702 23.3301008678322 6.47499249666312 14.0487667095699 36.8780300662733 + + +Goodness of fit (khi2 test) + +khi2 value 3.60463882826436 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.360463882826436 +p-value, i.e. P(X^2<=value) 0.0365745964008727 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yghJ.txt b/validation/validation_results/Berges_2021/Berges_2021/yghJ.txt new file mode 100644 index 0000000..cba328b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yghJ.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.9552000000000003E-2 NA NA +2.2613888888888889 7.8623999999999999E-2 NA NA +2.7741666666666664 0.102816 NA NA +3.2088888888888891 0.13759199999999999 NA NA +3.7063888888888892 0.17841599999999999 NA NA +4.2258333333333331 0.232848 NA NA +4.6355555555555554 0.31147199999999997 NA NA +4.9675000000000002 0.39463200000000004 NA NA +2.8 NA 12.0040519359193 0.642121338486451 +3.73333333333333 NA 10.6889169536251 1.11331926640123 +4.28333333333333 NA 10.7991816759313 1.52173946307116 +4.75 NA 10.2096208095365 1.95389277943886 +5.11666666666667 NA 9.11592179160751 2.25136932741518 +5.43333333333333 NA 8.23520105813273 2.61174756334985 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yghJ_res/KEIO_ROBOT5_6.pdf b/validation/validation_results/Berges_2021/Berges_2021/yghJ_res/KEIO_ROBOT5_6.pdf new file mode 100644 index 0000000..4926b69 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yghJ_res/KEIO_ROBOT5_6.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yghJ_res/KEIO_ROBOT5_6_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yghJ_res/KEIO_ROBOT5_6_log.txt new file mode 100644 index 0000000..83fa83d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yghJ_res/KEIO_ROBOT5_6_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.069552 NA NA + [2,] 0.078624 NA NA + [3,] 0.102816 NA NA + [4,] 0.137592 NA NA + [5,] 0.178416 NA NA + [6,] 0.232848 NA NA + [7,] 0.311472 NA NA + [8,] 0.394632 NA NA + [9,] NA 12.004052 0.6421213 +[10,] NA 10.688917 1.1133193 +[11,] NA 10.799182 1.5217395 +[12,] NA 10.209621 1.9538928 +[13,] NA 9.115922 2.2513693 +[14,] NA 8.235201 2.6117476 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0198053 12.6166178 0.3083246 0.5969638 -5.1708716 2.9105252 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.293515e-08 2.286452e-07 -3.844107e-07 -1.485026e-07 2.797518e-07 3.841469e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.004800947 0.512193603 0.228395530 0.054007263 0.957478739 0.421949328 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5333962 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.293515e-08 2.286452e-07 -3.844107e-07 -1.485026e-07 2.797518e-07 3.841469e-07 + +$result$normp +[1] 6.69403e-07 + +$result$res + [1] -0.52703225 -0.11145194 0.04691978 -0.15476295 0.12949361 0.69810258 0.18641588 -0.51768188 -0.27948721 1.09992735 -0.48592338 -0.74945227 0.07314878 0.34178674 0.41681307 -0.02372003 -0.32310252 -0.48347595 0.04225078 0.37123465 + +$result$prevres + [1] -0.52703337 -0.11145315 0.04691853 -0.15476413 0.12949268 0.69810226 0.18641643 -0.51768025 -0.27948717 1.09992755 -0.48592318 -0.74945217 0.07314866 0.34178632 0.41681391 -0.02371976 -0.32310258 -0.48347623 0.04225039 0.37123426 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 148.97877 0.000000 0 5.396259 0.0000000 0.0000000 + [2,] 192.86505 0.000000 0 8.637933 0.0000000 0.0000000 + [3,] 261.93610 0.000000 0 14.391596 0.0000000 0.0000000 + [4,] 339.54758 0.000000 0 21.579251 0.0000000 0.0000000 + [5,] 456.96356 0.000000 0 33.543904 0.0000000 0.0000000 + [6,] 623.09144 0.000000 0 52.148906 0.0000000 0.0000000 + [7,] 795.74811 0.000000 0 73.056432 0.0000000 0.0000000 + [8,] 970.14114 0.000000 0 95.445146 0.0000000 0.0000000 + [9,] -81.34959 2.173913 0 -2.856547 0.3115822 0.0000000 +[10,] -156.05564 2.173913 0 -7.753612 0.5977186 0.0000000 +[11,] -224.02461 2.173913 0 -13.169630 0.8580508 0.0000000 +[12,] -302.04335 2.173913 0 -20.165425 1.1568753 0.0000000 +[13,] -380.55804 2.173913 0 -27.847179 1.4575994 0.0000000 +[14,] -463.66580 2.173913 0 -36.537890 1.7759157 0.0000000 +[15,] 105.31513 0.000000 5 3.698084 0.0000000 0.7166391 +[16,] 202.02952 0.000000 5 10.037820 0.0000000 1.3747527 +[17,] 290.02211 0.000000 5 17.049394 0.0000000 1.9735169 +[18,] 391.02511 0.000000 5 26.106146 0.0000000 2.6608132 +[19,] 492.67018 0.000000 5 36.050939 0.0000000 3.3524786 +[20,] 600.26143 0.000000 5 47.301928 0.0000000 4.0846060 + +$result$retres +$result$retres$res + [1] -0.52703337 -0.11145315 0.04691853 -0.15476413 0.12949268 0.69810226 0.18641643 -0.51768025 -0.27948717 1.09992755 -0.48592318 -0.74945217 0.07314866 0.34178632 0.41681391 -0.02371976 -0.32310258 -0.48347623 0.04225039 0.37123426 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05901133 12.277017 0.4994758 + [2,] 0.07639494 12.126441 0.5842304 + [3,] 0.10375437 11.889455 0.7176225 + [4,] 0.13449672 11.623166 0.8675082 + [5,] 0.18100585 11.220306 1.0942656 + [6,] 0.24681005 10.650314 1.4150969 + [7,] 0.31520033 10.057921 1.7485368 + [8,] 0.38427839 9.459570 2.0853301 + [9,] 0.10536683 11.875488 0.7254841 + [10,] 0.18394085 11.194884 1.1085753 + [11,] 0.25542898 10.575657 1.4571189 + [12,] 0.33748721 9.864873 1.8571975 + [13,] 0.42006708 9.149570 2.2598194 + [14,] 0.50747782 8.392423 2.6859944 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0105406674 NA NA + [2,] 0.0022290631 NA NA + [3,] -0.0009383707 NA NA + [4,] 0.0030952827 NA NA + [5,] -0.0025898536 NA NA + [6,] -0.0139620452 NA NA + [7,] -0.0037283287 NA NA + [8,] 0.0103536051 NA NA + [9,] NA 0.12856410 -0.083362782 +[10,] NA -0.50596667 0.004743951 +[11,] NA 0.22352466 0.064620516 +[12,] NA 0.34474800 0.096695246 +[13,] NA -0.03364838 -0.008450078 +[14,] NA -0.15722171 -0.074246852 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yghJ_res/KEIO_ROBOT5_6_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yghJ_res/KEIO_ROBOT5_6_res.txt new file mode 100644 index 0000000..1174174 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yghJ_res/KEIO_ROBOT5_6_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0198052958549493 0.019669726384502 0.0195318777422147 0.00268943909382739 0.014697754036499 0.0250193823444112 +Glc 12.6166178419409 12.6645695083041 12.6584968759411 0.259318686904681 12.1283463143707 13.1369827477473 +Ace 0.308324559549922 0.32756907867025 0.331049283173537 0.100838501482276 0.15283718981993 0.51511743925647 +mu 0.5969638294539 0.599802554364587 0.600905928785594 0.0285823069381087 0.548345751846834 0.659374508144597 +qGlc -5.17087155048096 -5.30187161898844 -5.32462617337657 0.591394039101782 -6.38837842690535 -4.08682202570645 +qAce 2.91052523755882 2.88780554155782 2.88739398217918 0.23358580083897 2.37609063598164 3.28837795143941 +res 3.98316150378995 35.3339045053998 34.5195282043938 8.14587179461265 20.8177441739307 51.7055995527537 + + +Goodness of fit (khi2 test) + +khi2 value 3.98316150380147 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.284511535985819 +p-value, i.e. P(X^2<=value) 0.00443337335792262 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygiC.txt b/validation/validation_results/Berges_2021/Berges_2021/ygiC.txt new file mode 100644 index 0000000..c846451 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygiC.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.12096 NA NA NA +3.34194444444444 0.187488 NA NA NA +3.9975 0.273672 NA NA NA +4.52333333333333 0.394632 NA NA NA +1.95 NA 13.8863995516144 0.390771204974494 0 +3.25 NA 12.8779576462211 0.924860063833356 0 +4.08333333333333 NA 11.8069834377691 1.4562812857651 0 +4.76666666666667 NA 10.4997253332895 2.00612221760876 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygiC_res/KEIO_ROBOT2_34.pdf b/validation/validation_results/Berges_2021/Berges_2021/ygiC_res/KEIO_ROBOT2_34.pdf new file mode 100644 index 0000000..ef67444 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ygiC_res/KEIO_ROBOT2_34.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygiC_res/KEIO_ROBOT2_34_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ygiC_res/KEIO_ROBOT2_34_log.txt new file mode 100644 index 0000000..c146ab5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygiC_res/KEIO_ROBOT2_34_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.120960 NA NA NA +[2,] 0.187488 NA NA NA +[3,] 0.273672 NA NA NA +[4,] 0.394632 NA NA NA +[5,] NA 13.88640 0.3907712 0 +[6,] NA 12.87796 0.9248601 0 +[7,] NA 11.80698 1.4562813 0 +[8,] NA 10.49973 2.0061222 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.551207e-02 1.435297e+01 2.014073e-01 1.000000e-06 6.018280e-01 -5.527948e+00 2.632744e+00 -1.944373e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 7.142211e-10 4.257454e-08 -3.913141e-08 -6.352747e-22 -7.333068e-09 -7.406495e-08 8.526022e-08 -4.405874e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.005209842 0.334219613 0.146443785 0.139517936 0.049068462 0.750012982 0.327926752 0.316757848 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3123687 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 7.142211e-10 4.257454e-08 -3.913141e-08 -6.352747e-22 -7.333068e-09 -7.406495e-08 8.526022e-08 -4.405874e-13 + +$result$normp +[1] 1.270947e-07 + +$result$res + [1] -3.001540e-01 1.579859e-01 4.594979e-01 -3.235496e-01 -1.235093e-01 1.140596e-01 9.657059e-02 -8.712091e-02 2.995233e-01 -2.297479e-01 -3.173821e-01 2.476068e-01 4.079532e-06 2.498202e-06 6.005573e-07 -1.847090e-06 + +$result$prevres + [1] -3.001541e-01 1.579858e-01 4.594979e-01 -3.235495e-01 -1.235094e-01 1.140596e-01 9.657061e-02 -8.712086e-02 2.995234e-01 -2.297479e-01 -3.173822e-01 2.476067e-01 4.079533e-06 2.498202e-06 6.005583e-07 -1.847088e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.252991e+02 0.000000 0 0 1.437760e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.736422e+02 0.000000 0 0 3.185670e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.543690e+02 0.000000 0 0 5.653703e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.607400e+02 0.000000 0 0 8.778908e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.459841e+01 2.173913 0 0 -1.321513e+00 0.2058264 0.0000000 0.0000000 + [6,] -1.212169e+02 2.173913 0 0 -6.567731e+00 0.5594288 0.0000000 0.0000000 + [7,] -2.131614e+02 2.173913 0 0 -1.524996e+01 0.9837624 0.0000000 0.0000000 + [8,] -3.317546e+02 2.173913 0 0 -2.870871e+01 1.5310825 0.0000000 0.0000000 + [9,] 4.885307e+01 0.000000 5 0 1.447584e+00 0.0000000 0.4734007 0.0000000 +[10,] 1.327809e+02 0.000000 5 0 7.194290e+00 0.0000000 1.2866863 0.0000000 +[11,] 2.334969e+02 0.000000 5 0 1.670480e+01 0.0000000 2.2626535 0.0000000 +[12,] 3.634038e+02 0.000000 5 0 3.144750e+01 0.0000000 3.5214897 0.0000000 +[13,] -3.607969e-05 0.000000 0 5 -1.069091e-06 0.0000000 0.0000000 0.4734007 +[14,] -9.806331e-05 0.000000 0 5 -5.313232e-06 0.0000000 0.0000000 1.2866863 +[15,] -1.724455e-04 0.000000 0 5 -1.233708e-05 0.0000000 0.0000000 2.2626535 +[16,] -2.683863e-04 0.000000 0 5 -2.322507e-05 0.0000000 0.0000000 3.5214897 + +$result$retres +$result$retres$res + [1] -3.001541e-01 1.579858e-01 4.594979e-01 -3.235495e-01 -1.235094e-01 1.140596e-01 9.657061e-02 -8.712086e-02 2.995234e-01 -2.297479e-01 -3.173822e-01 2.476067e-01 4.079533e-06 2.498202e-06 6.005583e-07 -1.847088e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.11495692 13.53140 0.5926909 7.110235e-07 + [2,] 0.19064772 12.83616 0.9238062 4.664834e-07 + [3,] 0.28286196 11.98915 1.3272047 1.685596e-07 + [4,] 0.38816101 11.02195 1.7878437 -1.716382e-07 + [5,] 0.08249322 13.82959 0.4506759 8.159065e-07 + [6,] 0.18038484 12.93043 0.8789105 4.996404e-07 + [7,] 0.29785771 11.85141 1.3928048 1.201117e-07 + [8,] 0.44937829 10.45965 2.0556436 -3.694177e-07 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.006003082 NA NA NA +[2,] -0.003159716 NA NA NA +[3,] -0.009189959 NA NA NA +[4,] 0.006470990 NA NA NA +[5,] NA 0.05681432 -0.05990468 -8.159065e-07 +[6,] NA -0.05246743 0.04594958 -4.996404e-07 +[7,] NA -0.04442248 0.06347644 -1.201117e-07 +[8,] NA 0.04007560 -0.04952134 3.694177e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygiC_res/KEIO_ROBOT2_34_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ygiC_res/KEIO_ROBOT2_34_res.txt new file mode 100644 index 0000000..0cfebf9 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygiC_res/KEIO_ROBOT2_34_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0255120675434067 0.0256189434351319 0.024588877034376 0.00501625532807384 0.0178469050436385 0.0366534291137559 +Glc 14.3529721480033 14.2828297354234 14.3081172252046 0.339683053816284 13.5990158430927 15.0424538750491 +Ace 0.201407274463438 0.202521814405464 0.194557169979275 0.136517985991876 9.99999999973245e-07 0.481296017972113 +Lac 1e-06 0.0996971232930928 0.0901528379082807 0.0817203324088043 9.99999999998677e-07 0.287341838117712 +mu 0.601827998102792 0.60478002355078 0.611221039636448 0.0436941891005821 0.517077954408434 0.686306233189839 +qGlc -5.52794810735602 -5.40861219555676 -5.39960449492144 0.850341568992783 -6.9351612626156 -3.53652023470875 +qAce 2.63274420537007 2.65617921600455 2.63235685846519 0.383965897108386 1.94745030421735 3.34250383008715 +qLac -1.94437315405049e-06 -0.0408054725104993 -0.0503843321366832 0.195314118969477 -0.422741544657916 0.303361414887099 +res 0.780593616102683 19.8097613290296 19.6441126704778 5.88760108435253 10.1319024680932 31.8840768703737 + + +Goodness of fit (khi2 test) + +khi2 value 0.780593616102738 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.0975742020128422 +p-value, i.e. P(X^2<=value) 0.000709035076960447 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygjR.txt b/validation/validation_results/Berges_2021/Berges_2021/ygjR.txt new file mode 100644 index 0000000..87bb12d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygjR.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.149688 NA NA +3.67805555555556 0.240408 NA NA +4.09222222222222 0.328104 NA NA +4.565 0.403704 NA NA +0.05 NA 14.7354251643705 0.0163493647583599 +1.95 NA 13.9802041632523 0.436565993249894 +2.83333333333333 NA 14.1775044278096 0.827425882536883 +3.98333333333333 NA 11.9206260389382 1.50413871092459 +4.88333333333333 NA 9.34501468940612 2.23339644143888 +5.16666666666667 NA 8.91865948286593 2.62367370013252 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygjR_res/KEIO_ROBOT3_39.pdf b/validation/validation_results/Berges_2021/Berges_2021/ygjR_res/KEIO_ROBOT3_39.pdf new file mode 100644 index 0000000..7510576 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ygjR_res/KEIO_ROBOT3_39.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygjR_res/KEIO_ROBOT3_39_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ygjR_res/KEIO_ROBOT3_39_log.txt new file mode 100644 index 0000000..d1ad7fc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygjR_res/KEIO_ROBOT3_39_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.149688 NA NA + [2,] 0.240408 NA NA + [3,] 0.328104 NA NA + [4,] 0.403704 NA NA + [5,] NA 14.735425 0.01634936 + [6,] NA 13.980204 0.43656599 + [7,] NA 14.177504 0.82742588 + [8,] NA 11.920626 1.50413871 + [9,] NA 9.345015 2.23339644 +[10,] NA 8.918659 2.62367370 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03076304 14.94591374 0.15292019 0.56659109 -6.48112595 2.62556641 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.068894e-09 1.271576e-08 -7.964224e-09 -8.380828e-09 2.376453e-08 -3.040694e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.01271834 0.51153533 0.22067316 0.09849461 0.96348931 0.41351945 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7347389 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.068894e-09 1.271576e-08 -7.964224e-09 -8.380828e-09 2.376453e-08 -3.040694e-09 + +$result$normp +[1] 2.950422e-08 + +$result$res + [1] 0.36653525 0.34046068 -0.77510491 0.24613815 0.43560233 0.55503555 -1.37384240 0.03332639 0.77111536 -0.42123723 0.70333546 0.02070660 -0.53599793 -0.65927892 0.22402054 0.24721424 + +$result$prevres + [1] 0.36653516 0.34046064 -0.77510491 0.24613822 0.43560231 0.55503556 -1.37384238 0.03332641 0.77111536 -0.42123726 0.70333550 0.02070660 -0.53599794 -0.65927895 0.22402053 0.24721425 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 255.2067818 0.000000 0 2.258670e+01 0.000000000 0.000000000 + [2,] 401.8088797 0.000000 0 4.546393e+01 0.000000000 0.000000000 + [3,] 508.0803983 0.000000 0 6.396182e+01 0.000000000 0.000000000 + [4,] 664.1522272 0.000000 0 9.326906e+01 0.000000000 0.000000000 + [5,] -0.7145438 2.173913 0 -5.521332e-04 0.003391623 0.000000000 + [6,] -50.2009334 2.173913 0 -1.777510e+00 0.238281601 0.000000000 + [7,] -98.9595918 2.173913 0 -5.419956e+00 0.469717361 0.000000000 + [8,] -212.7028740 2.173913 0 -1.756298e+01 1.009606353 0.000000000 + [9,] -370.7290947 2.173913 0 -3.930016e+01 1.759686845 0.000000000 +[10,] -439.6173484 2.173913 0 -4.995723e+01 2.086668881 0.000000000 +[11,] 0.6657777 0.000000 5 5.144511e-04 0.000000000 0.007800733 +[12,] 46.7748251 0.000000 5 1.656199e+00 0.000000000 0.548047681 +[13,] 92.2058076 0.000000 5 5.050056e+00 0.000000000 1.080349930 +[14,] 198.1863497 0.000000 5 1.636434e+01 0.000000000 2.322094612 +[15,] 345.4276129 0.000000 5 3.661801e+01 0.000000000 4.047279744 +[16,] 409.6143881 0.000000 5 4.654775e+01 0.000000000 4.799338425 + +$result$retres +$result$retres$res + [1] 0.36653516 0.34046064 -0.77510491 0.24613822 0.43560231 0.55503556 -1.37384238 0.03332641 0.77111536 -0.42123726 0.70333550 0.02070660 -0.53599794 -0.65927895 0.22402053 0.24721425 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15701870 13.501700 0.7379852 + [2,] 0.24721721 12.469936 1.1559625 + [3,] 0.31260190 11.722013 1.4589532 + [4,] 0.40862676 10.623604 1.9039295 + [5,] 0.03164700 14.935802 0.1570165 + [6,] 0.09286682 14.235521 0.4407073 + [7,] 0.15318637 13.545537 0.7202263 + [8,] 0.29389866 11.935956 1.3722829 + [9,] 0.48939357 9.699728 2.2782005 + [10,] 0.57461552 8.724890 2.6731166 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.007330703 NA NA + [2,] -0.006809213 NA NA + [3,] 0.015502098 NA NA + [4,] -0.004922764 NA NA + [5,] NA -0.20037706 -0.140667101 + [6,] NA -0.25531636 -0.004141321 + [7,] NA 0.63196749 0.107199588 + [8,] NA -0.01533015 0.131855790 + [9,] NA -0.35471307 -0.044804106 +[10,] NA 0.19376914 -0.049442850 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ygjR_res/KEIO_ROBOT3_39_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ygjR_res/KEIO_ROBOT3_39_res.txt new file mode 100644 index 0000000..0a93aab --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ygjR_res/KEIO_ROBOT3_39_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0307630360888368 0.0309946766756984 0.0306531773384959 0.00403162382744919 0.0242053635582347 0.0389592821858509 +Glc 14.9459137443791 14.9459458650839 14.9286809598488 0.263239309984976 14.4177479129178 15.4703143688973 +Ace 0.152920189264307 0.171457581521335 0.181229367396435 0.103588854179551 1.00000000000034e-06 0.363811958828221 +mu 0.566591092522832 0.566739978742647 0.570685402449918 0.0281966867253031 0.513467539780394 0.618757779433491 +qGlc -6.48112595245288 -6.45734929084121 -6.41527410651195 0.534675518986764 -7.4667071781396 -5.53160813539266 +qAce 2.62556640812962 2.59674817052059 2.5797710061564 0.228555161995897 2.20695655525124 2.9706668431094 +res 5.39841242743241 23.0652964400787 22.7766721488282 7.11235474054475 11.1969099933395 38.8232527055261 + + +Goodness of fit (khi2 test) + +khi2 value 5.39841242743242 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.539841242743242 +p-value, i.e. P(X^2<=value) 0.136974032044 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhBT.txt b/validation/validation_results/Berges_2021/Berges_2021/yhBT.txt new file mode 100644 index 0000000..6095c33 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhBT.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.06048 NA NA +1.61361111111111 0.074088 NA NA +2.36138888888889 0.1134 NA NA +3.28638888888889 0.184464 NA NA +3.81944444444444 0.255528 NA NA +4.41083333333333 0.367416 NA NA +0.283333333333333 NA 14.62541617013 0.0385496186217581 +1.91666666666667 NA 14.0028029507351 0.394429318167872 +2.7 NA 13.3372872914484 0.668521227818107 +3.61666666666667 NA 12.8166938739041 1.13428741244258 +4.05 NA 11.8566291657028 1.36379254406572 +4.75 NA 10.7148438340949 1.85413374453115 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhBT_res/KEIO_ROBOT4_44.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhBT_res/KEIO_ROBOT4_44.pdf new file mode 100644 index 0000000..015faa5 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhBT_res/KEIO_ROBOT4_44.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhBT_res/KEIO_ROBOT4_44_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhBT_res/KEIO_ROBOT4_44_log.txt new file mode 100644 index 0000000..bdc03ab --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhBT_res/KEIO_ROBOT4_44_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.060480 NA NA + [3,] 0.074088 NA NA + [4,] 0.113400 NA NA + [5,] 0.184464 NA NA + [6,] 0.255528 NA NA + [7,] 0.367416 NA NA + [8,] NA 14.62542 0.03854962 + [9,] NA 14.00280 0.39442932 +[10,] NA 13.33729 0.66852123 +[11,] NA 12.81669 1.13428741 +[12,] NA 11.85663 1.36379254 +[13,] NA 10.71484 1.85413374 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03053724 14.57118772 0.12832299 0.55975937 -5.41002494 2.51545766 + +$result$lastp + X Glc Ace mu qGlc qAce + 5.978335e-09 1.173471e-07 -1.119223e-07 -5.348285e-08 -9.474950e-08 2.288857e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.004875003 0.254035962 0.110754704 0.040425445 0.665335516 0.291141994 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3759513 + +$result$laststep + X Glc Ace mu qGlc qAce + 5.978335e-09 1.173471e-07 -1.119223e-07 -5.348285e-08 -9.474950e-08 2.288857e-07 + +$result$normp +[1] 3.009306e-07 + +$result$res + [1] -0.211938073 -0.043392769 0.063238982 0.056039808 0.386774567 0.174747816 -0.337502848 -0.228159412 0.001315969 0.415688814 -0.402559539 0.350886195 -0.137172027 0.566792626 -0.010551508 -0.276948413 -0.520452086 -0.241753135 0.482912515 + +$result$prevres + [1] -0.211938372 -0.043393162 0.063238570 0.056039410 0.386774375 0.174747927 -0.337502124 -0.228159644 0.001315903 0.415688838 -0.402559432 0.350886313 -0.137171978 0.566793153 -0.010551248 -0.276948331 -0.520452245 -0.241753411 0.482912081 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.0000000 0.00000000 + [2,] 97.605663 0.000000 0 3.56182517 0.0000000 0.00000000 + [3,] 123.378520 0.000000 0 6.07950346 0.0000000 0.00000000 + [4,] 187.510096 0.000000 0 13.52140584 0.0000000 0.00000000 + [5,] 314.696964 0.000000 0 31.58211301 0.0000000 0.00000000 + [6,] 424.110073 0.000000 0 49.46619000 0.0000000 0.00000000 + [7,] 590.534779 0.000000 0 79.54187138 0.0000000 0.00000000 + [8,] -3.611049 2.173913 0 -0.01603455 0.0203828 0.00000000 + [9,] -40.419606 2.173913 0 -1.39043605 0.2281511 0.00000000 +[10,] -74.227523 2.173913 0 -3.80301594 0.4189820 0.00000000 +[11,] -138.083116 2.173913 0 -10.03777903 0.7794190 0.00000000 +[12,] -181.756080 2.173913 0 -15.16177986 1.0259339 0.00000000 +[13,] -279.020962 2.173913 0 -28.29837756 1.5749517 0.00000000 +[14,] 3.861704 0.000000 5 0.01714756 0.0000000 0.04688044 +[15,] 43.225261 0.000000 5 1.48695070 0.0000000 0.52474744 +[16,] 79.379895 0.000000 5 4.06699554 0.0000000 0.96365865 +[17,] 147.667910 0.000000 5 10.73453363 0.0000000 1.79266373 +[18,] 194.372355 0.000000 5 16.21420786 0.0000000 2.35964788 +[19,] 298.388706 0.000000 5 30.26265916 0.0000000 3.62238898 + +$result$retres +$result$retres$res + [1] -0.211938372 -0.043393162 0.063238570 0.056039410 0.386774375 0.174747927 -0.337502124 -0.228159644 0.001315903 0.415688838 -0.402559432 0.350886313 -0.137171978 0.566793153 -0.010551248 -0.276948331 -0.520452245 -0.241753411 0.482912081 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03053723 14.57119 0.1283231 + [2,] 0.05961214 14.29018 0.2589805 + [3,] 0.07535277 14.13805 0.3297160 + [4,] 0.11452079 13.75949 0.5057300 + [5,] 0.19219949 13.00874 0.8548040 + [6,] 0.25902296 12.36289 1.1550966 + [7,] 0.36066596 11.38052 1.6118618 + [8,] 0.03578559 14.52046 0.1519082 + [9,] 0.08928370 14.00341 0.3923191 + [10,] 0.13842063 13.52850 0.6131316 + [11,] 0.23122932 12.63152 1.0301970 + [12,] 0.29470426 12.01804 1.3154419 + [13,] 0.43607051 10.65174 1.9507162 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0042387674 NA NA + [2,] 0.0008678632 NA NA + [3,] -0.0012647714 NA NA + [4,] -0.0011207882 NA NA + [5,] -0.0077354875 NA NA + [6,] -0.0034949585 NA NA + [7,] 0.0067500425 NA NA + [8,] NA 0.1049534364 -0.11335863 + [9,] NA -0.0006053155 0.00211025 +[10,] NA -0.1912168657 0.05538967 +[11,] NA 0.1851773387 0.10409045 +[12,] NA -0.1614077040 0.04835068 +[13,] NA 0.0630991099 -0.09658242 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhBT_res/KEIO_ROBOT4_44_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhBT_res/KEIO_ROBOT4_44_res.txt new file mode 100644 index 0000000..45dd76a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhBT_res/KEIO_ROBOT4_44_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0305372385350279 0.0310030522879375 0.0308559779132326 0.00418498109753776 0.0232829588284869 0.0394742801142263 +Glc 14.5711877167846 14.5645015817058 14.545046623481 0.196713049995137 14.2452410816276 14.9499178359823 +Ace 0.128322988564822 0.135926804846726 0.131476180426146 0.0861247048592601 0.000310470301702839 0.314793367425173 +mu 0.559759370477829 0.559504497574752 0.557470063682796 0.0341822990840807 0.502847720637271 0.628797177171744 +qGlc -5.41002493584485 -5.36203992688383 -5.44351762179132 0.594919441712953 -6.64655133577924 -4.32705880689944 +qAce 2.51545766494414 2.49074587328903 2.48952342053026 0.253140439834237 1.9627934773048 2.91972239341235 +res 1.83741204236182 33.5295669593346 32.6842420468986 8.98396743786772 19.0866462869316 53.1026326725909 + + +Goodness of fit (khi2 test) + +khi2 value 1.83741204236376 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.141339387874136 +p-value, i.e. P(X^2<=value) 0.00013974561309669 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhaJ.txt b/validation/validation_results/Berges_2021/Berges_2021/yhaJ.txt new file mode 100644 index 0000000..0402cc3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhaJ.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.17388 NA NA +3.67805555555556 0.269136 NA NA +4.09222222222222 0.358344 NA NA +4.565 0.458136 NA NA +0.05 NA 14.7237931060179 0.0251301185273151 +1.95 NA 13.9753579978931 0.43126935119335 +2.83333333333333 NA 12.8369102180892 0.760592955974851 +3.98333333333333 NA 11.7403343326689 1.44175206108356 +4.88333333333333 NA 9.30155347394825 2.08421689172628 +5.16666666666667 NA 8.58618463549981 2.49793363754722 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhaJ_res/KEIO_ROBOT3_21.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhaJ_res/KEIO_ROBOT3_21.pdf new file mode 100644 index 0000000..a0d0302 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhaJ_res/KEIO_ROBOT3_21.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhaJ_res/KEIO_ROBOT3_21_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhaJ_res/KEIO_ROBOT3_21_log.txt new file mode 100644 index 0000000..e37cb74 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhaJ_res/KEIO_ROBOT3_21_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.173880 NA NA + [2,] 0.269136 NA NA + [3,] 0.358344 NA NA + [4,] 0.458136 NA NA + [5,] NA 14.723793 0.02513012 + [6,] NA 13.975358 0.43126935 + [7,] NA 12.836910 0.76059296 + [8,] NA 11.740334 1.44175206 + [9,] NA 9.301553 2.08421689 +[10,] NA 8.586185 2.49793364 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03663657 14.60349312 0.13996769 0.55213129 -5.64698365 2.19646526 + +$result$lastp + X Glc Ace mu qGlc qAce + 6.704505e-09 1.540107e-07 -1.062642e-07 -4.663746e-08 -1.091755e-07 1.379155e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.00932233 0.34370561 0.14794553 0.06074505 0.56535971 0.24183851 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4960091 + +$result$laststep + X Glc Ace mu qGlc qAce + 6.704505e-09 1.540107e-07 -1.062642e-07 -4.663746e-08 -1.091755e-07 1.379155e-07 + +$result$normp +[1] 2.610964e-07 + +$result$res + [1] 0.27492345 0.50163744 -0.37238379 -0.12882783 -0.28432262 -0.21056872 0.76157066 -0.30774239 0.26534641 -0.22428334 0.59458587 -0.04652535 -0.34876493 -0.66530328 0.35265167 0.11335602 + +$result$prevres + [1] 0.27492302 0.50163728 -0.37238365 -0.12882715 -0.28432295 -0.21056882 0.76157070 -0.30774222 0.26534656 -0.22428326 0.59458640 -0.04652509 -0.34876485 -0.66530345 0.35265133 0.11335567 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 244.8079861 0.000000 0 2.580309e+01 0.000000000 0.000000000 + [2,] 380.9974635 0.000000 0 5.133991e+01 0.000000000 0.000000000 + [3,] 478.8881730 0.000000 0 7.179729e+01 0.000000000 0.000000000 + [4,] 621.7278986 0.000000 0 1.039814e+02 0.000000000 0.000000000 + [5,] -0.6223536 2.173913 0 -5.726451e-04 0.004037712 0.000000000 + [6,] -43.0193096 2.173913 0 -1.807239e+00 0.279101152 0.000000000 + [7,] -84.0369943 2.173913 0 -5.455046e+00 0.545216140 0.000000000 + [8,] -178.2918404 2.173913 0 -1.743334e+01 1.156723772 0.000000000 + [9,] -307.3598658 2.173913 0 -3.857235e+01 1.994092733 0.000000000 +[10,] -363.1724023 2.173913 0 -4.885491e+01 2.356193924 0.000000000 +[11,] 0.5567661 0.000000 5 5.122962e-04 0.000000000 0.009286738 +[12,] 38.4856708 0.000000 5 1.616781e+00 0.000000000 0.641932650 +[13,] 75.1806603 0.000000 5 4.880160e+00 0.000000000 1.253997123 +[14,] 159.5023524 0.000000 5 1.559611e+01 0.000000000 2.660464676 +[15,] 274.9683973 0.000000 5 3.450736e+01 0.000000000 4.586413285 +[16,] 324.8990664 0.000000 5 4.370628e+01 0.000000000 5.419246025 + +$result$retres +$result$retres$res + [1] 0.27492302 0.50163728 -0.37238365 -0.12882715 -0.28432295 -0.21056882 0.76157070 -0.30774222 0.26534656 -0.22428326 0.59458640 -0.04652509 -0.34876485 -0.66530345 0.35265133 0.11335567 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.17937846 13.143585 0.7078175 + [2,] 0.27916875 12.122969 1.1047989 + [3,] 0.35089633 11.389367 1.3901425 + [4,] 0.45555946 10.318913 1.8065088 + [5,] 0.03766206 14.593005 0.1440474 + [6,] 0.10752279 13.878496 0.4219643 + [7,] 0.17511078 13.187233 0.6908400 + [8,] 0.33042174 11.598773 1.3086914 + [9,] 0.54309706 9.423613 2.1547472 + [10,] 0.63506367 8.483014 2.5206048 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.005498460 NA NA + [2,] -0.010032746 NA NA + [3,] 0.007447673 NA NA + [4,] 0.002576543 NA NA + [5,] NA 0.13078856 -0.118917279 + [6,] NA 0.09686166 0.009305018 + [7,] NA -0.35032252 0.069752970 + [8,] NA 0.14156142 0.133060691 + [9,] NA -0.12205942 -0.070530266 +[10,] NA 0.10317030 -0.022671133 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhaJ_res/KEIO_ROBOT3_21_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhaJ_res/KEIO_ROBOT3_21_res.txt new file mode 100644 index 0000000..4d294ee --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhaJ_res/KEIO_ROBOT3_21_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0366365689329854 0.0360025784189571 0.0352760756650119 0.00407691949611951 0.0291880322753987 0.0443853324344337 +Glc 14.6034931152554 14.6023709450702 14.5956466691772 0.262122527450755 14.0789435198149 15.0474988442721 +Ace 0.139967692087729 0.15056664593321 0.151528999903464 0.10317948587537 9.99999999992066e-07 0.368498848314072 +mu 0.552131285139854 0.55709637613225 0.560720993870666 0.0243827120202503 0.508665974963125 0.599655209584377 +qGlc -5.64698365421647 -5.6784826508717 -5.70924522978223 0.476894190381171 -6.54581835101766 -4.77345038297987 +qAce 2.1964652562704 2.18237384596264 2.1709393340155 0.187704123887419 1.89155947649228 2.53918031350477 +res 2.46025002993524 22.7520135171014 21.5715445391772 6.84364643422913 11.6458167174335 40.3830460031922 + + +Goodness of fit (khi2 test) + +khi2 value 2.4602500299368 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.24602500299368 +p-value, i.e. P(X^2<=value) 0.00855760378374936 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhbS.txt b/validation/validation_results/Berges_2021/Berges_2021/yhbS.txt new file mode 100644 index 0000000..8716098 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhbS.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.101304 NA NA NA +3.34194444444444 0.152712 NA NA NA +3.9975 0.201096 NA NA NA +4.52333333333333 0.29484 NA NA NA +1.95 NA 13.7814146604411 0.376391920331649 0 +3.25 NA 12.7779018509026 0.873336538656529 0 +4.08333333333333 NA 11.6694390242967 1.30674768933028 0 +4.76666666666667 NA 10.3946551803448 1.85720383516158 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhbS_res/KEIO_ROBOT2_40.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhbS_res/KEIO_ROBOT2_40.pdf new file mode 100644 index 0000000..4d34b1b Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhbS_res/KEIO_ROBOT2_40.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhbS_res/KEIO_ROBOT2_40_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhbS_res/KEIO_ROBOT2_40_log.txt new file mode 100644 index 0000000..09a2cca --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhbS_res/KEIO_ROBOT2_40_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.101304 NA NA NA +[2,] 0.152712 NA NA NA +[3,] 0.201096 NA NA NA +[4,] 0.294840 NA NA NA +[5,] NA 13.78141 0.3763919 0 +[6,] NA 12.77790 0.8733365 0 +[7,] NA 11.66944 1.3067477 0 +[8,] NA 10.39466 1.8572038 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.478318e-02 1.437089e+01 1.467420e-01 1.000000e-06 5.411289e-01 -7.170820e+00 3.097087e+00 -2.444539e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 8.650026e-09 2.249383e-07 -1.215468e-07 -2.117582e-22 -8.650875e-08 5.704503e-08 5.433299e-08 -1.067473e-12 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.006652467 0.382003185 0.165943616 0.154750148 0.065005529 1.051228859 0.456775827 0.435334884 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3320915 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 8.650026e-09 2.249383e-07 -1.215468e-07 -2.117582e-22 -8.650875e-08 5.704503e-08 5.433299e-08 -1.067473e-12 + +$result$normp +[1] 2.813106e-07 + +$result$res + [1] -2.681232e-01 -7.571763e-02 7.241556e-01 -4.150943e-01 -5.543827e-02 3.270353e-02 8.105174e-02 -5.831699e-02 1.797989e-01 -2.253890e-01 -4.673943e-02 9.232956e-02 3.951768e-06 2.310385e-06 4.589131e-07 -1.823237e-06 + +$result$prevres + [1] -2.681238e-01 -7.571809e-02 7.241556e-01 -4.150937e-01 -5.543844e-02 3.270360e-02 8.105185e-02 -5.831701e-02 1.797991e-01 -2.253891e-01 -4.673956e-02 9.232948e-02 3.951768e-06 2.310386e-06 4.589156e-07 -1.823234e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 1.935618e+02 0.000000 0 0 1.199935e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.050409e+02 0.000000 0 0 2.526471e+01 0.0000000 0.0000000 0.0000000 + [3,] 4.349304e+02 0.000000 0 0 4.308887e+01 0.0000000 0.0000000 0.0000000 + [4,] 5.780901e+02 0.000000 0 0 6.480537e+01 0.0000000 0.0000000 0.0000000 + [5,] -5.394418e+01 2.173913 0 0 -1.528581e+00 0.1864372 0.0000000 0.0000000 + [6,] -1.384131e+02 2.173913 0 0 -7.129676e+00 0.4783714 0.0000000 0.0000000 + [7,] -2.336936e+02 2.173913 0 0 -1.586167e+01 0.8076717 0.0000000 0.0000000 + [8,] -3.511377e+02 2.173913 0 0 -2.880239e+01 1.2135720 0.0000000 0.0000000 + [9,] 5.358670e+01 0.000000 5 0 1.518451e+00 0.0000000 0.4288056 0.0000000 +[10,] 1.374958e+02 0.000000 5 0 7.082429e+00 0.0000000 1.1002542 0.0000000 +[11,] 2.321450e+02 0.000000 5 0 1.575656e+01 0.0000000 1.8576449 0.0000000 +[12,] 3.488108e+02 0.000000 5 0 2.861152e+01 0.0000000 2.7912156 0.0000000 +[13,] -4.229611e-05 0.000000 0 5 -1.198517e-06 0.0000000 0.0000000 0.4288056 +[14,] -1.085258e-04 0.000000 0 5 -5.590178e-06 0.0000000 0.0000000 1.1002542 +[15,] -1.832326e-04 0.000000 0 5 -1.243669e-05 0.0000000 0.0000000 1.8576449 +[16,] -2.753172e-04 0.000000 0 5 -2.258314e-05 0.0000000 0.0000000 2.7912156 + +$result$retres +$result$retres$res + [1] -2.681238e-01 -7.571809e-02 7.241556e-01 -4.150937e-01 -5.543844e-02 3.270360e-02 8.105185e-02 -5.831701e-02 1.797991e-01 -2.253891e-01 -4.673956e-02 9.232948e-02 3.951768e-06 2.310386e-06 4.589156e-07 -1.823234e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09594152 13.42793 0.5540084 6.785437e-07 + [2,] 0.15119764 12.69570 0.8702602 4.289254e-07 + [3,] 0.21557911 11.84254 1.2387399 1.380835e-07 + [4,] 0.28653813 10.90222 1.6448654 -1.824723e-07 + [5,] 0.07119100 13.75591 0.4123517 7.903537e-07 + [6,] 0.14385906 12.79295 0.8282587 4.620773e-07 + [7,] 0.22582827 11.70672 1.2973998 9.178311e-08 + [8,] 0.32686470 10.36783 1.8756697 -3.646468e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.005362476 NA NA NA +[2,] 0.001514362 NA NA NA +[3,] -0.014483111 NA NA NA +[4,] 0.008301874 NA NA NA +[5,] NA 0.02550168 -0.035959829 -7.903537e-07 +[6,] NA -0.01504365 0.045077812 -4.620773e-07 +[7,] NA -0.03728385 0.009347913 -9.178311e-08 +[8,] NA 0.02682582 -0.018465895 3.646468e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhbS_res/KEIO_ROBOT2_40_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhbS_res/KEIO_ROBOT2_40_res.txt new file mode 100644 index 0000000..6af0be7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhbS_res/KEIO_ROBOT2_40_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0247831806581032 0.0247508263172739 0.0242793349703164 0.00631218678947716 0.0161575353933196 0.0391980146125788 +Glc 14.3708907859987 14.2944131899433 14.2882586942961 0.371943618471896 13.6811790403758 14.9920907462866 +Ace 0.14674196351127 0.148377642220888 0.110539171850548 0.128398729455662 9.99999999976541e-07 0.408981630259464 +Lac 1e-06 0.0863040809625743 0.0727653140622155 0.0790940119303902 9.99999999992887e-07 0.263126379135915 +mu 0.54112888762732 0.548040637261077 0.544830963252114 0.0574055897991643 0.441941919413702 0.644836742124073 +qGlc -7.17082045043399 -6.98341112117831 -6.91278106440461 1.08006738657194 -9.16908766029007 -5.0309239355423 +qAce 3.09708730392947 3.14741514268327 3.18609829503725 0.47183751614678 2.13216328954494 4.02304407632876 +qLac -2.44453949168623e-06 -0.00469201219863895 0.00177932998316118 0.248636384108684 -0.469194969106876 0.519574845616492 +res 0.882278200353405 20.2511525773471 19.8366616117344 5.88708987755491 11.589238055936 33.2539902820771 + + +Goodness of fit (khi2 test) + +khi2 value 0.88227820035456 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.11028477504432 +p-value, i.e. P(X^2<=value) 0.00111167836218313 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhbw.txt b/validation/validation_results/Berges_2021/Berges_2021/yhbw.txt new file mode 100644 index 0000000..df0aed5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhbw.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.3504000000000005E-2 NA NA +2.2613888888888889 8.0135999999999999E-2 NA NA +2.7741666666666664 0.114912 NA NA +3.2088888888888891 0.13608000000000001 NA NA +3.7063888888888892 0.17841599999999999 NA NA +4.2258333333333331 0.21923999999999999 NA NA +4.6355555555555554 0.296352 NA NA +4.9675000000000002 0.35985600000000001 NA NA +2.8 NA 12.6002044166502 0.625523777445662 +3.73333333333333 NA 11.6720381440824 1.04246183916201 +4.28333333333333 NA 11.2388065168285 1.39925793637895 +4.75 NA 10.3875799384651 1.73360238475236 +5.11666666666667 NA 9.70423369741814 2.05615132062483 +5.43333333333333 NA 8.67015221901749 2.32316528830458 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhbw_res/KEIO_ROBOT5_47.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhbw_res/KEIO_ROBOT5_47.pdf new file mode 100644 index 0000000..e51fafc Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhbw_res/KEIO_ROBOT5_47.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhbw_res/KEIO_ROBOT5_47_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhbw_res/KEIO_ROBOT5_47_log.txt new file mode 100644 index 0000000..537c906 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhbw_res/KEIO_ROBOT5_47_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.063504 NA NA + [2,] 0.080136 NA NA + [3,] 0.114912 NA NA + [4,] 0.136080 NA NA + [5,] 0.178416 NA NA + [6,] 0.219240 NA NA + [7,] 0.296352 NA NA + [8,] 0.359856 NA NA + [9,] NA 12.600204 0.6255238 +[10,] NA 11.672038 1.0424618 +[11,] NA 11.238807 1.3992579 +[12,] NA 10.387580 1.7336024 +[13,] NA 9.704234 2.0561513 +[14,] NA 8.670152 2.3231653 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02333659 13.52202023 0.27051085 0.54717362 -5.97115020 2.67656913 + +$result$lastp + X Glc Ace mu qGlc qAce + 7.211335e-10 1.202056e-08 -2.080586e-08 -7.109857e-09 1.812313e-08 2.463922e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.003537428 0.342239489 0.149270350 0.034088431 0.644118694 0.280519519 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.336279 + +$result$laststep + X Glc Ace mu qGlc qAce + 7.211335e-10 1.202056e-08 -2.080586e-08 -7.109857e-09 1.812313e-08 2.463922e-08 + +$result$normp +[1] 3.954727e-08 + +$result$res + [1] -0.001144683 0.014730852 -0.421513699 -0.050170748 -0.053870987 0.819786355 -0.074959638 -0.313839826 -0.004489906 0.305780208 -0.251600065 -0.079290626 -0.248257252 0.277857641 0.295584852 -0.028732835 -0.267087200 -0.208643913 -0.115637789 0.324516885 + +$result$prevres + [1] -0.001144740 0.014730793 -0.421513759 -0.050170803 -0.053871027 0.819786345 -0.074959608 -0.313839748 -0.004489901 0.305780220 -0.251600053 -0.079290622 -0.248257260 0.277857617 0.295584898 -0.028732817 -0.267087200 -0.208643927 -0.115637812 0.324516858 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 136.01195 0.000000 0 5.804994 0.0000000 0.0000000 + [2,] 172.32726 0.000000 0 9.094245 0.0000000 0.0000000 + [3,] 228.14328 0.000000 0 14.769903 0.0000000 0.0000000 + [4,] 289.40942 0.000000 0 21.672287 0.0000000 0.0000000 + [5,] 379.95820 0.000000 0 32.864287 0.0000000 0.0000000 + [6,] 504.86322 0.000000 0 49.787865 0.0000000 0.0000000 + [7,] 631.73925 0.000000 0 68.340329 0.0000000 0.0000000 + [8,] 757.56397 0.000000 0 87.820235 0.0000000 0.0000000 + [9,] -86.06387 2.173913 0 -3.503196 0.3363569 0.0000000 +[10,] -159.23148 2.173913 0 -9.148502 0.6223123 0.0000000 +[11,] -223.47344 2.173913 0 -15.178396 0.8733842 0.0000000 +[12,] -295.38553 2.173913 0 -22.774836 1.1544327 0.0000000 +[13,] -366.28286 2.173913 0 -30.947182 1.4315153 0.0000000 +[14,] -440.06777 2.173913 0 -40.038012 1.7198833 0.0000000 +[15,] 88.72973 0.000000 5 3.611709 0.0000000 0.7736208 +[16,] 164.16374 0.000000 5 9.431881 0.0000000 1.4313182 +[17,] 230.39561 0.000000 5 15.648552 0.0000000 2.0087836 +[18,] 304.53521 0.000000 5 23.480296 0.0000000 2.6551953 +[19,] 377.62862 0.000000 5 31.905783 0.0000000 3.2924853 +[20,] 453.69905 0.000000 5 41.278205 0.0000000 3.9557316 + +$result$retres +$result$retres$res + [1] -0.001144740 0.014730793 -0.421513759 -0.050170803 -0.053871027 0.819786345 -0.074959608 -0.313839748 -0.004489901 0.305780220 -0.251600053 -0.079290622 -0.248257260 0.277857617 0.295584898 -0.028732817 -0.267087200 -0.208643927 -0.115637812 0.324516858 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06348111 13.083935 0.4668828 + [2,] 0.08043062 12.898969 0.5497935 + [3,] 0.10648172 12.614681 0.6772258 + [4,] 0.13507658 12.302633 0.8171012 + [5,] 0.17733858 11.841440 1.0238311 + [6,] 0.23563573 11.205260 1.3089990 + [7,] 0.29485281 10.559041 1.5986668 + [8,] 0.35357921 9.918176 1.8859345 + [9,] 0.10799757 12.598139 0.6846408 + [10,] 0.17997250 11.812697 1.0367153 + [11,] 0.24316727 11.123070 1.3458405 + [12,] 0.31390715 10.351106 1.6918736 + [13,] 0.38364881 9.590035 2.0330238 + [14,] 0.45623099 8.797967 2.3880687 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 2.289479e-05 NA NA + [2,] -2.946159e-04 NA NA + [3,] 8.430275e-03 NA NA + [4,] 1.003416e-03 NA NA + [5,] 1.077421e-03 NA NA + [6,] -1.639573e-02 NA NA + [7,] 1.499192e-03 NA NA + [8,] 6.276795e-03 NA NA + [9,] NA 0.002065355 -0.059116980 +[10,] NA -0.140658901 0.005746563 +[11,] NA 0.115736025 0.053417440 +[12,] NA 0.036473686 0.041728785 +[13,] NA 0.114198340 0.023127562 +[14,] NA -0.127814504 -0.064903372 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhbw_res/KEIO_ROBOT5_47_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhbw_res/KEIO_ROBOT5_47_res.txt new file mode 100644 index 0000000..0a924f5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhbw_res/KEIO_ROBOT5_47_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0233365914377757 0.0239211592526212 0.0234606269994551 0.00321434508816916 0.0185804173702116 0.031006067115544 +Glc 13.5220202335309 13.5187792581823 13.5146963891145 0.222355603907059 13.1620788402705 13.9581954542804 +Ace 0.270510848148734 0.253393143269678 0.257664864007065 0.117910585334094 0.0361961186363031 0.48364763536176 +mu 0.54717361623728 0.543382921573893 0.544611680612113 0.0280077993429204 0.483942039621964 0.589400479591423 +qGlc -5.971150196645 -5.90570492755844 -5.8881793543509 0.512578933994505 -6.86361889425796 -4.94588768397763 +qAce 2.67656913222464 2.70428511010468 2.68284579713848 0.271275196403463 2.14953519684358 3.20407363654069 +res 1.5831703097495 35.4810317456769 34.7805111846156 9.02136015056967 22.3565592262865 54.66862525375 + + +Goodness of fit (khi2 test) + +khi2 value 1.58317030974954 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.113083593553538 +p-value, i.e. P(X^2<=value) 1.94073238808158e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhcB.txt b/validation/validation_results/Berges_2021/Berges_2021/yhcB.txt new file mode 100644 index 0000000..105f53e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhcB.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.154224 NA NA +3.67805555555556 0.223776 NA NA +4.09222222222222 0.328104 NA NA +4.565 0.424872 NA NA +0.05 NA 14.3210526563008 0.0181847279920677 +1.95 NA 14.3220582511991 0.425384959386593 +2.83333333333333 NA 13.7552929406227 0.72843790451005 +3.98333333333333 NA 12.2370181074885 1.31842397866389 +4.88333333333333 NA 9.92593205215286 1.84300478737474 +5.16666666666667 NA 9.48021867792967 2.48899841380413 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhcB_res/KEIO_ROBOT3_41.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhcB_res/KEIO_ROBOT3_41.pdf new file mode 100644 index 0000000..7ce99f5 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhcB_res/KEIO_ROBOT3_41.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhcB_res/KEIO_ROBOT3_41_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhcB_res/KEIO_ROBOT3_41_log.txt new file mode 100644 index 0000000..ce91ecd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhcB_res/KEIO_ROBOT3_41_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.154224 NA NA + [2,] 0.223776 NA NA + [3,] 0.328104 NA NA + [4,] 0.424872 NA NA + [5,] NA 14.321053 0.01818473 + [6,] NA 14.322058 0.42538496 + [7,] NA 13.755293 0.72843790 + [8,] NA 12.237018 1.31842398 + [9,] NA 9.925932 1.84300479 +[10,] NA 9.480219 2.48899841 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02430485 14.63299534 0.17092242 0.62674313 -5.60410322 2.36155017 + +$result$lastp + X Glc Ace mu qGlc qAce +-7.159615e-09 -1.642737e-07 -1.898759e-08 6.948010e-08 2.182316e-08 2.064454e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01051729 0.48360981 0.20969264 0.10255396 0.92113599 0.39876203 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7213246 + +$result$laststep + X Glc Ace mu qGlc qAce +-7.159615e-09 -1.642737e-07 -1.898759e-08 6.948010e-08 2.182316e-08 2.064454e-07 + +$result$normp +[1] 2.744468e-07 + +$result$res + [1] -0.3365478182 0.9953950795 -0.6098476667 -0.0006310842 0.6630967502 -0.4553084993 -0.4092199818 -0.0545161478 0.6230820649 -0.3671341862 0.7782649597 -0.1758829192 -0.5416522598 -0.6363864870 0.9533922902 -0.3777355838 + +$result$prevres + [1] -0.3365471200 0.9953955550 -0.6098475049 -0.0006315643 0.6630971029 -0.4553083880 -0.4092200240 -0.0545163576 0.6230819093 -0.3671342420 0.7782650576 -0.1758826861 -0.5416519829 -0.6363863084 0.9533920316 -0.3777361126 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 303.4230325 0.000000 0 2.121647e+01 0.000000000 0.000000000 + [2,] 501.3070614 0.000000 0 4.481415e+01 0.000000000 0.000000000 + [3,] 649.8846565 0.000000 0 6.463809e+01 0.000000000 0.000000000 + [4,] 874.0215990 0.000000 0 9.697415e+01 0.000000000 0.000000000 + [5,] -0.6187865 2.173913 0 -3.779516e-04 0.002683662 0.000000000 + [6,] -46.5445657 2.173913 0 -1.322243e+00 0.201862615 0.000000000 + [7,] -95.3418174 2.173913 0 -4.206872e+00 0.413495071 0.000000000 + [8,] -216.5477974 2.173913 0 -1.444920e+01 0.939162368 0.000000000 + [9,] -395.3804549 2.173913 0 -3.390160e+01 1.714755120 0.000000000 +[10,] -475.9881463 2.173913 0 -4.375458e+01 2.064348656 0.000000000 +[11,] 0.5997354 0.000000 5 3.663153e-04 0.000000000 0.006172422 +[12,] 45.1115584 0.000000 5 1.281534e+00 0.000000000 0.464284013 +[13,] 92.4064473 0.000000 5 4.077352e+00 0.000000000 0.951038664 +[14,] 209.8807551 0.000000 5 1.400434e+01 0.000000000 2.160073446 +[15,] 383.2075387 0.000000 5 3.285785e+01 0.000000000 3.943936775 +[16,] 461.3334922 0.000000 5 4.240747e+01 0.000000000 4.748001909 + +$result$retres +$result$retres$res + [1] -0.3365471200 0.9953955550 -0.6098475049 -0.0006315643 0.6630971029 -0.4553083880 -0.4092200240 -0.0545163576 0.6230819093 -0.3671342420 0.7782650576 -0.1758826861 -0.5416519829 -0.6363863084 0.9533920316 -0.3777361126 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.14749306 13.531492 0.6350921 + [2,] 0.24368391 12.671390 0.9975365 + [3,] 0.31590705 12.025597 1.2696712 + [4,] 0.42485937 11.051386 1.6802004 + [5,] 0.02507856 14.626077 0.1738377 + [6,] 0.08250221 14.112616 0.3902084 + [7,] 0.14351623 13.567052 0.6201075 + [8,] 0.29506706 12.211941 1.1911467 + [9,] 0.51867186 10.212550 2.0336832 + [10,] 0.61946031 9.311337 2.4134512 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 6.730942e-03 NA NA + [2,] -1.990791e-02 NA NA + [3,] 1.219695e-02 NA NA + [4,] 1.263129e-05 NA NA + [5,] NA -0.30502467 -0.15565301 + [6,] NA 0.20944186 0.03517654 + [7,] NA 0.18824121 0.10833040 + [8,] NA 0.02507752 0.12727726 + [9,] NA -0.28661768 -0.19067841 +[10,] NA 0.16888175 0.07554722 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhcB_res/KEIO_ROBOT3_41_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhcB_res/KEIO_ROBOT3_41_res.txt new file mode 100644 index 0000000..2c2d54f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhcB_res/KEIO_ROBOT3_41_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0243048480745447 0.0246293096522028 0.0245722944431419 0.00370408918087811 0.0181589606289755 0.0317025876932156 +Glc 14.6329953371077 14.6164959970819 14.6214013778171 0.275277280481916 14.1365242605293 15.1143439721051 +Ace 0.17092242404586 0.160954726543815 0.154106797261825 0.0865667480908952 9.99999999999634e-07 0.359566239014253 +mu 0.626743132515573 0.625835848924671 0.623230268856905 0.0325111645102899 0.572535358601394 0.690881537159372 +qGlc -5.60410321685475 -5.56300129436528 -5.59768137725119 0.50494117474405 -6.53140328129903 -4.54598710326686 +qAce 2.36155017143784 2.38966495731835 2.38652346680113 0.207929778056061 1.95195433463114 2.77119586477775 +res 5.20309238744173 23.476198487194 23.5207395454962 6.87817293003318 10.7761224805454 36.8057712668026 + + +Goodness of fit (khi2 test) + +khi2 value 5.20309238744341 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.520309238744341 +p-value, i.e. P(X^2<=value) 0.122795267691291 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhcH.txt b/validation/validation_results/Berges_2021/Berges_2021/yhcH.txt new file mode 100644 index 0000000..8af9e18 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhcH.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.167832 NA NA +3.67805555555556 0.254016 NA NA +4.09222222222222 0.328104 NA NA +4.565 0.403704 NA NA +0.05 NA 14.2749252258385 0.0194761220877897 +1.95 NA 13.895991186826 0.427761866323285 +2.83333333333333 NA 13.3183477997287 0.748493525781604 +3.98333333333333 NA 11.8448913038235 1.3844922466549 +4.88333333333333 NA 9.67378666974557 1.56103371821549 +5.16666666666667 NA 8.71644749451345 2.34502589208553 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhcH_res/KEIO_ROBOT3_5.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhcH_res/KEIO_ROBOT3_5.pdf new file mode 100644 index 0000000..b45092f Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhcH_res/KEIO_ROBOT3_5.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhcH_res/KEIO_ROBOT3_5_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhcH_res/KEIO_ROBOT3_5_log.txt new file mode 100644 index 0000000..6fb1d79 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhcH_res/KEIO_ROBOT3_5_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.167832 NA NA + [2,] 0.254016 NA NA + [3,] 0.328104 NA NA + [4,] 0.403704 NA NA + [5,] NA 14.274925 0.01947612 + [6,] NA 13.895991 0.42776187 + [7,] NA 13.318348 0.74849353 + [8,] NA 11.844891 1.38449225 + [9,] NA 9.673787 1.56103372 +[10,] NA 8.716447 2.34502589 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03765591 14.55542647 0.15258946 0.52216606 -5.71923198 2.04126390 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.108427e-08 1.574518e-07 1.674245e-07 7.056678e-08 -7.870681e-07 -2.107576e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01618153 0.54623725 0.23336706 0.10291006 0.97040339 0.40991439 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7763619 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.108427e-08 1.574518e-07 1.674245e-07 7.056678e-08 -7.870681e-07 -2.107576e-07 + +$result$normp +[1] 8.495996e-07 + +$result$res + [1] 0.06545024 0.14881021 -0.45331099 0.23339013 0.58606803 -0.15189972 -0.35076840 -0.38754468 0.02689554 0.27724923 0.68503616 -0.07436521 -0.48393260 -1.00426333 1.64728519 -0.76976021 + +$result$prevres + [1] 0.06545101 0.14881066 -0.45331090 0.23338956 0.58606769 -0.15190019 -0.35076884 -0.38754484 0.02689606 0.27725012 0.68503533 -0.07436563 -0.48393276 -1.00426308 1.64728574 -0.76975960 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 224.5875388 0.000000 0 2.433047e+01 0.000000000 0.000000000 + [2,] 341.2374394 0.000000 0 4.726158e+01 0.000000000 0.000000000 + [3,] 423.6223130 0.000000 0 6.527868e+01 0.000000000 0.000000000 + [4,] 542.2411155 0.000000 0 9.321086e+01 0.000000000 0.000000000 + [5,] -0.6298418 2.173913 0 -5.955118e-04 0.004146934 0.000000000 + [6,] -42.1037298 2.173913 0 -1.803726e+00 0.277214672 0.000000000 + [7,] -80.7328495 2.173913 0 -5.331895e+00 0.531552204 0.000000000 + [8,] -166.7735585 2.173913 0 -1.656004e+01 1.098051824 0.000000000 + [9,] -281.1075454 2.173913 0 -3.579829e+01 1.850836881 0.000000000 +[10,] -329.7272029 2.173913 0 -4.500454e+01 2.170952995 0.000000000 +[11,] 0.5170361 0.000000 5 4.888548e-04 0.000000000 0.009537949 +[12,] 34.5628824 0.000000 5 1.480676e+00 0.000000000 0.637593746 +[13,] 66.2734629 0.000000 5 4.376944e+00 0.000000000 1.222570069 +[14,] 136.9041390 0.000000 5 1.359411e+01 0.000000000 2.525519194 +[15,] 230.7607202 0.000000 5 2.938676e+01 0.000000000 4.256924826 +[16,] 270.6725168 0.000000 5 3.694415e+01 0.000000000 4.993191890 + +$result$retres +$result$retres$res + [1] 0.06545101 0.14881066 -0.45331090 0.23338956 0.58606769 -0.15190019 -0.35076884 -0.38754484 0.02689606 0.27725012 0.68503533 -0.07436563 -0.48393276 -1.00426308 1.64728574 -0.76975960 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.1691410 13.115283 0.6665941 + [2,] 0.2569922 12.153058 1.0100241 + [3,] 0.3190378 11.473479 1.2525742 + [4,] 0.4083718 10.495013 1.6018009 + [5,] 0.0386520 14.544516 0.1564832 + [6,] 0.1042419 13.826117 0.4128887 + [7,] 0.1653328 13.156994 0.6517070 + [8,] 0.3014040 11.666621 1.1836396 + [9,] 0.4822202 9.686159 1.8904909 + [10,] 0.5591109 8.843983 2.1910740 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.001309020 NA NA + [2,] -0.002976213 NA NA + [3,] 0.009066218 NA NA + [4,] -0.004667791 NA NA + [5,] NA -0.26959114 -0.13700707 + [6,] NA 0.06987409 0.01487313 + [7,] NA 0.16135367 0.09678655 + [8,] NA 0.17827063 0.20085262 + [9,] NA -0.01237219 -0.32945715 +[10,] NA -0.12753505 0.15395192 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhcH_res/KEIO_ROBOT3_5_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhcH_res/KEIO_ROBOT3_5_res.txt new file mode 100644 index 0000000..21cb336 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhcH_res/KEIO_ROBOT3_5_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0376559116764387 0.037354008376795 0.0366491304275644 0.00524538600284901 0.0286194278547466 0.0484777220436174 +Glc 14.5554264653835 14.5608071677601 14.5794024337331 0.271954102564839 14.005462382186 15.0946101518401 +Ace 0.152589461547017 0.165923948928383 0.140077702382463 0.109297002735848 9.99999999999179e-07 0.386895709266904 +mu 0.522166063920578 0.526195930494146 0.527847600665536 0.0298690862014792 0.465035476531743 0.583239706704271 +qGlc -5.7192319778831 -5.74926099166346 -5.80073763445829 0.501891424571414 -6.69715730131407 -4.83187875390126 +qAce 2.04126389699416 2.03647482333331 2.04445565832504 0.216070895630442 1.5906958957575 2.35845029431588 +res 6.02737875422086 23.740137809222 23.1752507462601 7.24590285067595 12.56056288292 41.3626766341426 + + +Goodness of fit (khi2 test) + +khi2 value 6.02737875422538 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.602737875422538 +p-value, i.e. P(X^2<=value) 0.187042224249324 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhdP.txt b/validation/validation_results/Berges_2021/Berges_2021/yhdP.txt new file mode 100644 index 0000000..c5e867b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhdP.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.033264 NA NA +1.195 0.06048 NA NA +1.61361111111111 0.077112 NA NA +2.36138888888889 0.119448 NA NA +3.28638888888889 0.201096 NA NA +3.81944444444444 0.273672 NA NA +4.41083333333333 0.382536 NA NA +0.283333333333333 NA 13.9822463273873 0.0441464588198056 +1.91666666666667 NA 13.864630146959 0.393354490728915 +2.7 NA 13.0031599671202 0.692292589341005 +3.61666666666667 NA 12.4010610792924 1.17185142532013 +4.05 NA 12.1556722855545 1.47804425109668 +4.75 NA 10.3853431707779 1.9376679481753 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhdP_res/KEIO_ROBOT4_21.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhdP_res/KEIO_ROBOT4_21.pdf new file mode 100644 index 0000000..3b5dd63 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhdP_res/KEIO_ROBOT4_21.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhdP_res/KEIO_ROBOT4_21_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhdP_res/KEIO_ROBOT4_21_log.txt new file mode 100644 index 0000000..75e16eb --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhdP_res/KEIO_ROBOT4_21_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.033264 NA NA + [2,] 0.060480 NA NA + [3,] 0.077112 NA NA + [4,] 0.119448 NA NA + [5,] 0.201096 NA NA + [6,] 0.273672 NA NA + [7,] 0.382536 NA NA + [8,] NA 13.98225 0.04414646 + [9,] NA 13.86463 0.39335449 +[10,] NA 13.00316 0.69229259 +[11,] NA 12.40106 1.17185143 +[12,] NA 12.15567 1.47804425 +[13,] NA 10.38534 1.93766795 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03192303 14.17125538 0.12856209 0.56219321 -4.71376070 2.52443198 + +$result$lastp + X Glc Ace mu qGlc qAce + 5.819074e-10 -1.339098e-08 -2.171692e-08 -5.028594e-09 6.329775e-08 5.456192e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.005553653 0.288155383 0.126244521 0.044036809 0.712164103 0.315191582 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4288435 + +$result$laststep + X Glc Ace mu qGlc qAce + 5.819074e-10 -1.339098e-08 -2.171692e-08 -5.028594e-09 6.329775e-08 5.456192e-08 + +$result$normp +[1] 8.752243e-08 + +$result$res + [1] -0.06704832 0.10094417 0.09851474 0.04799175 0.07195622 -0.01827960 -0.07167520 0.31041390 -0.46076506 0.46627978 -0.01480123 -0.70750443 0.40637704 0.54583908 0.06464559 -0.26515493 -0.45811976 -0.47875999 0.59155001 + +$result$prevres + [1] -0.06704835 0.10094413 0.09851470 0.04799171 0.07195620 -0.01827959 -0.07167512 0.31041393 -0.46076503 0.46627980 -0.01480123 -0.70750444 0.40637697 0.54583918 0.06464565 -0.26515490 -0.45811979 -0.47876004 0.59154989 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 97.889951 0.000000 0 3.73430824 0.00000000 0.00000000 + [3,] 123.864004 0.000000 0 6.38040341 0.00000000 0.00000000 + [4,] 188.590843 0.000000 0 14.21648610 0.00000000 0.00000000 + [5,] 317.224125 0.000000 0 33.28045906 0.00000000 0.00000000 + [6,] 428.070867 0.000000 0 52.19393213 0.00000000 0.00000000 + [7,] 596.908348 0.000000 0 84.04897999 0.00000000 0.00000000 + [8,] -3.147425 2.173913 0 -0.01461173 0.02131533 0.00000000 + [9,] -35.314365 2.173913 0 -1.27073828 0.23915971 0.00000000 +[10,] -64.939258 2.173913 0 -3.48086638 0.43978857 0.00000000 +[11,] -121.011363 2.173913 0 -9.20441253 0.81952605 0.00000000 +[12,] -159.421157 2.173913 0 -13.91545767 1.07964895 0.00000000 +[13,] -245.085327 2.173913 0 -26.01057828 1.65979297 0.00000000 +[14,] 3.876853 0.000000 5 0.01799806 0.00000000 0.04902525 +[15,] 43.498609 0.000000 5 1.56523689 0.00000000 0.55006733 +[16,] 79.989188 0.000000 5 4.28757092 0.00000000 1.01151370 +[17,] 149.056224 0.000000 5 11.33757148 0.00000000 1.88490992 +[18,] 196.367640 0.000000 5 17.14041994 0.00000000 2.48319258 +[19,] 301.884820 0.000000 5 32.03863253 0.00000000 3.81752384 + +$result$retres +$result$retres$res + [1] -0.06704835 0.10094413 0.09851470 0.04799171 0.07195620 -0.01827959 -0.07167512 0.31041393 -0.46076503 0.46627980 -0.01480123 -0.70750444 0.40637697 0.54583918 0.06464565 -0.26515490 -0.45811979 -0.47876004 0.59154989 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03192303 14.17126 0.1285621 + [2,] 0.06249888 13.91489 0.2658577 + [3,] 0.07908229 13.77584 0.3403227 + [4,] 0.12040783 13.42935 0.5258879 + [5,] 0.20253512 12.74074 0.8946664 + [6,] 0.27330641 12.14735 1.2124526 + [7,] 0.38110250 11.24353 1.6964924 + [8,] 0.03743537 14.12504 0.1533143 + [9,] 0.09377186 13.65268 0.4062836 + [10,] 0.14565626 13.21765 0.6392616 + [11,] 0.24385975 12.39425 1.0802275 + [12,] 0.31112984 11.83022 1.3822922 + [13,] 0.46116023 10.57228 2.0559779 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0013409670 NA NA + [2,] -0.0020188827 NA NA + [3,] -0.0019702940 NA NA + [4,] -0.0009598343 NA NA + [5,] -0.0014391240 NA NA + [6,] 0.0003655917 NA NA + [7,] 0.0014335024 NA NA + [8,] NA -0.142790406 -0.10916784 + [9,] NA 0.211951914 -0.01292913 +[10,] NA -0.214488709 0.05303098 +[11,] NA 0.006808565 0.09162396 +[12,] NA 0.325452044 0.09575201 +[13,] NA -0.186933408 -0.11830998 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhdP_res/KEIO_ROBOT4_21_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhdP_res/KEIO_ROBOT4_21_res.txt new file mode 100644 index 0000000..ccf8c8b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhdP_res/KEIO_ROBOT4_21_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0319230335818471 0.0320513869405823 0.0318600785363088 0.00418731708312795 0.025074201647263 0.0397515449508212 +Glc 14.1712553806655 14.1768479004482 14.1836001634973 0.19614378481954 13.7575767849109 14.5411333969193 +Ace 0.12856209211697 0.144113210653036 0.146347816039388 0.0730346458793841 0.0126327204708978 0.27768426986065 +mu 0.562193210443713 0.563128596491416 0.562788606177841 0.0309159041507762 0.505286568133691 0.617149857884304 +qGlc -4.71376069820039 -4.76876927434817 -4.69081857773072 0.609239140264535 -6.01910407654065 -3.73643905648612 +qAce 2.52443198271811 2.47105557448075 2.47420217525791 0.223124930216917 2.0862656844865 2.89385688426246 +res 2.39078743002655 32.1032233066316 31.061743774854 8.07554106525309 19.3690787856685 49.1460741546511 + + +Goodness of fit (khi2 test) + +khi2 value 2.39078743002661 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.183906725386662 +p-value, i.e. P(X^2<=value) 0.000611288772504132 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yheO.txt b/validation/validation_results/Berges_2021/Berges_2021/yheO.txt new file mode 100644 index 0000000..56c9e78 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yheO.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.0479999999999999E-2 NA NA +2.2613888888888889 8.9207999999999996E-2 NA NA +2.7741666666666664 0.119448 NA NA +3.2088888888888891 0.14363999999999999 NA NA +3.7063888888888892 0.18748799999999999 NA NA +4.2258333333333331 0.282744 NA NA +4.6355555555555554 0.33566400000000002 NA NA +4.9675000000000002 0.41882400000000003 NA NA +2.8 NA 12.1090531714474 0.711101868624168 +3.73333333333333 NA 11.3010195100032 1.27332343457624 +4.28333333333333 NA 10.5996375526303 1.72909038893188 +4.75 NA 9.66230992541059 2.28557783452589 +5.11666666666667 NA 8.83612015317222 2.61872931679765 +5.43333333333333 NA 7.89338818608231 3.03204178486208 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yheO_res/KEIO_ROBOT5_4.pdf b/validation/validation_results/Berges_2021/Berges_2021/yheO_res/KEIO_ROBOT5_4.pdf new file mode 100644 index 0000000..62a2854 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yheO_res/KEIO_ROBOT5_4.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yheO_res/KEIO_ROBOT5_4_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yheO_res/KEIO_ROBOT5_4_log.txt new file mode 100644 index 0000000..30a5911 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yheO_res/KEIO_ROBOT5_4_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.060480 NA NA + [2,] 0.089208 NA NA + [3,] 0.119448 NA NA + [4,] 0.143640 NA NA + [5,] 0.187488 NA NA + [6,] 0.282744 NA NA + [7,] 0.335664 NA NA + [8,] 0.418824 NA NA + [9,] NA 12.109053 0.7111019 +[10,] NA 11.301020 1.2733234 +[11,] NA 10.599638 1.7290904 +[12,] NA 9.662310 2.2855778 +[13,] NA 8.836120 2.6187293 +[14,] NA 7.893388 3.0320418 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02257824 13.06014024 0.29759149 0.58661560 -5.76040419 3.16395431 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.312519e-09 7.055483e-08 -6.705370e-08 -2.340745e-08 -2.203675e-09 5.566851e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.00358899 0.37845234 0.16905199 0.03547808 0.64145174 0.28299273 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3870572 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.312519e-09 7.055483e-08 -6.705370e-08 -2.340745e-08 -2.203675e-09 5.566851e-08 + +$result$normp +[1] 1.145918e-07 + +$result$res + [1] 0.2766157193 -0.2065677612 -0.2257117985 0.2339906048 0.5547991239 -0.6708492436 0.3418702233 -0.1346617889 0.0585816612 -0.0005970435 -0.1157206469 0.0494088774 -0.0309410384 0.0392681903 0.4704081630 -0.0468403247 -0.2540378787 -0.6709040036 0.0338054745 0.4675685695 + +$result$prevres + [1] 0.2766155225 -0.2065679717 -0.2257120139 0.2339904022 0.5547989684 -0.6708492908 0.3418703275 -0.1346615006 0.0585816312 -0.0005970275 -0.1157206166 0.0494089017 -0.0309410382 0.0392681495 0.4704082987 -0.0468402867 -0.2540378942 -0.6709040523 0.0338054153 0.4675685193 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 146.18571 0.000000 0 6.036459 0.0000000 0.0000000 + [2,] 188.40409 0.000000 0 9.619568 0.0000000 0.0000000 + [3,] 254.52333 0.000000 0 15.942270 0.0000000 0.0000000 + [4,] 328.45747 0.000000 0 23.797089 0.0000000 0.0000000 + [5,] 439.76858 0.000000 0 36.801473 0.0000000 0.0000000 + [6,] 596.43058 0.000000 0 56.906554 0.0000000 0.0000000 + [7,] 758.47688 0.000000 0 79.384215 0.0000000 0.0000000 + [8,] 921.53072 0.000000 0 103.356480 0.0000000 0.0000000 + [9,] -88.97944 2.173913 0 -3.550021 0.3487600 0.0000000 +[10,] -169.40085 2.173913 0 -9.558487 0.6639764 0.0000000 +[11,] -242.03128 2.173913 0 -16.155828 0.9486555 0.0000000 +[12,] -324.96686 2.173913 0 -24.633374 1.2737263 0.0000000 +[13,] -408.07409 2.173913 0 -33.902676 1.5994699 0.0000000 +[14,] -495.73409 2.173913 0 -44.352695 1.9430583 0.0000000 +[15,] 112.40736 0.000000 5 4.484726 0.0000000 0.8021481 +[16,] 214.00339 0.000000 5 12.075197 0.0000000 1.5271457 +[17,] 305.75711 0.000000 5 20.409591 0.0000000 2.1819077 +[18,] 410.52929 0.000000 5 31.119239 0.0000000 2.9295706 +[19,] 515.51831 0.000000 5 42.829110 0.0000000 3.6787808 +[20,] 626.25882 0.000000 5 56.030576 0.0000000 4.4690342 + +$result$retres +$result$retres$res + [1] 0.2766155225 -0.2065679717 -0.2257120139 0.2339904022 0.5547989684 -0.6708492908 0.3418703275 -0.1346615006 0.0585816312 -0.0005970275 -0.1157206166 0.0494089017 -0.0309410382 0.0392681495 0.4704082987 -0.0468402867 -0.2540378942 -0.6709040523 0.0338054153 0.4675685193 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06601231 12.633630 0.5318564 + [2,] 0.08507664 12.446423 0.6346813 + [3,] 0.11493376 12.153234 0.7957178 + [4,] 0.14831981 11.825392 0.9757879 + [5,] 0.19858398 11.331812 1.2468914 + [6,] 0.26932701 10.637135 1.6284491 + [7,] 0.34250141 9.918583 2.0231206 + [8,] 0.41613077 9.195562 2.4202459 + [9,] 0.11668876 12.136001 0.8051835 + [10,] 0.20174774 11.300745 1.2639554 + [11,] 0.27856647 10.546406 1.6782828 + [12,] 0.36628461 9.685038 2.1513970 + [13,] 0.45418430 8.821887 2.6254904 + [14,] 0.54689929 7.911452 3.1255555 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.005532310 NA NA + [2,] 0.004131359 NA NA + [3,] 0.004514240 NA NA + [4,] -0.004679808 NA NA + [5,] -0.011095979 NA NA + [6,] 0.013416986 NA NA + [7,] -0.006837407 NA NA + [8,] 0.002693230 NA NA + [9,] NA -0.0269475504 -0.094081660 +[10,] NA 0.0002746326 0.009368057 +[11,] NA 0.0532314836 0.050807579 +[12,] NA -0.0227280948 0.134180810 +[13,] NA 0.0142328776 -0.006761083 +[14,] NA -0.0180633488 -0.093513704 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yheO_res/KEIO_ROBOT5_4_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yheO_res/KEIO_ROBOT5_4_res.txt new file mode 100644 index 0000000..892c46b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yheO_res/KEIO_ROBOT5_4_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0225782386858367 0.022402839285546 0.0223180794219857 0.00284166451978321 0.0174068892012815 0.0281586106744657 +Glc 13.0601402411465 13.0260598836357 13.0562356833074 0.234875461789458 12.5869357303726 13.4801096544038 +Ace 0.297591486513995 0.304046881792273 0.31215082394767 0.110721694117984 0.0975618894050612 0.496767196957329 +mu 0.586615600512453 0.59020895550277 0.590136545983592 0.0267330596677539 0.538818565837131 0.641985619119398 +qGlc -5.76040418955509 -5.74481750020905 -5.7788502700838 0.523128653596055 -6.65469091466921 -4.8601487857762 +qAce 3.1639543061959 3.15531107605703 3.14899221294976 0.23134703580078 2.63566811465157 3.61779416185489 +res 2.09738620811954 36.0442983590482 35.1085502669083 8.0488541863611 23.6908256679508 52.7588054377372 + + +Goodness of fit (khi2 test) + +khi2 value 2.09738620811987 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.149813300579991 +p-value, i.e. P(X^2<=value) 0.000111341691727096 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yheS.txt b/validation/validation_results/Berges_2021/Berges_2021/yheS.txt new file mode 100644 index 0000000..0f9249f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yheS.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.184464 NA NA +3.67805555555556 0.291816 NA NA +4.09222222222222 0.387072 NA NA +4.565 0.603288 NA NA +0.05 NA 14.3820655622923 0.0231364495117968 +1.95 NA 13.7842195811724 0.462071457600599 +2.83333333333333 NA 13.7180840099783 0.804899534718986 +3.98333333333333 NA 11.5915057001821 1.47619675103515 +4.88333333333333 NA 9.03029479158426 2.25282044370515 +5.16666666666667 NA 8.01551032870301 2.71534066697037 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yheS_res/KEIO_ROBOT3_26.pdf b/validation/validation_results/Berges_2021/Berges_2021/yheS_res/KEIO_ROBOT3_26.pdf new file mode 100644 index 0000000..39fc73d Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yheS_res/KEIO_ROBOT3_26.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yheS_res/KEIO_ROBOT3_26_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yheS_res/KEIO_ROBOT3_26_log.txt new file mode 100644 index 0000000..d9ee9f0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yheS_res/KEIO_ROBOT3_26_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.184464 NA NA + [2,] 0.291816 NA NA + [3,] 0.387072 NA NA + [4,] 0.603288 NA NA + [5,] NA 14.382066 0.02313645 + [6,] NA 13.784220 0.46207146 + [7,] NA 13.718084 0.80489953 + [8,] NA 11.591506 1.47619675 + [9,] NA 9.030295 2.25282044 +[10,] NA 8.015510 2.71534067 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02008658 14.40982702 0.26202425 0.73829042 -5.40208792 2.08877479 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.609618e-09 3.280377e-08 -3.594838e-08 -1.945531e-08 3.899731e-09 4.580922e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008780998 0.556967323 0.240259333 0.102630341 0.852003368 0.365865730 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.8686136 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.609618e-09 3.280377e-08 -3.594838e-08 -1.945531e-08 3.899731e-09 4.580922e-08 + +$result$normp +[1] 6.97364e-08 + +$result$res + [1] -0.82229007 0.58637549 1.25210483 -0.95135730 0.04833610 0.33142617 -0.76461506 0.39733824 0.25834020 -0.27082566 1.20512411 -0.08549089 -0.69704034 -0.97555344 0.21653905 0.33642151 + +$result$prevres + [1] -0.82229027 0.58637536 1.25210482 -0.95135705 0.04833603 0.33142616 -0.76461503 0.39733831 0.25834023 -0.27082569 1.20512429 -0.08549078 -0.69704030 -0.97555350 0.21653892 0.33642137 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 418.2350506 0.000000 0 2.416895e+01 0.000000000 0.000000000 + [2,] 755.5880153 0.000000 0 5.582249e+01 0.000000000 0.000000000 + [3,] 1025.8446146 0.000000 0 8.432312e+01 0.000000000 0.000000000 + [4,] 1454.3565992 0.000000 0 1.333575e+02 0.000000000 0.000000000 + [5,] -0.5981559 2.173913 0 -3.022204e-04 0.002224122 0.000000000 + [6,] -51.2078314 2.173913 0 -1.235587e+00 0.190405999 0.000000000 + [7,] -112.9313542 2.173913 0 -4.259910e+00 0.419912477 0.000000000 + [8,] -285.2376326 2.173913 0 -1.633458e+01 1.060598641 0.000000000 + [9,] -569.3501740 2.173913 0 -4.191727e+01 2.117013858 0.000000000 +[10,] -705.5216761 2.173913 0 -5.567524e+01 2.623340140 0.000000000 +[11,] 0.5319517 0.000000 5 2.687706e-04 0.000000000 0.005115481 +[12,] 45.5401210 0.000000 5 1.098832e+00 0.000000000 0.437933798 +[13,] 100.4320510 0.000000 5 3.788421e+00 0.000000000 0.965798697 +[14,] 253.6673774 0.000000 5 1.452666e+01 0.000000000 2.439376875 +[15,] 506.3341893 0.000000 5 3.727784e+01 0.000000000 4.869131872 +[16,] 627.4341560 0.000000 5 4.951308e+01 0.000000000 6.033682322 + +$result$retres +$result$retres$res + [1] -0.82229027 0.58637536 1.25210482 -0.95135705 0.04833603 0.33142616 -0.76461503 0.39733831 0.25834023 -0.27082569 1.20512429 -0.08549078 -0.69704030 -0.97555350 0.21653892 0.33642137 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.16801819 13.327408 0.6805531 + [2,] 0.30354351 12.335766 1.0639820 + [3,] 0.41211410 11.541353 1.3711504 + [4,] 0.58426086 10.281751 1.8581888 + [5,] 0.02084192 14.404300 0.2641613 + [6,] 0.08475104 13.936676 0.4449733 + [7,] 0.16269456 13.366361 0.6654915 + [8,] 0.38028030 11.774281 1.2810861 + [9,] 0.73905328 9.149131 2.2961282 + [10,] 0.91100858 7.890931 2.7826249 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.01644581 NA NA + [2,] -0.01172751 NA NA + [3,] -0.02504210 NA NA + [4,] 0.01902714 NA NA + [5,] NA -0.02223457 -0.24102486 + [6,] NA -0.15245603 0.01709816 + [7,] NA 0.35172291 0.13940806 + [8,] NA -0.18277562 0.19511070 + [9,] NA -0.11883650 -0.04330778 +[10,] NA 0.12457982 -0.06728427 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yheS_res/KEIO_ROBOT3_26_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yheS_res/KEIO_ROBOT3_26_res.txt new file mode 100644 index 0000000..112afcb --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yheS_res/KEIO_ROBOT3_26_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0200865766425093 0.0201937056545526 0.0202963171129133 0.00189649857818897 0.0167841418512503 0.0240430739886352 +Glc 14.4098270236396 14.4004737667768 14.3882692513289 0.270074158782444 13.8339478237374 14.7970706839273 +Ace 0.262024254026113 0.265772994399141 0.282399149666558 0.0991425573181424 0.0750161365407558 0.453952070010775 +mu 0.738290424469099 0.738113958432512 0.73609232666739 0.0201639667157064 0.699110793590669 0.77785477618029 +qGlc -5.402087917608 -5.40690247847014 -5.35549795567156 0.441128037836594 -6.20118367739908 -4.48983963615595 +qAce 2.08877479070615 2.08945690852473 2.09486209583403 0.157223637588744 1.78462575393286 2.4147920613641 +res 7.54489531728016 23.3465828737611 23.1126512164217 6.39387890530597 14.0343751384666 35.6127703080601 + + +Goodness of fit (khi2 test) + +khi2 value 7.54489531728037 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.754489531728037 +p-value, i.e. P(X^2<=value) 0.32680542965351 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhhM.txt b/validation/validation_results/Berges_2021/Berges_2021/yhhM.txt new file mode 100644 index 0000000..21d47f5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhhM.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.110376 NA NA NA +3.34194444444444 0.161784 NA NA NA +3.9975 0.217728 NA NA NA +4.52333333333333 0.337176 NA NA NA +1.95 NA 13.6080125406627 0.381507943554176 0 +3.25 NA 12.8425429326873 0.884743386684842 0 +4.08333333333333 NA 11.6188437770134 1.32432077760131 0 +4.76666666666667 NA 10.3591578902369 1.79829177944067 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhhM_res/KEIO_ROBOT2_43.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhhM_res/KEIO_ROBOT2_43.pdf new file mode 100644 index 0000000..33785f4 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhhM_res/KEIO_ROBOT2_43.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhhM_res/KEIO_ROBOT2_43_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhhM_res/KEIO_ROBOT2_43_log.txt new file mode 100644 index 0000000..738d33f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhhM_res/KEIO_ROBOT2_43_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.110376 NA NA NA +[2,] 0.161784 NA NA NA +[3,] 0.217728 NA NA NA +[4,] 0.337176 NA NA NA +[5,] NA 13.60801 0.3815079 0 +[6,] NA 12.84254 0.8847434 0 +[7,] NA 11.61884 1.3243208 0 +[8,] NA 10.35916 1.7982918 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.271374e-02 1.417634e+01 2.213680e-01 1.000000e-06 5.883226e-01 -6.403048e+00 2.710277e+00 -2.284527e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 8.520760e-09 1.681510e-07 -1.282138e-07 0.000000e+00 -9.188877e-08 2.109644e-07 8.720415e-08 -6.125139e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.009032662 0.570019961 0.247166548 0.234707168 0.095711763 1.491930968 0.647403296 0.624046606 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5207129 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 8.520760e-09 1.681510e-07 -1.282138e-07 0.000000e+00 -9.188877e-08 2.109644e-07 8.720415e-08 -6.125139e-13 + +$result$normp +[1] 3.245616e-07 + +$result$res + [1] -5.714040e-01 2.308183e-02 1.043613e+00 -6.035336e-01 8.035855e-02 -1.996319e-01 1.595139e-01 -4.024053e-02 3.238660e-01 -2.996922e-01 -2.573910e-01 2.332171e-01 4.052089e-06 2.456776e-06 5.684922e-07 -1.842629e-06 + +$result$prevres + [1] -5.714047e-01 2.308128e-02 1.043613e+00 -6.035330e-01 8.035846e-02 -1.996318e-01 1.595139e-01 -4.024063e-02 3.238663e-01 -2.996922e-01 -2.573911e-01 2.332169e-01 4.052089e-06 2.456777e-06 5.684939e-07 -1.842627e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.178152e+02 0.000000 0 0 1.237536e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.571531e+02 0.000000 0 0 2.711079e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.252335e+02 0.000000 0 0 4.769023e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.156581e+02 0.000000 0 0 7.352799e+01 0.0000000 0.0000000 0.0000000 + [5,] -5.085593e+01 2.173913 0 0 -1.337014e+00 0.1804028 0.0000000 0.0000000 + [6,] -1.364453e+02 2.173913 0 0 -6.551083e+00 0.4840167 0.0000000 0.0000000 + [7,] -2.377527e+02 2.173913 0 0 -1.506637e+01 0.8433877 0.0000000 0.0000000 + [8,] -3.671107e+02 2.173913 0 0 -2.813500e+01 1.3022632 0.0000000 0.0000000 + [9,] 4.951038e+01 0.000000 5 0 1.301639e+00 0.0000000 0.4149265 0.0000000 +[10,] 1.328352e+02 0.000000 5 0 6.377754e+00 0.0000000 1.1132385 0.0000000 +[11,] 2.314623e+02 0.000000 5 0 1.466774e+01 0.0000000 1.9397917 0.0000000 +[12,] 3.573977e+02 0.000000 5 0 2.739060e+01 0.0000000 2.9952054 0.0000000 +[13,] -4.173293e-05 0.000000 0 5 -1.097168e-06 0.0000000 0.0000000 0.4149265 +[14,] -1.119685e-04 0.000000 0 5 -5.375890e-06 0.0000000 0.0000000 1.1132385 +[15,] -1.951025e-04 0.000000 0 5 -1.236363e-05 0.0000000 0.0000000 1.9397917 +[16,] -3.012551e-04 0.000000 0 5 -2.308789e-05 0.0000000 0.0000000 2.9952054 + +$result$retres +$result$retres$res + [1] -5.714047e-01 2.308128e-02 1.043613e+00 -6.035330e-01 8.035846e-02 -1.996318e-01 1.595139e-01 -4.024063e-02 3.238663e-01 -2.996922e-01 -2.573911e-01 2.332169e-01 4.052089e-06 2.456777e-06 5.684939e-07 -1.842627e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09894791 13.34664 0.5725626 7.039737e-07 + [2,] 0.16224563 12.65773 0.8641617 4.581811e-07 + [3,] 0.23860026 11.82672 1.2159111 1.616870e-07 + [4,] 0.32510534 10.88524 1.6144215 -1.742225e-07 + [5,] 0.07153586 13.64498 0.4462812 8.104179e-07 + [6,] 0.15370242 12.75071 0.8248050 4.913554e-07 + [7,] 0.25095842 11.69222 1.2728426 1.136988e-07 + [8,] 0.37514318 10.34065 1.8449352 -3.685254e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.0114280941 NA NA NA +[2,] -0.0004616255 NA NA NA +[3,] -0.0208722567 NA NA NA +[4,] 0.0120706597 NA NA NA +[5,] NA -0.03696489 -0.06477327 -8.104179e-07 +[6,] NA 0.09183062 0.05993843 -4.913554e-07 +[7,] NA -0.07337642 0.05147822 -1.136988e-07 +[8,] NA 0.01851069 -0.04664339 3.685254e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhhM_res/KEIO_ROBOT2_43_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhhM_res/KEIO_ROBOT2_43_res.txt new file mode 100644 index 0000000..c86d8a5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhhM_res/KEIO_ROBOT2_43_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0227137417778754 0.0225500022241814 0.0214958728665015 0.00531934976783309 0.015842261338684 0.0337638947481726 +Glc 14.1763364838519 14.0889102537521 14.0998881864654 0.327858038205569 13.4134474451372 14.7240057005502 +Ace 0.221367966157694 0.220197088292214 0.226693807276363 0.15213514257942 9.99999999990418e-07 0.491296790396283 +Lac 1e-06 0.075884417386228 0.0482447338156448 0.0840626460583609 9.99999999986122e-07 0.2554246573665 +mu 0.588322573459407 0.596377253227481 0.599520927032812 0.0525233400189233 0.491772452338243 0.672032100147791 +qGlc -6.40304828165528 -6.21605122369075 -6.2187756578669 0.925206146516209 -7.9331842037377 -4.41231875646267 +qAce 2.7102767542733 2.74901563628635 2.69445951245303 0.415625046846491 1.99958334597742 3.48542501019942 +qLac -2.28452734436001e-06 0.0286245934663456 0.0746909939358227 0.250403961287575 -0.503705559670473 0.414287315929487 +res 2.16913535938103 20.1375856385158 19.534716132582 5.96873569734281 11.2240306611446 32.620305828829 + + +Goodness of fit (khi2 test) + +khi2 value 2.16913535938258 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.271141919922822 +p-value, i.e. P(X^2<=value) 0.0246174291332529 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhhX.txt b/validation/validation_results/Berges_2021/Berges_2021/yhhX.txt new file mode 100644 index 0000000..cb85663 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhhX.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 5.7456E-2 NA NA +2.2613888888888889 7.8623999999999999E-2 NA NA +2.7741666666666664 0.114912 NA NA +3.2088888888888891 0.13910400000000001 NA NA +3.7063888888888892 0.18446399999999999 NA NA +4.2258333333333331 0.270648 NA NA +4.6355555555555554 0.32356800000000002 NA NA +4.9675000000000002 0.38253599999999999 NA NA +2.8 NA 12.1096661510357 0.631445219824516 +3.73333333333333 NA 11.5165617735442 1.11604401580182 +4.28333333333333 NA 10.9752369844451 1.50113969474825 +4.75 NA 9.99222209662007 1.89213040656483 +5.11666666666667 NA 9.20077219498303 2.21864387599059 +5.43333333333333 NA 8.03358963749831 2.48942786405758 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhhX_res/KEIO_ROBOT5_19.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhhX_res/KEIO_ROBOT5_19.pdf new file mode 100644 index 0000000..d1c2e64 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhhX_res/KEIO_ROBOT5_19.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhhX_res/KEIO_ROBOT5_19_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhhX_res/KEIO_ROBOT5_19_log.txt new file mode 100644 index 0000000..3596d54 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhhX_res/KEIO_ROBOT5_19_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.057456 NA NA + [2,] 0.078624 NA NA + [3,] 0.114912 NA NA + [4,] 0.139104 NA NA + [5,] 0.184464 NA NA + [6,] 0.270648 NA NA + [7,] 0.323568 NA NA + [8,] 0.382536 NA NA + [9,] NA 12.109666 0.6314452 +[10,] NA 11.516562 1.1160440 +[11,] NA 10.975237 1.5011397 +[12,] NA 9.992222 1.8921304 +[13,] NA 9.200772 2.2186439 +[14,] NA 8.033590 2.4894279 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02262978 13.23484704 0.30325494 0.57294132 -5.89183566 2.69081591 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.027378e-08 -6.157987e-07 1.335939e-08 1.026870e-07 5.970132e-07 2.660392e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.004080039 0.417131594 0.182276383 0.040344373 0.739692962 0.322466671 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.420357 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.027378e-08 -6.157987e-07 1.335939e-08 1.026870e-07 5.970132e-07 2.660392e-07 + +$result$normp +[1] 9.040124e-07 + +$result$res + [1] 0.35364340 0.20251921 -0.20019802 0.15862045 0.23685067 -0.79313543 -0.06847226 0.35772184 0.43557824 -0.05416803 -0.46850528 -0.13591904 -0.21333882 0.43635292 0.47087487 -0.08332076 -0.33745097 -0.39703169 -0.14099045 0.48791901 + +$result$prevres + [1] 0.35364426 0.20252013 -0.20019709 0.15862133 0.23685136 -0.79313517 -0.06847261 0.35772075 0.43557883 -0.05416783 -0.46850530 -0.13591922 -0.21333909 0.43635262 0.47087517 -0.08332043 -0.33745074 -0.39703167 -0.14099072 0.48791838 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 142.57509 0.000000 0 5.900808 0.0000000 0.0000000 + [2,] 182.66720 0.000000 0 9.347949 0.0000000 0.0000000 + [3,] 245.04881 0.000000 0 15.383872 0.0000000 0.0000000 + [4,] 314.35650 0.000000 0 22.827462 0.0000000 0.0000000 + [5,] 418.03533 0.000000 0 35.062629 0.0000000 0.0000000 + [6,] 562.94227 0.000000 0 53.834010 0.0000000 0.0000000 + [7,] 711.89030 0.000000 0 74.678463 0.0000000 0.0000000 + [8,] 861.01204 0.000000 0 96.789357 0.0000000 0.0000000 + [9,] -88.84166 2.173913 0 -3.536796 0.3412294 0.0000000 +[10,] -167.45945 2.173913 0 -9.422180 0.6431903 0.0000000 +[11,] -237.77077 2.173913 0 -15.822904 0.9132471 0.0000000 +[12,] -317.50650 2.173913 0 -23.991530 1.2195019 0.0000000 +[13,] -396.95767 2.173913 0 -32.873014 1.5246636 0.0000000 +[14,] -480.37257 2.173913 0 -42.839462 1.8450496 0.0000000 +[15,] 93.32065 0.000000 5 3.715105 0.0000000 0.7848277 +[16,] 175.90199 0.000000 5 9.897204 0.0000000 1.4793377 +[17,] 249.75810 0.000000 5 16.620623 0.0000000 2.1004683 +[18,] 333.51375 0.000000 5 25.201074 0.0000000 2.8048543 +[19,] 416.97048 0.000000 5 34.530323 0.0000000 3.5067263 +[20,] 504.59079 0.000000 5 44.999234 0.0000000 4.2436140 + +$result$retres +$result$retres$res + [1] 0.35364426 0.20252013 -0.20019709 0.15862133 0.23685136 -0.79313517 -0.06847261 0.35772075 0.43557883 -0.05416783 -0.46850530 -0.13591922 -0.21333909 0.43635262 0.47087517 -0.08332043 -0.33745074 -0.39703167 -0.14099072 0.48791838 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06452889 12.803979 0.5000338 + [2,] 0.08267440 12.617379 0.5852542 + [3,] 0.11090806 12.327039 0.7178534 + [4,] 0.14227643 12.004462 0.8651748 + [5,] 0.18920103 11.521914 1.0855559 + [6,] 0.25478530 10.847478 1.3935721 + [7,] 0.32219855 10.154235 1.7101782 + [8,] 0.38969041 9.460183 2.0271534 + [9,] 0.11256181 12.310032 0.7256203 + [10,] 0.19214450 11.491645 1.0993799 + [11,] 0.26331877 10.759725 1.4336495 + [12,] 0.34403311 9.929699 1.8127241 + [13,] 0.42445939 9.102636 2.1904457 + [14,] 0.50889807 8.234312 2.5870115 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.007072885 NA NA + [2,] -0.004050403 NA NA + [3,] 0.004003942 NA NA + [4,] -0.003172427 NA NA + [5,] -0.004737027 NA NA + [6,] 0.015862703 NA NA + [7,] 0.001369452 NA NA + [8,] -0.007154415 NA NA + [9,] NA -0.20036626 -0.09417503 +[10,] NA 0.02491720 0.01666409 +[11,] NA 0.21551244 0.06749015 +[12,] NA 0.06252284 0.07940633 +[13,] NA 0.09813598 0.02819814 +[14,] NA -0.20072221 -0.09758368 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhhX_res/KEIO_ROBOT5_19_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhhX_res/KEIO_ROBOT5_19_res.txt new file mode 100644 index 0000000..0131411 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhhX_res/KEIO_ROBOT5_19_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0226297787750074 0.0230403921542281 0.022533186483447 0.0034826500991087 0.0170131479578795 0.0300149972624033 +Glc 13.2348470423283 13.2931335601917 13.2886354213388 0.266469361673909 12.7658603900065 13.7883601299112 +Ace 0.303254943478683 0.304759929227384 0.299393425302241 0.112746996435433 0.128870611293453 0.53759284564427 +mu 0.572941316233946 0.5717939803583 0.572802025167574 0.0308577992054571 0.517472130999125 0.630758614465401 +qGlc -5.89183565759043 -5.97548524039683 -5.92493506338603 0.600909984820441 -7.16069481626227 -4.84438442480258 +qAce 2.69081590769339 2.68003415054539 2.67872504707949 0.262968730407767 2.21788761248307 3.17707481566346 +res 2.47379996267331 37.9325703692724 37.4960664544714 8.64979195308865 24.2940744382751 55.6439200112722 + + +Goodness of fit (khi2 test) + +khi2 value 2.4737999626795 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.17669999733425 +p-value, i.e. P(X^2<=value) 0.00030073209844088 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhiI.txt b/validation/validation_results/Berges_2021/Berges_2021/yhiI.txt new file mode 100644 index 0000000..f43e45e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhiI.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.18888888888889 0.065016 NA NA +2.27694444444444 0.10584 NA NA +3.12833333333333 0.157248 NA NA +3.77138888888889 0.214704 NA NA +4.41555555555556 0.297864 NA NA +4.82277777777778 0.358344 NA NA +0.0666666666666667 NA 15.5474287729818 0.00422290244344736 +1.71666666666667 NA 14.2353952432767 0.347969308314086 +2.8 NA 13.2111248705134 0.714151650729584 +3.63333333333333 NA 12.8085423817645 1.16342786145513 +4.26666666666667 NA 12.0108904953934 1.61239658092266 +4.88333333333333 NA 10.4492424724173 2.06011635267939 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhiI_res/KEIO_ROBOT1_2.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhiI_res/KEIO_ROBOT1_2.pdf new file mode 100644 index 0000000..d6a3115 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhiI_res/KEIO_ROBOT1_2.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhiI_res/KEIO_ROBOT1_2_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhiI_res/KEIO_ROBOT1_2_log.txt new file mode 100644 index 0000000..dd9491e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhiI_res/KEIO_ROBOT1_2_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.065016 NA NA + [3,] 0.105840 NA NA + [4,] 0.157248 NA NA + [5,] 0.214704 NA NA + [6,] 0.297864 NA NA + [7,] 0.358344 NA NA + [8,] NA 15.54743 0.004222902 + [9,] NA 14.23540 0.347969308 +[10,] NA 13.21112 0.714151651 +[11,] NA 12.80854 1.163427861 +[12,] NA 12.01089 1.612396581 +[13,] NA 10.44924 2.060116353 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0372152 15.1177297 0.0558675 0.4684237 -6.6110561 2.9576506 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.641618e-08 4.180384e-07 -1.473225e-07 -1.090335e-07 -3.401940e-07 2.567718e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.007330277 0.336996017 0.146684204 0.045675553 0.913890326 0.399207704 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4941311 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.641618e-08 4.180384e-07 -1.473225e-07 -1.090335e-07 -3.401940e-07 2.567718e-08 + +$result$normp +[1] 5.700957e-07 + +$result$res + [1] 0.273160179 -0.003288929 0.114272901 0.193225702 0.152058697 -0.171300668 -0.101346791 -0.970347791 0.508271274 1.048133254 -0.100567919 -0.529364721 0.043875903 0.295491747 -0.009814832 -0.105042275 -0.268905541 -0.288263675 0.376534575 + +$result$prevres + [1] 0.273159358 -0.003289941 0.114271858 0.193224897 0.152058371 -0.171300075 -0.101345281 -0.970348682 0.508270910 1.048133298 -0.100567594 -0.529364267 0.043876335 0.295492467 -0.009814595 -0.105042381 -0.268905848 -0.288264020 0.376534377 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.0000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 87.2630317 0.000000 0 3.860928626 0.000000000 0.00000000 + [3,] 145.2705809 0.000000 0 12.309780672 0.000000000 0.00000000 + [4,] 216.4606847 0.000000 0 25.200679885 0.000000000 0.00000000 + [5,] 292.5488006 0.000000 0 41.060085251 0.000000000 0.00000000 + [6,] 395.5884961 0.000000 0 65.005367004 0.000000000 0.00000000 + [7,] 478.7253827 0.000000 0 85.921908229 0.000000000 0.00000000 + [8,] -0.9732412 2.173913 0 -0.001213596 0.005478604 0.00000000 + [9,] -37.8836350 2.173913 0 -1.370578538 0.213255887 0.00000000 +[10,] -83.2095480 2.173913 0 -5.256910148 0.468406107 0.00000000 +[11,] -137.5927278 2.173913 0 -11.821782412 0.774541811 0.00000000 +[12,] -195.7093914 2.173913 0 -20.398746160 1.101694173 0.00000000 +[13,] -271.5291472 2.173913 0 -33.349605595 1.528501402 0.00000000 +[14,] 1.0014387 0.000000 5 0.001248757 0.000000000 0.01260079 +[15,] 38.9812280 0.000000 5 1.410287966 0.000000000 0.49048854 +[16,] 85.6203573 0.000000 5 5.409217283 0.000000000 1.07733405 +[17,] 141.5791673 0.000000 5 12.164291938 0.000000000 1.78144617 +[18,] 201.3796303 0.000000 5 20.989753899 0.000000000 2.53389660 +[19,] 279.3960929 0.000000 5 34.315835325 0.000000000 3.51555323 + +$result$retres +$result$retres$res + [1] 0.273159358 -0.003289941 0.114271858 0.193224897 0.152058371 -0.171300075 -0.101345281 -0.970348682 0.508270910 1.048133298 -0.100567594 -0.529364267 0.043876335 0.295492467 -0.009814595 -0.105042381 -0.268905848 -0.288264020 0.376534377 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03721519 15.11773 0.05586765 + [2,] 0.06495020 14.72629 0.23098785 + [3,] 0.10812544 14.11694 0.50359836 + [4,] 0.16111250 13.36912 0.83816119 + [5,] 0.21774517 12.56984 1.19574257 + [6,] 0.29443800 11.48744 1.67998477 + [7,] 0.35631709 10.61411 2.07069234 + [8,] 0.03839569 15.10107 0.06332140 + [9,] 0.08316649 14.46920 0.34600639 + [10,] 0.13814498 13.69327 0.69314317 + [11,] 0.20410956 12.76228 1.10964669 + [12,] 0.27460270 11.76738 1.55474378 + [13,] 0.36656898 10.46943 2.13542323 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -5.463187e-03 NA NA + [2,] 6.579881e-05 NA NA + [3,] -2.285437e-03 NA NA + [4,] -3.864498e-03 NA NA + [5,] -3.041167e-03 NA NA + [6,] 3.426001e-03 NA NA + [7,] 2.026906e-03 NA NA + [8,] NA 0.44636039 -0.059098493 + [9,] NA -0.23380462 0.001962919 +[10,] NA -0.48214132 0.021008476 +[11,] NA 0.04626109 0.053781170 +[12,] NA 0.24350756 0.057652804 +[13,] NA -0.02018311 -0.075306875 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhiI_res/KEIO_ROBOT1_2_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhiI_res/KEIO_ROBOT1_2_res.txt new file mode 100644 index 0000000..2f79d32 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhiI_res/KEIO_ROBOT1_2_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0372152035855683 0.0375110525939213 0.0375734281519996 0.00512770363554431 0.0288234689721486 0.0482988452836117 +Glc 15.1177297008332 15.1208208213802 15.0945356918388 0.210972715960488 14.7969670224419 15.5994583542971 +Ace 0.055867502673364 0.0909651747574786 0.0868829630085618 0.0668413407978039 9.99999999999549e-07 0.227709781415853 +mu 0.468423736689395 0.46739556664455 0.466222624600841 0.0318636119472597 0.40055746129412 0.526763904532251 +qGlc -6.61105612273386 -6.620062717808 -6.59804336205734 0.596792132200981 -7.76407192064926 -5.51359207242702 +qAce 2.95765056396752 2.88724683099819 2.83803816667692 0.239709401886783 2.47990788220322 3.40153016187557 +res 3.17415256288849 31.7484417550447 30.8565280005583 7.95612812921158 19.6642635856426 51.495534561115 + + +Goodness of fit (khi2 test) + +khi2 value 3.17415256289709 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.244165581761315 +p-value, i.e. P(X^2<=value) 0.0027699865084711 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhiN.txt b/validation/validation_results/Berges_2021/Berges_2021/yhiN.txt new file mode 100644 index 0000000..af980fd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhiN.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.133056 NA NA +3.67805555555556 0.19656 NA NA +4.09222222222222 0.261576 NA NA +4.565 0.337176 NA NA +0.05 NA 14.1391664366155 0.0197611940753023 +1.95 NA 13.9925800113837 0.382516934952005 +2.83333333333333 NA 13.574003475031 0.715849130395789 +3.98333333333333 NA 12.2095990348935 1.29327863169524 +4.88333333333333 NA 10.7721337804088 2.13725405523455 +5.16666666666667 NA 10.0646297656377 2.29887833388921 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhiN_res/KEIO_ROBOT3_2.pdf b/validation/validation_results/Berges_2021/Berges_2021/yhiN_res/KEIO_ROBOT3_2.pdf new file mode 100644 index 0000000..7977926 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yhiN_res/KEIO_ROBOT3_2.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhiN_res/KEIO_ROBOT3_2_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yhiN_res/KEIO_ROBOT3_2_log.txt new file mode 100644 index 0000000..b3b4497 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhiN_res/KEIO_ROBOT3_2_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.133056 NA NA + [2,] 0.196560 NA NA + [3,] 0.261576 NA NA + [4,] 0.337176 NA NA + [5,] NA 14.13917 0.01976119 + [6,] NA 13.99258 0.38251693 + [7,] NA 13.57400 0.71584913 + [8,] NA 12.20960 1.29327863 + [9,] NA 10.77213 2.13725406 +[10,] NA 10.06463 2.29887833 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02706313 14.37357824 0.11021110 0.55104366 -5.35528918 2.88347503 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.330886e-09 -1.316250e-08 -4.692316e-08 -2.152295e-08 1.370109e-07 7.726662e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.00747555 0.27985408 0.12444467 0.06591948 0.62430238 0.28173711 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4066473 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.330886e-09 -1.316250e-08 -4.692316e-08 -2.152295e-08 1.370109e-07 7.726662e-08 + +$result$normp +[1] 1.660898e-07 + +$result$res + [1] -0.048229430 0.441816108 -0.176145912 -0.116235821 0.493618504 -0.274465516 -0.414467223 0.141670904 -0.029891628 0.083534959 0.472029719 0.004082912 -0.362318641 -0.264972462 -0.402478576 0.553657048 + +$result$prevres + [1] -0.048229590 0.441816036 -0.176145886 -0.116235618 0.493618534 -0.274465448 -0.414467146 0.141670947 -0.029891703 0.083534816 0.472029951 0.004083026 -0.362318605 -0.264972541 -0.402478723 0.553656892 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 244.0431518 0.000000 0 1.900098e+01 0.000000000 0.000000000 + [2,] 379.4763501 0.000000 0 3.777295e+01 0.000000000 0.000000000 + [3,] 476.7614213 0.000000 0 5.280053e+01 0.000000000 0.000000000 + [4,] 618.6485913 0.000000 0 7.642981e+01 0.000000000 0.000000000 + [5,] -0.5901898 2.173913 0 -4.011431e-04 0.002982543 0.000000000 + [6,] -40.7463104 2.173913 0 -1.264097e+00 0.205912779 0.000000000 + [7,] -79.5426680 2.173913 0 -3.812701e+00 0.401971409 0.000000000 + [8,] -168.5921951 2.173913 0 -1.217203e+01 0.851986035 0.000000000 + [9,] -290.3995278 2.173913 0 -2.690857e+01 1.467543276 0.000000000 +[10,] -343.0403691 2.173913 0 -3.407256e+01 1.733565446 0.000000000 +[11,] 0.7308913 0.000000 5 4.967758e-04 0.000000000 0.006859849 +[12,] 50.4602467 0.000000 5 1.565458e+00 0.000000000 0.473599392 +[13,] 98.5056712 0.000000 5 4.721651e+00 0.000000000 0.924534242 +[14,] 208.7846405 0.000000 5 1.507385e+01 0.000000000 1.959567880 +[15,] 359.6308891 0.000000 5 3.332358e+01 0.000000000 3.375349534 +[16,] 424.8213275 0.000000 5 4.219548e+01 0.000000000 3.987200526 + +$result$retres +$result$retres$res + [1] -0.048229590 0.441816036 -0.176145886 -0.116235618 0.493618534 -0.274465448 -0.414467146 0.141670947 -0.029891703 0.083534816 0.472029951 0.004083026 -0.362318605 -0.264972541 -0.402478723 0.553656892 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.13209141 13.35287 0.6597981 + [2,] 0.20539632 12.64046 1.0433845 + [3,] 0.25805308 12.12871 1.3189243 + [4,] 0.33485129 11.38236 1.7207903 + [5,] 0.02781914 14.36623 0.1141672 + [6,] 0.07925792 13.86633 0.3833335 + [7,] 0.12895488 13.38335 0.6433854 + [8,] 0.24302462 12.27477 1.2402841 + [9,] 0.39905613 10.75838 2.0567583 + [10,] 0.46648746 10.10306 2.4096097 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0009645918 NA NA + [2,] -0.0088363207 NA NA + [3,] 0.0035229177 NA NA + [4,] 0.0023247124 NA NA + [5,] NA -0.22706453 -0.0944059903 + [6,] NA 0.12625411 -0.0008166052 + [7,] NA 0.19065489 0.0724637211 + [8,] NA -0.06516864 0.0529945082 + [9,] NA 0.01375018 0.0804957446 +[10,] NA -0.03842602 -0.1107313785 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yhiN_res/KEIO_ROBOT3_2_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yhiN_res/KEIO_ROBOT3_2_res.txt new file mode 100644 index 0000000..0d52702 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yhiN_res/KEIO_ROBOT3_2_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0270631276935114 0.0271862587977554 0.026964154357874 0.00479464282113166 0.0201957119481223 0.0371092908462191 +Glc 14.3735782445524 14.3910370812879 14.382245565284 0.258039380586258 13.9090443590111 14.8743928185027 +Ace 0.11021109670641 0.134264116180791 0.124708250591173 0.0915414612485553 9.99999999999265e-07 0.333355559752764 +mu 0.551043659137001 0.553148318938562 0.551947269394611 0.0360230845918042 0.481108831672612 0.613830961119027 +qGlc -5.35528918068873 -5.45828726757758 -5.48801082585505 0.577995928993711 -6.46185530802462 -4.40672579196923 +qAce 2.88347502907027 2.83556949562013 2.84144503353974 0.260512353320457 2.41506550757936 3.31446821155028 +res 1.65362062856542 24.2413625009508 23.0870868220011 6.88926649495695 13.8419466749704 38.7511454020739 + + +Goodness of fit (khi2 test) + +khi2 value 1.65362062856566 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.165362062856566 +p-value, i.e. P(X^2<=value) 0.00162817139108768 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yiaF.txt b/validation/validation_results/Berges_2021/Berges_2021/yiaF.txt new file mode 100644 index 0000000..fe64e86 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yiaF.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.167832 NA NA +3.67805555555556 0.273672 NA NA +4.09222222222222 0.361368 NA NA +4.565 0.485352 NA NA +0.05 NA 14.2021415637682 0.0217097011793847 +1.95 NA 13.7223841044811 0.425560724076706 +2.83333333333333 NA 13.1707178543112 0.765499968176382 +3.98333333333333 NA 11.8681908771965 1.45933861175214 +4.88333333333333 NA 9.55543305160112 2.12321235927536 +5.16666666666667 NA 8.61288982545572 2.47248101096773 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yiaF_res/KEIO_ROBOT3_43.pdf b/validation/validation_results/Berges_2021/Berges_2021/yiaF_res/KEIO_ROBOT3_43.pdf new file mode 100644 index 0000000..2b4e7c4 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yiaF_res/KEIO_ROBOT3_43.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yiaF_res/KEIO_ROBOT3_43_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yiaF_res/KEIO_ROBOT3_43_log.txt new file mode 100644 index 0000000..4666dcf --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yiaF_res/KEIO_ROBOT3_43_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.167832 NA NA + [2,] 0.273672 NA NA + [3,] 0.361368 NA NA + [4,] 0.485352 NA NA + [5,] NA 14.202142 0.0217097 + [6,] NA 13.722384 0.4255607 + [7,] NA 13.170718 0.7655000 + [8,] NA 11.868191 1.4593386 + [9,] NA 9.555433 2.1232124 +[10,] NA 8.612890 2.4724810 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0290279 14.3017496 0.1877333 0.6154760 -5.1939256 2.1730739 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.256244e-09 3.999458e-08 3.299208e-08 -9.706329e-09 -2.376698e-08 -9.561956e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.007332024 0.319857050 0.138649989 0.059937607 0.528676178 0.228771917 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4773943 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.256244e-09 3.999458e-08 3.299208e-08 -9.706329e-09 -2.376698e-08 -9.561956e-08 + +$result$normp +[1] 1.117667e-07 + +$result$res + [1] 0.1352122117 0.2775748456 -0.0536673846 -0.1685291722 0.1998965110 0.0236478712 -0.0544016034 -0.3584126265 0.0947046795 0.0945651682 0.8461332805 0.0001034848 -0.4704349099 -0.9222755026 0.1604704206 0.3860032266 + +$result$prevres + [1] 0.1352120807 0.2775747398 -0.0536674487 -0.1685291473 0.1998964249 0.0236478294 -0.0544016142 -0.3584125931 0.0947047332 0.0945652199 0.8461331156 0.0001033341 -0.4704350306 -0.9222755193 0.1604705982 0.3860035019 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 293.7453802 0.000000 0 2.453116e+01 0.000000000 0.000000000 + [2,] 480.9570732 0.000000 0 5.134998e+01 0.000000000 0.000000000 + [3,] 620.6005729 0.000000 0 7.372029e+01 0.000000000 0.000000000 + [4,] 830.2036755 0.000000 0 1.100123e+02 0.000000000 0.000000000 + [5,] -0.5733337 2.173913 0 -4.182012e-04 0.003204257 0.000000000 + [6,] -42.5742884 2.173913 0 -1.440376e+00 0.237939925 0.000000000 + [7,] -86.5776031 2.173913 0 -4.546178e+00 0.483866417 0.000000000 + [8,] -194.5975135 2.173913 0 -1.544425e+01 1.087569975 0.000000000 + [9,] -352.1913035 2.173913 0 -3.591414e+01 1.968332895 0.000000000 +[10,] -422.7836093 2.173913 0 -4.621954e+01 2.362860404 0.000000000 +[11,] 0.5517141 0.000000 5 4.024311e-04 0.000000000 0.007369792 +[12,] 40.9688733 0.000000 5 1.386062e+00 0.000000000 0.547261828 +[13,] 83.3128864 0.000000 5 4.374748e+00 0.000000000 1.112892759 +[14,] 187.2595215 0.000000 5 1.486187e+01 0.000000000 2.501410943 +[15,] 338.9106767 0.000000 5 3.455987e+01 0.000000000 4.527165660 +[16,] 406.8410483 0.000000 5 4.447666e+01 0.000000000 5.434578930 + +$result$retres +$result$retres$res + [1] 0.1352120807 0.2775747398 -0.0536674487 -0.1685291473 0.1998964249 0.0236478294 -0.0544016142 -0.3584125931 0.0947047332 0.0945652199 0.8461331156 0.0001033341 -0.4704350306 -0.9222755193 0.1604705982 0.3860035019 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.17053624 13.107578 0.6873597 + [2,] 0.27922349 12.190380 1.0711041 + [3,] 0.36029465 11.506231 1.3573437 + [4,] 0.48198142 10.479331 1.7869857 + [5,] 0.02993509 14.294094 0.1909363 + [6,] 0.09639321 13.733262 0.4255814 + [7,] 0.16601966 13.145693 0.6714130 + [8,] 0.33693960 11.703321 1.2748835 + [9,] 0.58630029 9.598997 2.1553065 + [10,] 0.69799851 8.656390 2.5496817 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.002704242 NA NA + [2,] -0.005551495 NA NA + [3,] 0.001073349 NA NA + [4,] 0.003370583 NA NA + [5,] NA -0.09195236 -1.692266e-01 + [6,] NA -0.01087800 -2.066683e-05 + [7,] NA 0.02502474 9.408701e-02 + [8,] NA 0.16486979 1.844551e-01 + [9,] NA -0.04356418 -3.209412e-02 +[10,] NA -0.04350000 -7.720070e-02 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yiaF_res/KEIO_ROBOT3_43_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yiaF_res/KEIO_ROBOT3_43_res.txt new file mode 100644 index 0000000..78efb8a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yiaF_res/KEIO_ROBOT3_43_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0290279031589361 0.0298237833269235 0.0292843173475079 0.00367050600536775 0.0245820903768376 0.0368827915506211 +Glc 14.3017495896067 14.2983485462394 14.2622201627478 0.24054587586286 13.8906735669923 14.8424547317979 +Ace 0.187733336587824 0.201173990093767 0.194676130767492 0.114329089724673 9.99999999999905e-07 0.411463754324341 +mu 0.615476016026177 0.611197492354444 0.612712492990737 0.0259435162757792 0.566409594083843 0.650078112369581 +qGlc -5.19392562131649 -5.16963828654846 -5.18958966148257 0.416099202521165 -5.95181557328071 -4.33388701033385 +qAce 2.17307387966187 2.13741652048237 2.12062883475836 0.214701887905425 1.79567490144182 2.60915096446759 +res 2.27905282980021 24.5536977585855 24.0742190896245 7.35394902950501 13.2565587740828 38.1540395663602 + + +Goodness of fit (khi2 test) + +khi2 value 2.27905282980043 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.227905282980043 +p-value, i.e. P(X^2<=value) 0.00628051551058084 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibL.txt b/validation/validation_results/Berges_2021/Berges_2021/yibL.txt new file mode 100644 index 0000000..6fe9ea5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yibL.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.134568 NA NA +3.67805555555556 0.21924 NA NA +4.09222222222222 0.290304 NA NA +4.565 0.40068 NA NA +0.05 NA 14.7166570151296 0.0210623236770538 +1.95 NA 14.2281331381886 0.418533579543459 +2.83333333333333 NA 13.6896131367391 0.797637533469356 +3.98333333333333 NA 11.8567617389417 1.46400231743666 +4.88333333333333 NA 9.43613274838426 1.96724346344096 +5.16666666666667 NA 8.62335214311137 2.44149586726273 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibL_res/KEIO_ROBOT3_3.pdf b/validation/validation_results/Berges_2021/Berges_2021/yibL_res/KEIO_ROBOT3_3.pdf new file mode 100644 index 0000000..1bc06ba Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yibL_res/KEIO_ROBOT3_3.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibL_res/KEIO_ROBOT3_3_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yibL_res/KEIO_ROBOT3_3_log.txt new file mode 100644 index 0000000..8155d7a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yibL_res/KEIO_ROBOT3_3_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.134568 NA NA + [2,] 0.219240 NA NA + [3,] 0.290304 NA NA + [4,] 0.400680 NA NA + [5,] NA 14.716657 0.02106232 + [6,] NA 14.228133 0.41853358 + [7,] NA 13.689613 0.79763753 + [8,] NA 11.856762 1.46400232 + [9,] NA 9.436133 1.96724346 +[10,] NA 8.623352 2.44149587 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02325473 14.81920288 0.20805065 0.61928557 -7.13905763 2.55715948 + +$result$lastp + X Glc Ace mu qGlc qAce +-5.764552e-09 -9.887836e-08 2.271153e-07 6.532728e-08 5.359817e-09 -5.036918e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.008644249 0.412685930 0.175636461 0.088103626 0.859509632 0.360817020 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6001098 + +$result$laststep + X Glc Ace mu qGlc qAce +-5.764552e-09 -9.887836e-08 2.271153e-07 6.532728e-08 5.359817e-09 -5.036918e-07 + +$result$normp +[1] 5.65149e-07 + +$result$res + [1] 0.17784685 0.38034299 0.14344594 -0.38915858 0.20459819 -0.08195409 -0.33085462 0.15487173 0.29322930 -0.23989051 0.95004068 0.07368749 -0.65230707 -1.10172209 0.60334731 0.12695369 + +$result$prevres + [1] 0.17784726 0.38034307 0.14344565 -0.38915956 0.20459840 -0.08195411 -0.33085477 0.15487151 0.29322930 -0.23989033 0.95003955 0.07368677 -0.65230746 -1.10172185 0.60334820 0.12695479 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 296.9824313 0.000000 0 1.986889e+01 0.000000000 0.000000000 + [2,] 487.7434147 0.000000 0 4.171777e+01 0.000000000 0.000000000 + [3,] 630.3510517 0.000000 0 5.998644e+01 0.000000000 0.000000000 + [4,] 844.7673901 0.000000 0 8.967870e+01 0.000000000 0.000000000 + [5,] -0.7881234 2.173913 0 -4.605546e-04 0.002567229 0.000000000 + [6,] -58.7789384 2.173913 0 -1.594648e+00 0.191466243 0.000000000 + [7,] -119.8244162 2.173913 0 -5.046730e+00 0.390315501 0.000000000 + [8,] -270.2769381 2.173913 0 -1.720838e+01 0.880398851 0.000000000 + [9,] -490.6139789 2.173913 0 -4.013733e+01 1.598123711 0.000000000 +[10,] -589.5200361 2.173913 0 -5.170452e+01 1.920299846 0.000000000 +[11,] 0.6492905 0.000000 5 3.794250e-04 0.000000000 0.005904628 +[12,] 48.4246607 0.000000 5 1.313741e+00 0.000000000 0.440372358 +[13,] 98.7165957 0.000000 5 4.157717e+00 0.000000000 0.897725651 +[14,] 222.6659646 0.000000 5 1.417701e+01 0.000000000 2.024917357 +[15,] 404.1892574 0.000000 5 3.306688e+01 0.000000000 3.675684536 +[16,] 485.6723939 0.000000 5 4.259645e+01 0.000000000 4.416689645 + +$result$retres +$result$retres$res + [1] 0.17784726 0.38034307 0.14344565 -0.38915956 0.20459840 -0.08195411 -0.33085477 0.15487151 0.29322930 -0.23989033 0.95003955 0.07368677 -0.65230746 -1.10172185 0.60334820 0.12695479 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.13812495 13.494991 0.6823737 + [2,] 0.22684686 12.472214 1.0487251 + [3,] 0.29317291 11.707615 1.3225993 + [4,] 0.39289681 10.558008 1.7343802 + [5,] 0.02398606 14.810772 0.2110702 + [6,] 0.07779798 14.190434 0.4332709 + [7,] 0.13444443 13.537420 0.6671760 + [8,] 0.27405512 11.928003 1.2436579 + [9,] 0.47851436 9.571018 2.0879131 + [10,] 0.57029310 8.513003 2.4668868 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.003556945 NA NA + [2,] -0.007606861 NA NA + [3,] -0.002868913 NA NA + [4,] 0.007783191 NA NA + [5,] NA -0.09411526 -0.19000791 + [6,] NA 0.03769889 -0.01473735 + [7,] NA 0.15219319 0.13046149 + [8,] NA -0.07124089 0.22034437 + [9,] NA -0.13488548 -0.12066964 +[10,] NA 0.11034955 -0.02539096 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibL_res/KEIO_ROBOT3_3_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yibL_res/KEIO_ROBOT3_3_res.txt new file mode 100644 index 0000000..4c5ed1d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yibL_res/KEIO_ROBOT3_3_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0232547276289379 0.0234146966158317 0.0230751973618059 0.00304572114845915 0.0188590219161672 0.0294033850130893 +Glc 14.8192028768422 14.839985108024 14.8740261269843 0.244575949072065 14.3029148792079 15.2880718522112 +Ace 0.208050645610615 0.216059793203441 0.204193456795288 0.106109037799498 0.0413260431369401 0.413804377717543 +mu 0.619285565007578 0.619873598401284 0.620957959180685 0.0272698840303627 0.571352932130211 0.665139958903363 +qGlc -7.1390576270892 -7.17722031577787 -7.25412661408502 0.601728789016429 -8.21685360942953 -5.92736926181188 +qAce 2.55715948345731 2.55329239905395 2.57129238326262 0.248972221466596 2.11536495802416 3.04816367956078 +res 3.60131767701558 22.8212180619113 21.0056871462219 8.06961830120253 11.617224620265 47.5426660324428 + + +Goodness of fit (khi2 test) + +khi2 value 3.6013176770212 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.36013176770212 +p-value, i.e. P(X^2<=value) 0.0364543153475653 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibN.txt b/validation/validation_results/Berges_2021/Berges_2021/yibN.txt new file mode 100644 index 0000000..cd5e653 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yibN.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.1512 NA NA +3.67805555555556 0.2268 NA NA +4.09222222222222 0.312984 NA NA +4.565 0.394632 NA NA +0.05 NA 14.4529712073308 0.0197742448771818 +1.95 NA 14.0277234679801 0.395203744023403 +2.83333333333333 NA 13.1206772769665 0.663788182160406 +3.98333333333333 NA 12.588155850013 1.31672575224479 +4.88333333333333 NA 9.9114861649474 1.46067362376866 +5.16666666666667 NA 9.68958935987407 2.18236262893008 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibN_res/KEIO_ROBOT3_4.pdf b/validation/validation_results/Berges_2021/Berges_2021/yibN_res/KEIO_ROBOT3_4.pdf new file mode 100644 index 0000000..b649848 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yibN_res/KEIO_ROBOT3_4.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibN_res/KEIO_ROBOT3_4_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yibN_res/KEIO_ROBOT3_4_log.txt new file mode 100644 index 0000000..da1bd17 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yibN_res/KEIO_ROBOT3_4_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.151200 NA NA + [2,] 0.226800 NA NA + [3,] 0.312984 NA NA + [4,] 0.394632 NA NA + [5,] NA 14.452971 0.01977424 + [6,] NA 14.027723 0.39520374 + [7,] NA 13.120677 0.66378818 + [8,] NA 12.588156 1.31672575 + [9,] NA 9.911486 1.46067362 +[10,] NA 9.689589 2.18236263 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02956671 14.51046092 0.16360307 0.56806425 -5.36709001 2.04494862 + +$result$lastp + X Glc Ace mu qGlc qAce + 4.568177e-09 2.397032e-08 -6.580131e-08 -3.791611e-08 1.274673e-07 8.892072e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.01589127 0.60427483 0.25993537 0.12812909 1.16097561 0.49622903 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.8814454 + +$result$laststep + X Glc Ace mu qGlc qAce + 4.568177e-09 2.397032e-08 -6.580131e-08 -3.791611e-08 1.274673e-07 8.892072e-08 + +$result$normp +[1] 1.746932e-07 + +$result$res + [1] 0.01767108 0.60470981 -0.53610236 0.03769374 0.10748174 -0.18180208 0.59192734 -1.04963977 0.87444247 -0.34240970 0.73447644 -0.07902927 -0.37200273 -1.18362725 1.50976163 -0.60957882 + +$result$prevres + [1] 0.01767074 0.60470963 -0.53610235 0.03769411 0.10748169 -0.18180203 0.59192744 -1.04963967 0.87444242 -0.34240986 0.73447677 -0.07902911 -0.37200268 -1.18362736 1.50976142 -0.60957904 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 256.2907107 0.000000 0 2.180054e+01 0.000000000 0.00000000 + [2,] 403.9919685 0.000000 0 4.393331e+01 0.000000000 0.00000000 + [3,] 511.1526576 0.000000 0 6.184615e+01 0.000000000 0.00000000 + [4,] 668.6337543 0.000000 0 9.024683e+01 0.000000000 0.00000000 + [5,] -0.5917433 2.173913 0 -4.394681e-04 0.003259848 0.00000000 + [6,] -41.6424962 2.173913 0 -1.417675e+00 0.229403865 0.00000000 + [7,] -82.1647744 2.173913 0 -4.327225e+00 0.452636575 0.00000000 + [8,] -176.8396053 2.173913 0 -1.404192e+01 0.974189654 0.00000000 + [9,] -308.5676965 2.173913 0 -3.145741e+01 1.699865011 0.00000000 +[10,] -366.0389935 2.173913 0 -4.000253e+01 2.016467974 0.00000000 +[11,] 0.5185668 0.000000 5 3.851222e-04 0.000000000 0.00749765 +[12,] 36.4928754 0.000000 5 1.242361e+00 0.000000000 0.52762889 +[13,] 72.0040619 0.000000 5 3.792109e+00 0.000000000 1.04106412 +[14,] 154.9711536 0.000000 5 1.230546e+01 0.000000000 2.24063621 +[15,] 270.4094019 0.000000 5 2.756730e+01 0.000000000 3.90968953 +[16,] 320.7736469 0.000000 5 3.505571e+01 0.000000000 4.63787634 + +$result$retres +$result$retres$res + [1] 0.01767074 0.60470963 -0.53610235 0.03769411 0.10748169 -0.18180203 0.59192744 -1.04963967 0.87444242 -0.34240986 0.73447677 -0.07902911 -0.37200268 -1.18362736 1.50976142 -0.60957904 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15155341 13.357926 0.6027375 + [2,] 0.23889419 12.532728 0.9171516 + [3,] 0.30226195 11.934027 1.1452663 + [4,] 0.39538588 11.054189 1.4804988 + [5,] 0.03041853 14.502413 0.1666696 + [6,] 0.08951213 13.944095 0.3793979 + [7,] 0.14784497 13.392964 0.5893876 + [8,] 0.28413178 12.105322 1.0800003 + [9,] 0.47375770 10.313730 1.7626259 + [10,] 0.55648908 9.532081 2.0604468 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0003534148 NA NA + [2,] -0.0120941925 NA NA + [3,] 0.0107220470 NA NA + [4,] -0.0007538821 NA NA + [5,] NA -0.04944158 -0.14689535 + [6,] NA 0.08362893 0.01580582 + [7,] NA -0.27228662 0.07440054 + [8,] NA 0.48283425 0.23672547 + [9,] NA -0.40224351 -0.30195228 +[10,] NA 0.15750853 0.12191581 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibN_res/KEIO_ROBOT3_4_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yibN_res/KEIO_ROBOT3_4_res.txt new file mode 100644 index 0000000..146c61a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yibN_res/KEIO_ROBOT3_4_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0295667052910226 0.0297217818727344 0.0297813470382014 0.00401469422200018 0.0225130908088709 0.0368504977985624 +Glc 14.5104609210556 14.4677545094365 14.4698754764551 0.259404393908939 14.0604868853353 15.0582141537623 +Ace 0.163603070887612 0.169477158441373 0.162138740379913 0.0979295981530859 0.021833761018171 0.375297989088429 +mu 0.568064245177755 0.56882202603863 0.567174341511779 0.030326633711262 0.519234316851903 0.626886954619351 +qGlc -5.36709000896124 -5.2249149729913 -5.19172973788655 0.532095961293194 -6.17143179826412 -4.27765302884789 +qAce 2.04494862191046 2.03724268598811 2.02792813456432 0.199410399069433 1.66590689603652 2.41609046446924 +res 7.76946005697556 23.6925137511917 22.9746386805745 6.8624597148878 12.0057429927166 38.0489687594974 + + +Goodness of fit (khi2 test) + +khi2 value 7.76946005697615 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.776946005697615 +p-value, i.e. P(X^2<=value) 0.348655781790648 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibT.txt b/validation/validation_results/Berges_2021/Berges_2021/yibT.txt new file mode 100644 index 0000000..e4b32d1 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yibT.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.15876 NA NA +3.67805555555556 0.2646 NA NA +4.09222222222222 0.350784 NA NA +4.565 0.439992 NA NA +0.05 NA 14.2239748988211 0.0253711784673284 +1.95 NA 14.0587094887824 0.449572722387344 +2.83333333333333 NA 13.4454002024926 0.88391608495911 +3.98333333333333 NA 12.0967834520228 1.75911716081899 +4.88333333333333 NA 9.53669100535613 2.32528201562731 +5.16666666666667 NA 8.45933924038288 3.08529104118186 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibT_res/KEIO_ROBOT3_1.pdf b/validation/validation_results/Berges_2021/Berges_2021/yibT_res/KEIO_ROBOT3_1.pdf new file mode 100644 index 0000000..af291e9 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yibT_res/KEIO_ROBOT3_1.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibT_res/KEIO_ROBOT3_1_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yibT_res/KEIO_ROBOT3_1_log.txt new file mode 100644 index 0000000..e1fa555 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yibT_res/KEIO_ROBOT3_1_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.158760 NA NA + [2,] 0.264600 NA NA + [3,] 0.350784 NA NA + [4,] 0.439992 NA NA + [5,] NA 14.223975 0.02537118 + [6,] NA 14.058709 0.44957272 + [7,] NA 13.445400 0.88391608 + [8,] NA 12.096783 1.75911716 + [9,] NA 9.536691 2.32528202 +[10,] NA 8.459339 3.08529104 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03072816 14.60342033 0.16501751 0.58617207 -5.80381511 2.76916355 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.111865e-09 1.242324e-08 3.022051e-08 1.652202e-08 -1.199404e-07 -2.243995e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.01242473 0.51912200 0.22790879 0.09615994 0.90631067 0.40035444 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7603377 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.111865e-09 1.242324e-08 3.022051e-08 1.652202e-08 -1.199404e-07 -2.243995e-08 + +$result$normp +[1] 1.274139e-07 + +$result$res + [1] 0.35848429 0.03887145 -0.62431962 0.31682282 0.80520965 -0.22878767 -0.30254946 -0.72078231 0.09829542 0.34861436 0.71981927 0.12777867 -0.49985673 -1.19958052 1.17820444 -0.32636512 + +$result$prevres + [1] 0.35848446 0.03887156 -0.62431960 0.31682267 0.80520963 -0.22878774 -0.30254954 -0.72078236 0.09829550 0.34861451 0.71981912 0.12777860 -0.49985673 -1.19958045 1.17820452 -0.32636506 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 269.9960760 0.000000 0 2.386852e+01 0.000000000 0.000000000 + [2,] 431.8146162 0.000000 0 4.880365e+01 0.000000000 0.000000000 + [3,] 550.4682561 0.000000 0 6.921945e+01 0.000000000 0.000000000 + [4,] 726.2529786 0.000000 0 1.018745e+02 0.000000000 0.000000000 + [5,] -0.6401851 2.173913 0 -4.941950e-04 0.003389445 0.000000000 + [6,] -45.9819720 2.173913 0 -1.634520e+00 0.243450508 0.000000000 + [7,] -91.7719753 2.173913 0 -5.053088e+00 0.485884642 0.000000000 + [8,] -200.7927440 2.173913 0 -1.668583e+01 1.063092629 0.000000000 + [9,] -355.2549523 2.173913 0 -3.791487e+01 1.880889288 0.000000000 +[10,] -423.3276770 2.173913 0 -4.843411e+01 2.241298784 0.000000000 +[11,] 0.7025358 0.000000 5 5.423271e-04 0.000000000 0.007795725 +[12,] 50.4603756 0.000000 5 1.793714e+00 0.000000000 0.559936168 +[13,] 100.7100857 0.000000 5 5.545233e+00 0.000000000 1.117534676 +[14,] 220.3489071 0.000000 5 1.831094e+01 0.000000000 2.445113047 +[15,] 389.8549267 0.000000 5 4.160758e+01 0.000000000 4.326045361 +[16,] 464.5575787 0.000000 5 5.315134e+01 0.000000000 5.154987204 + +$result$retres +$result$retres$res + [1] 0.35848446 0.03887156 -0.62431960 0.31682267 0.80520963 -0.22878774 -0.30254954 -0.72078236 0.09829550 0.34861451 0.71981912 0.12777860 -0.49985673 -1.19958045 1.17820452 -0.32636506 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.16592969 13.264761 0.8037295 + [2,] 0.26537743 12.280108 1.2735354 + [3,] 0.33829761 11.558109 1.6180211 + [4,] 0.44632845 10.488473 2.1283748 + [5,] 0.03164209 14.594371 0.1693350 + [6,] 0.09637195 13.953467 0.4751284 + [7,] 0.16174168 13.306227 0.7839447 + [8,] 0.31737955 11.765224 1.5192011 + [9,] 0.53788954 9.581907 2.5609229 + [10,] 0.63507005 8.619702 3.0200180 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0071696892 NA NA + [2,] -0.0007774312 NA NA + [3,] 0.0124863920 NA NA + [4,] -0.0063364535 NA NA + [5,] NA -0.37039643 -0.14396382 + [6,] NA 0.10524236 -0.02555572 + [7,] NA 0.13917279 0.09997135 + [8,] NA 0.33155989 0.23991609 + [9,] NA -0.04521593 -0.23564090 +[10,] NA -0.16036268 0.06527301 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yibT_res/KEIO_ROBOT3_1_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yibT_res/KEIO_ROBOT3_1_res.txt new file mode 100644 index 0000000..c2e0336 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yibT_res/KEIO_ROBOT3_1_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.030728164700611 0.0309967461458584 0.0307322637853863 0.00395115875658258 0.0244117195346096 0.0386929770470898 +Glc 14.6034203274241 14.6020487273623 14.5749614155616 0.280976229687464 14.1244540298928 15.1309100311813 +Ace 0.165017505693836 0.17589081016516 0.168610954549555 0.113267342764515 9.99999999998355e-07 0.403564806535719 +mu 0.586172065610439 0.586320601865316 0.587978665964049 0.0272767923744953 0.536161004757446 0.634062198894021 +qGlc -5.80381510705651 -5.7577638141033 -5.79398966243515 0.447709536001033 -6.64766768562106 -4.87527217783333 +qAce 2.76916354797863 2.75796665022571 2.76056924817162 0.215111322983658 2.3721599416833 3.16288469797097 +res 5.78113455953328 24.4535171773497 23.4229431535896 7.49501888062105 13.1736042353819 41.5243699301667 + + +Goodness of fit (khi2 test) + +khi2 value 5.78113455953341 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.578113455953341 +p-value, i.e. P(X^2<=value) 0.166696117409175 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yicH.txt b/validation/validation_results/Berges_2021/Berges_2021/yicH.txt new file mode 100644 index 0000000..e2fd210 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yicH.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.154224 NA NA +3.67805555555556 0.21924 NA NA +4.09222222222222 0.30996 NA NA +4.565 0.391608 NA NA +0.05 NA 14.3764910555735 0.0204726672033415 +1.95 NA 13.5841916665707 0.419875197235342 +2.83333333333333 NA 13.3217819952524 0.745015294124994 +3.98333333333333 NA 11.9993860046612 1.50616358516577 +4.88333333333333 NA 9.61562982329746 1.89775138721661 +5.16666666666667 NA 9.24517902131765 2.61322025561566 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yicH_res/KEIO_ROBOT3_6.pdf b/validation/validation_results/Berges_2021/Berges_2021/yicH_res/KEIO_ROBOT3_6.pdf new file mode 100644 index 0000000..1884396 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yicH_res/KEIO_ROBOT3_6.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yicH_res/KEIO_ROBOT3_6_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yicH_res/KEIO_ROBOT3_6_log.txt new file mode 100644 index 0000000..a6c8083 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yicH_res/KEIO_ROBOT3_6_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.154224 NA NA + [2,] 0.219240 NA NA + [3,] 0.309960 NA NA + [4,] 0.391608 NA NA + [5,] NA 14.376491 0.02047267 + [6,] NA 13.584192 0.41987520 + [7,] NA 13.321782 0.74501529 + [8,] NA 11.999386 1.50616359 + [9,] NA 9.615630 1.89775139 +[10,] NA 9.245179 2.61322026 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03011513 14.38206580 0.13939492 0.56108837 -5.74283141 2.58376601 + +$result$lastp + X Glc Ace mu qGlc qAce + 7.918998e-09 6.691449e-08 -1.123000e-07 -6.502769e-08 1.706812e-07 1.233638e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01323491 0.50977842 0.22241273 0.10478752 0.99066902 0.43317975 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7387038 + +$result$laststep + X Glc Ace mu qGlc qAce + 7.918998e-09 6.691449e-08 -1.123000e-07 -6.502769e-08 1.706812e-07 1.233638e-07 + +$result$normp +[1] 2.563803e-07 + +$result$res + [1] -0.146327575 0.896081378 -0.537794539 -0.075537030 -0.006945651 0.403369837 -0.310009362 -0.413020682 0.654680626 -0.328074767 0.614339288 -0.024943278 -0.322135796 -1.046475545 1.253128709 -0.473913377 + +$result$prevres + [1] -0.146328149 0.896081096 -0.537794492 -0.075536369 -0.006945792 0.403369902 -0.310009200 -0.413020497 0.654680574 -0.328074986 0.614339843 -0.024943042 -0.322135762 -1.046475774 1.253128396 -0.473913661 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 251.1984468 0.000000 0 2.176372e+01 0.000000000 0.000000000 + [2,] 393.7583626 0.000000 0 4.361468e+01 0.000000000 0.000000000 + [3,] 496.7672237 0.000000 0 6.122049e+01 0.000000000 0.000000000 + [4,] 647.6767281 0.000000 0 8.903970e+01 0.000000000 0.000000000 + [5,] -0.6330594 2.173913 0 -4.788451e-04 0.003319732 0.000000000 + [6,] -44.2016787 2.173913 0 -1.529939e+00 0.231791395 0.000000000 + [7,] -86.8325839 2.173913 0 -4.647092e+00 0.455345732 0.000000000 + [8,] -185.7126482 2.173913 0 -1.497925e+01 0.973867849 0.000000000 + [9,] -322.3342961 2.173913 0 -3.337482e+01 1.690304945 0.000000000 +[10,] -381.7092306 2.173913 0 -4.236665e+01 2.001664135 0.000000000 +[11,] 0.6550876 0.000000 5 4.955071e-04 0.000000000 0.007635383 +[12,] 45.7397387 0.000000 5 1.583175e+00 0.000000000 0.533120208 +[13,] 89.8540467 0.000000 5 4.808795e+00 0.000000000 1.047295184 +[14,] 192.1747828 0.000000 5 1.550047e+01 0.000000000 2.239896052 +[15,] 333.5503745 0.000000 5 3.453615e+01 0.000000000 3.887701373 +[16,] 394.9913439 0.000000 5 4.384086e+01 0.000000000 4.603827510 + +$result$retres +$result$retres$res + [1] -0.146328149 0.896081096 -0.537794492 -0.075536369 -0.006945792 0.403369902 -0.310009200 -0.413020497 0.654680574 -0.328074986 0.614339843 -0.024943042 -0.322135762 -1.046475774 1.253128396 -0.473913661 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15129744 13.141745 0.6974296 + [2,] 0.23716162 12.262911 1.0928271 + [3,] 0.29920411 11.627896 1.3785276 + [4,] 0.39009727 10.697590 1.7970831 + [5,] 0.03097195 14.373296 0.1433406 + [6,] 0.08994064 13.769742 0.4148866 + [7,] 0.14764016 13.179178 0.6805881 + [8,] 0.28147107 11.809397 1.2968684 + [9,] 0.46638398 9.916783 2.1483771 + [10,] 0.54674599 9.094265 2.5184375 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.002926563 NA NA + [2,] -0.017921622 NA NA + [3,] 0.010755890 NA NA + [4,] 0.001510727 NA NA + [5,] NA 0.003195064 -0.122867969 + [6,] NA -0.185550155 0.004988608 + [7,] NA 0.142604232 0.064427152 + [8,] NA 0.189989429 0.209295155 + [9,] NA -0.301153064 -0.250625679 +[10,] NA 0.150914494 0.094782732 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yicH_res/KEIO_ROBOT3_6_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yicH_res/KEIO_ROBOT3_6_res.txt new file mode 100644 index 0000000..b02c69d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yicH_res/KEIO_ROBOT3_6_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0301151298372338 0.0300579716787064 0.0297630824152232 0.0039117106560353 0.0227679340952329 0.0375722034876315 +Glc 14.3820658018102 14.3638643131946 14.3641651749033 0.234857189840551 13.9469660799361 14.8454781061268 +Ace 0.139394915148412 0.158069001469361 0.143611026707226 0.0954975284696038 0.00355130611378582 0.360045093814059 +mu 0.561088366533586 0.56405009171912 0.565378428583706 0.0283260972109907 0.512465418528457 0.624912423156057 +qGlc -5.74283141415235 -5.77949779349059 -5.81037753306453 0.49556315949404 -6.63328170577915 -4.80900026522847 +qAce 2.58376601241385 2.55495865089822 2.57588596307594 0.258122562366633 2.05314614179176 2.98942695892057 +res 5.45683245259455 24.2196602750677 23.955144944461 6.16099142883082 15.4400095081016 38.1359065194946 + + +Goodness of fit (khi2 test) + +khi2 value 5.4568324525962 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.54568324525962 +p-value, i.e. P(X^2<=value) 0.141349664970745 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yidB.txt b/validation/validation_results/Berges_2021/Berges_2021/yidB.txt new file mode 100644 index 0000000..5a63498 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yidB.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.14364 NA NA +3.67805555555556 0.220752 NA NA +4.09222222222222 0.299376 NA NA +4.565 0.388584 NA NA +0.05 NA 14.7619304781925 0.0195914551719206 +1.95 NA 14.1696160821856 0.455989129129805 +2.83333333333333 NA 13.5653796217929 0.944400045728813 +3.98333333333333 NA 11.8606880439163 1.42244715287056 +4.88333333333333 NA 9.77909046723852 2.19572515332932 +5.16666666666667 NA 9.19366468901344 2.53738194026599 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yidB_res/KEIO_ROBOT3_35.pdf b/validation/validation_results/Berges_2021/Berges_2021/yidB_res/KEIO_ROBOT3_35.pdf new file mode 100644 index 0000000..36b6159 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yidB_res/KEIO_ROBOT3_35.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yidB_res/KEIO_ROBOT3_35_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yidB_res/KEIO_ROBOT3_35_log.txt new file mode 100644 index 0000000..f942e31 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yidB_res/KEIO_ROBOT3_35_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.143640 NA NA + [2,] 0.220752 NA NA + [3,] 0.299376 NA NA + [4,] 0.388584 NA NA + [5,] NA 14.761930 0.01959146 + [6,] NA 14.169616 0.45598913 + [7,] NA 13.565380 0.94440005 + [8,] NA 11.860688 1.42244715 + [9,] NA 9.779090 2.19572515 +[10,] NA 9.193665 2.53738194 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02967174 14.79112125 0.19117741 0.56042731 -6.36363902 2.65357516 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.359807e-08 2.227989e-07 -1.668686e-07 -1.137891e-07 8.428300e-08 1.480394e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.009632678 0.379546621 0.164258369 0.077390105 0.756318807 0.326321415 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5447589 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.359807e-08 2.227989e-07 -1.668686e-07 -1.137891e-07 8.428300e-08 1.480394e-07 + +$result$normp +[1] 3.458852e-07 + +$result$res + [1] 0.25733078 0.61751854 -0.26867856 -0.26941917 0.04264401 -0.10111774 -0.18698589 0.27520839 0.32165627 -0.35140504 0.87789222 0.06872902 -1.03116791 -0.31048509 0.11860683 0.27642493 + +$result$prevres + [1] 0.25732981 0.61751807 -0.26867846 -0.26941799 0.04264353 -0.10111777 -0.18698568 0.27520876 0.32165636 -0.35140520 0.87789304 0.06872932 -1.03116793 -0.31048548 0.11860642 0.27642462 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 250.7212024 0.000000 0 2.140254e+01 0.000000000 0.000000000 + [2,] 392.8022137 0.000000 0 4.286817e+01 0.000000000 0.000000000 + [3,] 495.4252927 0.000000 0 6.015616e+01 0.000000000 0.000000000 + [4,] 645.7253147 0.000000 0 8.746440e+01 0.000000000 0.000000000 + [5,] -0.7014823 2.173913 0 -5.227846e-04 0.003270799 0.000000000 + [6,] -48.9427434 2.173913 0 -1.668811e+00 0.228205190 0.000000000 + [7,] -96.1063505 2.173913 0 -5.066559e+00 0.448114808 0.000000000 + [8,] -205.4244689 2.173913 0 -1.632099e+01 0.957832087 0.000000000 + [9,] -356.3683383 2.173913 0 -3.634556e+01 1.661637638 0.000000000 +[10,] -421.9434435 2.173913 0 -4.613012e+01 1.967394495 0.000000000 +[11,] 0.6727758 0.000000 5 5.013911e-04 0.000000000 0.007522838 +[12,] 46.9398798 0.000000 5 1.600519e+00 0.000000000 0.524871938 +[13,] 92.1734302 0.000000 5 4.859222e+00 0.000000000 1.030664057 +[14,] 197.0179685 0.000000 5 1.565309e+01 0.000000000 2.203013801 +[15,] 341.7848244 0.000000 5 3.485820e+01 0.000000000 3.821766568 +[16,] 404.6764267 0.000000 5 4.424236e+01 0.000000000 4.525007338 + +$result$retres +$result$retres$res + [1] 0.25732981 0.61751807 -0.26867846 -0.26941799 0.04264353 -0.10111777 -0.18698568 0.27520876 0.32165636 -0.35140520 0.87789304 0.06872932 -1.03116793 -0.31048548 0.11860642 0.27642462 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.14878660 13.438575 0.7551761 + [2,] 0.23310236 12.481171 1.1544039 + [3,] 0.29400243 11.789653 1.4427604 + [4,] 0.38319564 10.776866 1.8650825 + [5,] 0.03051492 14.781547 0.1951701 + [6,] 0.08850225 14.123102 0.4697350 + [7,] 0.14519420 13.479366 0.7381665 + [8,] 0.27659759 11.987284 1.3603501 + [9,] 0.45803628 9.927052 2.2194464 + [10,] 0.53685936 9.032018 2.5926669 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.005146596 NA NA + [2,] -0.012350361 NA NA + [3,] 0.005373569 NA NA + [4,] 0.005388360 NA NA + [5,] NA -0.01961602 -0.17557861 + [6,] NA 0.04651417 -0.01374586 + [7,] NA 0.08601341 0.20623359 + [8,] NA -0.12659603 0.06209710 + [9,] NA -0.14796192 -0.02372128 +[10,] NA 0.16164639 -0.05528492 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yidB_res/KEIO_ROBOT3_35_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yidB_res/KEIO_ROBOT3_35_res.txt new file mode 100644 index 0000000..6dcf4ce --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yidB_res/KEIO_ROBOT3_35_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0296717355694871 0.0292091640229822 0.0291687583930889 0.00403659738991279 0.0219790306249302 0.0372908866622075 +Glc 14.7911212504413 14.7616546036597 14.7729358974274 0.277247284488512 14.1898421023407 15.2451602966107 +Ace 0.191177413842807 0.198267521296434 0.187343598448037 0.100907057582681 0.000739282594217679 0.426630554721363 +mu 0.56042731193353 0.565353214594073 0.56142477214635 0.030067806236579 0.51002771531941 0.623034359189893 +qGlc -6.36363902026757 -6.37632055165354 -6.38192329324967 0.601808492612301 -7.5336877882995 -5.25844124160816 +qAce 2.65357516457945 2.66414247335735 2.66490312987319 0.24081042290522 2.18834667936752 3.18621582601957 +res 2.96762308270312 24.0603468775479 23.4500331212532 7.57721903403664 12.4076364700261 41.3994141054561 + + +Goodness of fit (khi2 test) + +khi2 value 2.9676230827075 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.29676230827075 +p-value, i.e. P(X^2<=value) 0.017824247092041 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yidR.txt b/validation/validation_results/Berges_2021/Berges_2021/yidR.txt new file mode 100644 index 0000000..f12527a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yidR.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.195 0.069552 NA NA +1.61361111111111 0.089208 NA NA +2.36138888888889 0.142128 NA NA +3.28638888888889 0.250992 NA NA +3.81944444444444 0.322056 NA NA +4.41083333333333 0.470232 NA NA +0.283333333333333 NA 14.0191187652122 0.0479320468276319 +1.91666666666667 NA 13.6557131974353 0.407257059405972 +2.7 NA 13.6637753116276 0.756647284009168 +3.61666666666667 NA 12.4841921872832 1.18047172085733 +4.05 NA 11.3697911793177 1.50149795472268 +4.75 NA 10.0592376750674 1.87184987041629 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yidR_res/KEIO_ROBOT4_36.pdf b/validation/validation_results/Berges_2021/Berges_2021/yidR_res/KEIO_ROBOT4_36.pdf new file mode 100644 index 0000000..3ad61bd Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yidR_res/KEIO_ROBOT4_36.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yidR_res/KEIO_ROBOT4_36_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yidR_res/KEIO_ROBOT4_36_log.txt new file mode 100644 index 0000000..483f1a8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yidR_res/KEIO_ROBOT4_36_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.069552 NA NA + [3,] 0.089208 NA NA + [4,] 0.142128 NA NA + [5,] 0.250992 NA NA + [6,] 0.322056 NA NA + [7,] 0.470232 NA NA + [8,] NA 14.01912 0.04793205 + [9,] NA 13.65571 0.40725706 +[10,] NA 13.66378 0.75664728 +[11,] NA 12.48419 1.18047172 +[12,] NA 11.36979 1.50149795 +[13,] NA 10.05924 1.87184987 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03622241 14.33200935 0.17892362 0.57945997 -4.61130394 2.01455361 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.053337e-08 -1.033548e-07 -2.186623e-07 -7.627052e-08 6.538017e-07 3.939457e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.007222709 0.383177720 0.166622549 0.050295838 0.791764179 0.344356606 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5748686 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.053337e-08 -1.033548e-07 -2.186623e-07 -7.627052e-08 6.538017e-07 3.939457e-07 + +$result$normp +[1] 8.044088e-07 + +$result$res + [1] -0.003279480 0.142133462 0.153016907 0.009104022 -0.388083950 0.460027912 -0.179103420 0.568387122 0.194192305 -0.916329507 -0.451744670 0.516452137 0.089042614 0.767305233 0.140484144 -0.508216804 -0.517518018 -0.661242850 0.779188295 + +$result$prevres + [1] -0.003280007 0.142132739 0.153016133 0.009103234 -0.388084439 0.460027920 -0.179102355 0.568387362 0.194192610 -0.916329235 -0.451744597 0.516452000 0.089041860 0.767306273 0.140484725 -0.508216562 -0.517518288 -0.661243402 0.779187253 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 99.930782 0.000000 0 4.32558062 0.00000000 0.00000000 + [3,] 127.363624 0.000000 0 7.44425953 0.00000000 0.00000000 + [4,] 196.439310 0.000000 0 16.80247028 0.00000000 0.00000000 + [5,] 335.745716 0.000000 0 39.96746961 0.00000000 0.00000000 + [6,] 457.253743 0.000000 0 63.26080109 0.00000000 0.00000000 + [7,] 644.145549 0.000000 0 102.91575836 0.00000000 0.00000000 + [8,] -3.086758 2.173913 0 -0.01627295 0.02424689 0.00000000 + [9,] -35.227281 2.173913 0 -1.44468424 0.27671489 0.00000000 +[10,] -65.401855 2.173913 0 -3.99995728 0.51374012 0.00000000 +[11,] -123.369481 2.173913 0 -10.71639322 0.96908338 0.00000000 +[12,] -163.521825 2.173913 0 -16.30482203 1.28448530 0.00000000 +[13,] -253.975233 2.173913 0 -30.79846883 1.99500863 0.00000000 +[14,] 3.101597 0.000000 5 0.01635118 0.00000000 0.05576785 +[15,] 35.396628 0.000000 5 1.45162923 0.00000000 0.63644425 +[16,] 65.716260 0.000000 5 4.01918616 0.00000000 1.18160227 +[17,] 123.962551 0.000000 5 10.76790984 0.00000000 2.22889178 +[18,] 164.307919 0.000000 5 16.38320374 0.00000000 2.95431618 +[19,] 255.196161 0.000000 5 30.94652545 0.00000000 4.58851984 + +$result$retres +$result$retres$res + [1] -0.003280007 0.142132739 0.153016133 0.009103234 -0.388084439 0.460027920 -0.179102355 0.568387362 0.194192610 -0.916329235 -0.451744597 0.516452000 0.089041860 0.767306273 0.140484725 -0.508216562 -0.517518288 -0.661243402 0.779187253 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03622240 14.33201 0.1789238 + [2,] 0.07239465 14.04415 0.3046805 + [3,] 0.09226832 13.88600 0.3737733 + [4,] 0.14231006 13.48777 0.5477487 + [5,] 0.24323031 12.68465 0.8986084 + [6,] 0.33125656 11.98415 1.2046408 + [7,] 0.46664995 10.90670 1.6753501 + [8,] 0.04268545 14.28058 0.2013933 + [9,] 0.10998120 13.74504 0.4353540 + [10,] 0.17316066 13.24226 0.6550040 + [11,] 0.29453315 12.27639 1.0769681 + [12,] 0.37860404 11.60736 1.3692493 + [13,] 0.56799519 10.10020 2.0276873 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 6.560014e-05 NA NA + [2,] -2.842655e-03 NA NA + [3,] -3.060323e-03 NA NA + [4,] -1.820647e-04 NA NA + [5,] 7.761689e-03 NA NA + [6,] -9.200558e-03 NA NA + [7,] 3.582047e-03 NA NA + [8,] NA -0.26145819 -0.15346125 + [9,] NA -0.08932860 -0.02809694 +[10,] NA 0.42151145 0.10164331 +[11,] NA 0.20780251 0.10350366 +[12,] NA -0.23756792 0.13224868 +[13,] NA -0.04095926 -0.15583745 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yidR_res/KEIO_ROBOT4_36_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yidR_res/KEIO_ROBOT4_36_res.txt new file mode 100644 index 0000000..a02a351 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yidR_res/KEIO_ROBOT4_36_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0362224103942646 0.0359822071161371 0.0359618737431146 0.00410587385062906 0.0286504518030313 0.0455536891546555 +Glc 14.332009352722 14.3401177940302 14.339090642554 0.207206979689531 13.9340889878737 14.7449349567057 +Ace 0.17892362424999 0.188661529892981 0.191978695703076 0.079662990558209 0.0141785229221454 0.328665089508921 +mu 0.579459973510883 0.583430125139392 0.58062893524368 0.0268349914334854 0.524361640517545 0.634639891153392 +qGlc -4.61130394296527 -4.62654488359141 -4.59498633157554 0.469328042115273 -5.62953311439473 -3.8508800775229 +qAce 2.01455360824761 2.02593871189271 1.9952316591745 0.209921933654598 1.68607252099424 2.46479842922938 +res 4.29616042131757 33.1286109080084 31.4889379901777 8.50377278949786 20.8129235047671 51.9171187505367 + + +Goodness of fit (khi2 test) + +khi2 value 4.29616042132494 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.330473878563457 +p-value, i.e. P(X^2<=value) 0.0123863013185808 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yieP.txt b/validation/validation_results/Berges_2021/Berges_2021/yieP.txt new file mode 100644 index 0000000..5d46c90 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yieP.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.031752 NA NA +1.195 0.055944 NA NA +1.61361111111111 0.072576 NA NA +2.36138888888889 0.101304 NA NA +3.28638888888889 0.175392 NA NA +3.81944444444444 0.208656 NA NA +4.41083333333333 0.343224 NA NA +0.283333333333333 NA 13.903186828493 0.0495412792779493 +1.91666666666667 NA 14.0282024359144 0.423095821093594 +2.7 NA 13.518335349278 0.653951374237332 +3.61666666666667 NA 12.910480136563 1.33096152800549 +4.05 NA 12.541208768241 1.68246365595337 +4.75 NA 11.136058891521 2.44781943452811 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yieP_res/KEIO_ROBOT4_33.pdf b/validation/validation_results/Berges_2021/Berges_2021/yieP_res/KEIO_ROBOT4_33.pdf new file mode 100644 index 0000000..314edf3 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yieP_res/KEIO_ROBOT4_33.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yieP_res/KEIO_ROBOT4_33_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yieP_res/KEIO_ROBOT4_33_log.txt new file mode 100644 index 0000000..5b3f060 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yieP_res/KEIO_ROBOT4_33_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.031752 NA NA + [2,] 0.055944 NA NA + [3,] 0.072576 NA NA + [4,] 0.101304 NA NA + [5,] 0.175392 NA NA + [6,] 0.208656 NA NA + [7,] 0.343224 NA NA + [8,] NA 13.90319 0.04954128 + [9,] NA 14.02820 0.42309582 +[10,] NA 13.51834 0.65395137 +[11,] NA 12.91048 1.33096153 +[12,] NA 12.54121 1.68246366 +[13,] NA 11.13606 2.44781943 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02575705 14.24048948 0.06350977 0.57791453 -4.49016270 3.76335978 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.653477e-09 1.136067e-08 1.871900e-08 1.652140e-08 -1.286901e-07 5.125817e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.006562387 0.357600940 0.160898039 0.064207225 1.043326691 0.490844250 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5370087 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.653477e-09 1.136067e-08 1.871900e-08 1.652140e-08 -1.286901e-07 5.125817e-09 + +$result$normp +[1] 1.316912e-07 + +$result$res + [1] -0.29974743 -0.22802712 -0.35645958 -0.02393475 -0.16559298 1.27538975 -0.68262909 0.65586692 -0.42047629 -0.06613042 -0.19138757 -0.38969792 0.41182529 0.21904660 -0.09774891 0.20158328 -0.39468636 -0.22241716 0.29422254 + +$result$prevres + [1] -0.29974735 -0.22802701 -0.35645946 -0.02393463 -0.16559290 1.27538976 -0.68262923 0.65586689 -0.42047633 -0.06613046 -0.19138758 -0.38969791 0.41182539 0.21904652 -0.09774893 0.20158330 -0.39468632 -0.22241711 0.29422254 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 99.746388 0.000000 0 3.07016173 0.00000000 0.00000000 + [3,] 127.046388 0.000000 0 5.28028505 0.00000000 0.00000000 + [4,] 195.723687 0.000000 0 11.90438804 0.00000000 0.00000000 + [5,] 334.044703 0.000000 0 28.27611335 0.00000000 0.00000000 + [6,] 454.562476 0.000000 0 44.71878033 0.00000000 0.00000000 + [7,] 639.769262 0.000000 0 72.68422923 0.00000000 0.00000000 + [8,] -3.004991 2.173913 0 -0.01126406 0.01723762 0.00000000 + [9,] -34.241878 2.173913 0 -0.99815839 0.19642270 0.00000000 +[10,] -63.517776 2.173913 0 -2.76098985 0.36435891 0.00000000 +[11,] -119.684198 2.173913 0 -7.38836366 0.68654802 0.00000000 +[12,] -158.550219 2.173913 0 -11.23485821 0.90949633 0.00000000 +[13,] -246.027243 2.173913 0 -21.20174552 1.41129339 0.00000000 +[14,] 5.792749 0.000000 5 0.02171384 0.00000000 0.03964653 +[15,] 66.008382 0.000000 5 1.92415905 0.00000000 0.45177222 +[16,] 122.443798 0.000000 5 5.32238540 0.00000000 0.83802548 +[17,] 230.716323 0.000000 5 14.24261623 0.00000000 1.57906044 +[18,] 305.638708 0.000000 5 21.65753898 0.00000000 2.09184156 +[19,] 474.268968 0.000000 5 40.87079885 0.00000000 3.24597479 + +$result$retres +$result$retres$res + [1] -0.29974735 -0.22802701 -0.35645946 -0.02393463 -0.16559290 1.27538976 -0.68262923 0.65586689 -0.42047633 -0.06613046 -0.19138758 -0.38969791 0.41182539 0.21904652 -0.09774893 0.20158330 -0.39468632 -0.22241711 0.29422254 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02575705 14.24049 0.06350976 + [2,] 0.05138346 14.04138 0.23038805 + [3,] 0.06544681 13.93212 0.32196812 + [4,] 0.10082531 13.65724 0.55235170 + [5,] 0.17208014 13.10362 1.01636077 + [6,] 0.23416380 12.62125 1.42064743 + [7,] 0.32957142 11.87997 2.04193863 + [8,] 0.03033951 14.20489 0.09335058 + [9,] 0.07797420 13.83478 0.40354604 + [10,] 0.12261847 13.48792 0.69426803 + [11,] 0.20826944 12.82244 1.25202426 + [12,] 0.26753817 12.36195 1.63798023 + [13,] 0.40093624 11.32550 2.50666394 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0059949470 NA NA + [2,] 0.0045605401 NA NA + [3,] 0.0071291892 NA NA + [4,] 0.0004786925 NA NA + [5,] 0.0033118579 NA NA + [6,] -0.0255077952 NA NA + [7,] 0.0136525846 NA NA + [8,] NA -0.30169877 -0.04380930 + [9,] NA 0.19341911 0.01954979 +[10,] NA 0.03042001 -0.04031666 +[11,] NA 0.08803829 0.07893726 +[12,] NA 0.17926104 0.04448342 +[13,] NA -0.18943968 -0.05884451 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yieP_res/KEIO_ROBOT4_33_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yieP_res/KEIO_ROBOT4_33_res.txt new file mode 100644 index 0000000..b83db40 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yieP_res/KEIO_ROBOT4_33_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0257570513095491 0.0260985047643686 0.0259976286195887 0.00425443092410839 0.019551127789614 0.0334275967228443 +Glc 14.2404894790609 14.2336717554977 14.2292236907405 0.219048589541707 13.8049741896626 14.6172694767688 +Ace 0.0635097744051745 0.0875099182176409 0.0793032738086709 0.0664815433640716 9.99999999998355e-07 0.230847758801507 +mu 0.577914525032327 0.579542110928262 0.578872284724222 0.040371682006533 0.511586453359705 0.65283108497213 +qGlc -4.49016269764889 -4.43552133190465 -4.37797648445948 0.726397752395364 -5.95225304965848 -3.00406912426411 +qAce 3.7633597767458 3.6691696941252 3.67532558436328 0.249194177081044 3.22040361691288 4.14962253721757 +res 3.74891811606322 31.5110028645225 29.4424131848709 8.54545908708316 17.5392963666615 51.112846385233 + + +Goodness of fit (khi2 test) + +khi2 value 3.74891811606334 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.288378316620257 +p-value, i.e. P(X^2<=value) 0.00641926278861184 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yifL.txt b/validation/validation_results/Berges_2021/Berges_2021/yifL.txt new file mode 100644 index 0000000..e28f3a0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yifL.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.146664 NA NA +3.67805555555556 0.229824 NA NA +4.09222222222222 0.3024 NA NA +4.565 0.40068 NA NA +0.05 NA 14.444934978885 0.02241015192845 +1.95 NA 13.5773994502269 0.3976994661129 +2.83333333333333 NA 13.5372183559725 0.734114951225064 +3.98333333333333 NA 12.2523825713812 1.35708132461315 +4.88333333333333 NA 10.0246977969158 1.97885634959353 +5.16666666666667 NA 9.37853080527562 2.33452925972428 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yifL_res/KEIO_ROBOT3_38.pdf b/validation/validation_results/Berges_2021/Berges_2021/yifL_res/KEIO_ROBOT3_38.pdf new file mode 100644 index 0000000..b7680db Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yifL_res/KEIO_ROBOT3_38.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yifL_res/KEIO_ROBOT3_38_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yifL_res/KEIO_ROBOT3_38_log.txt new file mode 100644 index 0000000..6c1c2ac --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yifL_res/KEIO_ROBOT3_38_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.146664 NA NA + [2,] 0.229824 NA NA + [3,] 0.302400 NA NA + [4,] 0.400680 NA NA + [5,] NA 14.444935 0.02241015 + [6,] NA 13.577399 0.39769947 + [7,] NA 13.537218 0.73411495 + [8,] NA 12.252383 1.35708132 + [9,] NA 10.024698 1.97885635 +[10,] NA 9.378531 2.33452926 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02735268 14.43249715 0.15834737 0.58621491 -5.52070181 2.42394573 + +$result$lastp + X Glc Ace mu qGlc qAce + 4.343989e-09 2.772441e-08 -5.921876e-08 -3.881098e-08 1.236181e-07 6.220666e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008262282 0.337403444 0.146829303 0.071860764 0.659020991 0.286946081 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4955526 + +$result$laststep + X Glc Ace mu qGlc qAce + 4.343989e-09 2.772441e-08 -5.921876e-08 -3.881098e-08 1.236181e-07 6.220666e-08 + +$result$normp +[1] 1.579613e-07 + +$result$res + [1] 0.05282811 0.32195100 -0.06057443 -0.16514436 -0.04369537 0.66247112 -0.44168563 -0.48553316 0.33762889 -0.02918584 0.69650676 0.01146015 -0.46737517 -0.71729694 0.23304821 0.24365699 + +$result$prevres + [1] 0.05282776 0.32195081 -0.06057443 -0.16514399 -0.04369543 0.66247117 -0.44168553 -0.48553306 0.33762884 -0.02918599 0.69650706 0.01146028 -0.46737515 -0.71729706 0.23304804 0.24365684 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 270.0294035 0.000000 0 2.124919e+01 0.000000000 0.000000000 + [2,] 431.8827616 0.000000 0 4.344942e+01 0.000000000 0.000000000 + [3,] 550.5649093 0.000000 0 6.162652e+01 0.000000000 0.000000000 + [4,] 726.3952304 0.000000 0 9.070133e+01 0.000000000 0.000000000 + [5,] -0.6089572 2.173913 0 -4.184493e-04 0.003017118 0.000000000 + [6,] -43.7411189 2.173913 0 -1.384078e+00 0.216718241 0.000000000 + [7,] -87.3020029 2.173913 0 -4.278981e+00 0.432543496 0.000000000 + [8,] -191.0201336 2.173913 0 -1.413023e+01 0.946421773 0.000000000 + [9,] -337.9757937 2.173913 0 -3.210891e+01 1.674523224 0.000000000 +[10,] -402.7418683 2.173913 0 -4.101777e+01 1.995410985 0.000000000 +[11,] 0.6149548 0.000000 5 4.225708e-04 0.000000000 0.006939372 +[12,] 44.1719229 0.000000 5 1.397710e+00 0.000000000 0.498451953 +[13,] 88.1618358 0.000000 5 4.321124e+00 0.000000000 0.994850040 +[14,] 192.9014809 0.000000 5 1.426940e+01 0.000000000 2.176770078 +[15,] 341.3044997 0.000000 5 3.242515e+01 0.000000000 3.851403414 +[16,] 406.7084520 0.000000 5 4.142176e+01 0.000000000 4.589445266 + +$result$retres +$result$retres$res + [1] 0.05282776 0.32195081 -0.06057443 -0.16514399 -0.04369543 0.66247117 -0.44168553 -0.48553306 0.33762884 -0.02918599 0.69650706 0.01146028 -0.46737515 -0.71729706 0.23304804 0.24365684 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.14772056 13.298928 0.6560577 + [2,] 0.23626302 12.465076 1.0221727 + [3,] 0.30118851 11.853638 1.2906338 + [4,] 0.39737712 10.947778 1.6883649 + [5,] 0.02816627 14.424835 0.1617116 + [6,] 0.08579268 13.882136 0.3999915 + [7,] 0.14399187 13.334043 0.6406399 + [8,] 0.28256371 12.029037 1.2136219 + [9,] 0.47890273 10.180007 2.0254660 + [10,] 0.56543297 9.365105 2.3832606 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.001056555 NA NA + [2,] -0.006439016 NA NA + [3,] 0.001211489 NA NA + [4,] 0.003302880 NA NA + [5,] NA 0.02009990 -0.139301411 + [6,] NA -0.30473674 -0.002292056 + [7,] NA 0.20317534 0.093475030 + [8,] NA 0.22334521 0.143459412 + [9,] NA -0.15530927 -0.046609608 +[10,] NA 0.01342556 -0.048731368 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yifL_res/KEIO_ROBOT3_38_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yifL_res/KEIO_ROBOT3_38_res.txt new file mode 100644 index 0000000..f4b8c69 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yifL_res/KEIO_ROBOT3_38_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0273526839547211 0.0277711327439192 0.0279781931548997 0.00382686208904028 0.0211636242828156 0.0358242753332812 +Glc 14.4324971487721 14.4207663323365 14.42578384295 0.268966474687705 13.9902652548739 14.9225744536752 +Ace 0.158347371970155 0.172474984672377 0.154977265390792 0.113288736522441 9.99999999998664e-07 0.408425767067716 +mu 0.586214913174367 0.585416749217215 0.583945870908426 0.0294904775667714 0.52966307771051 0.644526334803524 +qGlc -5.52070181168059 -5.49799198204911 -5.49084601707945 0.532930658238406 -6.61522656869759 -4.50634720936901 +qAce 2.42394573245727 2.38754460269703 2.3800605863934 0.219247076433145 2.00338087865444 2.80232357924383 +res 2.4557238225748 24.4107069413133 23.8019302268257 6.50453279014623 12.5387902040085 37.6276187438854 + + +Goodness of fit (khi2 test) + +khi2 value 2.45572382257533 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.245572382257533 +p-value, i.e. P(X^2<=value) 0.00849466089840894 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigA.txt b/validation/validation_results/Berges_2021/Berges_2021/yigA.txt new file mode 100644 index 0000000..1fafbd2 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yigA.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.140616 NA NA +3.67805555555556 0.23436 NA NA +4.09222222222222 0.328104 NA NA +4.565 0.412776 NA NA +0.05 NA 14.7170631759896 0.026094171729559 +1.95 NA 14.0573065473163 0.433474203285139 +2.83333333333333 NA 13.8350329085433 0.823857473125033 +3.98333333333333 NA 11.8880835114118 1.47301185995261 +4.88333333333333 NA 9.75966997247163 2.15943873908748 +5.16666666666667 NA 8.80758975249589 2.50741580746059 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigA_res/KEIO_ROBOT3_10.pdf b/validation/validation_results/Berges_2021/Berges_2021/yigA_res/KEIO_ROBOT3_10.pdf new file mode 100644 index 0000000..b5e92b3 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yigA_res/KEIO_ROBOT3_10.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigA_res/KEIO_ROBOT3_10_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yigA_res/KEIO_ROBOT3_10_log.txt new file mode 100644 index 0000000..8bd3f0b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yigA_res/KEIO_ROBOT3_10_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.140616 NA NA + [2,] 0.234360 NA NA + [3,] 0.328104 NA NA + [4,] 0.412776 NA NA + [5,] NA 14.71706 0.02609417 + [6,] NA 14.05731 0.43347420 + [7,] NA 13.83503 0.82385747 + [8,] NA 11.88808 1.47301186 + [9,] NA 9.75967 2.15943874 +[10,] NA 8.80759 2.50741581 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02689719 14.80276511 0.19346925 0.59943886 -6.33512317 2.51866128 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.577804e-08 2.842508e-07 9.530523e-08 -1.356906e-07 2.638258e-07 -6.075432e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.009422887 0.412395666 0.177663316 0.083211319 0.789186201 0.338037735 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6019127 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.577804e-08 2.842508e-07 9.530523e-08 -1.356906e-07 2.638258e-07 -6.075432e-07 + +$result$normp +[1] 7.39767e-07 + +$result$res + [1] 0.51387351 0.47740140 -0.77309928 0.11496982 0.16750677 0.24964053 -0.65557390 0.22519511 0.03998125 -0.02674977 0.85406799 0.05356415 -0.62876430 -0.80967001 0.15853516 0.37226700 + +$result$prevres + [1] 0.51387203 0.47740033 -0.77309977 0.11497050 0.16750616 0.24964045 -0.65557368 0.22519557 0.03998141 -0.02674991 0.85406751 0.05356344 -0.62876503 -0.80967035 0.15853597 0.37226847 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 280.5005483 0.000000 0 2.170560e+01 0.00000000 0.000000000 + [2,] 453.4082419 0.000000 0 4.485536e+01 0.00000000 0.000000000 + [3,] 581.1800261 0.000000 0 6.397003e+01 0.00000000 0.000000000 + [4,] 771.5966956 0.000000 0 9.474096e+01 0.00000000 0.000000000 + [5,] -0.6990236 2.173913 0 -4.723919e-04 0.00296786 0.000000000 + [6,] -50.9689614 2.173913 0 -1.591307e+00 0.21640005 0.000000000 + [7,] -102.5884252 2.173913 0 -4.965805e+00 0.43556195 0.000000000 + [8,] -227.2011241 2.173913 0 -1.660931e+01 0.96463285 0.000000000 + [9,] -406.1121180 2.173913 0 -3.813717e+01 1.72423922 0.000000000 +[10,] -485.5431740 2.173913 0 -4.888150e+01 2.06148141 0.000000000 +[11,] 0.6391966 0.000000 5 4.319616e-04 0.00000000 0.006826078 +[12,] 46.6067060 0.000000 5 1.455113e+00 0.00000000 0.497720111 +[13,] 93.8082402 0.000000 5 4.540799e+00 0.00000000 1.001792484 +[14,] 207.7557734 0.000000 5 1.518778e+01 0.00000000 2.218655545 +[15,] 371.3544002 0.000000 5 3.487314e+01 0.00000000 3.965750197 +[16,] 443.9872295 0.000000 5 4.469790e+01 0.00000000 4.741407243 + +$result$retres +$result$retres$res + [1] 0.51387203 0.47740033 -0.77309977 0.11497050 0.16750616 0.24964045 -0.65557368 0.22519557 0.03998141 -0.02674991 0.85406751 0.05356344 -0.62876503 -0.80967035 0.15853597 0.37226847 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15089344 13.492320 0.7144641 + [2,] 0.24390801 12.509303 1.1052832 + [3,] 0.31264200 11.782893 1.3940828 + [4,] 0.41507541 10.700334 1.8244771 + [5,] 0.02771554 14.794116 0.1969077 + [6,] 0.08656774 14.172141 0.4441869 + [7,] 0.14699987 13.533469 0.6981045 + [8,] 0.29288690 11.991673 1.3110778 + [9,] 0.50234223 9.778061 2.1911459 + [10,] 0.59533405 8.795285 2.5818695 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.010277441 NA NA + [2,] -0.009548007 NA NA + [3,] 0.015461995 NA NA + [4,] -0.002299410 NA NA + [5,] NA -0.07705284 -0.17081350 + [6,] NA -0.11483461 -0.01071269 + [7,] NA 0.30156390 0.12575301 + [8,] NA -0.10358996 0.16193407 + [9,] NA -0.01839145 -0.03170719 +[10,] NA 0.01230496 -0.07445369 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigA_res/KEIO_ROBOT3_10_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yigA_res/KEIO_ROBOT3_10_res.txt new file mode 100644 index 0000000..d400a42 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yigA_res/KEIO_ROBOT3_10_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0268971896757069 0.026224094062042 0.0257655987368602 0.00334011810213751 0.0205340083177414 0.0328368449713781 +Glc 14.8027651050573 14.7753001118622 14.7854406491905 0.251308441898386 14.2574369852751 15.212275055641 +Ace 0.193469251999351 0.196069085100228 0.19766757300603 0.110507290632646 9.99999999999677e-07 0.431560926319428 +mu 0.599438855123368 0.606305384722488 0.605925664202764 0.0266570493853661 0.555962747835201 0.655405883589572 +qGlc -6.33512316757032 -6.34066217054467 -6.35040727188857 0.550018477369059 -7.26754166888898 -5.26690454759234 +qAce 2.51866128049422 2.56287172514073 2.55761922635526 0.2487490184224 2.0651434829345 3.05894126155517 +res 3.62298900410806 23.7760768279959 22.5112635180722 7.1360926346185 13.060868085205 38.141169526952 + + +Goodness of fit (khi2 test) + +khi2 value 3.62298900411653 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.362298900411653 +p-value, i.e. P(X^2<=value) 0.0372435759028056 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigB.txt b/validation/validation_results/Berges_2021/Berges_2021/yigB.txt new file mode 100644 index 0000000..2986ce7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yigB.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.17388 NA NA +3.67805555555556 0.273672 NA NA +4.09222222222222 0.338688 NA NA +4.565 0.44604 NA NA +0.05 NA 14.3490289264296 0.015564125649493 +1.95 NA 13.9387887631948 0.442082809620383 +2.83333333333333 NA 13.1644787872888 0.713539824170145 +3.98333333333333 NA 11.8624528761568 1.40379553792848 +4.88333333333333 NA 8.97132036194999 2.27300153701105 +5.16666666666667 NA 8.38575338676279 2.51224615005264 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigB_res/KEIO_ROBOT3_12.pdf b/validation/validation_results/Berges_2021/Berges_2021/yigB_res/KEIO_ROBOT3_12.pdf new file mode 100644 index 0000000..f2c18e1 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yigB_res/KEIO_ROBOT3_12.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigB_res/KEIO_ROBOT3_12_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yigB_res/KEIO_ROBOT3_12_log.txt new file mode 100644 index 0000000..08f3db0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yigB_res/KEIO_ROBOT3_12_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.173880 NA NA + [2,] 0.273672 NA NA + [3,] 0.338688 NA NA + [4,] 0.446040 NA NA + [5,] NA 14.349029 0.01556413 + [6,] NA 13.938789 0.44208281 + [7,] NA 13.164479 0.71353982 + [8,] NA 11.862453 1.40379554 + [9,] NA 8.971320 2.27300154 +[10,] NA 8.385753 2.51224615 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03516591 14.58521796 0.11220426 0.55583165 -5.95045704 2.36294242 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.824478e-10 3.422690e-08 2.024912e-08 1.955751e-09 -8.382150e-08 -3.845678e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008380942 0.317589334 0.136859130 0.056860849 0.539425620 0.231144314 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4572181 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.824478e-10 3.422690e-08 2.024912e-08 1.955751e-09 -8.382150e-08 -3.845678e-08 + +$result$normp +[1] 1.004509e-07 + +$result$res + [1] 0.00703125 -0.10188415 0.16308553 -0.06591854 0.49039051 -0.19561347 -0.04598669 -0.75330189 0.66927991 -0.16476836 0.50426577 -0.18723808 -0.14377988 -0.36385203 -0.26879512 0.45939933 + +$result$prevres + [1] 0.007031271 -0.101884142 0.163085529 -0.065918557 0.490390431 -0.195613536 -0.045986738 -0.753301889 0.669279986 -0.164768255 0.504265668 -0.187238146 -0.143779919 -0.363852014 -0.268795032 0.459399443 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 247.4280375 0.000000 0 2.503238e+01 0.000000000 0.000000000 + [2,] 386.2182764 0.000000 0 4.995431e+01 0.000000000 0.000000000 + [3,] 486.1949301 0.000000 0 6.996671e+01 0.000000000 0.000000000 + [4,] 632.3192989 0.000000 0 1.015077e+02 0.000000000 0.000000000 + [5,] -0.6558603 2.173913 0 -5.792689e-04 0.003875992 0.000000000 + [6,] -45.5240454 2.173913 0 -1.837465e+00 0.269037209 0.000000000 + [7,] -89.1360521 2.173913 0 -5.560667e+00 0.526774685 0.000000000 + [8,] -189.7393523 2.173913 0 -1.783394e+01 1.121318313 0.000000000 + [9,] -328.0121645 2.173913 0 -3.957266e+01 1.938480565 0.000000000 +[10,] -387.9287180 2.173913 0 -5.016826e+01 2.292574367 0.000000000 +[11,] 0.5990209 0.000000 5 5.290671e-04 0.000000000 0.008914781 +[12,] 41.5787579 0.000000 5 1.678224e+00 0.000000000 0.618785580 +[13,] 81.4111818 0.000000 5 5.078758e+00 0.000000000 1.211581776 +[14,] 173.2958161 0.000000 5 1.628839e+01 0.000000000 2.579032119 +[15,] 299.5853789 0.000000 5 3.614314e+01 0.000000000 4.458505300 +[16,] 354.3093353 0.000000 5 4.582049e+01 0.000000000 5.272921044 + +$result$retres +$result$retres$res + [1] 0.007031271 -0.101884142 0.163085529 -0.065918557 0.490390431 -0.195613536 -0.045986738 -0.753301889 0.669279986 -0.164768255 0.504265668 -0.187238146 -0.143779919 -0.363852014 -0.268795032 0.459399443 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.17402063 13.098708 0.7025012 + [2,] 0.27163432 12.053705 1.1174749 + [3,] 0.34194971 11.300943 1.4163985 + [4,] 0.44472163 10.200718 1.8533009 + [5,] 0.03615693 14.574609 0.1164173 + [6,] 0.10395403 13.848807 0.4046352 + [7,] 0.16985301 13.143325 0.6847838 + [8,] 0.32186744 11.515934 1.3310251 + [9,] 0.53080158 9.279189 2.2192425 + [10,] 0.62133719 8.309960 2.6041260 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0001406254 NA NA + [2,] 0.0020376828 NA NA + [3,] -0.0032617106 NA NA + [4,] 0.0013183711 NA NA + [5,] NA -0.22557960 -0.10085313 + [6,] NA 0.08998223 0.03744763 + [7,] NA 0.02115390 0.02875598 + [8,] NA 0.34651887 0.07277040 + [9,] NA -0.30786879 0.05375901 +[10,] NA 0.07579340 -0.09187989 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigB_res/KEIO_ROBOT3_12_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yigB_res/KEIO_ROBOT3_12_res.txt new file mode 100644 index 0000000..e0911d0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yigB_res/KEIO_ROBOT3_12_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0351659063736591 0.0352202985960977 0.0350826533948914 0.0037258728904141 0.0286671324733749 0.0417092856656293 +Glc 14.5852179629545 14.5813550161471 14.5805563721967 0.272976724859819 14.0914923146293 15.1102206947028 +Ace 0.112204256633837 0.115940042092045 0.0974441049347834 0.0966103628555684 9.99999999994061e-07 0.325560073768584 +mu 0.555831651674711 0.55692164111545 0.556713577791596 0.0227493901904344 0.518931383359718 0.598453166565372 +qGlc -5.95045703758119 -5.92220629036301 -5.93434614753562 0.478619055954893 -6.83848633156298 -4.99222127590492 +qAce 2.36294241918222 2.34482183993827 2.36179951996251 0.193693608192914 1.93980401556589 2.71129911786253 +res 2.09048374439181 22.8065235378212 22.8420651929412 5.53090709080463 12.5887074490535 34.0976753868865 + + +Goodness of fit (khi2 test) + +khi2 value 2.09048374439187 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.209048374439187 +p-value, i.e. P(X^2<=value) 0.0044015696982364 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigI.txt b/validation/validation_results/Berges_2021/Berges_2021/yigI.txt new file mode 100644 index 0000000..1b96f13 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yigI.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.176904 NA NA +3.67805555555556 0.263088 NA NA +4.09222222222222 0.361368 NA NA +4.565 0.443016 NA NA +0.05 NA 14.7262240944497 0.0169896726758757 +1.95 NA 13.7144519850134 0.417202524396899 +2.83333333333333 NA 13.1841589090987 0.760968344250234 +3.98333333333333 NA 11.7089315292934 1.38732591784723 +4.88333333333333 NA 9.35286899452021 2.08086414836527 +5.16666666666667 NA 8.74023778965753 1.94272827277521 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigI_res/KEIO_ROBOT3_45.pdf b/validation/validation_results/Berges_2021/Berges_2021/yigI_res/KEIO_ROBOT3_45.pdf new file mode 100644 index 0000000..52e4379 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yigI_res/KEIO_ROBOT3_45.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigI_res/KEIO_ROBOT3_45_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yigI_res/KEIO_ROBOT3_45_log.txt new file mode 100644 index 0000000..4e6c054 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yigI_res/KEIO_ROBOT3_45_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.176904 NA NA + [2,] 0.263088 NA NA + [3,] 0.361368 NA NA + [4,] 0.443016 NA NA + [5,] NA 14.726224 0.01698967 + [6,] NA 13.714452 0.41720252 + [7,] NA 13.184159 0.76096834 + [8,] NA 11.708932 1.38732592 + [9,] NA 9.352869 2.08086415 +[10,] NA 8.740238 1.94272827 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0411238 14.6423756 0.1771996 0.5203788 -5.5422122 1.8700379 + +$result$lastp + X Glc Ace mu qGlc qAce + 3.061037e-09 3.592885e-08 -2.965210e-08 -1.839532e-08 2.615022e-08 2.665107e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.01629257 0.54047043 0.23017561 0.09491371 0.88239607 0.37088030 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7692196 + +$result$laststep + X Glc Ace mu qGlc qAce + 3.061037e-09 3.592885e-08 -2.965210e-08 -1.839532e-08 2.615022e-08 2.665107e-08 + +$result$normp +[1] 6.254599e-08 + +$result$res + [1] 0.34332908 0.78664181 -0.77438120 -0.03296581 -0.20737791 0.34275852 -0.03717958 -0.23779839 0.36399816 -0.22440081 0.82052761 0.09947143 -0.42985292 -0.91711288 -0.87695348 1.30392024 + +$result$prevres + [1] 0.34332888 0.78664172 -0.77438118 -0.03296560 -0.20737799 0.34275852 -0.03717953 -0.23779833 0.36399817 -0.22440084 0.82052776 0.09947149 -0.42985291 -0.91711294 -0.87695356 1.30392017 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 223.4357887 0.000000 0 2.643489e+01 0.000000000 0.00000000 + [2,] 339.0017806 0.000000 0 5.127593e+01 0.000000000 0.00000000 + [3,] 420.5355161 0.000000 0 7.077097e+01 0.000000000 0.00000000 + [4,] 537.8353638 0.000000 0 1.009679e+02 0.000000000 0.00000000 + [5,] -0.6103199 2.173913 0 -6.301876e-04 0.004528638 0.00000000 + [6,] -40.7177041 2.173913 0 -1.904091e+00 0.302129672 0.00000000 + [7,] -77.9892854 2.173913 0 -5.621597e+00 0.578688749 0.00000000 + [8,] -160.8521231 2.173913 0 -1.743022e+01 1.193539772 0.00000000 + [9,] -270.7660533 2.173913 0 -3.762743e+01 2.009112763 0.00000000 +[10,] -317.4593536 2.173913 0 -4.728315e+01 2.355581991 0.00000000 +[11,] 0.4736446 0.000000 5 4.890633e-04 0.000000000 0.01041587 +[12,] 31.5993665 0.000000 5 1.477688e+00 0.000000000 0.69489825 +[13,] 60.5243363 0.000000 5 4.362695e+00 0.000000000 1.33098412 +[14,] 124.8308398 0.000000 5 1.352689e+01 0.000000000 2.74514148 +[15,] 210.1306042 0.000000 5 2.920113e+01 0.000000000 4.62095935 +[16,] 246.3673897 0.000000 5 3.669454e+01 0.000000000 5.41783858 + +$result$retres +$result$retres$res + [1] 0.34332888 0.78664172 -0.77438118 -0.03296560 -0.20737799 0.34275852 -0.03717953 -0.23779833 0.36399817 -0.22440084 0.82052776 0.09947149 -0.42985291 -0.91711294 -0.87695356 1.30392017 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.18377058 13.123139 0.6898163 + [2,] 0.27882083 12.110821 1.0313897 + [3,] 0.34588038 11.396614 1.2723754 + [4,] 0.44235669 10.369109 1.6190735 + [5,] 0.04220784 14.630830 0.1810952 + [6,] 0.11344587 13.872121 0.4370968 + [7,] 0.17964700 13.167056 0.6749978 + [8,] 0.32682652 11.599544 1.2039033 + [9,] 0.52205371 9.520308 1.9054734 + [10,] 0.60498953 8.637013 2.2035123 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0068665775 NA NA + [2,] -0.0157328343 NA NA + [3,] 0.0154876236 NA NA + [4,] 0.0006593121 NA NA + [5,] NA 0.09539387 -0.16410555 + [6,] NA -0.15766892 -0.01989430 + [7,] NA 0.01710259 0.08597058 + [8,] NA 0.10938723 0.18342259 + [9,] NA -0.16743916 0.17539071 +[10,] NA 0.10322439 -0.26078403 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yigI_res/KEIO_ROBOT3_45_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yigI_res/KEIO_ROBOT3_45_res.txt new file mode 100644 index 0000000..4808e73 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yigI_res/KEIO_ROBOT3_45_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0411238039205637 0.0416950491277377 0.0424702692370956 0.00492118766083973 0.0318550101577876 0.0495387414254724 +Glc 14.6423756468387 14.639281013131 14.6461994683185 0.252487335245217 14.1573076966205 15.1361457873233 +Ace 0.177199581456556 0.199676510030907 0.194193723758849 0.103243939651057 0.00435557420913021 0.40724331803709 +mu 0.520378840898001 0.518915360415816 0.514781208488682 0.026846280444944 0.477308927454283 0.574871086045799 +qGlc -5.54221217019421 -5.53300917359211 -5.52159844969351 0.462364132406117 -6.36105959330236 -4.65722137969705 +qAce 1.87003792592364 1.82742040394307 1.82960627074867 0.178106841510179 1.49507467126059 2.11057347430646 +res 5.91698805238345 23.4340750476067 23.3277744727215 7.26730185418752 11.7796404286139 37.9562580315943 + + +Goodness of fit (khi2 test) + +khi2 value 5.91698805238361 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.591698805238361 +p-value, i.e. P(X^2<=value) 0.177811361431156 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yiiD.txt b/validation/validation_results/Berges_2021/Berges_2021/yiiD.txt new file mode 100644 index 0000000..77bf510 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yiiD.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.146664 NA NA +3.67805555555556 0.229824 NA NA +4.09222222222222 0.293328 NA NA +4.565 0.37044 NA NA +0.05 NA 14.6788694841786 0.00969732549029215 +1.95 NA 13.9851874366527 0.389157633746909 +2.83333333333333 NA 13.2879607060215 0.671834804013516 +3.98333333333333 NA 11.9266877433073 1.48085534120295 +4.88333333333333 NA 9.88494057302357 2.15324077749882 +5.16666666666667 NA 9.3173698737326 2.40169668174886 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yiiD_res/KEIO_ROBOT3_8.pdf b/validation/validation_results/Berges_2021/Berges_2021/yiiD_res/KEIO_ROBOT3_8.pdf new file mode 100644 index 0000000..df8d2ad Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yiiD_res/KEIO_ROBOT3_8.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yiiD_res/KEIO_ROBOT3_8_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yiiD_res/KEIO_ROBOT3_8_log.txt new file mode 100644 index 0000000..b9f29bc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yiiD_res/KEIO_ROBOT3_8_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.146664 NA NA + [2,] 0.229824 NA NA + [3,] 0.293328 NA NA + [4,] 0.370440 NA NA + [5,] NA 14.678869 0.009697325 + [6,] NA 13.985187 0.389157634 + [7,] NA 13.287961 0.671834804 + [8,] NA 11.926688 1.480855341 + [9,] NA 9.884941 2.153240777 +[10,] NA 9.317370 2.401696682 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03516763 14.67722498 0.07993118 0.51457021 -6.01716602 2.66147652 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.832968e-09 4.684229e-08 -9.492911e-08 -1.581184e-08 -9.108504e-08 2.190951e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.007933042 0.271549900 0.118290990 0.054030107 0.533050689 0.232511508 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3839282 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.832968e-09 4.684229e-08 -9.492911e-08 -1.581184e-08 -9.108504e-08 2.190951e-07 + +$result$normp +[1] 2.603042e-07 + +$result$res + [1] 0.39428734 0.17868586 -0.22456082 -0.10255591 -0.02687449 -0.04000282 0.07253247 -0.06895644 0.28047383 -0.21717255 0.37487236 0.02505282 0.03914789 -0.85146483 -0.05340879 0.46580055 + +$result$prevres + [1] 0.39428729 0.17868594 -0.22456063 -0.10255554 -0.02687459 -0.04000285 0.07253249 -0.06895639 0.28047387 -0.21717253 0.37487283 0.02505311 0.03914805 -0.85146493 -0.05340916 0.46580010 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 219.7329497 0.000000 0 2.223155e+01 0.000000000 0.000000000 + [2,] 331.8359981 0.000000 0 4.292249e+01 0.000000000 0.000000000 + [3,] 410.6571570 0.000000 0 5.909922e+01 0.000000000 0.000000000 + [4,] 523.7613094 0.000000 0 8.408476e+01 0.000000000 0.000000000 + [5,] -0.6625261 2.173913 0 -5.849848e-04 0.003872168 0.000000000 + [6,] -43.9162985 2.173913 0 -1.753521e+00 0.256671031 0.000000000 + [7,] -83.8159137 2.173913 0 -5.156236e+00 0.489866353 0.000000000 + [8,] -171.9872759 2.173913 0 -1.589955e+01 1.005188344 0.000000000 + [9,] -288.2632498 2.173913 0 -3.416964e+01 1.684769163 0.000000000 +[10,] -337.4987455 2.173913 0 -4.287636e+01 1.972528511 0.000000000 +[11,] 0.6740024 0.000000 5 5.951177e-04 0.000000000 0.008905985 +[12,] 44.6770181 0.000000 5 1.783895e+00 0.000000000 0.590343370 +[13,] 85.2677759 0.000000 5 5.245552e+00 0.000000000 1.126692611 +[14,] 174.9664454 0.000000 5 1.617496e+01 0.000000000 2.311933192 +[15,] 293.2565558 0.000000 5 3.476153e+01 0.000000000 3.874969074 +[16,] 343.3449104 0.000000 5 4.361907e+01 0.000000000 4.536815574 + +$result$retres +$result$retres$res + [1] 0.39428729 0.17868594 -0.22456063 -0.10255554 -0.02687459 -0.04000285 0.07253249 -0.06895639 0.28047387 -0.21717253 0.37487283 0.02505311 0.03914805 -0.85146493 -0.05340916 0.46580010 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15454975 13.281221 0.69740321 + [2,] 0.23339772 12.359206 1.10522318 + [3,] 0.28883679 11.710925 1.39196687 + [4,] 0.36838889 10.780677 1.80342876 + [5,] 0.03608418 14.666507 0.08467189 + [6,] 0.09592225 13.966786 0.39416826 + [7,] 0.15112012 13.321326 0.67966441 + [8,] 0.27309803 11.894968 1.31056236 + [9,] 0.43395637 10.013959 2.14255895 + [10,] 0.50206967 9.217471 2.49485670 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.007885746 NA NA + [2,] -0.003573719 NA NA + [3,] 0.004491213 NA NA + [4,] 0.002051111 NA NA + [5,] NA 0.01236231 -0.074974566 + [6,] NA 0.01840131 -0.005010622 + [7,] NA -0.03336495 -0.007829610 + [8,] NA 0.03171994 0.170292985 + [9,] NA -0.12901798 0.010681831 +[10,] NA 0.09989936 -0.093160019 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yiiD_res/KEIO_ROBOT3_8_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yiiD_res/KEIO_ROBOT3_8_res.txt new file mode 100644 index 0000000..34d7d9f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yiiD_res/KEIO_ROBOT3_8_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0351676328341826 0.0348147019824719 0.0349883112420751 0.00516980181144143 0.0258984854747649 0.0441436653472328 +Glc 14.6772249761474 14.6397772547173 14.6512338871558 0.269461006638838 14.1595299534216 15.1432258728639 +Ace 0.0799311828533061 0.0989946079964341 0.0778944781193838 0.0895633535872395 9.99999999987122e-07 0.31277014201785 +mu 0.514570205142069 0.51845301886927 0.515327137841512 0.0321977622158773 0.466446371563031 0.578179808591381 +qGlc -6.01716601766082 -5.98873094708177 -6.01007216659279 0.576830765979968 -7.06405675985612 -4.6484110728648 +qAce 2.66147651611924 2.66920180691358 2.69541374987721 0.213377581394882 2.18582770350405 2.98982015828262 +res 1.47400882042945 24.0995080588339 22.621710679343 7.58378997797327 12.6245221927291 40.0864843809574 + + +Goodness of fit (khi2 test) + +khi2 value 1.47400882043034 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.147400882043034 +p-value, i.e. P(X^2<=value) 0.000986000118524901 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjaG.txt b/validation/validation_results/Berges_2021/Berges_2021/yjaG.txt new file mode 100644 index 0000000..ce20990 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjaG.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.12852 NA NA +3.67805555555556 0.199584 NA NA +4.09222222222222 0.27972 NA NA +4.565 0.38556 NA NA +0.05 NA 14.0186146817498 0.016160653103321 +1.95 NA 13.8178654038851 0.353153324548443 +2.83333333333333 NA 13.3597374126371 0.65295572843308 +3.98333333333333 NA 12.4627892982391 1.2416052489721 +4.88333333333333 NA 10.1502984901254 1.79636579697607 +5.16666666666667 NA 9.80617464530447 2.13860836496595 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjaG_res/KEIO_ROBOT3_7.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjaG_res/KEIO_ROBOT3_7.pdf new file mode 100644 index 0000000..fd54270 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjaG_res/KEIO_ROBOT3_7.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjaG_res/KEIO_ROBOT3_7_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjaG_res/KEIO_ROBOT3_7_log.txt new file mode 100644 index 0000000..b2bda23 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjaG_res/KEIO_ROBOT3_7_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.128520 NA NA + [2,] 0.199584 NA NA + [3,] 0.279720 NA NA + [4,] 0.385560 NA NA + [5,] NA 14.018615 0.01616065 + [6,] NA 13.817865 0.35315332 + [7,] NA 13.359737 0.65295573 + [8,] NA 12.462789 1.24160525 + [9,] NA 10.150298 1.79636580 +[10,] NA 9.806175 2.13860836 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01878661 14.17927660 0.17749952 0.65900425 -5.43140136 2.43312160 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.092514e-08 -3.418740e-07 8.036187e-08 2.638462e-07 -3.209499e-07 3.508104e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.007531268 0.379966805 0.165617627 0.094732203 0.832286360 0.363302727 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5756198 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.092514e-08 -3.418740e-07 8.036187e-08 2.638462e-07 -3.209499e-07 3.508104e-07 + +$result$normp +[1] 6.476614e-07 + +$result$res + [1] -0.17131442 0.62517339 -0.05378071 -0.25275739 0.33798923 -0.09449211 -0.05960169 -0.57868387 0.68645530 -0.29166686 0.81831224 0.02860224 -0.48021367 -0.87958808 0.22275626 0.29013102 + +$result$prevres + [1] -0.17131220 0.62517491 -0.05378023 -0.25275911 0.33798997 -0.09449202 -0.05960200 -0.57868452 0.68645513 -0.29166655 0.81831185 0.02860243 -0.48021315 -0.87958743 0.22275609 0.29013021 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 332.9328619 0.000000 0 1.799439e+01 0.000000000 0.000000000 + [2,] 564.4638072 0.000000 0 3.900348e+01 0.000000000 0.000000000 + [3,] 741.6027703 0.000000 0 5.701374e+01 0.000000000 0.000000000 + [4,] 1012.7008894 0.000000 0 8.685022e+01 0.000000000 0.000000000 + [5,] -0.6002038 2.173913 0 -2.834433e-04 0.002076041 0.000000000 + [6,] -46.8508233 2.173913 0 -1.037096e+00 0.162051975 0.000000000 + [7,] -98.0063631 2.173913 0 -3.376535e+00 0.338993503 0.000000000 + [8,] -229.4279754 2.173913 0 -1.196923e+01 0.793566772 0.000000000 + [9,] -429.6774878 2.173913 0 -2.881386e+01 1.486208367 0.000000000 +[10,] -521.5628679 2.173913 0 -3.749571e+01 1.804030046 0.000000000 +[11,] 0.6184128 0.000000 5 2.920424e-04 0.000000000 0.004774893 +[12,] 48.2721834 0.000000 5 1.068559e+00 0.000000000 0.372719543 +[13,] 100.9796798 0.000000 5 3.478972e+00 0.000000000 0.779685058 +[14,] 236.3883606 0.000000 5 1.233235e+01 0.000000000 1.825203574 +[15,] 442.7130421 0.000000 5 2.968802e+01 0.000000000 3.418279245 +[16,] 537.3860405 0.000000 5 3.863325e+01 0.000000000 4.149269107 + +$result$retres +$result$retres$res + [1] -0.17131220 0.62517491 -0.05378023 -0.25275911 0.33798997 -0.09449202 -0.05960200 -0.57868452 0.68645513 -0.29166655 0.81831185 0.02860243 -0.48021315 -0.87958743 0.22275609 0.29013021 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.12509376 13.303111 0.5699980 + [2,] 0.21208750 12.586123 0.8911893 + [3,] 0.27864440 12.037573 1.1369253 + [4,] 0.38050482 11.198056 1.5130061 + [5,] 0.01941597 14.174090 0.1798230 + [6,] 0.06791137 13.774399 0.3588738 + [7,] 0.12154975 13.332320 0.5569131 + [8,] 0.25934992 12.196594 1.0656878 + [9,] 0.46931856 10.466068 1.8409170 + [10,] 0.56566361 9.672008 2.1966344 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.003426244 NA NA + [2,] -0.012503498 NA NA + [3,] 0.001075605 NA NA + [4,] 0.005055182 NA NA + [5,] NA -0.15547538 -0.163662369 + [6,] NA 0.04346633 -0.005720487 + [7,] NA 0.02741692 0.096042629 + [8,] NA 0.26619488 0.175917487 + [9,] NA -0.31576936 -0.044551218 +[10,] NA 0.13416662 -0.058026043 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjaG_res/KEIO_ROBOT3_7_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjaG_res/KEIO_ROBOT3_7_res.txt new file mode 100644 index 0000000..99c52d2 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjaG_res/KEIO_ROBOT3_7_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0187866130041831 0.0189405286776319 0.01876404762105 0.00279797477373489 0.0141786584289258 0.0256601332939224 +Glc 14.1792765961622 14.2183863710502 14.233894496914 0.265222008133526 13.7158359850124 14.7546723769484 +Ace 0.17749952361032 0.200572311163739 0.19892475557322 0.111587410713142 0.00945432391343102 0.427457899994516 +mu 0.659004247005835 0.659855284811777 0.65995496422197 0.0309990644138315 0.594846333247352 0.71845548727198 +qGlc -5.43140136029437 -5.498952383838 -5.43967694955482 0.606053797832586 -6.71600375514347 -4.41812613426232 +qAce 2.43312159722314 2.37661437034217 2.36155610906065 0.241401445401068 1.90111880425972 2.84897522556103 +res 3.3133820839749 23.7435484995064 23.0381948269308 6.59264476520307 12.2248028387082 36.0335363547342 + + +Goodness of fit (khi2 test) + +khi2 value 3.31338208398814 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.331338208398814 +p-value, i.e. P(X^2<=value) 0.026941722716672 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjbD.txt b/validation/validation_results/Berges_2021/Berges_2021/yjbD.txt new file mode 100644 index 0000000..36542eb --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjbD.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.15876 NA NA +3.67805555555556 0.23436 NA NA +4.09222222222222 0.341712 NA NA +4.565 0.427896 NA NA +0.05 NA 14.4972743631277 0.0224215535040479 +1.95 NA 13.8493797638207 0.402884772845815 +2.83333333333333 NA 13.5447835068454 0.724070665095931 +3.98333333333333 NA 11.963860780573 1.35027272935491 +4.88333333333333 NA 9.70584728531748 1.63017469373458 +5.16666666666667 NA 8.90495394423364 2.26666583933783 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjbD_res/KEIO_ROBOT3_9.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjbD_res/KEIO_ROBOT3_9.pdf new file mode 100644 index 0000000..a6232b5 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjbD_res/KEIO_ROBOT3_9.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjbD_res/KEIO_ROBOT3_9_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjbD_res/KEIO_ROBOT3_9_log.txt new file mode 100644 index 0000000..b407467 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjbD_res/KEIO_ROBOT3_9_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.158760 NA NA + [2,] 0.234360 NA NA + [3,] 0.341712 NA NA + [4,] 0.427896 NA NA + [5,] NA 14.497274 0.02242155 + [6,] NA 13.849380 0.40288477 + [7,] NA 13.544784 0.72407067 + [8,] NA 11.963861 1.35027273 + [9,] NA 9.705847 1.63017469 +[10,] NA 8.904954 2.26666584 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02848795 14.57025084 0.18629619 0.59452629 -5.76930485 2.03635437 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.756118e-09 1.927021e-08 -1.554733e-08 -1.489409e-08 3.528110e-08 7.799624e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.01243075 0.51733943 0.22107692 0.10374198 0.94394127 0.39928349 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7585652 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.756118e-09 1.927021e-08 -1.554733e-08 -1.489409e-08 3.528110e-08 7.799624e-09 + +$result$normp +[1] 4.629869e-08 + +$result$res + [1] -0.05926038 0.96737258 -0.85850238 0.09893198 0.14051158 0.25230901 -0.40882383 -0.15023156 0.21779918 -0.05156438 0.83409379 -0.01556535 -0.54721957 -1.09811873 1.18858054 -0.36177068 + +$result$prevres + [1] -0.05926052 0.96737249 -0.85850239 0.09893212 0.14051154 0.25230902 -0.40882380 -0.15023151 0.21779917 -0.05156442 0.83409387 -0.01556532 -0.54721958 -1.09811877 1.18858050 -0.36177070 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 276.5639738 0.000000 0 2.266670e+01 0.000000000 0.000000000 + [2,] 445.2891272 0.000000 0 4.665750e+01 0.000000000 0.000000000 + [3,] 569.6127674 0.000000 0 6.640489e+01 0.000000000 0.000000000 + [4,] 754.4851539 0.000000 0 9.811889e+01 0.000000000 0.000000000 + [5,] -0.6365121 2.173913 0 -4.555687e-04 0.003142999 0.000000000 + [6,] -46.1529229 2.173913 0 -1.524251e+00 0.227896079 0.000000000 + [7,] -92.6040994 2.173913 0 -4.740063e+00 0.457264889 0.000000000 + [8,] -204.1669435 2.173913 0 -1.577905e+01 1.008145162 0.000000000 + [9,] -363.5569658 2.173913 0 -3.609082e+01 1.795188730 0.000000000 +[10,] -434.1284311 2.173913 0 -4.620125e+01 2.143659839 0.000000000 +[11,] 0.5167308 0.000000 5 3.698382e-04 0.000000000 0.007228898 +[12,] 37.4676895 0.000000 5 1.237412e+00 0.000000000 0.524160982 +[13,] 75.1775059 0.000000 5 3.848060e+00 0.000000000 1.051709244 +[14,] 165.7460276 0.000000 5 1.280969e+01 0.000000000 2.318733871 +[15,] 295.1414261 0.000000 5 2.929911e+01 0.000000000 4.128934079 +[16,] 352.4324833 0.000000 5 3.750692e+01 0.000000000 4.930417630 + +$result$retres +$result$retres$res + [1] -0.05926052 0.96737249 -0.85850239 0.09893212 0.14051154 0.25230902 -0.40882380 -0.15023151 0.21779917 -0.05156442 0.83409387 -0.01556532 -0.54721958 -1.09811877 1.18858050 -0.36177070 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15757479 13.317587 0.6284407 + [2,] 0.25370745 12.384713 0.9577116 + [3,] 0.32454195 11.697332 1.2003319 + [4,] 0.42987464 10.675180 1.5611143 + [5,] 0.02934750 14.561910 0.1892403 + [6,] 0.09081344 13.965442 0.3997717 + [7,] 0.15354171 13.356725 0.6146267 + [8,] 0.30419760 11.894754 1.1306490 + [9,] 0.51943993 9.806035 1.8678908 + [10,] 0.61474054 8.881234 2.1943117 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.001185210 NA NA + [2,] -0.019347450 NA NA + [3,] 0.017170048 NA NA + [4,] -0.001978642 NA NA + [5,] NA -0.06463531 -0.166818774 + [6,] NA -0.11606215 0.003113064 + [7,] NA 0.18805895 0.109443916 + [8,] NA 0.06910650 0.219623754 + [9,] NA -0.10018762 -0.237716100 +[10,] NA 0.02371963 0.072354140 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjbD_res/KEIO_ROBOT3_9_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjbD_res/KEIO_ROBOT3_9_res.txt new file mode 100644 index 0000000..b9b147d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjbD_res/KEIO_ROBOT3_9_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0284879474871803 0.0286502998799535 0.029034327814633 0.00353069810423208 0.0219022960600162 0.0353919432789575 +Glc 14.5702508351608 14.5327678593692 14.5232578277651 0.241308468543846 14.0873855687955 15.0227116765704 +Ace 0.186296192199615 0.187558225656476 0.179992291765991 0.113141201200569 1.00000000000265e-06 0.417084428552903 +mu 0.594526293062147 0.595203377400871 0.591912166845226 0.0264174756308962 0.550839827899677 0.64846111392099 +qGlc -5.76930485134989 -5.71863109181499 -5.74705123197669 0.466914421792953 -6.5687322662678 -4.83639517384878 +qAce 2.0363543717684 2.02280102224873 2.0401337475488 0.216797796939247 1.57834602250139 2.43131226250079 +res 5.75421098787827 22.8777917787703 22.9859057194467 5.83040925736319 13.3270136502273 35.3478671358579 + + +Goodness of fit (khi2 test) + +khi2 value 5.75421098787833 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.575421098787833 +p-value, i.e. P(X^2<=value) 0.164526722640516 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjbR.txt b/validation/validation_results/Berges_2021/Berges_2021/yjbR.txt new file mode 100644 index 0000000..05e6f3f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjbR.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.170856 NA NA +3.67805555555556 0.278208 NA NA +4.09222222222222 0.353808 NA NA +4.565 0.449064 NA NA +0.05 NA 14.6138323257702 0.0128583435122086 +1.95 NA 14.0321213378892 0.415370641213447 +2.83333333333333 NA 13.2181193292946 0.696633311211932 +3.98333333333333 NA 11.8791493698714 1.23375653933195 +4.88333333333333 NA 9.55195135172094 2.05327891957715 +5.16666666666667 NA 8.59499181739816 2.31222308179105 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjbR_res/KEIO_ROBOT3_13.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjbR_res/KEIO_ROBOT3_13.pdf new file mode 100644 index 0000000..cecf7f2 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjbR_res/KEIO_ROBOT3_13.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjbR_res/KEIO_ROBOT3_13_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjbR_res/KEIO_ROBOT3_13_log.txt new file mode 100644 index 0000000..f698863 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjbR_res/KEIO_ROBOT3_13_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.170856 NA NA + [2,] 0.278208 NA NA + [3,] 0.353808 NA NA + [4,] 0.449064 NA NA + [5,] NA 14.613832 0.01285834 + [6,] NA 14.032121 0.41537064 + [7,] NA 13.218119 0.69663331 + [8,] NA 11.879149 1.23375654 + [9,] NA 9.551951 2.05327892 +[10,] NA 8.594992 2.31222308 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03610906 14.69015498 0.10901204 0.55357524 -5.63218151 2.10375431 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.757137e-09 -8.666774e-08 -1.377642e-07 -1.980188e-08 2.597030e-07 2.567428e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.005714377 0.210752310 0.090428311 0.037776383 0.349838758 0.148887190 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3042932 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.757137e-09 -8.666774e-08 -1.377642e-07 -1.980188e-08 2.597030e-07 2.567428e-07 + +$result$normp +[1] 4.003155e-07 + +$result$res + [1] 0.33378457 -0.07968095 -0.29571765 0.14527935 0.14350431 -0.12137510 0.16577975 -0.33499394 0.04572103 0.10136395 0.50002489 -0.19856265 -0.33132620 -0.08603890 -0.16440471 0.28030757 + +$result$prevres + [1] 0.33378440 -0.07968100 -0.29571756 0.14527967 0.14350450 -0.12137490 0.16577992 -0.33499390 0.04572080 0.10136358 0.50002558 -0.19856220 -0.33132594 -0.08603902 -0.16440527 0.28030684 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 245.8270569 0.000000 0 2.553744e+01 0.000000000 0.000000000 + [2,] 383.0262627 0.000000 0 5.087015e+01 0.000000000 0.000000000 + [3,] 481.7262358 0.000000 0 7.118291e+01 0.000000000 0.000000000 + [4,] 625.8395682 0.000000 0 1.031621e+02 0.000000000 0.000000000 + [5,] -0.6207448 2.173913 0 -5.629475e-04 0.003979721 0.000000000 + [6,] -42.9776609 2.173913 0 -1.780164e+00 0.275538517 0.000000000 + [7,] -84.0314763 2.173913 0 -5.378754e+00 0.538742870 0.000000000 + [8,] -178.5113080 2.173913 0 -1.721329e+01 1.144472270 0.000000000 + [9,] -308.0746693 2.173913 0 -3.812835e+01 1.975129307 0.000000000 +[10,] -364.1465784 2.173913 0 -4.830998e+01 2.334617710 0.000000000 +[11,] 0.5332848 0.000000 5 4.836311e-04 0.000000000 0.009153358 +[12,] 36.9223142 0.000000 5 1.529347e+00 0.000000000 0.633738590 +[13,] 72.1918435 0.000000 5 4.620914e+00 0.000000000 1.239108601 +[14,] 153.3599191 0.000000 5 1.478802e+01 0.000000000 2.632286221 +[15,] 264.6684229 0.000000 5 3.275624e+01 0.000000000 4.542797407 +[16,] 312.8400683 0.000000 5 4.150333e+01 0.000000000 5.369620734 + +$result$retres +$result$retres$res + [1] 0.33378440 -0.07968100 -0.29571756 0.14527967 0.14350450 -0.12137490 0.16577992 -0.33499390 0.04572080 0.10136358 0.50002558 -0.19856220 -0.33132594 -0.08603902 -0.16440527 0.28030684 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.17753169 13.251294 0.6464611 + [2,] 0.27661438 12.243207 1.0230054 + [3,] 0.34789365 11.517998 1.2938883 + [4,] 0.45196959 10.459110 1.6894085 + [5,] 0.03712248 14.679844 0.1128635 + [6,] 0.10627346 13.976289 0.3756582 + [7,] 0.17329703 13.294378 0.6303681 + [8,] 0.32754277 11.725052 1.2165487 + [9,] 0.53906511 9.572983 2.0203979 + [10,] 0.63060690 8.641619 2.3682845 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.006675688 NA NA + [2,] 0.001593620 NA NA + [3,] 0.005914351 NA NA + [4,] -0.002905593 NA NA + [5,] NA -0.06601207 -0.10000512 + [6,] NA 0.05583245 0.03971244 + [7,] NA -0.07625877 0.06626519 + [8,] NA 0.15409719 0.01720780 + [9,] NA -0.02103157 0.03288105 +[10,] NA -0.04662725 -0.05606137 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjbR_res/KEIO_ROBOT3_13_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjbR_res/KEIO_ROBOT3_13_res.txt new file mode 100644 index 0000000..c0ef918 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjbR_res/KEIO_ROBOT3_13_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0361090645914074 0.0361680872526514 0.0358577184855162 0.00452190469443736 0.0281694945580987 0.045277558119095 +Glc 14.6901549835449 14.7006992239667 14.6938753104274 0.24526383934047 14.2228158188913 15.1436074153389 +Ace 0.109012038260373 0.134001962797163 0.120493974899021 0.104879155191611 9.99999999994061e-07 0.355315311655201 +mu 0.553575238023881 0.555085239949794 0.554515524080914 0.0265975205952413 0.506927454359445 0.604826380703283 +qGlc -5.63218151297634 -5.65902827489169 -5.72123253575856 0.499175096067276 -6.60064804822933 -4.7833142872829 +qAce 2.10375430783616 2.08545534759896 2.09795011343786 0.188383221377764 1.6851080118775 2.44458044364192 +res 0.925943548247519 22.7661791393703 22.2774088234646 6.55626286998275 11.7170453943343 36.5795567990363 + + +Goodness of fit (khi2 test) + +khi2 value 0.925943548249575 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.0925943548249576 +p-value, i.e. P(X^2<=value) 0.000120776902460869 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjcO.txt b/validation/validation_results/Berges_2021/Berges_2021/yjcO.txt new file mode 100644 index 0000000..296dcdf --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjcO.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.170856 NA NA +3.67805555555556 0.260064 NA NA +4.09222222222222 0.344736 NA NA +4.565 0.470232 NA NA +0.05 NA 14.3510862509306 0.0183467586771119 +1.95 NA 13.9600229135777 0.434851702014233 +2.83333333333333 NA 13.115477531153 0.752318873846327 +3.98333333333333 NA 11.9909314640952 1.42183570103192 +4.88333333333333 NA 9.17662013928018 2.09099125097709 +5.16666666666667 NA 8.30584725462062 2.42765474293743 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjcO_res/KEIO_ROBOT3_11.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjcO_res/KEIO_ROBOT3_11.pdf new file mode 100644 index 0000000..6e782e2 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjcO_res/KEIO_ROBOT3_11.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjcO_res/KEIO_ROBOT3_11_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjcO_res/KEIO_ROBOT3_11_log.txt new file mode 100644 index 0000000..49f6f60 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjcO_res/KEIO_ROBOT3_11_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.170856 NA NA + [2,] 0.260064 NA NA + [3,] 0.344736 NA NA + [4,] 0.470232 NA NA + [5,] NA 14.351086 0.01834676 + [6,] NA 13.960023 0.43485170 + [7,] NA 13.115478 0.75231887 + [8,] NA 11.990931 1.42183570 + [9,] NA 9.176620 2.09099125 +[10,] NA 8.305847 2.42765474 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02852523 14.50640705 0.18417353 0.61105467 -5.89494816 2.20660091 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.536473e-09 1.665723e-08 -1.345188e-08 -1.295240e-08 3.379222e-08 3.165164e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.008547637 0.376973590 0.161763749 0.071120569 0.648864598 0.276271686 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5559212 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.536473e-09 1.665723e-08 -1.345188e-08 -1.295240e-08 3.379222e-08 3.165164e-09 + +$result$normp +[1] 4.219567e-08 + +$result$res + [1] -0.26955229 0.49491201 0.14855698 -0.30303559 0.31909414 -0.18348215 0.24309908 -0.75608366 0.35978815 0.01758443 0.84511267 -0.07280982 -0.44675153 -0.82939759 0.13140315 0.37244313 + +$result$prevres + [1] -0.26955242 0.49491193 0.14855696 -0.30303547 0.31909411 -0.18348214 0.24309911 -0.75608362 0.35978815 0.01758439 0.84511273 -0.07280980 -0.44675154 -0.82939763 0.13140312 0.37244312 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 290.0326115 0.000000 0 2.380167e+01 0.00000000 0.000000000 + [2,] 473.1990210 0.000000 0 4.964681e+01 0.00000000 0.000000000 + [3,] 609.4729350 0.000000 0 7.114474e+01 0.00000000 0.000000000 + [4,] 813.6152725 0.000000 0 1.059471e+02 0.00000000 0.000000000 + [5,] -0.6506441 2.173913 0 -4.663570e-04 0.00314842 0.000000000 + [6,] -48.0723068 2.173913 0 -1.596431e+00 0.23261845 0.000000000 + [7,] -97.4807381 2.173913 0 -5.022943e+00 0.47170231 0.000000000 + [8,] -218.2106265 2.173913 0 -1.699076e+01 1.05590560 0.000000000 + [9,] -393.5710338 2.173913 0 -3.937245e+01 1.90446205 0.000000000 +[10,] -471.9293195 2.173913 0 -5.061341e+01 2.28363218 0.000000000 +[11,] 0.5601639 0.000000 5 4.015043e-04 0.00000000 0.007241367 +[12,] 41.3872526 0.000000 5 1.374427e+00 0.00000000 0.535022436 +[13,] 83.9248249 0.000000 5 4.324440e+00 0.00000000 1.084915315 +[14,] 187.8657156 0.000000 5 1.462798e+01 0.00000000 2.428582869 +[15,] 338.8400698 0.000000 5 3.389722e+01 0.00000000 4.380262712 +[16,] 406.3016580 0.000000 5 4.357498e+01 0.00000000 5.252354018 + +$result$retres +$result$retres$res + [1] -0.26955242 0.49491193 0.14855696 -0.30303547 0.31909411 -0.18348214 0.24309911 -0.75608362 0.35978815 0.01758439 0.84511273 -0.07280980 -0.44675154 -0.82939763 0.13140312 0.37244312 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.16546495 13.185326 0.6786813 + [2,] 0.26996224 12.177223 1.0560352 + [3,] 0.34770714 11.427205 1.3367825 + [4,] 0.46417129 10.303656 1.7573502 + [5,] 0.02941021 14.497870 0.1873693 + [6,] 0.09391082 13.875621 0.4202897 + [7,] 0.16111375 13.227303 0.6629686 + [8,] 0.32532462 11.643133 1.2559562 + [9,] 0.56384124 9.342123 2.1172719 + [10,] 0.67042033 8.313936 2.5021434 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.005391048 NA NA + [2,] -0.009898239 NA NA + [3,] -0.002971139 NA NA + [4,] 0.006060709 NA NA + [5,] NA -0.146783290 -0.16902255 + [6,] NA 0.084401784 0.01456196 + [7,] NA -0.111825592 0.08935031 + [8,] NA 0.347798465 0.16587953 + [9,] NA -0.165502548 -0.02628062 +[10,] NA -0.008088819 -0.07448862 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjcO_res/KEIO_ROBOT3_11_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjcO_res/KEIO_ROBOT3_11_res.txt new file mode 100644 index 0000000..f72fd34 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjcO_res/KEIO_ROBOT3_11_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0285252336906324 0.0285276932689114 0.0283525773208979 0.0035213443973611 0.0222029856450048 0.0359699035992833 +Glc 14.5064070539719 14.4700597115985 14.4553333384319 0.263738114946642 13.9020340499368 14.9364350875325 +Ace 0.184173530362495 0.191232750218973 0.181545655229856 0.106527250407898 1.00000000000009e-06 0.410874364841943 +mu 0.611054666275424 0.612750955742172 0.612170484916302 0.026258900773894 0.558509269647036 0.666220084884651 +qGlc -5.89494815720173 -5.89603270993185 -5.90210198429462 0.49133645660275 -6.81332195287803 -4.99040013134821 +qAce 2.20660090595011 2.19429346623823 2.20642869523995 0.186760304195237 1.81226245757715 2.51945815774251 +res 3.09048390569372 24.13591151423 23.1501547130338 6.57869063447584 11.8634690341941 35.5439519042883 + + +Goodness of fit (khi2 test) + +khi2 value 3.09048390569378 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.309048390569378 +p-value, i.e. P(X^2<=value) 0.0207863093510393 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjcZ.txt b/validation/validation_results/Berges_2021/Berges_2021/yjcZ.txt new file mode 100644 index 0000000..611a171 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjcZ.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.652799999999999E-2 NA NA +2.2613888888888889 8.9207999999999996E-2 NA NA +2.7741666666666664 0.13910400000000001 NA NA +3.2088888888888891 0.14968800000000002 NA NA +3.7063888888888892 0.195048 NA NA +4.2258333333333331 0.28576800000000002 NA NA +4.6355555555555554 0.371952 NA NA +4.9675000000000002 0.51559200000000005 NA NA +2.8 NA 12.2609257071251 0.650129196448217 +3.73333333333333 NA 11.6535279969914 1.13566070976477 +4.28333333333333 NA 10.9605184097475 1.4947301250087 +4.75 NA 10.0865706870416 1.90158963127429 +5.11666666666667 NA 9.22044899385263 2.20030922094117 +5.43333333333333 NA 8.38827039474486 2.64151264872402 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjcZ_res/KEIO_ROBOT5_5.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjcZ_res/KEIO_ROBOT5_5.pdf new file mode 100644 index 0000000..7c4ded7 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjcZ_res/KEIO_ROBOT5_5.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjcZ_res/KEIO_ROBOT5_5_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjcZ_res/KEIO_ROBOT5_5_log.txt new file mode 100644 index 0000000..9b3105f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjcZ_res/KEIO_ROBOT5_5_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.066528 NA NA + [2,] 0.089208 NA NA + [3,] 0.139104 NA NA + [4,] 0.149688 NA NA + [5,] 0.195048 NA NA + [6,] 0.285768 NA NA + [7,] 0.371952 NA NA + [8,] 0.515592 NA NA + [9,] NA 12.260926 0.6501292 +[10,] NA 11.653528 1.1356607 +[11,] NA 10.960518 1.4947301 +[12,] NA 10.086571 1.9015896 +[13,] NA 9.220449 2.2003092 +[14,] NA 8.388270 2.6415126 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01762075 13.00036411 0.41017228 0.66996550 -4.75594721 2.33080117 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.901435e-08 5.937513e-07 -4.403036e-07 -2.409482e-07 -7.874216e-10 2.764780e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.00482688 0.60602823 0.26579790 0.06031851 0.97706668 0.42678902 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6745748 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.901435e-08 5.937513e-07 -4.403036e-07 -2.409482e-07 -7.874216e-10 2.764780e-07 + +$result$normp +[1] 8.253885e-07 + +$result$res + [1] -0.32632415 -0.45197799 -1.30358657 0.07801026 0.80152461 0.65855570 1.07068420 -1.21273155 0.10461620 -0.11690244 -0.08808798 0.05202124 0.10981974 -0.06146677 0.49421833 -0.19537473 -0.32504562 -0.37574493 0.18785797 0.21408897 + +$result$prevres + [1] -0.32632606 -0.45198013 -1.30358889 0.07800795 0.80152265 0.65855479 1.07068495 -1.21272866 0.10461588 -0.11690233 -0.08808771 0.05202148 0.10981979 -0.06146711 0.49421925 -0.19537451 -0.32504578 -0.37574530 0.18785758 0.21408875 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 170.25816 0.000000 0 5.486802 0.0000000 0.0000000 + [2,] 227.48313 0.000000 0 9.064596 0.0000000 0.0000000 + [3,] 320.73641 0.000000 0 15.678511 0.0000000 0.0000000 + [4,] 429.17665 0.000000 0 24.266927 0.0000000 0.0000000 + [5,] 598.94907 0.000000 0 39.116942 0.0000000 0.0000000 + [6,] 848.25946 0.000000 0 63.163340 0.0000000 0.0000000 + [7,] 1116.20119 0.000000 0 91.173428 0.0000000 0.0000000 + [8,] 1394.20245 0.000000 0 122.035933 0.0000000 0.0000000 + [9,] -85.28916 2.173913 0 -2.726208 0.3159954 0.0000000 +[10,] -172.79675 2.173913 0 -7.837746 0.6402101 0.0000000 +[11,] -256.65976 2.173913 0 -13.785873 0.9509217 0.0000000 +[12,] -356.52945 2.173913 0 -21.755562 1.3209379 0.0000000 +[13,] -460.10486 2.173913 0 -30.772950 1.7046837 0.0000000 +[14,] -572.49353 2.173913 0 -41.230485 2.1210825 0.0000000 +[15,] 96.13683 0.000000 5 3.072946 0.0000000 0.7267895 +[16,] 194.77425 0.000000 5 8.834606 0.0000000 1.4724833 +[17,] 289.30356 0.000000 5 15.539257 0.0000000 2.1871200 +[18,] 401.87537 0.000000 5 24.522587 0.0000000 3.0381571 +[19,] 518.62424 0.000000 5 34.686870 0.0000000 3.9207725 +[20,] 645.30728 0.000000 5 46.474468 0.0000000 4.8784898 + +$result$retres +$result$retres$res + [1] -0.32632606 -0.45198013 -1.30358889 0.07800795 0.80152265 0.65855479 1.07068495 -1.21272866 0.10461588 -0.11690233 -0.08808771 0.05202148 0.10981979 -0.06146711 0.49421925 -0.19537451 -0.32504578 -0.37574530 0.18785758 0.21408875 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06000148 12.699511 0.5576147 + [2,] 0.08016840 12.556351 0.6277751 + [3,] 0.11303222 12.323057 0.7421079 + [4,] 0.15124816 12.051770 0.8750606 + [5,] 0.21107845 11.627047 1.0832093 + [6,] 0.29893910 11.003343 1.3888751 + [7,] 0.39336570 10.333028 1.7173839 + [8,] 0.49133743 9.637547 2.0582261 + [9,] 0.11500555 12.309049 0.7489730 + [10,] 0.21492341 11.599753 1.0965858 + [11,] 0.31067983 10.919998 1.4297210 + [12,] 0.42471297 10.110501 1.8264406 + [13,] 0.54297739 9.270966 2.2378807 + [14,] 0.67130494 8.359996 2.6843304 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.006526521 NA NA + [2,] 0.009039603 NA NA + [3,] 0.026071778 NA NA + [4,] -0.001560159 NA NA + [5,] -0.016030453 NA NA + [6,] -0.013171096 NA NA + [7,] -0.021413699 NA NA + [8,] 0.024254573 NA NA + [9,] NA -0.04812330 -0.09884385 +[10,] NA 0.05377507 0.03907490 +[11,] NA 0.04052034 0.06500916 +[12,] NA -0.02392988 0.07514906 +[13,] NA -0.05051710 -0.03757152 +[14,] NA 0.02827487 -0.04281775 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjcZ_res/KEIO_ROBOT5_5_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjcZ_res/KEIO_ROBOT5_5_res.txt new file mode 100644 index 0000000..04026b9 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjcZ_res/KEIO_ROBOT5_5_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0176207536625543 0.0176306564528979 0.0174024792388567 0.00205995916812782 0.0145114405778482 0.0213720170352603 +Glc 13.0003641146995 13.0146473576043 12.9803366991049 0.252856832226459 12.5538679708557 13.525183427589 +Ace 0.41017227607194 0.409892211630086 0.396368335089701 0.11145086892886 0.199919256409951 0.641861917597226 +mu 0.669965496696073 0.671277813242032 0.671886469220862 0.02360602823675 0.630680993029934 0.711280914118756 +qGlc -4.75594721114039 -4.76376986900039 -4.78729747192364 0.500738858974535 -5.71180364573364 -3.71948274288614 +qAce 2.3308011729092 2.33118722748521 2.31309895885239 0.200026954552412 1.99921657934318 2.71979466175558 +res 6.37071651834938 37.6479550942681 37.4113751001974 8.39800527146576 22.8868447126238 55.5975373607175 + + +Goodness of fit (khi2 test) + +khi2 value 6.37071651838594 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.45505117988471 +p-value, i.e. P(X^2<=value) 0.0437347398264997 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjeI.txt b/validation/validation_results/Berges_2021/Berges_2021/yjeI.txt new file mode 100644 index 0000000..b1c579c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjeI.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.17388 NA NA +3.67805555555556 0.260064 NA NA +4.09222222222222 0.387072 NA NA +4.565 0.585144 NA NA +0.05 NA 14.2784240020622 0.016276507034326 +1.95 NA 14.0533709587791 0.457798012854761 +2.83333333333333 NA 13.3983720876595 0.807518707502987 +3.98333333333333 NA 11.6058235351541 1.5000907466349 +4.88333333333333 NA 9.04485444159311 2.32366248013975 +5.16666666666667 NA 8.18635881642296 2.59865781448822 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjeI_res/KEIO_ROBOT3_44.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjeI_res/KEIO_ROBOT3_44.pdf new file mode 100644 index 0000000..3826a38 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjeI_res/KEIO_ROBOT3_44.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjeI_res/KEIO_ROBOT3_44_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjeI_res/KEIO_ROBOT3_44_log.txt new file mode 100644 index 0000000..5d99c51 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjeI_res/KEIO_ROBOT3_44_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.173880 NA NA + [2,] 0.260064 NA NA + [3,] 0.387072 NA NA + [4,] 0.585144 NA NA + [5,] NA 14.278424 0.01627651 + [6,] NA 14.053371 0.45779801 + [7,] NA 13.398372 0.80751871 + [8,] NA 11.605824 1.50009075 + [9,] NA 9.044854 2.32366248 +[10,] NA 8.186359 2.59865781 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.01760248 14.31791254 0.28918722 0.76112656 -5.48216725 2.13310462 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.706085e-10 -5.370381e-08 9.270504e-08 4.653049e-09 1.507679e-07 -2.126288e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.008841806 0.604016564 0.260670046 0.117706795 0.968849779 0.416288323 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.9487019 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.706085e-10 -5.370381e-08 9.270504e-08 4.653049e-09 1.507679e-07 -2.126288e-07 + +$result$normp +[1] 2.818545e-07 + +$result$res + [1] -0.832113868 1.462401056 0.472648497 -0.844095454 0.075153393 -0.365167080 -0.107031763 0.456488251 0.401420405 -0.460863205 1.374121431 -0.001591996 -0.706911459 -1.186688717 -0.272915840 0.793986580 + +$result$prevres + [1] -0.832113897 1.462400948 0.472648312 -0.844095782 0.075153510 -0.365166993 -0.107031706 0.456488238 0.401420300 -0.460863347 1.374120969 -0.001592372 -0.706911733 -1.186688713 -0.272915391 0.793987240 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 446.6350546 0.000000 0 2.261821e+01 0.000000000 0.000000000 + [2,] 821.7931912 0.000000 0 5.320528e+01 0.000000000 0.000000000 + [3,] 1126.3324578 0.000000 0 8.113341e+01 0.000000000 0.000000000 + [4,] 1614.1531673 0.000000 0 1.297058e+02 0.000000000 0.000000000 + [5,] -0.6073716 2.173913 0 -2.689764e-04 0.001950187 0.000000000 + [6,] -53.4161846 2.173913 0 -1.135612e+00 0.171512000 0.000000000 + [7,] -119.6440730 2.173913 0 -3.981023e+00 0.384160615 0.000000000 + [8,] -309.0108046 2.173913 0 -1.561821e+01 0.992191069 0.000000000 + [9,] -628.4198305 2.173913 0 -4.083077e+01 2.017769392 0.000000000 +[10,] -783.4308272 2.173913 0 -5.455576e+01 2.515488320 0.000000000 +[11,] 0.5435534 0.000000 5 2.407144e-04 0.000000000 0.004485429 +[12,] 47.8036004 0.000000 5 1.016290e+00 0.000000000 0.394477601 +[13,] 107.0727440 0.000000 5 3.562726e+00 0.000000000 0.883569414 +[14,] 276.5421967 0.000000 5 1.397716e+01 0.000000000 2.282039458 +[15,] 562.3900452 0.000000 5 3.654057e+01 0.000000000 4.640869602 +[16,] 701.1136138 0.000000 5 4.882343e+01 0.000000000 5.785623137 + +$result$retres +$result$retres$res + [1] -0.832113897 1.462400948 0.472648312 -0.844095782 0.075153510 -0.365166993 -0.107031706 0.456488238 0.401420300 -0.460863347 1.374120969 -0.001592372 -0.706911733 -1.186688713 -0.272915391 0.793987240 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15723772 13.312162 0.6805236 + [2,] 0.28931202 12.360870 1.0506701 + [3,] 0.39652497 11.588647 1.3511411 + [4,] 0.56826208 10.351676 1.8324451 + [5,] 0.01828528 14.312995 0.2911007 + [6,] 0.07765196 13.885394 0.4574795 + [7,] 0.15210411 13.349138 0.6661364 + [8,] 0.36498665 11.815808 1.2627530 + [9,] 0.72406030 9.229508 2.2690794 + [10,] 0.89832077 7.974362 2.7574553 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.016642278 NA NA + [2,] -0.029248019 NA NA + [3,] -0.009452966 NA NA + [4,] 0.016881916 NA NA + [5,] NA -0.03457061 -0.2748241938 + [6,] NA 0.16797682 0.0003184744 + [7,] NA 0.04923458 0.1413823466 + [8,] NA -0.20998459 0.2373377426 + [9,] NA -0.18465334 0.0545830783 +[10,] NA 0.21199714 -0.1587974479 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjeI_res/KEIO_ROBOT3_44_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjeI_res/KEIO_ROBOT3_44_res.txt new file mode 100644 index 0000000..8c8c2a8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjeI_res/KEIO_ROBOT3_44_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0176024831582201 0.0176682207500672 0.0175833160637533 0.00204746974455858 0.0139810711070222 0.0217103956391261 +Glc 14.3179125372788 14.3275801271673 14.3270641229934 0.243220828253725 13.8870052946357 14.7665476371231 +Ace 0.289187215458872 0.309852593051253 0.310137145191593 0.114423704500364 0.132540974151381 0.570586639140252 +mu 0.761126562834309 0.761506260240125 0.762162258897595 0.0247678322345622 0.715335050820122 0.809030303921727 +qGlc -5.48216725304386 -5.50792598787472 -5.50362042922977 0.370129150792213 -6.22117266690605 -4.78940968909084 +qAce 2.13310462433081 2.10606423877708 2.08688262150119 0.180437527531491 1.70874005374218 2.46540414569392 +res 9.00035356969153 23.7906074411713 23.3097496997664 7.01514177970318 12.6966278938327 38.9117559032645 + + +Goodness of fit (khi2 test) + +khi2 value 9.00035356969282 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.900035356969282 +p-value, i.e. P(X^2<=value) 0.467929978406739 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgJ.txt b/validation/validation_results/Berges_2021/Berges_2021/yjgJ.txt new file mode 100644 index 0000000..13b6623 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjgJ.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.18144 NA NA +3.67805555555556 0.29484 NA NA +4.09222222222222 0.367416 NA NA +4.565 0.535248 NA NA +0.05 NA 14.4257568227242 0.0155794999525615 +1.95 NA 13.8666582896826 0.459922264552166 +2.83333333333333 NA 13.5465255011823 0.796622018740592 +3.98333333333333 NA 11.8718988671023 1.37832355822617 +4.88333333333333 NA 9.43063999213425 2.19070589623816 +5.16666666666667 NA 8.54317842865009 2.52337221070657 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgJ_res/KEIO_ROBOT3_36.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjgJ_res/KEIO_ROBOT3_36.pdf new file mode 100644 index 0000000..a6c7fa5 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjgJ_res/KEIO_ROBOT3_36.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgJ_res/KEIO_ROBOT3_36_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjgJ_res/KEIO_ROBOT3_36_log.txt new file mode 100644 index 0000000..86ad58e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjgJ_res/KEIO_ROBOT3_36_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.181440 NA NA + [2,] 0.294840 NA NA + [3,] 0.367416 NA NA + [4,] 0.535248 NA NA + [5,] NA 14.425757 0.0155795 + [6,] NA 13.866658 0.4599223 + [7,] NA 13.546526 0.7966220 + [8,] NA 11.871899 1.3783236 + [9,] NA 9.430640 2.1907059 +[10,] NA 8.543178 2.5233722 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02762361 14.51577622 0.20397307 0.64428259 -5.21475514 2.07801301 + +$result$lastp + X Glc Ace mu qGlc qAce +-5.520356e-09 -5.823644e-08 6.619349e-08 4.822422e-08 -9.539557e-08 -4.926922e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.008119474 0.384878586 0.166271171 0.069567045 0.603013839 0.259572809 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5808125 + +$result$laststep + X Glc Ace mu qGlc qAce +-5.520356e-09 -5.823644e-08 6.619349e-08 4.822422e-08 -9.539557e-08 -4.926922e-08 + +$result$normp +[1] 1.471628e-07 + +$result$res + [1] -0.25656823 0.02870365 0.91725722 -0.60613875 0.17978177 0.18988831 -0.42315628 -0.09415369 0.24071271 -0.09307282 0.95655203 -0.16045668 -0.64424349 -0.51770266 -0.02247457 0.38832537 + +$result$prevres + [1] -0.25656769 0.02870398 0.91725727 -0.60613928 0.17978189 0.18988829 -0.42315639 -0.09415385 0.24071273 -0.09307267 0.95655170 -0.16045683 -0.64424350 -0.51770251 -0.02247438 0.38832552 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 319.1266605 0.000000 0 2.536151e+01 0.000000000 0.000000000 + [2,] 534.7129068 0.000000 0 5.432747e+01 0.000000000 0.000000000 + [3,] 698.2452010 0.000000 0 7.893102e+01 0.000000000 0.000000000 + [4,] 946.8804073 0.000000 0 1.194033e+02 0.000000000 0.000000000 + [5,] -0.5760499 2.173913 0 -3.999505e-04 0.003051453 0.000000000 + [6,] -44.2099174 2.173913 0 -1.433709e+00 0.234188906 0.000000000 + [7,] -91.5963827 2.173913 0 -4.618910e+00 0.485204631 0.000000000 + [8,] -211.4753351 2.173913 0 -1.613858e+01 1.120227775 0.000000000 + [9,] -391.4741429 2.173913 0 -3.839712e+01 2.073717997 0.000000000 +[10,] -473.3985973 2.173913 0 -4.977869e+01 2.507688461 0.000000000 +[11,] 0.5279615 0.000000 5 3.665627e-04 0.000000000 0.007018342 +[12,] 40.5192969 0.000000 5 1.314024e+00 0.000000000 0.538634485 +[13,] 83.9499650 0.000000 5 4.233326e+00 0.000000000 1.115970652 +[14,] 193.8214858 0.000000 5 1.479134e+01 0.000000000 2.576523883 +[15,] 358.7940882 0.000000 5 3.519175e+01 0.000000000 4.769551393 +[16,] 433.8795324 0.000000 5 4.562319e+01 0.000000000 5.767683460 + +$result$retres +$result$retres$res + [1] -0.25656769 0.02870398 0.91725727 -0.60613928 0.17978189 0.18988829 -0.42315639 -0.09415385 0.24071273 -0.09307267 0.95655170 -0.16045683 -0.64424350 -0.51770251 -0.02247438 0.38832552 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.17630865 13.312335 0.6835288 + [2,] 0.29541408 12.348308 1.0676812 + [3,] 0.38576115 11.617049 1.3590787 + [4,] 0.52312521 10.505239 1.8021209 + [5,] 0.02852797 14.508456 0.2068898 + [6,] 0.09703017 13.954007 0.4278309 + [7,] 0.17142370 13.351874 0.6677733 + [8,] 0.35962549 11.828588 1.2747831 + [9,] 0.64221135 9.541368 2.1862110 + [10,] 0.77082717 8.500365 2.6010373 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0051313538 NA NA + [2,] -0.0005740796 NA NA + [3,] -0.0183451454 NA NA + [4,] 0.0121227856 NA NA + [5,] NA -0.08269967 -0.191310341 + [6,] NA -0.08734861 0.032091366 + [7,] NA 0.19465194 0.128848700 + [8,] NA 0.04331077 0.103540501 + [9,] NA -0.11072785 0.004494877 +[10,] NA 0.04281343 -0.077665103 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgJ_res/KEIO_ROBOT3_36_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjgJ_res/KEIO_ROBOT3_36_res.txt new file mode 100644 index 0000000..b8a0f56 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjgJ_res/KEIO_ROBOT3_36_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0276236104295162 0.0274996924011147 0.0273212000261104 0.00329728470299992 0.0212931601471107 0.0338829251930803 +Glc 14.5157762219723 14.4749080878714 14.4458784321918 0.271327725784973 14.0028877429667 15.0732446648312 +Ace 0.203973065808915 0.200315659298037 0.198048230649987 0.0900261250412971 0.00672025006120095 0.375369577785796 +mu 0.64428258796705 0.646659949900832 0.645316622339015 0.0262283252335545 0.601880789924073 0.699355261348099 +qGlc -5.21475513710454 -5.16024420528927 -5.09605645399624 0.423753111731605 -6.11365362093447 -4.54479169283474 +qAce 2.07801301373033 2.09051121009933 2.11466269576136 0.161670241105083 1.75490743802188 2.3387820798935 +res 3.37343206812484 23.9974924629487 22.2006483960391 6.3518356054934 14.8663164463163 38.6261687131956 + + +Goodness of fit (khi2 test) + +khi2 value 3.37343206812587 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.337343206812587 +p-value, i.e. P(X^2<=value) 0.0287778609706861 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgM.txt b/validation/validation_results/Berges_2021/Berges_2021/yjgM.txt new file mode 100644 index 0000000..d9dabb7 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjgM.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.195 0.065016 NA NA +1.61361111111111 0.0756 NA NA +2.36138888888889 0.1134 NA NA +3.28638888888889 0.193536 NA NA +3.81944444444444 0.270648 NA NA +4.41083333333333 0.379512 NA NA +0.283333333333333 NA 14.4476033350557 0.0402521349432851 +1.91666666666667 NA 13.7060223078962 0.376074952331173 +2.7 NA 13.2140232047146 0.631352838619626 +3.61666666666667 NA 12.5559723530953 1.07462832181763 +4.05 NA 12.2401503685218 1.30890601580277 +4.75 NA 10.5748333437957 1.96380525852192 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgM_res/KEIO_ROBOT4_5.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjgM_res/KEIO_ROBOT4_5.pdf new file mode 100644 index 0000000..22d5aad Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjgM_res/KEIO_ROBOT4_5.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgM_res/KEIO_ROBOT4_5_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjgM_res/KEIO_ROBOT4_5_log.txt new file mode 100644 index 0000000..c45194e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjgM_res/KEIO_ROBOT4_5_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.065016 NA NA + [3,] 0.075600 NA NA + [4,] 0.113400 NA NA + [5,] 0.193536 NA NA + [6,] 0.270648 NA NA + [7,] 0.379512 NA NA + [8,] NA 14.44760 0.04025213 + [9,] NA 13.70602 0.37607495 +[10,] NA 13.21402 0.63135284 +[11,] NA 12.55597 1.07462832 +[12,] NA 12.24015 1.30890602 +[13,] NA 10.57483 1.96380526 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0308060 14.3516392 0.0865491 0.5677853 -4.8825486 2.5403242 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.325029e-09 1.434138e-08 -1.656108e-08 -1.137269e-08 1.564294e-08 2.030678e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.003957906 0.207865286 0.090996475 0.032478849 0.524309878 0.231602468 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3097991 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.325029e-09 1.434138e-08 -1.656108e-08 -1.137269e-08 1.564294e-08 2.030678e-08 + +$result$normp +[1] 3.561047e-08 + +$result$res + [1] -0.274099977 -0.214982705 0.070341798 0.216956670 0.276862692 -0.060558210 -0.128036564 -0.309130756 0.269535431 0.381359768 -0.009586875 -0.575257113 0.243079545 0.351764825 -0.090642307 -0.220944838 -0.257617512 0.069497995 0.147941836 + +$result$prevres + [1] -0.274100043 -0.214982794 0.070341703 0.216956575 0.276862636 -0.060558205 -0.128036429 -0.309130784 0.269535430 0.381359780 -0.009586856 -0.575257099 0.243079529 0.351764902 -0.090642276 -0.220944835 -0.257617541 0.069497956 0.147941794 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 98.546299 0.000000 0 3.62780156 0.00000000 0.00000000 + [3,] 124.986750 0.000000 0 6.21295415 0.00000000 0.00000000 + [4,] 191.097732 0.000000 0 13.90139385 0.00000000 0.00000000 + [5,] 323.107931 0.000000 0 32.71160629 0.00000000 0.00000000 + [6,] 437.312282 0.000000 0 51.45495130 0.00000000 0.00000000 + [7,] 611.814715 0.000000 0 83.13346165 0.00000000 0.00000000 + [8,] -3.262779 2.173913 0 -0.01462099 0.02058621 0.00000000 + [9,] -36.810350 2.173913 0 -1.28005315 0.23225158 0.00000000 +[10,] -67.899714 2.173913 0 -3.51854887 0.42840711 0.00000000 +[11,] -127.027547 2.173913 0 -9.34352189 0.80146883 0.00000000 +[12,] -167.676765 2.173913 0 -14.15488904 1.05794140 0.00000000 +[13,] -258.630406 2.173913 0 -26.54811811 1.63180518 0.00000000 +[14,] 3.904434 0.000000 5 0.01749634 0.00000000 0.04734828 +[15,] 44.049436 0.000000 5 1.53178709 0.00000000 0.53417863 +[16,] 81.252802 0.000000 5 4.21050309 0.00000000 0.98533636 +[17,] 152.008654 0.000000 5 11.18100934 0.00000000 1.84337832 +[18,] 200.651906 0.000000 5 16.93857502 0.00000000 2.43326522 +[19,] 309.492396 0.000000 5 31.76904382 0.00000000 3.75315192 + +$result$retres +$result$retres$res + [1] -0.274100043 -0.214982794 0.070341703 0.216956575 0.276862636 -0.060558205 -0.128036429 -0.309130784 0.269535430 0.381359780 -0.009586856 -0.575257099 0.243079529 0.351764902 -0.090642276 -0.220944835 -0.257617541 0.069497956 0.147941794 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03080600 14.35164 0.08654912 + [2,] 0.06071634 14.09443 0.22037077 + [3,] 0.07700683 13.95435 0.29325593 + [4,] 0.11773913 13.60408 0.47549600 + [5,] 0.19907325 12.90466 0.83939239 + [6,] 0.26943684 12.29958 1.15420558 + [7,] 0.37695127 11.37504 1.63523512 + [8,] 0.03618273 14.30540 0.11060512 + [9,] 0.09146576 13.83001 0.35794650 + [10,] 0.14269791 13.38945 0.58716387 + [11,] 0.24013463 12.55156 1.02310481 + [12,] 0.30712046 11.97553 1.32280561 + [13,] 0.45700292 10.68665 1.99339362 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.005482001 NA NA + [2,] 0.004299656 NA NA + [3,] -0.001406834 NA NA + [4,] -0.004339132 NA NA + [5,] -0.005537253 NA NA + [6,] 0.001211164 NA NA + [7,] 0.002560729 NA NA + [8,] NA 0.142200160 -0.07035298 + [9,] NA -0.123986298 0.01812846 +[10,] NA -0.175425499 0.04418897 +[11,] NA 0.004409954 0.05152351 +[12,] NA 0.264618266 -0.01389959 +[13,] NA -0.111816583 -0.02958836 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgM_res/KEIO_ROBOT4_5_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjgM_res/KEIO_ROBOT4_5_res.txt new file mode 100644 index 0000000..ff6f690 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjgM_res/KEIO_ROBOT4_5_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0308060004632028 0.0311109134277678 0.0308650577304097 0.00416169136378312 0.0238709186322632 0.0392864461132094 +Glc 14.3516392444832 14.3481910555123 14.3500982912139 0.212818538758919 14.0008219414895 14.7257412492725 +Ace 0.0865491028334201 0.114992823650505 0.103045272398291 0.0679161020152207 1.0000000000001e-06 0.2495343011576 +mu 0.567785322614211 0.568267775412908 0.567840040418628 0.0317342283577746 0.509423587322513 0.628051156959458 +qGlc -4.88254855279366 -4.87827854844736 -4.90256453153307 0.544016752563431 -5.95014547661064 -4.01303517316957 +qAce 2.54032418071342 2.48001174385021 2.47665415154764 0.232418384058887 2.03332107116475 2.93662580873854 +res 1.24768158245716 32.1098712455226 31.3457933588069 7.01665960067082 20.6434800220657 46.6992167809201 + + +Goodness of fit (khi2 test) + +khi2 value 1.24768158245723 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.0959755063428641 +p-value, i.e. P(X^2<=value) 1.45287027159715e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgR.txt b/validation/validation_results/Berges_2021/Berges_2021/yjgR.txt new file mode 100644 index 0000000..71021df --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjgR.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.160272 NA NA +3.67805555555556 0.261576 NA NA +4.09222222222222 0.35532 NA NA +4.565 0.452088 NA NA +0.05 NA 14.3240305944491 0.0190858599367402 +1.95 NA 14.1909248302424 0.452301978525108 +2.83333333333333 NA 13.5108438732476 0.790423360206847 +3.98333333333333 NA 11.8669482968738 1.51058373812616 +4.88333333333333 NA 9.43833541843536 2.03123542099359 +5.16666666666667 NA 8.53528178650291 2.60494153152395 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgR_res/KEIO_ROBOT3_14.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjgR_res/KEIO_ROBOT3_14.pdf new file mode 100644 index 0000000..b5d35af Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjgR_res/KEIO_ROBOT3_14.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgR_res/KEIO_ROBOT3_14_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjgR_res/KEIO_ROBOT3_14_log.txt new file mode 100644 index 0000000..ee605b0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjgR_res/KEIO_ROBOT3_14_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.160272 NA NA + [2,] 0.261576 NA NA + [3,] 0.355320 NA NA + [4,] 0.452088 NA NA + [5,] NA 14.324031 0.01908586 + [6,] NA 14.190925 0.45230198 + [7,] NA 13.510844 0.79042336 + [8,] NA 11.866948 1.51058374 + [9,] NA 9.438335 2.03123542 +[10,] NA 8.535282 2.60494153 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02957642 14.64711332 0.18586313 0.59902934 -5.86569964 2.30484688 + +$result$lastp + X Glc Ace mu qGlc qAce +-1.240622e-08 -4.165510e-07 -1.404131e-07 9.833879e-08 3.099438e-07 5.464464e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01013093 0.43245487 0.18629393 0.08138649 0.74920650 0.32094946 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6350286 + +$result$laststep + X Glc Ace mu qGlc qAce +-1.240622e-08 -4.165510e-07 -1.404131e-07 9.833879e-08 3.099438e-07 5.464464e-07 + +$result$normp +[1] 7.73126e-07 + +$result$res + [1] 0.27282916 0.31120047 -0.60556953 0.17402779 0.68321129 -0.40339948 -0.33714689 -0.17110749 0.21800651 0.01043607 0.85118639 -0.07135519 -0.48569531 -1.00682391 0.80970641 -0.09701839 + +$result$prevres + [1] 0.27283030 0.31120125 -0.60556924 0.17402712 0.68321219 -0.40339907 -0.33714682 -0.17110786 0.21800598 0.01043559 0.85118710 -0.07135440 -0.48569460 -1.00682369 0.80970550 -0.09701992 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 280.1700806 0.000000 0 2.383960e+01 0.000000000 0.000000000 + [2,] 452.7254311 0.000000 0 4.924917e+01 0.000000000 0.000000000 + [3,] 580.2063249 0.000000 0 7.022430e+01 0.000000000 0.000000000 + [4,] 770.1547631 0.000000 0 1.039835e+02 0.000000000 0.000000000 + [5,] -0.6472203 2.173913 0 -4.809506e-04 0.003263458 0.000000000 + [6,] -47.1697959 2.173913 0 -1.619220e+00 0.237842730 0.000000000 + [7,] -94.9167583 2.173913 0 -5.051446e+00 0.478595686 0.000000000 + [8,] -210.1317209 2.173913 0 -1.688905e+01 1.059540349 0.000000000 + [9,] -375.4822941 2.173913 0 -3.876697e+01 1.893282173 0.000000000 +[10,] -448.8762294 2.173913 0 -4.968358e+01 2.263354028 0.000000000 +[11,] 0.5849276 0.000000 5 4.346607e-04 0.000000000 0.007505953 +[12,] 42.6298657 0.000000 5 1.463376e+00 0.000000000 0.547038278 +[13,] 85.7813476 0.000000 5 4.565261e+00 0.000000000 1.100770079 +[14,] 189.9072674 0.000000 5 1.526354e+01 0.000000000 2.436942803 +[15,] 339.3434181 0.000000 5 3.503578e+01 0.000000000 4.354548997 +[16,] 405.6734402 0.000000 5 4.490171e+01 0.000000000 5.205714264 + +$result$retres +$result$retres$res + [1] 0.27283030 0.31120125 -0.60556924 0.17402712 0.68321219 -0.40339907 -0.33714682 -0.17110786 0.21800598 0.01043559 0.85118710 -0.07135440 -0.48569460 -1.00682369 0.80970550 -0.09701992 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.16572861 13.313910 0.7097273 + [2,] 0.26780002 12.314426 1.1024609 + [3,] 0.34320862 11.576024 1.3926057 + [4,] 0.45556854 10.475795 1.8249258 + [5,] 0.03047569 14.638308 0.1893233 + [6,] 0.09511481 14.005361 0.4380311 + [7,] 0.16145512 13.355756 0.6932844 + [8,] 0.32153643 11.788239 1.3092190 + [9,] 0.55127686 9.538618 2.1931765 + [10,] 0.65325144 8.540082 2.5855375 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.005456606 NA NA + [2,] -0.006224025 NA NA + [3,] 0.012111385 NA NA + [4,] -0.003480542 NA NA + [5,] NA -0.31427761 -0.17023742 + [6,] NA 0.18556357 0.01427088 + [7,] NA 0.15508754 0.09713892 + [8,] NA 0.07870962 0.20136474 + [9,] NA -0.10028275 -0.16194110 +[10,] NA -0.00480037 0.01940398 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjgR_res/KEIO_ROBOT3_14_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjgR_res/KEIO_ROBOT3_14_res.txt new file mode 100644 index 0000000..eb61249 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjgR_res/KEIO_ROBOT3_14_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0295764158833289 0.0295801661526934 0.029601132093086 0.00370800570128125 0.0232884108968434 0.037428690326122 +Glc 14.6471133196899 14.6540232467889 14.6216815046172 0.240145856273933 14.228262828618 15.1318980971381 +Ace 0.18586312533769 0.186114787601695 0.173817843822779 0.10037139193753 0.0119214137263941 0.397866288992325 +mu 0.599029338270931 0.601000631531111 0.601254828162867 0.0262900955306249 0.553551482751716 0.652671077301019 +qGlc -5.86569964037787 -5.86233759270917 -5.88422213359189 0.472310217261048 -6.73798562804155 -4.96887932122344 +qAce 2.30484687578187 2.31142468105014 2.33105171072822 0.198607072016745 1.90967802870555 2.68564605668765 +res 4.03261318322006 24.0241091405851 23.6933863957443 6.93325724630499 13.6013453728124 40.5631698096436 + + +Goodness of fit (khi2 test) + +khi2 value 4.03261318322858 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.403261318322858 +p-value, i.e. P(X^2<=value) 0.0541362506478487 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjhC.txt b/validation/validation_results/Berges_2021/Berges_2021/yjhC.txt new file mode 100644 index 0000000..2504a8f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjhC.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.195 0.069552 NA NA +1.61361111111111 0.089208 NA NA +2.36138888888889 0.142128 NA NA +3.28638888888889 0.23436 NA NA +3.81944444444444 0.328104 NA NA +4.41083333333333 0.452088 NA NA +0.283333333333333 NA 14.3239257508663 0.0424464810222213 +1.91666666666667 NA 14.0354517970522 0.397463085096435 +2.7 NA 13.2991306641651 0.676758743900355 +3.61666666666667 NA 12.4451477913562 1.1302034571788 +4.05 NA 11.717445593621 1.43892358577569 +4.75 NA 10.3058905193315 2.01755243565745 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjhC_res/KEIO_ROBOT4_4.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjhC_res/KEIO_ROBOT4_4.pdf new file mode 100644 index 0000000..edf050b Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjhC_res/KEIO_ROBOT4_4.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjhC_res/KEIO_ROBOT4_4_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjhC_res/KEIO_ROBOT4_4_log.txt new file mode 100644 index 0000000..721c62b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjhC_res/KEIO_ROBOT4_4_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.069552 NA NA + [3,] 0.089208 NA NA + [4,] 0.142128 NA NA + [5,] 0.234360 NA NA + [6,] 0.328104 NA NA + [7,] 0.452088 NA NA + [8,] NA 14.32393 0.04244648 + [9,] NA 14.03545 0.39746309 +[10,] NA 13.29913 0.67675874 +[11,] NA 12.44515 1.13020346 +[12,] NA 11.71745 1.43892359 +[13,] NA 10.30589 2.01755244 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03675297 14.46302478 0.10737112 0.56926054 -4.63301354 2.20060389 + +$result$lastp + X Glc Ace mu qGlc qAce + 8.316844e-09 7.437834e-08 -4.413460e-08 -5.847541e-08 1.241464e-07 -3.597386e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.003321197 0.173492717 0.075644509 0.022842522 0.364376388 0.159460445 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.2591005 + +$result$laststep + X Glc Ace mu qGlc qAce + 8.316844e-09 7.437834e-08 -4.413460e-08 -5.847541e-08 1.241464e-07 -3.597386e-08 + +$result$normp +[1] 1.66358e-07 + +$result$res + [1] -0.05235125 0.15066017 0.14418261 -0.05848094 0.21488938 -0.24185713 0.02840151 0.18857659 -0.35638045 0.15634300 -0.05898430 0.09729293 -0.02684777 0.44895907 -0.04567787 -0.25358573 -0.25743465 -0.24353034 0.35126952 + +$result$prevres + [1] -0.05235167 0.15065960 0.14418200 -0.05848156 0.21488897 -0.24185718 0.02840223 0.18857645 -0.35638044 0.15634308 -0.05898420 0.09729300 -0.02684789 0.44895926 -0.04567785 -0.25358579 -0.25743477 -0.24353044 0.35126959 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 98.720183 0.000000 0 4.33577022 0.00000000 0.00000000 + [3,] 125.284635 0.000000 0 7.43000467 0.00000000 0.00000000 + [4,] 191.764614 0.000000 0 16.64287630 0.00000000 0.00000000 + [5,] 324.678252 0.000000 0 39.21611372 0.00000000 0.00000000 + [6,] 439.783351 0.000000 0 61.73498995 0.00000000 0.00000000 + [7,] 615.808853 0.000000 0 99.82951850 0.00000000 0.00000000 + [8,] -3.096691 2.173913 0 -0.01655669 0.02456556 0.00000000 + [9,] -34.987292 2.173913 0 -1.45207602 0.27754867 0.00000000 +[10,] -64.589653 2.173913 0 -3.99504913 0.51237953 0.00000000 +[11,] -120.960933 2.173913 0 -10.62073431 0.95956400 0.00000000 +[12,] -159.751927 2.173913 0 -16.09854365 1.26728684 0.00000000 +[13,] -246.622163 2.173913 0 -30.22061363 1.95641472 0.00000000 +[14,] 3.383016 0.000000 5 0.01808754 0.00000000 0.05650079 +[15,] 38.222269 0.000000 5 1.58633714 0.00000000 0.63836193 +[16,] 70.561708 0.000000 5 4.36443733 0.00000000 1.17847291 +[17,] 132.145161 0.000000 5 11.60274325 0.00000000 2.20699721 +[18,] 174.522828 0.000000 5 17.58703901 0.00000000 2.91475973 +[19,] 269.425216 0.000000 5 33.01485665 0.00000000 4.49975385 + +$result$retres +$result$retres$res + [1] -0.05235167 0.15065960 0.14418200 -0.05848156 0.21488897 -0.24185718 0.02840223 0.18857645 -0.35638044 0.15634308 -0.05898420 0.09729300 -0.02684789 0.44895926 -0.04567785 -0.25358579 -0.25743477 -0.24353044 0.35126959 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03675297 14.46302 0.1073712 + [2,] 0.07256519 14.17156 0.2458113 + [3,] 0.09209164 14.01264 0.3212952 + [4,] 0.14095837 13.61493 0.5102004 + [5,] 0.23865778 12.81979 0.8878793 + [6,] 0.32326686 12.13119 1.2149546 + [7,] 0.45265604 11.07813 1.7151374 + [8,] 0.04318570 14.41067 0.1322383 + [9,] 0.10943183 13.87152 0.3883275 + [10,] 0.17092461 13.37105 0.6260416 + [11,] 0.28802427 12.41802 1.0787165 + [12,] 0.36860454 11.76220 1.3902175 + [13,] 0.54905948 10.29354 2.0878064 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0010470334 NA NA + [2,] -0.0030131920 NA NA + [3,] -0.0028836400 NA NA + [4,] 0.0011696312 NA NA + [5,] -0.0042977794 NA NA + [6,] 0.0048371436 NA NA + [7,] -0.0005680446 NA NA + [8,] NA -0.08674517 -0.08979185 + [9,] NA 0.16393500 0.00913557 +[10,] NA -0.07191782 0.05071716 +[11,] NA 0.02713273 0.05148695 +[12,] NA -0.04475478 0.04870609 +[13,] NA 0.01235003 -0.07025392 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjhC_res/KEIO_ROBOT4_4_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjhC_res/KEIO_ROBOT4_4_res.txt new file mode 100644 index 0000000..8062390 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjhC_res/KEIO_ROBOT4_4_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0367529749524084 0.036526115896209 0.0357672760996392 0.00410443211257293 0.0296516785738717 0.0438232234350614 +Glc 14.4630247769606 14.4844586519216 14.4600706065583 0.181470363790248 14.1910318759927 14.8759251257544 +Ace 0.107371117683833 0.121323552782122 0.109327000962749 0.0775400639166407 0.0155233533074166 0.295455869554176 +mu 0.569260536227155 0.572561143403753 0.575417979084032 0.0268428178840288 0.522103999763018 0.617251465020131 +qGlc -4.63301354050355 -4.6738107565994 -4.62100424294654 0.488256896901126 -5.65914133071372 -3.90199854346133 +qAce 2.20060388546538 2.19622356591387 2.23390206629695 0.212927121595297 1.75959286429178 2.60215822256696 +res 0.872730231499633 31.5957162165784 31.2543513807985 6.58297280746998 18.3538105817792 43.3674834050313 + + +Goodness of fit (khi2 test) + +khi2 value 0.87273023150168 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.0671330947308984 +p-value, i.e. P(X^2<=value) 1.67195457336893e-06 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjhU.txt b/validation/validation_results/Berges_2021/Berges_2021/yjhU.txt new file mode 100644 index 0000000..41b597b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjhU.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.195 0.06804 NA NA +1.61361111111111 0.086184 NA NA +2.36138888888889 0.130032 NA NA +3.28638888888889 0.207144 NA NA +3.81944444444444 0.303912 NA NA +4.41083333333333 0.40068 NA NA +0.283333333333333 NA 14.2827094622355 0.0443724387172147 +1.91666666666667 NA 13.771767092751 0.35957383264004 +2.7 NA 13.6090739301599 0.662578405109277 +3.61666666666667 NA 12.4894674024543 1.1119015055361 +4.05 NA 12.0346244824963 1.35310756356421 +4.75 NA 10.6785360020135 1.88549375503308 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjhU_res/KEIO_ROBOT4_6.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjhU_res/KEIO_ROBOT4_6.pdf new file mode 100644 index 0000000..06559af Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjhU_res/KEIO_ROBOT4_6.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjhU_res/KEIO_ROBOT4_6_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjhU_res/KEIO_ROBOT4_6_log.txt new file mode 100644 index 0000000..7ee5c43 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjhU_res/KEIO_ROBOT4_6_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.068040 NA NA + [3,] 0.086184 NA NA + [4,] 0.130032 NA NA + [5,] 0.207144 NA NA + [6,] 0.303912 NA NA + [7,] 0.400680 NA NA + [8,] NA 14.28271 0.04437244 + [9,] NA 13.77177 0.35957383 +[10,] NA 13.60907 0.66257841 +[11,] NA 12.48947 1.11190151 +[12,] NA 12.03462 1.35310756 +[13,] NA 10.67854 1.88549376 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03591989 14.39852459 0.10036991 0.54828914 -4.48426116 2.26676396 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.459133e-08 -4.462340e-08 -2.981245e-07 -1.091387e-07 6.430676e-07 5.804085e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.004670368 0.235035359 0.102672765 0.033026231 0.536936738 0.236070951 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3480511 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.459133e-08 -4.462340e-08 -2.981245e-07 -1.091387e-07 6.430676e-07 5.804085e-07 + +$result$normp +[1] 9.237984e-07 + +$result$res + [1] -0.09400555 0.05625594 0.04127190 0.05375816 0.52850223 -0.61460780 0.13145273 0.14443837 0.17451927 -0.45175338 0.14943767 -0.10600278 0.08936086 0.40477715 0.08518680 -0.29050831 -0.40632134 -0.16576750 0.37263320 + +$result$prevres + [1] -0.09400628 0.05625499 0.04127090 0.05375719 0.52850171 -0.61460765 0.13145424 0.14443849 0.17451953 -0.45175311 0.14943778 -0.10600286 0.08936017 0.40477856 0.08518755 -0.29050803 -0.40632173 -0.16576824 0.37263189 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 96.276923 0.000000 0 4.13261471 0.00000000 0.00000000 + [3,] 121.115983 0.000000 0 7.01996819 0.00000000 0.00000000 + [4,] 182.499446 0.000000 0 15.47974762 0.00000000 0.00000000 + [5,] 303.055116 0.000000 0 35.77464915 0.00000000 0.00000000 + [6,] 405.931050 0.000000 0 55.69129023 0.00000000 0.00000000 + [7,] 561.401023 0.000000 0 88.94645775 0.00000000 0.00000000 + [8,] -2.988140 2.173913 0 -0.01559913 0.02393563 0.00000000 + [9,] -33.073525 2.173913 0 -1.33432605 0.26492585 0.00000000 +[10,] -60.355174 2.173913 0 -3.62377544 0.48345756 0.00000000 +[11,] -111.378079 2.173913 0 -9.48223740 0.89216170 0.00000000 +[12,] -146.017109 2.173913 0 -14.26244929 1.16962757 0.00000000 +[13,] -222.650323 2.173913 0 -26.43561006 1.78347563 0.00000000 +[14,] 3.474114 0.000000 5 0.01813608 0.00000000 0.05505194 +[15,] 38.452408 0.000000 5 1.55133299 0.00000000 0.60932945 +[16,] 70.170985 0.000000 5 4.21312496 0.00000000 1.11195240 +[17,] 129.491955 0.000000 5 11.02437271 0.00000000 2.05197191 +[18,] 169.764473 0.000000 5 16.58201014 0.00000000 2.69014341 +[19,] 258.860861 0.000000 5 30.73494217 0.00000000 4.10199394 + +$result$retres +$result$retres$res + [1] -0.09400628 0.05625499 0.04127090 0.05375719 0.52850171 -0.61460765 0.13145424 0.14443849 0.17451953 -0.45175311 0.14943778 -0.10600286 0.08936017 0.40477856 0.08518755 -0.29050803 -0.40632173 -0.16576824 0.37263189 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03591987 14.39852 0.1003702 + [2,] 0.06916510 14.12662 0.2378142 + [3,] 0.08700942 13.98068 0.3115870 + [4,] 0.13110714 13.62002 0.4938979 + [5,] 0.21771403 12.91170 0.8519522 + [6,] 0.29161985 12.30725 1.1574971 + [7,] 0.40330908 11.39378 1.6192481 + [8,] 0.04195675 14.34915 0.1253282 + [9,] 0.10273763 13.85205 0.3766113 + [10,] 0.15785418 13.40127 0.6044768 + [11,] 0.26093470 12.55821 1.0306372 + [12,] 0.33091521 11.98586 1.3199539 + [13,] 0.48573571 10.71964 1.9600201 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0018801256 NA NA + [2,] -0.0011250997 NA NA + [3,] -0.0008254181 NA NA + [4,] -0.0010751437 NA NA + [5,] -0.0105700342 NA NA + [6,] 0.0122921530 NA NA + [7,] -0.0026290848 NA NA + [8,] NA -0.06644171 -0.08095571 + [9,] NA -0.08027898 -0.01703751 +[10,] NA 0.20780643 0.05810161 +[11,] NA -0.06874138 0.08126435 +[12,] NA 0.04876132 0.03315365 +[13,] NA -0.04110568 -0.07452638 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjhU_res/KEIO_ROBOT4_6_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjhU_res/KEIO_ROBOT4_6_res.txt new file mode 100644 index 0000000..a51d628 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjhU_res/KEIO_ROBOT4_6_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0359198890272431 0.0350468003415863 0.0349288386577567 0.0042081853586445 0.0278840956698534 0.0445265701803803 +Glc 14.3985245860431 14.399545858305 14.3753716972927 0.235348659152356 13.8948332324753 14.8837563037756 +Ace 0.100369908162001 0.132650618784782 0.1274691428946 0.082634292380655 9.99999999998766e-07 0.310716074616334 +mu 0.548289136309997 0.555794961063805 0.556726588774 0.0292009008214475 0.492348532639203 0.608333967799715 +qGlc -4.48426115897039 -4.51870903173034 -4.5491447763775 0.52725195083409 -5.4527541563245 -3.54310623567573 +qAce 2.26676395556563 2.21788696199966 2.23555101356933 0.256744855896495 1.66533260128997 2.72086593768665 +res 1.57481417314099 32.9886853377102 31.8888448496007 7.71255793671661 22.0061008644123 50.6297844757425 + + +Goodness of fit (khi2 test) + +khi2 value 1.57481417315287 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.12113955178099 +p-value, i.e. P(X^2<=value) 5.73718133178989e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjjA.txt b/validation/validation_results/Berges_2021/Berges_2021/yjjA.txt new file mode 100644 index 0000000..8f4dd32 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjjA.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.195 0.069552 NA NA +1.61361111111111 0.078624 NA NA +2.36138888888889 0.119448 NA NA +3.28638888888889 0.199584 NA NA +3.81944444444444 0.258552 NA NA +4.41083333333333 0.391608 NA NA +0.283333333333333 NA 14.7268995255352 0.048785976122723 +1.91666666666667 NA 13.6143971840184 0.371287038524459 +2.7 NA 13.1519126457566 0.62514944144353 +3.61666666666667 NA 13.0023993561484 1.11295957806906 +4.05 NA 12.0957443660908 1.37095920429961 +4.75 NA 10.5814554662605 1.42063869682816 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjjA_res/KEIO_ROBOT4_1.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjjA_res/KEIO_ROBOT4_1.pdf new file mode 100644 index 0000000..d806ae9 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjjA_res/KEIO_ROBOT4_1.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjjA_res/KEIO_ROBOT4_1_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjjA_res/KEIO_ROBOT4_1_log.txt new file mode 100644 index 0000000..1c9c3bc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjjA_res/KEIO_ROBOT4_1_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.069552 NA NA + [3,] 0.078624 NA NA + [4,] 0.119448 NA NA + [5,] 0.199584 NA NA + [6,] 0.258552 NA NA + [7,] 0.391608 NA NA + [8,] NA 14.72690 0.04878598 + [9,] NA 13.61440 0.37128704 +[10,] NA 13.15191 0.62514944 +[11,] NA 13.00240 1.11295958 +[12,] NA 12.09574 1.37095920 +[13,] NA 10.58146 1.42063870 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03308111 14.49264735 0.19496261 0.55282546 -4.94086868 1.90906270 + +$result$lastp + X Glc Ace mu qGlc qAce + 4.685362e-09 5.064473e-08 -7.338701e-08 -3.787139e-08 4.662792e-08 1.450748e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01018404 0.51693121 0.22397607 0.07811890 1.27009076 0.54773417 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7647939 + +$result$laststep + X Glc Ace mu qGlc qAce + 4.685362e-09 5.064473e-08 -7.338701e-08 -3.787139e-08 4.662792e-08 1.450748e-07 + +$result$normp +[1] 1.806311e-07 + +$result$res + [1] -0.2359444 -0.2753406 0.1048864 0.1299021 0.1967759 0.7357398 -0.6332949 -0.6182321 0.6975623 0.6979638 -0.8639353 -0.1777209 0.2643622 0.8277387 0.1951694 -0.1810209 -0.9431991 -1.0914454 1.1927572 + +$result$prevres + [1] -0.2359447 -0.2753409 0.1048860 0.1299018 0.1967757 0.7357399 -0.6332944 -0.6182322 0.6975623 0.6979639 -0.8639352 -0.1777209 0.2643621 0.8277391 0.1951696 -0.1810209 -0.9431992 -1.0914456 1.1927569 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 96.800240 0.000000 0 3.82669960 0.00000000 0.00000000 + [3,] 122.005774 0.000000 0 6.51267326 0.00000000 0.00000000 + [4,] 184.464861 0.000000 0 14.40990758 0.00000000 0.00000000 + [5,] 307.606871 0.000000 0 33.44221360 0.00000000 0.00000000 + [6,] 413.025476 0.000000 0 52.18636757 0.00000000 0.00000000 + [7,] 572.747028 0.000000 0 83.57252490 0.00000000 0.00000000 + [8,] -3.294577 2.173913 0 -0.01584291 0.02205852 0.00000000 + [9,] -36.627465 2.173913 0 -1.36251599 0.24523563 0.00000000 +[10,] -67.007330 2.173913 0 -3.71071127 0.44864107 0.00000000 +[11,] -124.046777 2.173913 0 -9.74299226 0.83054315 0.00000000 +[12,] -162.883892 2.173913 0 -14.67906570 1.09057328 0.00000000 +[13,] -249.031232 2.173913 0 -27.28257462 1.66736443 0.00000000 +[14,] 2.927820 0.000000 5 0.01407925 0.00000000 0.05073459 +[15,] 32.550041 0.000000 5 1.21083869 0.00000000 0.56404196 +[16,] 59.547975 0.000000 5 3.29762938 0.00000000 1.03187447 +[17,] 110.237705 0.000000 5 8.65838790 0.00000000 1.91024924 +[18,] 144.751415 0.000000 5 13.04497031 0.00000000 2.50831854 +[19,] 221.308706 0.000000 5 24.24543791 0.00000000 3.83493820 + +$result$retres +$result$retres$res + [1] -0.2359447 -0.2753409 0.1048860 0.1299018 0.1967757 0.7357399 -0.6332944 -0.6182322 0.6975623 0.6979639 -0.8639352 -0.1777209 0.2643621 0.8277391 0.1951696 -0.1810209 -0.9431992 -1.0914456 1.1927569 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03308111 14.49265 0.1949627 + [2,] 0.06404518 14.21591 0.3018904 + [3,] 0.08072172 14.06686 0.3594792 + [4,] 0.12204604 13.69752 0.5021837 + [5,] 0.20351951 12.96936 0.7835346 + [6,] 0.27326680 12.34599 1.0243917 + [7,] 0.37894211 11.40152 1.3893184 + [8,] 0.03869058 14.44251 0.2143338 + [9,] 0.09544446 13.93528 0.4103210 + [10,] 0.14717041 13.47298 0.5889453 + [11,] 0.24428800 12.60499 0.9243197 + [12,] 0.31041360 12.01399 1.1526701 + [13,] 0.45709143 10.70306 1.6591901 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.004718893 NA NA + [2,] 0.005506818 NA NA + [3,] -0.002097721 NA NA + [4,] -0.002598035 NA NA + [5,] -0.003935515 NA NA + [6,] -0.014714797 NA NA + [7,] 0.012665888 NA NA + [8,] NA 0.2843868 -0.16554781 + [9,] NA -0.3208787 -0.03903393 +[10,] NA -0.3210634 0.03620417 +[11,] NA 0.3974102 0.18863983 +[12,] NA 0.0817516 0.21828911 +[13,] NA -0.1216066 -0.23855138 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjjA_res/KEIO_ROBOT4_1_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjjA_res/KEIO_ROBOT4_1_res.txt new file mode 100644 index 0000000..8a121d6 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjjA_res/KEIO_ROBOT4_1_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0330811114776679 0.0334707716498514 0.0328602764720495 0.00420494334958804 0.0261137253786152 0.0426979995380011 +Glc 14.4926473467723 14.4726555265924 14.4686320352198 0.200856257147792 14.1116520807417 14.8479081213642 +Ace 0.194962613452308 0.199357537516703 0.197431866474525 0.0769837861285357 0.0565128391481121 0.371548543318613 +mu 0.552825458366717 0.550933437522473 0.552144694650531 0.0286911437466585 0.491196841828976 0.608123254004277 +qGlc -4.94086868196499 -4.90078588441727 -4.82367181945656 0.58085577323334 -5.9439180071101 -4.07266505980009 +qAce 1.90906270414612 1.89487269700457 1.87896487274151 0.241357854275443 1.4292337139347 2.35132360954785 +res 7.60382643487859 32.8142148202921 32.9192541724711 7.10228267080002 19.1521398780532 47.9691024526976 + + +Goodness of fit (khi2 test) + +khi2 value 7.60382643487961 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.58490972575997 +p-value, i.e. P(X^2<=value) 0.131581197770469 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjjV.txt b/validation/validation_results/Berges_2021/Berges_2021/yjjV.txt new file mode 100644 index 0000000..470093d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjjV.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.17388 NA NA +3.67805555555556 0.250992 NA NA +4.09222222222222 0.328104 NA NA +4.565 0.40068 NA NA +0.05 NA 14.2184598326757 0.0195619228705754 +1.95 NA 13.7939260960113 0.449797129977092 +2.83333333333333 NA 13.6662179958184 0.74767558187474 +3.98333333333333 NA 11.2765990976244 1.43204612449238 +4.88333333333333 NA 9.18929625610824 2.22854704573432 +5.16666666666667 NA 8.56358929312523 2.48828726101493 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjjV_res/KEIO_ROBOT3_34.pdf b/validation/validation_results/Berges_2021/Berges_2021/yjjV_res/KEIO_ROBOT3_34.pdf new file mode 100644 index 0000000..64cf04e Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yjjV_res/KEIO_ROBOT3_34.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjjV_res/KEIO_ROBOT3_34_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yjjV_res/KEIO_ROBOT3_34_log.txt new file mode 100644 index 0000000..5f21c39 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjjV_res/KEIO_ROBOT3_34_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.173880 NA NA + [2,] 0.250992 NA NA + [3,] 0.328104 NA NA + [4,] 0.400680 NA NA + [5,] NA 14.218460 0.01956192 + [6,] NA 13.793926 0.44979713 + [7,] NA 13.666218 0.74767558 + [8,] NA 11.276599 1.43204612 + [9,] NA 9.189296 2.22854705 +[10,] NA 8.563589 2.48828726 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.04006587 14.59196615 0.09760636 0.50651298 -6.08584664 2.44980051 + +$result$lastp + X Glc Ace mu qGlc qAce + 7.410771e-09 2.813739e-07 4.053995e-08 -4.527772e-08 -3.252465e-07 -2.025129e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01284677 0.42731950 0.18426858 0.07687684 0.75730997 0.32471461 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6005901 + +$result$laststep + X Glc Ace mu qGlc qAce + 7.410771e-09 2.813739e-07 4.053995e-08 -4.527772e-08 -3.252465e-07 -2.025129e-07 + +$result$normp +[1] 4.792875e-07 + +$result$res + [1] -0.09193606 0.35747157 -0.48551907 0.19311882 0.78512802 -0.02856987 -1.33652125 0.38367025 0.37600998 -0.17971713 0.41507390 -0.12828490 -0.14968046 -0.35456776 -0.12885919 0.34631840 + +$result$prevres + [1] -0.09193653 0.35747133 -0.48551906 0.19311926 0.78512741 -0.02857015 -1.33652133 0.38367046 0.37601035 -0.17971674 0.41507370 -0.12828518 -0.14968074 -0.35456786 -0.12885887 0.34631895 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 214.6980977 0.000000 0 2.474766e+01 0.000000000 0.00000000 + [2,] 322.1463864 0.000000 0 4.747293e+01 0.000000000 0.00000000 + [3,] 397.3378278 0.000000 0 6.514687e+01 0.000000000 0.00000000 + [4,] 504.8467783 0.000000 0 9.233680e+01 0.000000000 0.00000000 + [5,] -0.6699527 2.173913 0 -6.738882e-04 0.004410599 0.00000000 + [6,] -44.0135147 2.173913 0 -1.997890e+00 0.289760722 0.00000000 + [7,] -83.5877947 2.173913 0 -5.842110e+00 0.550295971 0.00000000 + [8,] -170.3108075 2.173913 0 -1.787769e+01 1.121232489 0.00000000 + [9,] -283.7559007 2.173913 0 -3.818327e+01 1.868092457 0.00000000 +[10,] -331.5761578 2.173913 0 -4.781746e+01 2.182914673 0.00000000 +[11,] 0.6202714 0.000000 5 6.239151e-04 0.000000000 0.01014438 +[12,] 40.7496294 0.000000 5 1.849734e+00 0.000000000 0.66644966 +[13,] 77.3892219 0.000000 5 5.408880e+00 0.000000000 1.26568073 +[14,] 157.6811654 0.000000 5 1.655194e+01 0.000000000 2.57883473 +[15,] 262.7135750 0.000000 5 3.535174e+01 0.000000000 4.29661265 +[16,] 306.9876523 0.000000 5 4.427149e+01 0.000000000 5.02070375 + +$result$retres +$result$retres$res + [1] -0.09193653 0.35747133 -0.48551906 0.19311926 0.78512741 -0.02857015 -1.33652133 0.38367046 0.37601035 -0.17971674 0.41507370 -0.12828518 -0.14968074 -0.35456786 -0.12885887 0.34631895 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.17204127 13.006257 0.7359185 + [2,] 0.25814143 11.971748 1.1523505 + [3,] 0.31839362 11.247807 1.4437663 + [4,] 0.40454239 10.212714 1.8604334 + [5,] 0.04109351 14.579618 0.1025767 + [6,] 0.10757894 13.780784 0.4241401 + [7,] 0.16828261 13.051418 0.7177394 + [8,] 0.30130853 11.453088 1.3611326 + [9,] 0.47532391 9.362261 2.2027753 + [10,] 0.54867623 8.480920 2.5575511 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.001838731 NA NA + [2,] -0.007149427 NA NA + [3,] 0.009710381 NA NA + [4,] -0.003862385 NA NA + [5,] NA -0.36115861 -0.08301474 + [6,] NA 0.01314227 0.02565704 + [7,] NA 0.61479981 0.02993615 + [8,] NA -0.17648841 0.07091357 + [9,] NA -0.17296476 0.02577177 +[10,] NA 0.08266970 -0.06926379 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yjjV_res/KEIO_ROBOT3_34_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yjjV_res/KEIO_ROBOT3_34_res.txt new file mode 100644 index 0000000..92758ee --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yjjV_res/KEIO_ROBOT3_34_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0400658652785982 0.0397350676862337 0.0388183986633998 0.00532586188289853 0.0308471353340554 0.0512694627398342 +Glc 14.5919661496607 14.5927228806907 14.6078904027059 0.242404618507856 14.108849784293 15.0063634237419 +Ace 0.0976063618335788 0.110264679503818 0.10544401403545 0.0903949057472699 9.99999999994061e-07 0.316713201607873 +mu 0.506512981763243 0.510409321798609 0.511735713134559 0.0286586627570808 0.455307366354209 0.563207430892405 +qGlc -6.08584663535571 -6.11204678350891 -6.14817666132768 0.476134999509629 -7.02484197310014 -5.21252466369645 +qAce 2.44980051469618 2.45416411252234 2.4551001279112 0.200816122749728 2.03057834789276 2.77931519730483 +res 3.60708473841952 24.0729465678032 23.1997685380243 6.78856830932765 13.6071000551314 36.9265197088049 + + +Goodness of fit (khi2 test) + +khi2 value 3.60708473842131 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.360708473842131 +p-value, i.e. P(X^2<=value) 0.0366633350172238 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ykgE.txt b/validation/validation_results/Berges_2021/Berges_2021/ykgE.txt new file mode 100644 index 0000000..af9f347 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ykgE.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.195 0.061992 NA NA +1.61361111111111 0.074088 NA NA +2.36138888888889 0.101304 NA NA +3.28638888888889 0.152712 NA NA +3.81944444444444 0.19656 NA NA +4.41083333333333 0.27972 NA NA +0.283333333333333 NA 14.1593961585884 0.0481690115701082 +1.91666666666667 NA 13.7979001787151 0.402307986864453 +2.7 NA 13.8758350689874 0.700593449659948 +3.61666666666667 NA 12.7196996718939 1.19159009024844 +4.05 NA 12.2513454648613 1.48469092360463 +4.75 NA 11.5809690407766 2.09040369206891 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ykgE_res/KEIO_ROBOT4_29.pdf b/validation/validation_results/Berges_2021/Berges_2021/ykgE_res/KEIO_ROBOT4_29.pdf new file mode 100644 index 0000000..d776660 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ykgE_res/KEIO_ROBOT4_29.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ykgE_res/KEIO_ROBOT4_29_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ykgE_res/KEIO_ROBOT4_29_log.txt new file mode 100644 index 0000000..f6db177 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ykgE_res/KEIO_ROBOT4_29_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.061992 NA NA + [3,] 0.074088 NA NA + [4,] 0.101304 NA NA + [5,] 0.152712 NA NA + [6,] 0.196560 NA NA + [7,] 0.279720 NA NA + [8,] NA 14.15940 0.04816901 + [9,] NA 13.79790 0.40230799 +[10,] NA 13.87584 0.70059345 +[11,] NA 12.71970 1.19159009 +[12,] NA 12.25135 1.48469092 +[13,] NA 11.58097 2.09040369 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03287806 14.33553897 0.04833327 0.47889826 -4.70279855 3.46957191 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.582586e-08 1.065663e-08 -1.691965e-07 -1.302932e-07 6.564845e-07 1.123977e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.005393114 0.247929155 0.110448700 0.042387704 0.758374296 0.350943681 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3552906 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.582586e-08 1.065663e-08 -1.691965e-07 -1.302932e-07 6.564845e-07 1.123977e-07 + +$result$normp +[1] 6.996949e-07 + +$result$res + [1] -0.17049679 -0.18609497 -0.14415641 0.02816361 0.29651197 0.41094619 -0.39491843 0.28091923 0.11315770 -0.85626371 0.24753505 0.35079650 -0.13614477 0.17390140 0.02137516 -0.11256381 -0.17574918 -0.08879156 0.18182799 + +$result$prevres + [1] -0.17049759 -0.18609592 -0.14415738 0.02816273 0.29651155 0.41094635 -0.39491716 0.28091924 0.11315788 -0.85626349 0.24753516 0.35079647 -0.13614526 0.17390216 0.02137534 -0.11256391 -0.17574952 -0.08879191 0.18182784 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 88.615482 0.000000 0 3.48163738 0.00000000 0.00000000 + [3,] 108.286313 0.000000 0 5.74484705 0.00000000 0.00000000 + [4,] 154.916821 0.000000 0 12.02741015 0.00000000 0.00000000 + [5,] 241.258589 0.000000 0 26.06800326 0.00000000 0.00000000 + [6,] 311.421963 0.000000 0 39.10708677 0.00000000 0.00000000 + [7,] 413.378639 0.000000 0 59.94800122 0.00000000 0.00000000 + [8,] -3.102370 2.173913 0 -0.01477666 0.02168918 0.00000000 + [9,] -32.107200 2.173913 0 -1.16426914 0.22446675 0.00000000 +[10,] -56.439474 2.173913 0 -3.03047514 0.39457772 0.00000000 +[11,] -99.311215 2.173913 0 -7.52938599 0.69430116 0.00000000 +[12,] -127.138293 2.173913 0 -11.04335395 0.88884487 0.00000000 +[13,] -186.274461 2.173913 0 -19.63614320 1.30227561 0.00000000 +[14,] 5.264303 0.000000 5 0.02507400 0.00000000 0.04988512 +[15,] 54.481582 0.000000 5 1.97560750 0.00000000 0.51627353 +[16,] 95.770166 0.000000 5 5.14230705 0.00000000 0.90752875 +[17,] 168.517720 0.000000 5 12.77635117 0.00000000 1.59689266 +[18,] 215.736514 0.000000 5 18.73908024 0.00000000 2.04434320 +[19,] 316.082604 0.000000 5 33.31988313 0.00000000 2.99523391 + +$result$retres +$result$retres$res + [1] -0.17049759 -0.18609592 -0.14415738 0.02816273 0.29651155 0.41094635 -0.39491716 0.28091924 0.11315788 -0.85626349 0.24753516 0.35079647 -0.13614526 0.17390216 0.02137534 -0.11256391 -0.17574952 -0.08879191 0.18182784 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03287805 14.33554 0.04833344 + [2,] 0.05827008 14.08619 0.23229623 + [3,] 0.07120485 13.95917 0.32600737 + [4,] 0.10186725 13.65806 0.54815346 + [5,] 0.15864223 13.10053 0.95948260 + [6,] 0.20477893 12.64747 1.29373843 + [7,] 0.27182166 11.98910 1.77945642 + [8,] 0.03765603 14.28862 0.08294944 + [9,] 0.08232656 13.84995 0.40658306 + [10,] 0.11980086 13.48195 0.67808067 + [11,] 0.18582791 12.83357 1.15644019 + [12,] 0.22868458 12.41271 1.46693254 + [13,] 0.31976059 11.51834 2.12676926 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0034099517 NA NA + [2,] 0.0037219184 NA NA + [3,] 0.0028831476 NA NA + [4,] -0.0005632545 NA NA + [5,] -0.0059302310 NA NA + [6,] -0.0082189271 NA NA + [7,] 0.0078983432 NA NA + [8,] NA -0.12922285 -0.034780432 + [9,] NA -0.05205263 -0.004275069 +[10,] NA 0.39388121 0.022512783 +[11,] NA -0.11386618 0.035149904 +[12,] NA -0.16136637 0.017758382 +[13,] NA 0.06262682 -0.036365568 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ykgE_res/KEIO_ROBOT4_29_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ykgE_res/KEIO_ROBOT4_29_res.txt new file mode 100644 index 0000000..dfe894b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ykgE_res/KEIO_ROBOT4_29_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0328780641141495 0.0329446000326248 0.0329378127326288 0.00451286267490989 0.0258722572595884 0.0422115855408714 +Glc 14.3355389657203 14.3121027341477 14.3019013103215 0.215356687120695 13.9194740857305 14.7057673888928 +Ace 0.0483332695064938 0.0697930727519941 0.0534462698162151 0.0647041836870012 9.99999999994061e-07 0.201446682887364 +mu 0.478898256511836 0.479811705414341 0.484278132815448 0.0339312936415401 0.411597654384729 0.535297827368604 +qGlc -4.70279854894383 -4.60732412783658 -4.59926160695744 0.73092812416535 -6.34567956707707 -3.39502518844248 +qAce 3.46957190883001 3.43729509090145 3.43106393856805 0.292978476832772 2.89245378656648 3.92945420933562 +res 1.64100878088593 31.6047130883827 30.9674090595517 7.80942310244318 19.457535830712 47.4459401242984 + + +Goodness of fit (khi2 test) + +khi2 value 1.64100878089244 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.126231444684034 +p-value, i.e. P(X^2<=value) 7.28850978542766e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ykgG.txt b/validation/validation_results/Berges_2021/Berges_2021/ykgG.txt new file mode 100644 index 0000000..faa190c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ykgG.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.195 0.061992 NA NA +1.61361111111111 0.074088 NA NA +2.36138888888889 0.10584 NA NA +3.28638888888889 0.182952 NA NA +3.81944444444444 0.27972 NA NA +4.41083333333333 0.397656 NA NA +0.283333333333333 NA 14.3045842150125 0.0365469407387741 +1.91666666666667 NA 13.9649044992727 0.376279830836948 +2.7 NA 13.4137964341271 0.638528516633187 +3.61666666666667 NA 12.3966379718939 0.964351715607452 +4.05 NA 12.041288163394 1.2213030239497 +4.75 NA 10.4940405095319 1.85496527217179 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ykgG_res/KEIO_ROBOT4_7.pdf b/validation/validation_results/Berges_2021/Berges_2021/ykgG_res/KEIO_ROBOT4_7.pdf new file mode 100644 index 0000000..1eac882 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ykgG_res/KEIO_ROBOT4_7.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ykgG_res/KEIO_ROBOT4_7_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ykgG_res/KEIO_ROBOT4_7_log.txt new file mode 100644 index 0000000..bdebd60 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ykgG_res/KEIO_ROBOT4_7_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.061992 NA NA + [3,] 0.074088 NA NA + [4,] 0.105840 NA NA + [5,] 0.182952 NA NA + [6,] 0.279720 NA NA + [7,] 0.397656 NA NA + [8,] NA 14.30458 0.03654694 + [9,] NA 13.96490 0.37627983 +[10,] NA 13.41380 0.63852852 +[11,] NA 12.39664 0.96435172 +[12,] NA 12.04129 1.22130302 +[13,] NA 10.49404 1.85496527 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02637186 14.37288042 0.11890114 0.61322328 -5.17374877 2.35434845 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.131268e-09 -2.578519e-08 2.002805e-08 2.082797e-08 -3.750145e-08 -9.697799e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.004392026 0.250913379 0.109284285 0.041703057 0.645797993 0.281875711 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3806408 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.131268e-09 -2.578519e-08 2.002805e-08 2.082797e-08 -3.750145e-08 -9.697799e-09 + +$result$normp +[1] 5.481562e-08 + +$result$res + [1] -0.49580709 -0.35573636 -0.15751734 0.31841020 0.74567636 -0.26760754 -0.16758087 0.05668736 -0.19620926 0.03567530 0.33603200 -0.24409752 0.01191213 0.50783350 -0.15327426 -0.45328829 -0.08244339 0.04850246 0.13266998 + +$result$prevres + [1] -0.49580698 -0.35573621 -0.15751717 0.31841038 0.74567648 -0.26760753 -0.16758109 0.05668740 -0.19620926 0.03567527 0.33603197 -0.24409754 0.01191216 0.50783341 -0.15327430 -0.45328829 -0.08244335 0.04850251 0.13267001 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 104.045136 0.000000 0 3.27891723 0.00000000 0.00000000 + [3,] 134.494980 0.000000 0 5.72328954 0.00000000 0.00000000 + [4,] 212.742305 0.000000 0 13.24836072 0.00000000 0.00000000 + [5,] 375.145186 0.000000 0 32.51315391 0.00000000 0.00000000 + [6,] 520.190546 0.000000 0 52.39663792 0.00000000 0.00000000 + [7,] 747.585441 0.000000 0 86.96054475 0.00000000 0.00000000 + [8,] -3.480326 2.173913 0 -0.01337888 0.01774007 0.00000000 + [9,] -41.070803 2.173913 0 -1.23678256 0.20934791 0.00000000 +[10,] -77.707448 2.173913 0 -3.49722017 0.39609383 0.00000000 +[11,] -150.165641 2.173913 0 -9.61396764 0.76543093 0.00000000 +[12,] -201.456262 2.173913 0 -14.81201015 1.02687175 0.00000000 +[13,] -319.292930 2.173913 0 -28.56290317 1.62751401 0.00000000 +[14,] 3.642614 0.000000 5 0.01400274 0.00000000 0.04080216 +[15,] 42.985942 0.000000 5 1.29445392 0.00000000 0.48150020 +[16,] 81.330959 0.000000 5 3.66029609 0.00000000 0.91101582 +[17,] 157.167889 0.000000 5 10.06226847 0.00000000 1.76049115 +[18,] 210.850199 0.000000 5 15.50269652 0.00000000 2.36180503 +[19,] 334.181609 0.000000 5 29.89479585 0.00000000 3.74328223 + +$result$retres +$result$retres$res + [1] -0.49580698 -0.35573621 -0.15751717 0.31841038 0.74567648 -0.26760753 -0.16758109 0.05668740 -0.19620926 0.03567527 0.33603197 -0.24409754 0.01191216 0.50783341 -0.15327430 -0.45328829 -0.08244335 0.04850251 0.13267001 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02637186 14.37288 0.1189011 + [2,] 0.05487728 14.13238 0.2283420 + [3,] 0.07093766 13.99688 0.2900026 + [4,] 0.11220821 13.64868 0.4484527 + [5,] 0.19786553 12.92599 0.7773169 + [6,] 0.27436785 12.28054 1.0710323 + [7,] 0.39430438 11.26864 1.5315047 + [8,] 0.03137603 14.33066 0.1381136 + [9,] 0.08542528 13.87465 0.3456250 + [10,] 0.13810308 13.43021 0.5478709 + [11,] 0.24228668 12.55121 0.9478630 + [12,] 0.31603462 11.92900 1.2310035 + [13,] 0.48546541 10.49952 1.8814993 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.009916140 NA NA + [2,] 0.007114724 NA NA + [3,] 0.003150343 NA NA + [4,] -0.006368208 NA NA + [5,] -0.014913530 NA NA + [6,] 0.005352151 NA NA + [7,] 0.003351622 NA NA + [8,] NA -0.026076206 -0.101566682 + [9,] NA 0.090256260 0.030654859 +[10,] NA -0.016410626 0.090657658 +[11,] NA -0.154574705 0.016488669 +[12,] NA 0.112284870 -0.009700502 +[13,] NA -0.005479592 -0.026534002 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ykgG_res/KEIO_ROBOT4_7_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ykgG_res/KEIO_ROBOT4_7_res.txt new file mode 100644 index 0000000..7614328 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ykgG_res/KEIO_ROBOT4_7_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.026371858291114 0.0270053744466672 0.0271471518159053 0.00353102863488198 0.0198618193079481 0.0333733738866969 +Glc 14.3728804214466 14.3338907132279 14.3239903311724 0.185741461057941 13.9972870133518 14.6974500319623 +Ace 0.118901141887782 0.135177589289411 0.131148649601675 0.0823455049080079 0.00557108016015015 0.305661387202953 +mu 0.613223280853282 0.609942286425093 0.606840319722107 0.0317979637667382 0.556283420146158 0.677796587321749 +qGlc -5.17374877315302 -5.06611997647168 -5.01225776104809 0.520020190498221 -6.06975488278972 -4.09092599692535 +qAce 2.35434844909562 2.32201262054134 2.28918038540119 0.252603535199448 1.81692449748129 2.82000497007603 +res 1.88353630058523 31.5984699618886 29.9732156208574 7.90743487066241 20.096691996543 48.4452540538884 + + +Goodness of fit (khi2 test) + +khi2 value 1.88353630058542 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.14488740773734 +p-value, i.e. P(X^2<=value) 0.000160983887933723 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ymbA.txt b/validation/validation_results/Berges_2021/Berges_2021/ymbA.txt new file mode 100644 index 0000000..32e0017 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ymbA.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.195 0.065016 NA NA +1.61361111111111 0.084672 NA NA +2.36138888888889 0.123984 NA NA +3.28638888888889 0.202608 NA NA +3.81944444444444 0.291816 NA NA +4.41083333333333 0.40068 NA NA +0.283333333333333 NA 14.1617650337321 0.0415821364729121 +1.91666666666667 NA 13.3538173700289 0.423790952706184 +2.7 NA 13.6725930721131 0.78316382187463 +3.61666666666667 NA 12.4662589971182 1.12353431522877 +4.05 NA 11.8114266489631 1.34328874400729 +4.75 NA 10.3259246523844 1.70216406577499 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ymbA_res/KEIO_ROBOT4_8.pdf b/validation/validation_results/Berges_2021/Berges_2021/ymbA_res/KEIO_ROBOT4_8.pdf new file mode 100644 index 0000000..e6e5bca Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ymbA_res/KEIO_ROBOT4_8.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ymbA_res/KEIO_ROBOT4_8_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ymbA_res/KEIO_ROBOT4_8_log.txt new file mode 100644 index 0000000..db1ecab --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ymbA_res/KEIO_ROBOT4_8_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.065016 NA NA + [3,] 0.084672 NA NA + [4,] 0.123984 NA NA + [5,] 0.202608 NA NA + [6,] 0.291816 NA NA + [7,] 0.400680 NA NA + [8,] NA 14.16177 0.04158214 + [9,] NA 13.35382 0.42379095 +[10,] NA 13.67259 0.78316382 +[11,] NA 12.46626 1.12353432 +[12,] NA 11.81143 1.34328874 +[13,] NA 10.32592 1.70216407 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03368159 14.26700000 0.20078756 0.56044488 -4.76802309 2.04753138 + +$result$lastp + X Glc Ace mu qGlc qAce + 4.823364e-09 -2.271353e-08 -9.537434e-08 -3.795719e-08 2.636450e-07 1.933449e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.007483897 0.384771622 0.167229021 0.056281905 0.906350834 0.393719391 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5718674 + +$result$laststep + X Glc Ace mu qGlc qAce + 4.823364e-09 -2.271353e-08 -9.537434e-08 -3.795719e-08 2.636450e-07 1.933449e-07 + +$result$normp +[1] 3.434634e-07 + +$result$res + [1] -0.20592073 0.03940747 -0.07341694 0.12666830 0.49299688 -0.26865302 -0.08362471 0.12156834 0.78441175 -0.91376323 -0.19098633 -0.06727217 0.26604164 0.90191061 0.07096780 -0.73308743 -0.55863919 -0.37357966 0.69242787 + +$result$prevres + [1] -0.20592097 0.03940715 -0.07341728 0.12666796 0.49299668 -0.26865300 -0.08362423 0.12156840 0.78441185 -0.91376312 -0.19098629 -0.06727221 0.26604137 0.90191106 0.07096805 -0.73308733 -0.55863931 -0.37357990 0.69242743 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 97.685651 0.000000 0 3.93179754 0.00000000 0.00000000 + [3,] 123.515068 0.000000 0 6.71291706 0.00000000 0.00000000 + [4,] 187.813868 0.000000 0 14.93783432 0.00000000 0.00000000 + [5,] 315.406714 0.000000 0 34.91261282 0.00000000 0.00000000 + [6,] 425.221938 0.000000 0 54.70264481 0.00000000 0.00000000 + [7,] 592.323026 0.000000 0 87.99778248 0.00000000 0.00000000 + [8,] -3.182847 2.173913 0 -0.01558890 0.02248381 0.00000000 + [9,] -35.650579 2.173913 0 -1.35289707 0.25183766 0.00000000 +[10,] -65.494318 2.173913 0 -3.70191194 0.46265548 0.00000000 +[11,] -121.895725 2.173913 0 -9.77598730 0.86107814 0.00000000 +[12,] -160.487575 2.173913 0 -14.77007448 1.13369310 0.00000000 +[13,] -246.470434 2.173913 0 -27.57875027 1.74108077 0.00000000 +[14,] 3.143662 0.000000 5 0.01539698 0.00000000 0.05171276 +[15,] 35.211666 0.000000 5 1.33624085 0.00000000 0.57922661 +[16,] 64.687983 0.000000 5 3.65633576 0.00000000 1.06410761 +[17,] 120.395003 0.000000 5 9.65563000 0.00000000 1.98047973 +[18,] 158.511728 0.000000 5 14.58823236 0.00000000 2.60749414 +[19,] 243.436007 0.000000 5 27.23921382 0.00000000 4.00448578 + +$result$retres +$result$retres$res + [1] -0.20592097 0.03940715 -0.07341728 0.12666796 0.49299668 -0.26865300 -0.08362423 0.12156840 0.78441185 -0.91376312 -0.19098629 -0.06727221 0.26604137 0.90191106 0.07096805 -0.73308733 -0.55863931 -0.37357990 0.69242743 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03368158 14.26700 0.2007877 + [2,] 0.06580414 13.99372 0.3181443 + [3,] 0.08320365 13.84569 0.3817117 + [4,] 0.12651736 13.47719 0.5399542 + [5,] 0.21246793 12.74596 0.8539663 + [6,] 0.28644294 12.11662 1.1242268 + [7,] 0.39900752 11.15896 1.5354705 + [8,] 0.03947801 14.21769 0.2219643 + [9,] 0.09860650 13.71465 0.4379846 + [10,] 0.15295632 13.25226 0.6365464 + [11,] 0.25567154 12.37841 1.0118065 + [12,] 0.32595295 11.78048 1.2685728 + [13,] 0.48254032 10.44830 1.8406496 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.004118419 NA NA + [2,] -0.000788143 NA NA + [3,] 0.001468346 NA NA + [4,] -0.002533359 NA NA + [5,] -0.009859934 NA NA + [6,] 0.005373060 NA NA + [7,] 0.001672485 NA NA + [8,] NA -0.05592146 -0.18038221 + [9,] NA -0.36082945 -0.01419361 +[10,] NA 0.42033104 0.14661747 +[11,] NA 0.08785369 0.11172786 +[12,] NA 0.03094521 0.07471598 +[13,] NA -0.12237903 -0.13848549 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ymbA_res/KEIO_ROBOT4_8_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ymbA_res/KEIO_ROBOT4_8_res.txt new file mode 100644 index 0000000..986530d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ymbA_res/KEIO_ROBOT4_8_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0336815854976682 0.0341382792075969 0.0343429228042942 0.00373597798898164 0.0263387172639932 0.0402744088632504 +Glc 14.2670000043206 14.2513151796809 14.2556922260192 0.213795749516303 13.8326073018371 14.5958420484827 +Ace 0.200787555592905 0.20880798509387 0.212094492821827 0.0869571525142588 0.0621959543204961 0.368851259311817 +mu 0.560444881471446 0.558561068868321 0.553192266369077 0.0274669675380835 0.515646963390271 0.621771886145858 +qGlc -4.76802309182123 -4.70822173066738 -4.74569271370765 0.522562107597472 -5.66369722162639 -3.73000478226747 +qAce 2.04753137695243 1.99428081918121 2.01737613121923 0.243842807709386 1.54484469611118 2.46472495803058 +res 4.25142024804289 33.931080406008 33.3562165194258 8.13228333432033 19.7652496939626 51.3467509053521 + + +Goodness of fit (khi2 test) + +khi2 value 4.25142024804425 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.327032326772634 +p-value, i.e. P(X^2<=value) 0.0117889557504833 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ymjA.txt b/validation/validation_results/Berges_2021/Berges_2021/ymjA.txt new file mode 100644 index 0000000..e161834 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ymjA.txt @@ -0,0 +1,15 @@ +time X Glc Ace +1.8288888888888888 6.3504000000000005E-2 NA NA +2.2613888888888889 8.6184000000000011E-2 NA NA +2.7741666666666664 0.12700800000000001 NA NA +3.2088888888888891 0.1512 NA NA +3.7063888888888892 0.198072 NA NA +4.2258333333333331 0.27972000000000002 NA NA +4.6355555555555554 0.35380800000000001 NA NA +4.9675000000000002 0.42184800000000006 NA NA +2.8 NA 12.4326789780036 0.517039229483191 +3.73333333333333 NA 12.1444575423758 0.933574004359544 +4.28333333333333 NA 11.7850059873822 1.27312149008071 +4.75 NA 10.8773517870334 1.60663619482483 +5.11666666666667 NA 10.0651763936054 1.86721942944502 +5.43333333333333 NA 9.61448570323251 2.22481578895208 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ymjA_res/KEIO_ROBOT5_10.pdf b/validation/validation_results/Berges_2021/Berges_2021/ymjA_res/KEIO_ROBOT5_10.pdf new file mode 100644 index 0000000..b483cb0 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ymjA_res/KEIO_ROBOT5_10.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ymjA_res/KEIO_ROBOT5_10_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ymjA_res/KEIO_ROBOT5_10_log.txt new file mode 100644 index 0000000..5072d87 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ymjA_res/KEIO_ROBOT5_10_log.txt @@ -0,0 +1,200 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.828889 2.261389 2.774167 3.208889 3.706389 4.225833 4.635556 4.967500 2.800000 3.733333 4.283333 4.750000 5.116667 5.433333 + +$sys$data_meas + X Glc Ace + [1,] 0.063504 NA NA + [2,] 0.086184 NA NA + [3,] 0.127008 NA NA + [4,] 0.151200 NA NA + [5,] 0.198072 NA NA + [6,] 0.279720 NA NA + [7,] 0.353808 NA NA + [8,] 0.421848 NA NA + [9,] NA 12.432679 0.5170392 +[10,] NA 12.144458 0.9335740 +[11,] NA 11.785006 1.2731215 +[12,] NA 10.877352 1.6066362 +[13,] NA 10.065176 1.8672194 +[14,] NA 9.614486 2.2248158 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0236097 13.3288666 0.2118060 0.5818356 -4.0693619 2.2293727 + +$result$lastp + X Glc Ace mu qGlc qAce +-7.542394e-10 -3.725350e-08 1.276125e-09 7.216481e-09 3.884342e-08 1.450690e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.003182284 0.321428889 0.141777305 0.030116129 0.535771212 0.234678963 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3351077 + +$result$laststep + X Glc Ace mu qGlc qAce +-7.542394e-10 -3.725350e-08 1.276125e-09 7.216481e-09 3.884342e-08 1.450690e-08 + +$result$normp +[1] 5.622597e-08 + +$result$res + [1] 0.246159522 0.091140422 -0.420340229 0.076742776 0.296876187 -0.186039992 -0.175417019 0.154134352 0.476639946 -0.217073102 -0.623969750 -0.004458666 0.407360968 -0.038499396 0.328100547 -0.090966491 -0.291382387 -0.253303021 0.149596021 0.157955330 + +$result$prevres + [1] 0.246159586 0.091140491 -0.420340158 0.076742843 0.296876240 -0.186039972 -0.175417045 0.154134269 0.476639985 -0.217073087 -0.623969749 -0.004458677 0.407360949 -0.038499420 0.328100564 -0.090966471 -0.291382372 -0.253303019 0.149596006 0.157955292 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 144.91331 0.000000 0 6.257287 0.0000000 0.0000000 + [2,] 186.37852 0.000000 0 9.950881 0.0000000 0.0000000 + [3,] 251.17051 0.000000 0 16.450974 0.0000000 0.0000000 + [4,] 323.45788 0.000000 0 24.505459 0.0000000 0.0000000 + [5,] 432.04603 0.000000 0 37.806932 0.0000000 0.0000000 + [6,] 584.50387 0.000000 0 58.316331 0.0000000 0.0000000 + [7,] 741.85544 0.000000 0 81.191677 0.0000000 0.0000000 + [8,] 899.90707 0.000000 0 105.542159 0.0000000 0.0000000 + [9,] -62.33007 2.173913 0 -2.596354 0.3616277 0.0000000 +[10,] -118.25121 2.173913 0 -6.964766 0.6860720 0.0000000 +[11,] -168.58278 2.173913 0 -11.745320 0.9780866 0.0000000 +[12,] -225.91728 2.173913 0 -17.873583 1.3107310 0.0000000 +[13,] -283.25724 2.173913 0 -24.561045 1.6434070 0.0000000 +[14,] -343.64017 2.173913 0 -32.088132 1.9937378 0.0000000 +[15,] 78.53835 0.000000 5 3.271509 0.0000000 0.8317437 +[16,] 149.00121 0.000000 5 8.775881 0.0000000 1.5779657 +[17,] 212.42098 0.000000 5 14.799568 0.0000000 2.2495993 +[18,] 284.66472 0.000000 5 22.521422 0.0000000 3.0146813 +[19,] 356.91533 0.000000 5 30.947888 0.0000000 3.7798361 +[20,] 433.00021 0.000000 5 40.432317 0.0000000 4.5855969 + +$result$retres +$result$retres$res + [1] 0.246159586 0.091140491 -0.420340158 0.076742843 0.296876240 -0.186039972 -0.175417045 0.154134269 0.476639985 -0.217073087 -0.623969749 -0.004458677 0.407360949 -0.038499420 0.328100564 -0.090966471 -0.291382372 -0.253303019 0.149596006 0.157955292 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.06842719 13.015413 0.3835296 + [2,] 0.08800681 12.878473 0.4585512 + [3,] 0.11860120 12.664496 0.5757773 + [4,] 0.15273486 12.425764 0.7065644 + [5,] 0.20400952 12.067149 0.9030295 + [6,] 0.27599920 11.563653 1.1788665 + [7,] 0.35029966 11.043995 1.4635576 + [8,] 0.42493069 10.522025 1.7495152 + [9,] 0.12039733 12.651933 0.5826593 + [10,] 0.20723303 12.044604 0.9153807 + [11,] 0.28538910 11.497980 1.2148450 + [12,] 0.37441949 10.875301 1.5559756 + [13,] 0.46345836 10.252562 1.8971386 + [14,] 0.55722243 9.596776 2.2564068 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.004923192 NA NA + [2,] -0.001822810 NA NA + [3,] 0.008406803 NA NA + [4,] -0.001534857 NA NA + [5,] -0.005937525 NA NA + [6,] 0.003720799 NA NA + [7,] 0.003508341 NA NA + [8,] -0.003082685 NA NA + [9,] NA -0.219254393 -0.06562011 +[10,] NA 0.099853620 0.01819329 +[11,] NA 0.287026085 0.05827647 +[12,] NA 0.002050992 0.05066060 +[13,] NA -0.187386037 -0.02991920 +[14,] NA 0.017709733 -0.03159106 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ymjA_res/KEIO_ROBOT5_10_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ymjA_res/KEIO_ROBOT5_10_res.txt new file mode 100644 index 0000000..6eab424 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ymjA_res/KEIO_ROBOT5_10_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0236096973483841 0.0234663401029169 0.0232975594362035 0.00288209105915111 0.0184076635049523 0.0289458351148408 +Glc 13.3288665946931 13.3309521787507 13.2872878979393 0.253630200274786 12.8930645511618 13.7853248420611 +Ace 0.211805993597646 0.230522312203986 0.2202860986195 0.103087650736904 0.0537720107701162 0.432234567964558 +mu 0.581835638463168 0.584749688273615 0.58210177955723 0.0253943837654363 0.536880715115086 0.634412766184165 +qGlc -4.06936188001748 -4.06013185526312 -4.08864960862215 0.492144705222659 -5.0180012850362 -2.9508311238584 +qAce 2.22937266723733 2.21916306689414 2.21657890332212 0.216286589315572 1.84407360362646 2.60433369210843 +res 1.57216082985697 35.692376140955 34.3720624712499 8.57194503339307 23.0243323626922 52.9803588602934 + + +Goodness of fit (khi2 test) + +khi2 value 1.57216082985701 +data points 20 +fitted parameters 6 +degrees of freedom 14 +khi2 reduced value 0.112297202132643 +p-value, i.e. P(X^2<=value) 1.85702824775455e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ynbE.txt b/validation/validation_results/Berges_2021/Berges_2021/ynbE.txt new file mode 100644 index 0000000..21f8482 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ynbE.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.18888888888889 0.071064 NA NA +2.27694444444444 0.10584 NA NA +3.12833333333333 0.167832 NA NA +3.77138888888889 0.223776 NA NA +4.41555555555556 0.31752 NA NA +4.82277777777778 0.406728 NA NA +0.0666666666666667 NA 15.6406768471495 0.0154677789283352 +1.71666666666667 NA 15.0532151702385 0.354303861436694 +2.8 NA 13.5672154911836 0.776772560250913 +3.63333333333333 NA 12.5865359286506 1.33251820574266 +4.26666666666667 NA 11.5146648491023 1.86534198113067 +4.88333333333333 NA 10.3493329230653 2.61784264595442 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ynbE_res/KEIO_ROBOT1_32.pdf b/validation/validation_results/Berges_2021/Berges_2021/ynbE_res/KEIO_ROBOT1_32.pdf new file mode 100644 index 0000000..8f802a5 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ynbE_res/KEIO_ROBOT1_32.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ynbE_res/KEIO_ROBOT1_32_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ynbE_res/KEIO_ROBOT1_32_log.txt new file mode 100644 index 0000000..09f9ebe --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ynbE_res/KEIO_ROBOT1_32_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.071064 NA NA + [3,] 0.105840 NA NA + [4,] 0.167832 NA NA + [5,] 0.223776 NA NA + [6,] 0.317520 NA NA + [7,] 0.406728 NA NA + [8,] NA 15.64068 0.01546778 + [9,] NA 15.05322 0.35430386 +[10,] NA 13.56722 0.77677256 +[11,] NA 12.58654 1.33251821 +[12,] NA 11.51466 1.86534198 +[13,] NA 10.34933 2.61784265 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03517498 15.48287942 0.02014814 0.50203170 -7.28285634 3.51232974 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.060644e-09 4.094518e-08 -7.424131e-09 -7.410262e-09 -5.349981e-08 -1.216060e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.006028884 0.301808111 0.131908282 0.039431398 0.792133842 0.351605525 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4473025 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.060644e-09 4.094518e-08 -7.424131e-09 -7.410262e-09 -5.349981e-08 -1.216060e-08 + +$result$normp +[1] 6.926595e-08 + +$result$res + [1] -0.05565091 -0.35859733 0.22426551 0.06650625 0.49215305 0.26482303 -0.53425793 -0.38079287 -0.58287142 0.74970864 0.53151364 0.28857882 -0.60613681 0.06528076 0.01183826 0.00465026 -0.16727008 0.02275740 0.06274340 + +$result$prevres + [1] -0.055650959 -0.358597403 0.224265438 0.066506188 0.492153029 0.264823073 -0.534257817 -0.380792960 -0.582871464 0.749708633 0.531513669 0.288578873 -0.606136751 0.065280792 0.011838265 0.004650244 -0.167270102 0.022757385 0.062743416 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 90.820308 0.000000 0 3.798027532 0.000000000 0.00000000 + [3,] 156.823552 0.000000 0 12.560229944 0.000000000 0.00000000 + [4,] 240.458018 0.000000 0 26.459775523 0.000000000 0.00000000 + [5,] 332.081291 0.000000 0 44.053416465 0.000000000 0.00000000 + [6,] 458.872264 0.000000 0 71.270700990 0.000000000 0.00000000 + [7,] 562.960994 0.000000 0 95.501331272 0.000000000 0.00000000 + [8,] -1.073348 2.173913 0 -0.001265520 0.005184092 0.00000000 + [9,] -43.125087 2.173913 0 -1.486770607 0.208286975 0.00000000 +[10,] -97.079743 2.173913 0 -5.865484408 0.468878961 0.00000000 +[11,] -163.891636 2.173913 0 -13.493074195 0.791569258 0.00000000 +[12,] -237.042758 2.173913 0 -23.699883108 1.144876973 0.00000000 +[13,] -334.499695 2.173913 0 -39.437643953 1.615577721 0.00000000 +[14,] 1.190589 0.000000 5 0.001403752 0.000000000 0.01192341 +[15,] 47.835615 0.000000 5 1.649169694 0.000000000 0.47906004 +[16,] 107.683707 0.000000 5 6.506167853 0.000000000 1.07842161 +[17,] 181.793424 0.000000 5 14.966914829 0.000000000 1.82060929 +[18,] 262.934800 0.000000 5 26.288607533 0.000000000 2.63321704 +[19,] 371.036902 0.000000 5 43.745394828 0.000000000 3.71582876 + +$result$retres +$result$retres$res + [1] -0.055650959 -0.358597403 0.224265438 0.066506188 0.492153029 0.264823073 -0.534257817 -0.380792960 -0.582871464 0.749708633 0.531513669 0.288578873 -0.606136751 0.065280792 0.011838265 0.004650244 -0.167270102 0.022757385 0.062743416 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03517498 15.48288 0.02014815 + [2,] 0.06389205 15.06629 0.22105941 + [3,] 0.11032531 14.39269 0.54591720 + [4,] 0.16916212 13.53916 0.95755315 + [5,] 0.23361906 12.60410 1.40850877 + [6,] 0.32281646 11.31013 2.03255439 + [7,] 0.39604284 10.24785 2.54486307 + [8,] 0.03637217 15.46551 0.02852394 + [9,] 0.08327565 14.78509 0.35667151 + [10,] 0.14345535 13.91208 0.77770261 + [11,] 0.21797570 12.83103 1.29906419 + [12,] 0.29956667 11.64741 1.86989346 + [13,] 0.40826775 10.07051 2.63039133 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.001113019 NA NA + [2,] 0.007171948 NA NA + [3,] -0.004485309 NA NA + [4,] -0.001330124 NA NA + [5,] -0.009843061 NA NA + [6,] -0.005296461 NA NA + [7,] 0.010685156 NA NA + [8,] NA 0.1751648 -0.0130561585 + [9,] NA 0.2681209 -0.0023676529 +[10,] NA -0.3448660 -0.0009300488 +[11,] NA -0.2444963 0.0334540204 +[12,] NA -0.1327463 -0.0045514770 +[13,] NA 0.2788229 -0.0125486831 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ynbE_res/KEIO_ROBOT1_32_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ynbE_res/KEIO_ROBOT1_32_res.txt new file mode 100644 index 0000000..2ab640b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ynbE_res/KEIO_ROBOT1_32_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0351749818860597 0.0347000305830143 0.03495937727262 0.00429239460080713 0.0270284371710033 0.043431791334884 +Glc 15.4828794249793 15.4800831705471 15.4965681154074 0.192416464751431 15.0998251354254 15.8522082501628 +Ace 0.0201481392864976 0.0603599076155648 0.0499752201521533 0.0576819843779411 9.99999999990592e-07 0.18700232497786 +mu 0.502031695094681 0.50718061953106 0.504830327002653 0.0276578638387094 0.454491429311 0.55786065300198 +qGlc -7.28285634074209 -7.33372241246068 -7.31673829084321 0.596682979257275 -8.52285463295073 -6.23821066359277 +qAce 3.5123297429778 3.4632226044086 3.4379205153828 0.237476426924837 3.08953449016553 3.92205975564724 +res 2.60103350239893 32.0824180162833 31.3819292534611 8.03725613064202 20.9347520473069 49.3345965762603 + + +Goodness of fit (khi2 test) + +khi2 value 2.60103350239898 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.200079500184537 +p-value, i.e. P(X^2<=value) 0.000967087920764836 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yncE.txt b/validation/validation_results/Berges_2021/Berges_2021/yncE.txt new file mode 100644 index 0000000..561684e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yncE.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.033264 NA NA +1.18888888888889 0.054432 NA NA +2.27694444444444 0.108864 NA NA +3.12833333333333 0.167832 NA NA +3.77138888888889 0.247968 NA NA +4.41555555555556 0.374976 NA NA +4.82277777777778 0.563976 NA NA +0.0666666666666667 NA 15.5383550759938 0.0149737194835105 +1.71666666666667 NA 15.0903881164794 0.3543776106721 +2.8 NA 13.7424499696057 0.786506957906757 +3.63333333333333 NA 12.3943811644296 1.21048178880181 +4.26666666666667 NA 11.2646218445713 1.69300876325496 +4.88333333333333 NA 9.89553471672848 2.25012066304426 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yncE_res/KEIO_ROBOT1_31.pdf b/validation/validation_results/Berges_2021/Berges_2021/yncE_res/KEIO_ROBOT1_31.pdf new file mode 100644 index 0000000..bb3f95a Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yncE_res/KEIO_ROBOT1_31.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yncE_res/KEIO_ROBOT1_31_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yncE_res/KEIO_ROBOT1_31_log.txt new file mode 100644 index 0000000..2950138 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yncE_res/KEIO_ROBOT1_31_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.033264 NA NA + [2,] 0.054432 NA NA + [3,] 0.108864 NA NA + [4,] 0.167832 NA NA + [5,] 0.247968 NA NA + [6,] 0.374976 NA NA + [7,] 0.563976 NA NA + [8,] NA 15.538355 0.01497372 + [9,] NA 15.090388 0.35437761 +[10,] NA 13.742450 0.78650696 +[11,] NA 12.394381 1.21048179 +[12,] NA 11.264622 1.69300876 +[13,] NA 9.895535 2.25012066 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02163861 15.26686914 0.18497290 0.66428752 -7.18589492 2.73218924 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.628636e-09 -9.372335e-08 3.498364e-08 2.820001e-08 2.560844e-08 -7.690982e-09 + +$result$hci + X Glc Ace mu qGlc qAce +0.008423287 0.603807328 0.261079502 0.087207393 1.537204018 0.654926484 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.9546869 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.628636e-09 -9.372335e-08 3.498364e-08 2.820001e-08 2.560844e-08 -7.690982e-09 + +$result$normp +[1] 1.073546e-07 + +$result$res + [1] -0.58126963 -0.33824090 -0.53310837 0.25234968 0.85207494 1.57810287 -1.55762603 -0.61322844 -0.69914107 0.55402865 1.06748842 0.54946808 -0.85861564 0.87014569 0.09987657 -0.59412643 -0.60023517 -0.41210291 0.63644226 + +$result$prevres + [1] -0.58126950 -0.33824069 -0.53310809 0.25234996 0.85207514 1.57810281 -1.55762641 -0.61322824 -0.69914097 0.55402865 1.06748834 0.54946796 -0.85861574 0.87014551 0.09987648 -0.59412643 -0.60023510 -0.41210281 0.63644234 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000e+00 0.000000000 0.000000000 + [2,] 110.143826 0.000000 0 2.833549e+00 0.000000000 0.000000000 + [3,] 226.913461 0.000000 0 1.118001e+01 0.000000000 0.000000000 + [4,] 399.468816 0.000000 0 2.704116e+01 0.000000000 0.000000000 + [5,] 612.353339 0.000000 0 4.997269e+01 0.000000000 0.000000000 + [6,] 939.381167 0.000000 0 8.975457e+01 0.000000000 0.000000000 + [7,] 1231.186914 0.000000 0 1.284845e+02 0.000000000 0.000000000 + [8,] -1.064839 2.173913 0 -7.737229e-04 0.003206508 0.000000000 + [9,] -50.039978 2.173913 0 -1.102328e+00 0.150683469 0.000000000 +[10,] -127.546375 2.173913 0 -4.997878e+00 0.384075512 0.000000000 +[11,] -239.250623 2.173913 0 -1.286541e+01 0.720446234 0.000000000 +[12,] -376.691008 2.173913 0 -2.467863e+01 1.134315198 0.000000000 +[13,] -579.308461 2.173913 0 -4.482912e+01 1.744449371 0.000000000 +[14,] 0.931197 0.000000 5 6.766176e-04 0.000000000 0.007374968 +[15,] 43.759753 0.000000 5 9.639809e-01 0.000000000 0.346571979 +[16,] 111.538775 0.000000 5 4.370624e+00 0.000000000 0.883373677 +[17,] 209.223676 0.000000 5 1.125075e+01 0.000000000 1.657026339 +[18,] 329.414721 0.000000 5 2.158136e+01 0.000000000 2.608924956 +[19,] 506.602841 0.000000 5 3.920287e+01 0.000000000 4.012233554 + +$result$retres +$result$retres$res + [1] -0.58126950 -0.33824069 -0.53310809 0.25234996 0.85207514 1.57810281 -1.55762641 -0.61322824 -0.69914097 0.55402865 1.06748834 0.54946796 -0.85861574 0.87014551 0.09987648 -0.59412643 -0.60023510 -0.41210281 0.63644234 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02163861 15.266869 0.1849729 + [2,] 0.04766719 14.985306 0.2920274 + [3,] 0.09820184 14.438651 0.4998745 + [4,] 0.17287900 13.630834 0.8070188 + [5,] 0.26500950 12.634217 1.1859481 + [6,] 0.40653806 11.103240 1.7680497 + [7,] 0.53282347 9.737154 2.2874568 + [8,] 0.02261843 15.256270 0.1890028 + [9,] 0.06768330 14.768783 0.3743529 + [10,] 0.13900143 13.997303 0.6676817 + [11,] 0.24178698 12.885426 1.0904348 + [12,] 0.36825385 11.517377 1.6105882 + [13,] 0.55469392 9.500571 2.3774091 + + +$result$it +[1] 9 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.011625390 NA NA + [2,] 0.006764814 NA NA + [3,] 0.010662162 NA NA + [4,] -0.005046999 NA NA + [5,] -0.017041503 NA NA + [6,] -0.031562056 NA NA + [7,] 0.031152528 NA NA + [8,] NA 0.2820850 -0.17402910 + [9,] NA 0.3216048 -0.01997530 +[10,] NA -0.2548532 0.11882529 +[11,] NA -0.4910446 0.12004702 +[12,] NA -0.2527553 0.08242056 +[13,] NA 0.3949632 -0.12728847 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yncE_res/KEIO_ROBOT1_31_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yncE_res/KEIO_ROBOT1_31_res.txt new file mode 100644 index 0000000..d48fb06 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yncE_res/KEIO_ROBOT1_31_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0216386074615539 0.0218102867841072 0.0219803029193241 0.0027584231936789 0.0162279868585637 0.027386295390047 +Glc 15.2668691429121 15.2954306119757 15.2676444382189 0.217535267352102 14.8961497997505 15.706758048102 +Ace 0.184972895766392 0.191984276266356 0.197595248066941 0.0729409482000523 0.0723876843137459 0.331120795987037 +mu 0.664287518986084 0.664299633130839 0.661604290562988 0.0298290983930622 0.609755245469163 0.724882101607798 +qGlc -7.18589491835906 -7.29320767758724 -7.24884749792876 0.508416406607088 -8.25508347746275 -6.28368562397388 +qAce 2.73218923534158 2.72100085080334 2.70520949125753 0.214936511136257 2.35282643472249 3.08680583123514 +res 11.8485528802954 29.800031035934 28.9679891364717 7.6009507169344 17.3068311485367 43.3469685737922 + + +Goodness of fit (khi2 test) + +khi2 value 11.848552880296 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.911427144638153 +p-value, i.e. P(X^2<=value) 0.459900000292 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ynfK.txt b/validation/validation_results/Berges_2021/Berges_2021/ynfK.txt new file mode 100644 index 0000000..4db9a39 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ynfK.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.142128 NA NA +3.67805555555556 0.214704 NA NA +4.09222222222222 0.27972 NA NA +4.565 0.358344 NA NA +0.05 NA 14.4601076395555 0.0156733765642051 +1.95 NA 13.8478203192971 0.403604465788866 +2.83333333333333 NA 13.4241166561814 0.671706548829245 +3.98333333333333 NA 12.4450579333334 1.23384657057831 +4.88333333333333 NA 10.0124169164251 1.90753749440342 +5.16666666666667 NA 9.60619377069378 1.90702546980389 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ynfK_res/KEIO_ROBOT3_40.pdf b/validation/validation_results/Berges_2021/Berges_2021/ynfK_res/KEIO_ROBOT3_40.pdf new file mode 100644 index 0000000..2afc5df Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ynfK_res/KEIO_ROBOT3_40.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ynfK_res/KEIO_ROBOT3_40_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ynfK_res/KEIO_ROBOT3_40_log.txt new file mode 100644 index 0000000..0895758 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ynfK_res/KEIO_ROBOT3_40_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.142128 NA NA + [2,] 0.214704 NA NA + [3,] 0.279720 NA NA + [4,] 0.358344 NA NA + [5,] NA 14.460108 0.01567338 + [6,] NA 13.847820 0.40360447 + [7,] NA 13.424117 0.67170655 + [8,] NA 12.445058 1.23384657 + [9,] NA 10.012417 1.90753749 +[10,] NA 9.606194 1.90702547 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03043674 14.56397205 0.15184734 0.53903969 -5.84653537 2.24957543 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.475971e-08 4.545431e-08 -1.982074e-07 -1.189684e-07 5.541408e-07 2.533145e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01137743 0.40780467 0.17525637 0.08934611 0.84719251 0.36137862 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5833819 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.475971e-08 4.545431e-08 -1.982074e-07 -1.189684e-07 5.541408e-07 2.533145e-07 + +$result$normp +[1] 6.534247e-07 + +$result$res + [1] 0.06933589 0.31596673 -0.17053962 -0.09162415 0.20618685 0.22137826 -0.10966498 -0.81962477 0.63267758 -0.13095295 0.69822000 -0.07692836 -0.30933085 -0.60817052 -0.58182813 0.87803786 + +$result$prevres + [1] 0.06933487 0.31596620 -0.17053960 -0.09162312 0.20618676 0.22137850 -0.10966461 -0.81962447 0.63267735 -0.13095353 0.69822098 -0.07692792 -0.30933074 -0.60817088 -0.58182872 0.87803728 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 235.7591194 0.000000 0 20.644190565 0.000000000 0.000000000 + [2,] 363.0866051 0.000000 0 40.646803254 0.000000000 0.000000000 + [3,] 453.9076259 0.000000 0 56.535934072 0.000000000 0.000000000 + [4,] 585.6601986 0.000000 0 81.373758470 0.000000000 0.000000000 + [5,] -0.6441344 2.173913 0 -0.000492335 0.003353326 0.000000000 + [6,] -43.8770302 2.173913 0 -1.526102963 0.228421241 0.000000000 + [7,] -85.0160863 2.173913 0 -4.564522318 0.442588748 0.000000000 + [8,] -178.2701610 2.173913 0 -14.406106461 0.928063980 0.000000000 + [9,] -304.3037127 2.173913 0 -31.551617812 1.584187243 0.000000000 +[10,] -358.4069321 2.173913 0 -39.832345184 1.865845423 0.000000000 +[11,] 0.5700412 0.000000 5 0.000435703 0.000000000 0.007712649 +[12,] 38.8299605 0.000000 5 1.350558994 0.000000000 0.525368853 +[13,] 75.2368895 0.000000 5 4.039476248 0.000000000 1.017954121 +[14,] 157.7641713 0.000000 5 12.749006536 0.000000000 2.134547155 +[15,] 269.3003854 0.000000 5 27.922310778 0.000000000 3.643630659 +[16,] 317.1802410 0.000000 5 35.250525912 0.000000000 4.291444474 + +$result$retres +$result$retres$res + [1] 0.06933487 0.31596620 -0.17053960 -0.09162312 0.20618676 0.22137850 -0.10966461 -0.81962447 0.63267735 -0.13095353 0.69822098 -0.07692792 -0.30933074 -0.60817088 -0.58182872 0.87803728 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.14351470 13.337505 0.6237559 + [2,] 0.22102332 12.496831 0.9472227 + [3,] 0.27630921 11.897189 1.1779473 + [4,] 0.35651154 11.027298 1.5126558 + [5,] 0.03126821 14.554954 0.1553176 + [6,] 0.08707567 13.949654 0.3882189 + [7,] 0.14018028 13.373671 0.6098404 + [8,] 0.26055790 12.068031 1.1122124 + [9,] 0.42324912 10.303448 1.7911718 + [10,] 0.49308861 9.545955 2.0826329 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.001386697 NA NA + [2,] -0.006319324 NA NA + [3,] 0.003410792 NA NA + [4,] 0.001832462 NA NA + [5,] NA -0.09484591 -0.13964420 + [6,] NA -0.10183411 0.01538558 + [7,] NA 0.05044572 0.06186615 + [8,] NA 0.37702725 0.12163418 + [9,] NA -0.29103158 0.11636574 +[10,] NA 0.06023862 -0.17560746 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ynfK_res/KEIO_ROBOT3_40_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ynfK_res/KEIO_ROBOT3_40_res.txt new file mode 100644 index 0000000..97f880d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ynfK_res/KEIO_ROBOT3_40_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0304367371566433 0.0314244282488794 0.0313360677284604 0.00411707827783472 0.0249038751470938 0.0398162018527114 +Glc 14.5639720495808 14.6005442072075 14.6313927828068 0.278345150261545 14.0315156838767 15.1194034149683 +Ace 0.151847338227954 0.156830074130154 0.14713582312256 0.109106661336496 9.99999999987122e-07 0.383111104213228 +mu 0.539039694842188 0.533852343255965 0.531805654873856 0.0286572207851448 0.480311790788787 0.581981118305514 +qGlc -5.84653537012831 -5.86017146321331 -5.90419611928222 0.637541019954809 -7.08437892230054 -4.66060386158795 +qAce 2.24957542667316 2.22208531307016 2.23542861623573 0.228456804178826 1.74138104092549 2.59135675717252 +res 3.40334387754646 23.9485989340162 23.4224518256367 6.95422721216931 11.7997400697203 35.8927508499811 + + +Goodness of fit (khi2 test) + +khi2 value 3.40334387755179 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.340334387755179 +p-value, i.e. P(X^2<=value) 0.0297212194306756 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yniA.txt b/validation/validation_results/Berges_2021/Berges_2021/yniA.txt new file mode 100644 index 0000000..8088862 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yniA.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.040824 NA NA +1.18888888888889 0.0756 NA NA +2.27694444444444 0.1134 NA NA +3.12833333333333 0.170856 NA NA +3.77138888888889 0.223776 NA NA +4.41555555555556 0.337176 NA NA +4.82277777777778 0.421848 NA NA +0.0666666666666667 NA 15.5166926082726 0.0174035384868996 +1.71666666666667 NA 14.5798659684985 0.341600022513609 +2.8 NA 13.8260381664558 0.794918895409562 +3.63333333333333 NA 12.4078871067612 1.31076522874841 +4.26666666666667 NA 11.5394548554352 1.97228866864887 +4.88333333333333 NA 10.1795510008452 2.74913263568995 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yniA_res/KEIO_ROBOT1_45.pdf b/validation/validation_results/Berges_2021/Berges_2021/yniA_res/KEIO_ROBOT1_45.pdf new file mode 100644 index 0000000..8311397 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yniA_res/KEIO_ROBOT1_45.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yniA_res/KEIO_ROBOT1_45_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yniA_res/KEIO_ROBOT1_45_log.txt new file mode 100644 index 0000000..99cc6df --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yniA_res/KEIO_ROBOT1_45_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.040824 NA NA + [2,] 0.075600 NA NA + [3,] 0.113400 NA NA + [4,] 0.170856 NA NA + [5,] 0.223776 NA NA + [6,] 0.337176 NA NA + [7,] 0.421848 NA NA + [8,] NA 15.51669 0.01740354 + [9,] NA 14.57987 0.34160002 +[10,] NA 13.82604 0.79491890 +[11,] NA 12.40789 1.31076523 +[12,] NA 11.53945 1.97228867 +[13,] NA 10.17955 2.74913264 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.0352878999 15.3189390502 0.0002675208 0.5102578194 -6.9374689971 3.5950485424 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.395311e-09 6.151315e-08 -1.282970e-08 -1.618990e-08 -2.114565e-08 -4.637885e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.005604368 0.284527748 0.124790349 0.036477240 0.721363151 0.324583578 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4240193 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.395311e-09 6.151315e-08 -1.282970e-08 -1.618990e-08 -2.114565e-08 -4.637885e-08 + +$result$normp +[1] 8.254972e-08 + +$result$res + [1] -0.27680501 -0.54364497 -0.03139576 0.16365233 0.89890141 -0.06718589 -0.42271933 -0.46598892 0.14531081 -0.06434198 0.71198088 0.05938375 -0.38634454 -0.04266538 0.03511095 -0.02840687 0.14156254 -0.13809839 0.03249715 + +$result$prevres + [1] -0.27680512 -0.54364513 -0.03139594 0.16365218 0.89890132 -0.06718583 -0.42271912 -0.46598905 0.14531076 -0.06434197 0.71198094 0.05938382 -0.38634448 -0.04266532 0.03511095 -0.02840691 0.14156249 -0.13809841 0.03249721 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.00000000 + [2,] 91.712885 0.000000 0 3.847666343 0.000000000 0.00000000 + [3,] 159.788609 0.000000 0 12.838788199 0.000000000 0.00000000 + [4,] 246.726294 0.000000 0 27.236684557 0.000000000 0.00000000 + [5,] 342.545240 0.000000 0 45.587422461 0.000000000 0.00000000 + [6,] 475.846263 0.000000 0 74.144305229 0.000000000 0.00000000 + [7,] 585.744188 0.000000 0 99.685277631 0.000000000 0.00000000 + [8,] -1.022727 2.173913 0 -0.001209816 0.005202168 0.00000000 + [9,] -41.412774 2.173913 0 -1.435164557 0.210648830 0.00000000 +[10,] -93.793589 2.173913 0 -5.701263855 0.477087329 0.00000000 +[11,] -159.159177 2.173913 0 -13.188779988 0.809573742 0.00000000 +[12,] -231.152509 2.173913 0 -23.266983603 1.175772615 0.00000000 +[13,] -327.560662 2.173913 0 -38.886241667 1.666159100 0.00000000 +[14,] 1.218965 0.000000 5 0.001441953 0.000000000 0.01196499 +[15,] 49.358945 0.000000 5 1.710540050 0.000000000 0.48449231 +[16,] 111.790449 0.000000 5 6.795206939 0.000000000 1.09730086 +[17,] 189.698209 0.000000 5 15.719407410 0.000000000 1.86201961 +[18,] 275.505427 0.000000 5 27.731389470 0.000000000 2.70427701 +[19,] 390.412116 0.000000 5 46.347628514 0.000000000 3.83216593 + +$result$retres +$result$retres$res + [1] -0.27680512 -0.54364513 -0.03139594 0.16365218 0.89890132 -0.06718583 -0.42271912 -0.46598905 0.14531076 -0.06434197 0.71198094 0.05938382 -0.38634448 -0.04266532 0.03511095 -0.02840691 0.14156249 -0.13809841 0.03249721 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03528790 15.31894 0.0002675337 + [2,] 0.06472710 14.91868 0.2076829745 + [3,] 0.11277208 14.26546 0.5461864518 + [4,] 0.17412904 13.43125 0.9784801769 + [5,] 0.24175403 12.51182 1.4549355737 + [6,] 0.33583228 11.23274 2.1177689124 + [7,] 0.41339362 10.17821 2.6642313984 + [8,] 0.03650894 15.30234 0.0088704751 + [9,] 0.08473110 14.64671 0.3486222121 + [10,] 0.14726917 13.79644 0.7892375131 + [11,] 0.22530992 12.73540 1.3390777259 + [12,] 0.31126360 11.56677 1.9446689860 + [13,] 0.42636644 10.00183 2.7556320774 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0055361025 NA NA + [2,] 0.0108729026 NA NA + [3,] 0.0006279187 NA NA + [4,] -0.0032730435 NA NA + [5,] -0.0179780265 NA NA + [6,] 0.0013437166 NA NA + [7,] 0.0084543824 NA NA + [8,] NA 0.21435496 0.008533063 + [9,] NA -0.06684295 -0.007022190 +[10,] NA 0.02959731 0.005681382 +[11,] NA -0.32751123 -0.028312497 +[12,] NA -0.02731656 0.027619683 +[13,] NA 0.17771846 -0.006499442 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yniA_res/KEIO_ROBOT1_45_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yniA_res/KEIO_ROBOT1_45_res.txt new file mode 100644 index 0000000..829116a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yniA_res/KEIO_ROBOT1_45_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0352878998988987 0.0343898581568749 0.0339121595290474 0.00448780100286631 0.0261902252042533 0.0442938421689172 +Glc 15.3189390502442 15.3308885424033 15.2981341560771 0.232565262704697 14.8867493925072 15.8696566369754 +Ace 0.00026752082261913 0.046596256678505 0.0288681048994938 0.0539503236208273 9.99999999984466e-07 0.186445760683564 +mu 0.510257819353429 0.518236362111828 0.519591459278906 0.0305068486440159 0.459609043185488 0.576094218076951 +qGlc -6.93746899708203 -7.05105717169669 -7.01501701611978 0.557607668310953 -8.26755723196072 -6.12284426311253 +qAce 3.59504854237613 3.54854910425718 3.58204627920499 0.236989496316546 3.13172463349436 4.01173485322168 +res 2.33730131313767 31.3143438180243 29.769790468561 7.76006344723401 17.7572143043042 46.7129169447743 + + +Goodness of fit (khi2 test) + +khi2 value 2.33730131313788 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.179792408702914 +p-value, i.e. P(X^2<=value) 0.000539804813019072 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yoaC.txt b/validation/validation_results/Berges_2021/Berges_2021/yoaC.txt new file mode 100644 index 0000000..e3ec2e9 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yoaC.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.195 0.065016 NA NA +1.61361111111111 0.081648 NA NA +2.36138888888889 0.110376 NA NA +3.28638888888889 0.207144 NA NA +3.81944444444444 0.29484 NA NA +4.41083333333333 0.4158 NA NA +0.283333333333333 NA 13.8749605176937 0.0331536713143921 +1.91666666666667 NA 14.1369431072721 0.393264174271561 +2.7 NA 13.3623172462628 0.668538281644571 +3.61666666666667 NA 12.3994239676507 1.10184096898217 +4.05 NA 11.7825238306134 1.39748464065918 +4.75 NA 10.39662210413 1.97471715582031 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yoaC_res/KEIO_ROBOT4_17.pdf b/validation/validation_results/Berges_2021/Berges_2021/yoaC_res/KEIO_ROBOT4_17.pdf new file mode 100644 index 0000000..90826bb Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yoaC_res/KEIO_ROBOT4_17.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yoaC_res/KEIO_ROBOT4_17_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yoaC_res/KEIO_ROBOT4_17_log.txt new file mode 100644 index 0000000..45d72bb --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yoaC_res/KEIO_ROBOT4_17_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.065016 NA NA + [3,] 0.081648 NA NA + [4,] 0.110376 NA NA + [5,] 0.207144 NA NA + [6,] 0.294840 NA NA + [7,] 0.415800 NA NA + [8,] NA 13.87496 0.03315367 + [9,] NA 14.13694 0.39326417 +[10,] NA 13.36232 0.66853828 +[11,] NA 12.39942 1.10184097 +[12,] NA 11.78252 1.39748464 +[13,] NA 10.39662 1.97471716 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02965485 14.26687941 0.12211413 0.59801412 -4.81061567 2.41132641 + +$result$lastp + X Glc Ace mu qGlc qAce + 3.493789e-09 -3.745624e-08 -7.337408e-08 -3.078943e-08 2.732504e-07 1.386825e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.005354226 0.296171602 0.129442110 0.045351766 0.707932392 0.311419125 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.447467 + +$result$laststep + X Glc Ace mu qGlc qAce + 3.493789e-09 -3.745624e-08 -7.337408e-08 -3.078943e-08 2.732504e-07 1.386825e-07 + +$result$normp +[1] 3.18819e-07 + +$result$res + [1] -0.33165750 -0.22092827 -0.19066279 0.56748154 0.22528599 -0.18640992 -0.05892001 0.75624546 -0.83053260 -0.12145387 0.06879449 0.07591077 0.05103576 0.55519279 -0.07259426 -0.32503539 -0.29762529 -0.23793847 0.37800063 + +$result$prevres + [1] -0.33165767 -0.22092851 -0.19066306 0.56748126 0.22528582 -0.18640992 -0.05891964 0.75624554 -0.83053249 -0.12145377 0.06879452 0.07591072 0.05103549 0.55519314 -0.07259407 -0.32503532 -0.29762539 -0.23793866 0.37800031 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 102.171208 0.000000 0 3.62069643 0.00000000 0.00000000 + [3,] 131.234432 0.000000 0 6.27974998 0.00000000 0.00000000 + [4,] 205.237321 0.000000 0 14.37207695 0.00000000 0.00000000 + [5,] 356.855187 0.000000 0 34.77816381 0.00000000 0.00000000 + [6,] 490.833431 0.000000 0 55.59426767 0.00000000 0.00000000 + [7,] 699.078996 0.000000 0 91.44134031 0.00000000 0.00000000 + [8,] -3.228886 2.173913 0 -0.01394777 0.01990434 0.00000000 + [9,] -37.531902 2.173913 0 -1.26606160 0.23136389 0.00000000 +[10,] -70.406479 2.173913 0 -3.54613666 0.43401788 0.00000000 +[11,] -134.578046 2.173913 0 -9.63573004 0.82960090 0.00000000 +[12,] -179.561285 2.173913 0 -14.76175484 1.10689825 0.00000000 +[13,] -281.996652 2.173913 0 -28.20161886 1.73835690 0.00000000 +[14,] 3.722510 0.000000 5 0.01608007 0.00000000 0.04577998 +[15,] 43.269682 0.000000 5 1.45961381 0.00000000 0.53213694 +[16,] 81.170039 0.000000 5 4.08826084 0.00000000 0.99824113 +[17,] 155.151989 0.000000 5 11.10881547 0.00000000 1.90808207 +[18,] 207.012149 0.000000 5 17.01849367 0.00000000 2.54586597 +[19,] 325.107569 0.000000 5 32.51300926 0.00000000 3.99822088 + +$result$retres +$result$retres$res + [1] -0.33165767 -0.22092851 -0.19066306 0.56748126 0.22528582 -0.18640992 -0.05891964 0.75624554 -0.83053249 -0.12145377 0.06879452 0.07591072 0.05103549 0.55519314 -0.07259407 -0.32503532 -0.29762539 -0.23793866 0.37800031 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02965485 14.26688 0.1221142 + [2,] 0.06059743 14.01797 0.2468816 + [3,] 0.07783474 13.87931 0.3163863 + [4,] 0.12172563 13.52623 0.4933641 + [5,] 0.21164972 12.80285 0.8559581 + [6,] 0.29111180 12.16364 1.1763669 + [7,] 0.41462161 11.17008 1.6743859 + [8,] 0.03513026 14.22283 0.1441923 + [9,] 0.09329993 13.75490 0.3787454 + [10,] 0.14904731 13.30645 0.6035312 + [11,] 0.25786686 12.43107 1.0423159 + [12,] 0.33414762 11.81744 1.3498969 + [13,] 0.50785338 10.42010 2.0503172 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.006633153 NA NA + [2,] 0.004418570 NA NA + [3,] 0.003813261 NA NA + [4,] -0.011349625 NA NA + [5,] -0.004505716 NA NA + [6,] 0.003728198 NA NA + [7,] 0.001178393 NA NA + [8,] NA -0.34787295 -0.11103863 + [9,] NA 0.38204495 0.01451881 +[10,] NA 0.05586874 0.06500706 +[11,] NA -0.03164548 0.05952508 +[12,] NA -0.03491893 0.04758773 +[13,] NA -0.02347632 -0.07560006 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yoaC_res/KEIO_ROBOT4_17_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yoaC_res/KEIO_ROBOT4_17_res.txt new file mode 100644 index 0000000..9519eb2 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yoaC_res/KEIO_ROBOT4_17_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0296548500511324 0.0292244744471661 0.0293123516064947 0.0038049934432527 0.0220518073553281 0.0376867131092815 +Glc 14.2668794091975 14.2836587894349 14.2712925408159 0.162727670858077 13.9387556645694 14.597635792231 +Ace 0.122114131621348 0.130187389354597 0.122222097793799 0.0710630076135334 9.99999999997531e-07 0.259353795790771 +mu 0.598014118522438 0.602976056248773 0.598770809546783 0.0315418217422765 0.542877272923891 0.670854335673123 +qGlc -4.8106156656242 -4.89396185595073 -4.85010273781974 0.52099493802801 -5.83967236002012 -3.91660571912299 +qAce 2.4113264148823 2.40366758830052 2.41156159892581 0.206571460466935 1.98277138522821 2.75974892247521 +res 2.60294697604089 31.9740555915326 31.4589044096911 8.02548331434529 20.0786256199212 52.078912986263 + + +Goodness of fit (khi2 test) + +khi2 value 2.60294697604174 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.200226690464749 +p-value, i.e. P(X^2<=value) 0.00097093449679273 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yodD.txt b/validation/validation_results/Berges_2021/Berges_2021/yodD.txt new file mode 100644 index 0000000..44afc25 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yodD.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.195 0.069552 NA NA +1.61361111111111 0.086184 NA NA +2.36138888888889 0.12852 NA NA +3.28638888888889 0.210168 NA NA +3.81944444444444 0.297864 NA NA +4.41083333333333 0.40068 NA NA +0.283333333333333 NA 14.1934205104655 0.0420318658572477 +1.91666666666667 NA 14.2593358436625 0.413806170738773 +2.7 NA 13.7506259084186 0.646448399206399 +3.61666666666667 NA 12.6997310557603 1.09762073054799 +4.05 NA 11.8613201599422 1.36539491742683 +4.75 NA 10.4826723440425 1.24823893513997 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yodD_res/KEIO_ROBOT4_16.pdf b/validation/validation_results/Berges_2021/Berges_2021/yodD_res/KEIO_ROBOT4_16.pdf new file mode 100644 index 0000000..deecb76 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yodD_res/KEIO_ROBOT4_16.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yodD_res/KEIO_ROBOT4_16_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yodD_res/KEIO_ROBOT4_16_log.txt new file mode 100644 index 0000000..2908517 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yodD_res/KEIO_ROBOT4_16_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.069552 NA NA + [3,] 0.086184 NA NA + [4,] 0.128520 NA NA + [5,] 0.210168 NA NA + [6,] 0.297864 NA NA + [7,] 0.400680 NA NA + [8,] NA 14.19342 0.04203187 + [9,] NA 14.25934 0.41380617 +[10,] NA 13.75063 0.64644840 +[11,] NA 12.69973 1.09762073 +[12,] NA 11.86132 1.36539492 +[13,] NA 10.48267 1.24823894 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03631531 14.63622779 0.24153633 0.54448816 -4.97222213 1.58256846 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.390225e-08 5.847254e-08 -1.271946e-07 -1.001016e-07 4.155179e-07 1.742113e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.01059540 0.52852821 0.22801648 0.07419433 1.21279486 0.51766398 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7787751 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.390225e-08 5.847254e-08 -1.271946e-07 -1.001016e-07 4.155179e-07 1.742113e-07 + +$result$normp +[1] 4.825099e-07 + +$result$res + [1] -0.074234713 0.002880563 0.062269275 0.142301781 0.360514861 -0.364161434 0.014484304 0.842367525 -0.506770489 -0.489717498 -0.234891310 0.213152098 0.175859674 1.085556246 0.109420807 -0.256708047 -1.026710599 -1.359315815 1.447757408 + +$result$prevres + [1] -0.074235408 0.002879647 0.062268308 0.142300820 0.360514275 -0.364161441 0.014485481 0.842367432 -0.506770369 -0.489717306 -0.234891160 0.213152131 0.175859272 1.085556840 0.109421073 -0.256707987 -1.026710796 -1.359316121 1.447756990 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 95.840608 0.000000 0 4.15917318 0.00000000 0.00000000 + [3,] 120.375414 0.000000 0 7.05384983 0.00000000 0.00000000 + [4,] 180.868733 0.000000 0 15.51031257 0.00000000 0.00000000 + [5,] 299.293045 0.000000 0 35.71947911 0.00000000 0.00000000 + [6,] 400.080457 0.000000 0 55.49285561 0.00000000 0.00000000 + [7,] 552.067310 0.000000 0 88.43052804 0.00000000 0.00000000 + [8,] -3.311469 2.173913 0 -0.01747427 0.02418575 0.00000000 + [9,] -36.516313 2.173913 0 -1.48797840 0.26670177 0.00000000 +[10,] -66.499222 2.173913 0 -4.03160360 0.48568595 0.00000000 +[11,] -122.391045 2.173913 0 -10.51922841 0.89389936 0.00000000 +[12,] -160.242568 2.173913 0 -15.80018756 1.17035301 0.00000000 +[13,] -243.798370 2.173913 0 -29.21864302 1.78061397 0.00000000 +[14,] 2.424155 0.000000 5 0.01279201 0.00000000 0.05562723 +[15,] 26.731705 0.000000 5 1.08927206 0.00000000 0.61341407 +[16,] 48.680642 0.000000 5 2.95132856 0.00000000 1.11707769 +[17,] 89.596157 0.000000 5 7.70058329 0.00000000 2.05596852 +[18,] 117.305300 0.000000 5 11.56650046 0.00000000 2.69181192 +[19,] 178.472183 0.000000 5 21.38945799 0.00000000 4.09541214 + +$result$retres +$result$retres$res + [1] -0.074235408 0.002879647 0.062268308 0.142300820 0.360514275 -0.364161441 0.014485481 0.842367432 -0.506770369 -0.489717306 -0.234891160 0.213152131 0.175859272 1.085556840 0.109421073 -0.256707987 -1.026710796 -1.359316121 1.447756990 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03631529 14.63623 0.2415365 + [2,] 0.06960959 14.33219 0.3383071 + [3,] 0.08742937 14.16946 0.3901007 + [4,] 0.13136602 13.76823 0.5178037 + [5,] 0.21737829 12.98278 0.7678004 + [6,] 0.29058077 12.31430 0.9805652 + [7,] 0.40096971 11.30623 1.3014133 + [8,] 0.04237297 14.58091 0.2591432 + [9,] 0.10311464 14.02622 0.4356904 + [10,] 0.15796243 13.52536 0.5951068 + [11,] 0.26020544 12.59168 0.8922786 + [12,] 0.32944729 11.95937 1.0935317 + [13,] 0.48229606 10.56357 1.5377903 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 1.484708e-03 NA NA + [2,] -5.759294e-05 NA NA + [3,] -1.245366e-03 NA NA + [4,] -2.846016e-03 NA NA + [5,] -7.210286e-03 NA NA + [6,] 7.283229e-03 NA NA + [7,] -2.897096e-04 NA NA + [8,] NA -0.38748902 -0.21711137 + [9,] NA 0.23311437 -0.02188421 +[10,] NA 0.22526996 0.05134160 +[11,] NA 0.10804993 0.20534216 +[12,] NA -0.09804998 0.27186322 +[13,] NA -0.08089527 -0.28955140 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yodD_res/KEIO_ROBOT4_16_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yodD_res/KEIO_ROBOT4_16_res.txt new file mode 100644 index 0000000..bf72403 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yodD_res/KEIO_ROBOT4_16_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0363153057443121 0.0362210230303396 0.0363079881201301 0.00448205327683854 0.0276130002028747 0.044460491101716 +Glc 14.6362277854517 14.6031790799045 14.6109895840744 0.227479772815867 14.0937732857023 14.9847476289394 +Ace 0.241536327253948 0.239084114533576 0.242236694183368 0.0879412612465601 0.0765732752548153 0.408470927696627 +mu 0.544488161051759 0.546365555404844 0.542977768220543 0.029231540020365 0.492884981803195 0.605784203030927 +qGlc -4.97222213046008 -4.92396913074143 -4.96920741301691 0.5647425035447 -5.79251867031999 -3.63174164132413 +qAce 1.58256846482457 1.61135874982285 1.6069366207389 0.24332994032094 1.10521178481574 2.07720113525441 +res 7.88437758057422 31.4096343590866 31.3235825753647 8.6053243352528 16.9994251313913 48.6031692848793 + + +Goodness of fit (khi2 test) + +khi2 value 7.8843775805803 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.606490583121561 +p-value, i.e. P(X^2<=value) 0.148949622242724 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yohn.txt b/validation/validation_results/Berges_2021/Berges_2021/yohn.txt new file mode 100644 index 0000000..6403c9b --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yohn.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.0378 NA NA +1.195 0.066528 NA NA +1.61361111111111 0.084672 NA NA +2.36138888888889 0.131544 NA NA +3.28638888888889 0.222264 NA NA +3.81944444444444 0.319032 NA NA +4.41083333333333 0.473256 NA NA +0.283333333333333 NA 14.2365888360043 0.0428267843015613 +1.91666666666667 NA 13.9662064673537 0.418747833656797 +2.7 NA 13.1349493013761 0.706958570425758 +3.61666666666667 NA 12.3550822077908 1.05808404966855 +4.05 NA 11.7818472561659 1.56802288134891 +4.75 NA 9.94304422316229 2.17894316936432 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yohn_res/KEIO_ROBOT4_45.pdf b/validation/validation_results/Berges_2021/Berges_2021/yohn_res/KEIO_ROBOT4_45.pdf new file mode 100644 index 0000000..52125a4 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yohn_res/KEIO_ROBOT4_45.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yohn_res/KEIO_ROBOT4_45_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yohn_res/KEIO_ROBOT4_45_log.txt new file mode 100644 index 0000000..34f3c02 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yohn_res/KEIO_ROBOT4_45_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.037800 NA NA + [2,] 0.066528 NA NA + [3,] 0.084672 NA NA + [4,] 0.131544 NA NA + [5,] 0.222264 NA NA + [6,] 0.319032 NA NA + [7,] 0.473256 NA NA + [8,] NA 14.236589 0.04282678 + [9,] NA 13.966206 0.41874783 +[10,] NA 13.134949 0.70695857 +[11,] NA 12.355082 1.05808405 +[12,] NA 11.781847 1.56802288 +[13,] NA 9.943044 2.17894317 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03009985 14.35328528 0.11987946 0.62161064 -4.92609778 2.41854266 + +$result$lastp + X Glc Ace mu qGlc qAce +-7.077372e-09 -4.603230e-08 8.576338e-08 6.053756e-08 -2.044153e-07 -7.409329e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.00437134 0.25317826 0.11058651 0.03630727 0.55521103 0.24385896 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3861067 + +$result$laststep + X Glc Ace mu qGlc qAce +-7.077372e-09 -4.603230e-08 8.576338e-08 6.053756e-08 -2.044153e-07 -7.409329e-08 + +$result$normp +[1] 2.458956e-07 + +$result$res + [1] -0.38500747 -0.16310990 -0.13015945 -0.04559693 0.49419335 0.21577400 -0.31252201 0.15382299 -0.34691434 0.38938558 -0.04834870 -0.32027892 0.17233338 0.49803288 -0.15238806 -0.38429458 0.26881441 -0.56661860 0.33645395 + +$result$prevres + [1] -0.38500711 -0.16310938 -0.13015889 -0.04559633 0.49419377 0.21577406 -0.31252275 0.15382308 -0.34691439 0.38938548 -0.04834880 -0.32027896 0.17233360 0.49803248 -0.15238823 -0.38429459 0.26881457 -0.56661838 0.33645416 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 105.093208 0.000000 0 3.78013229 0.00000000 0.00000000 + [3,] 136.327592 0.000000 0 6.62135817 0.00000000 0.00000000 + [4,] 216.997825 0.000000 0 15.42365634 0.00000000 0.00000000 + [5,] 385.629523 0.000000 0 38.14640992 0.00000000 0.00000000 + [6,] 537.124601 0.000000 0 61.75038704 0.00000000 0.00000000 + [7,] 775.760386 0.000000 0 102.99418122 0.00000000 0.00000000 + [8,] -3.317788 2.173913 0 -0.01456260 0.02027263 0.00000000 + [9,] -39.481588 2.173913 0 -1.35984461 0.24124373 0.00000000 +[10,] -75.055873 2.173913 0 -3.86546559 0.45861274 0.00000000 +[11,] -145.923235 2.173913 0 -10.69484764 0.89163249 0.00000000 +[12,] -196.358460 2.173913 0 -16.52895326 1.19980606 0.00000000 +[13,] -312.797062 2.173913 0 -32.03868927 1.91127904 0.00000000 +[14,] 3.746513 0.000000 5 0.01644439 0.00000000 0.04662705 +[15,] 44.583402 0.000000 5 1.53556384 0.00000000 0.55486059 +[16,] 84.754599 0.000000 5 4.36496136 0.00000000 1.05480930 +[17,] 164.779447 0.000000 5 12.07683670 0.00000000 2.05075472 +[18,] 221.731916 0.000000 5 18.66482591 0.00000000 2.75955394 +[19,] 353.216723 0.000000 5 36.17873123 0.00000000 4.39594180 + +$result$retres +$result$retres$res + [1] -0.38500711 -0.16310938 -0.13015889 -0.04559633 0.49419377 0.21577406 -0.31252275 0.15382308 -0.34691439 0.38938548 -0.04834880 -0.32027896 0.17233360 0.49803248 -0.15238823 -0.38429459 0.26881457 -0.56661838 0.33645416 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.03009986 14.35329 0.1198794 + [2,] 0.06326581 14.09045 0.2489204 + [3,] 0.08206882 13.94145 0.3220786 + [4,] 0.13063207 13.55659 0.5110269 + [5,] 0.23214788 12.75211 0.9060014 + [6,] 0.32334748 12.02938 1.2608379 + [7,] 0.46700554 10.89092 1.8197782 + [8,] 0.03589663 14.30735 0.1424333 + [9,] 0.09908130 13.80663 0.3882702 + [10,] 0.16123598 13.31407 0.6300997 + [11,] 0.28505403 12.33284 1.1118470 + [12,] 0.37317345 11.63452 1.4546992 + [13,] 0.57661265 10.02232 2.2462340 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0077001423 NA NA + [2,] 0.0032621877 NA NA + [3,] 0.0026031778 NA NA + [4,] 0.0009119265 NA NA + [5,] -0.0098838755 NA NA + [6,] -0.0043154812 NA NA + [7,] 0.0062504551 NA NA + [8,] NA -0.07075861 -0.09960650 + [9,] NA 0.15958062 0.03047765 +[10,] NA -0.17911732 0.07685892 +[11,] NA 0.02224045 -0.05376291 +[12,] NA 0.14732832 0.11332368 +[13,] NA -0.07927346 -0.06729083 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yohn_res/KEIO_ROBOT4_45_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yohn_res/KEIO_ROBOT4_45_res.txt new file mode 100644 index 0000000..8b95525 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yohn_res/KEIO_ROBOT4_45_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.030099850648799 0.0303832872858017 0.0302689279106407 0.00324493858735272 0.025222024153899 0.0379342050780065 +Glc 14.353285281034 14.3099734976912 14.325735095043 0.171523238415642 13.9814073726027 14.5668570910492 +Ace 0.119879464484701 0.132575267262139 0.132637070770558 0.0718316947268976 9.99999999998766e-07 0.282131848235743 +mu 0.621610644942215 0.622039928299487 0.62244180410657 0.0251881042099956 0.574750120853323 0.661747929982801 +qGlc -4.92609777717394 -4.81937906698861 -4.80966194735561 0.465524936168611 -5.73302071539947 -3.98797799212925 +qAce 2.4185426607533 2.39928809490686 2.4051215450868 0.216388484904718 2.00214134701494 2.81578721444335 +res 1.93801910061906 30.5704729324549 29.4999056162975 7.05105364452232 20.1988167726651 44.7449489769139 + + +Goodness of fit (khi2 test) + +khi2 value 1.93801910062133 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.149078392355487 +p-value, i.e. P(X^2<=value) 0.000189317612672058 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ypeB.txt b/validation/validation_results/Berges_2021/Berges_2021/ypeB.txt new file mode 100644 index 0000000..bd424bd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ypeB.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.033264 NA NA +1.195 0.057456 NA NA +1.61361111111111 0.069552 NA NA +2.36138888888889 0.102816 NA NA +3.28638888888889 0.179928 NA NA +3.81944444444444 0.214704 NA NA +4.41083333333333 0.343224 NA NA +0.283333333333333 NA 14.5589845720817 0.034691247082268 +1.91666666666667 NA 13.4312241601009 0.294080570845657 +2.7 NA 13.7639661775108 0.525256807620769 +3.61666666666667 NA 13.1136155665091 0.88837476411074 +4.05 NA 11.9594720788419 0.978532519552988 +4.75 NA 10.8892054215161 1.3948075948802 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ypeB_res/KEIO_ROBOT4_39.pdf b/validation/validation_results/Berges_2021/Berges_2021/ypeB_res/KEIO_ROBOT4_39.pdf new file mode 100644 index 0000000..2773acb Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ypeB_res/KEIO_ROBOT4_39.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ypeB_res/KEIO_ROBOT4_39_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ypeB_res/KEIO_ROBOT4_39_log.txt new file mode 100644 index 0000000..356c4d3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ypeB_res/KEIO_ROBOT4_39_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.033264 NA NA + [2,] 0.057456 NA NA + [3,] 0.069552 NA NA + [4,] 0.102816 NA NA + [5,] 0.179928 NA NA + [6,] 0.214704 NA NA + [7,] 0.343224 NA NA + [8,] NA 14.55898 0.03469125 + [9,] NA 13.43122 0.29408057 +[10,] NA 13.76397 0.52525681 +[11,] NA 13.11362 0.88837476 +[12,] NA 11.95947 0.97853252 +[13,] NA 10.88921 1.39480759 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02722207 14.45404752 0.11057678 0.56642360 -5.33059443 2.04297214 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.302196e-08 7.891699e-08 -1.423198e-07 -1.249204e-07 4.777713e-07 2.148170e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.00807762 0.42266604 0.18298604 0.07504903 1.21623685 0.52359478 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6275273 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.302196e-08 7.891699e-08 -1.423198e-07 -1.249204e-07 4.777713e-07 2.148170e-07 + +$result$normp +[1] 5.627338e-07 + +$result$res + [1] -0.30209659 -0.19452776 -0.08267011 0.04457462 -0.24000827 1.10758904 -0.60607395 -0.32507493 1.13120201 -0.51319296 -0.84903634 0.45817698 0.09792522 0.46488839 0.04535032 -0.29864602 -0.57194743 0.03662671 0.32372804 + +$result$prevres + [1] -0.30209724 -0.19452864 -0.08267105 0.04457367 -0.24000886 1.10758903 -0.60607275 -0.32507506 1.13120211 -0.51319277 -0.84903617 0.45817704 0.09792484 0.46488905 0.04535060 -0.29864598 -0.57194766 0.03662636 0.32372762 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 98.386082 0.000000 0 3.20053427 0.00000000 0.00000000 + [3,] 124.712441 0.000000 0 5.47809508 0.00000000 0.00000000 + [4,] 190.484284 0.000000 0 12.24468377 0.00000000 0.00000000 + [5,] 321.665322 0.000000 0 28.77690655 0.00000000 0.00000000 + [6,] 435.043900 0.000000 0 45.23287477 0.00000000 0.00000000 + [7,] 608.151264 0.000000 0 73.02190711 0.00000000 0.00000000 + [8,] -3.561482 2.173913 0 -0.01410192 0.01818762 0.00000000 + [9,] -40.126535 2.173913 0 -1.23260513 0.20491648 0.00000000 +[10,] -73.960963 2.173913 0 -3.38526828 0.37770070 0.00000000 +[11,] -138.234181 2.173913 0 -8.98032938 0.70592843 0.00000000 +[12,] -182.382000 2.173913 0 -13.59784921 0.93138063 0.00000000 +[13,] -281.085747 2.173913 0 -25.48227556 1.43543673 0.00000000 +[14,] 3.139390 0.000000 5 0.01243062 0.00000000 0.04183154 +[15,] 35.370909 0.000000 5 1.08652201 0.00000000 0.47130791 +[16,] 65.195424 0.000000 5 2.98406065 0.00000000 0.86871161 +[17,] 121.851253 0.000000 5 7.91601887 0.00000000 1.62363539 +[18,] 160.766860 0.000000 5 11.98628985 0.00000000 2.14217546 +[19,] 247.772658 0.000000 5 22.46222445 0.00000000 3.30150447 + +$result$retres +$result$retres$res + [1] -0.30209724 -0.19452864 -0.08267105 0.04457367 -0.24000886 1.10758903 -0.60607275 -0.32507506 1.13120211 -0.51319277 -0.84903617 0.45817704 0.09792484 0.46488905 0.04535060 -0.29864598 -0.57194766 0.03662636 0.32372762 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02722206 14.45405 0.1105769 + [2,] 0.05356543 14.20613 0.2055920 + [3,] 0.06789858 14.07124 0.2572886 + [4,] 0.10370747 13.73425 0.3864438 + [5,] 0.17512782 13.06211 0.6440421 + [6,] 0.23685578 12.48119 0.8666819 + [7,] 0.33110255 11.59424 1.2066103 + [8,] 0.03196093 14.40945 0.1276691 + [9,] 0.08061405 13.95158 0.3031507 + [10,] 0.12563383 13.52790 0.4655276 + [11,] 0.21115518 12.72306 0.7739852 + [12,] 0.26989785 12.17023 0.9858578 + [13,] 0.40123215 10.93425 1.4595531 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0060419449 NA NA + [2,] 0.0038905729 NA NA + [3,] 0.0016534209 NA NA + [4,] -0.0008914734 NA NA + [5,] 0.0048001772 NA NA + [6,] -0.0221517806 NA NA + [7,] 0.0121214550 NA NA + [8,] NA 0.14953453 -0.092977811 + [9,] NA -0.52035297 -0.009070121 +[10,] NA 0.23606867 0.059729195 +[11,] NA 0.39055664 0.114389533 +[12,] NA -0.21076144 -0.007325273 +[13,] NA -0.04504543 -0.064745524 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ypeB_res/KEIO_ROBOT4_39_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ypeB_res/KEIO_ROBOT4_39_res.txt new file mode 100644 index 0000000..198ae8c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ypeB_res/KEIO_ROBOT4_39_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0272220681617303 0.0275058873925733 0.0275615649069779 0.0042647181236046 0.0183696438993509 0.0363785876299815 +Glc 14.4540475168526 14.4412198713477 14.4399733504236 0.176567134275492 14.1092492491322 14.7351407288333 +Ace 0.110576784850372 0.127607269653345 0.125915159915646 0.0731982214345277 0.0207365685189398 0.254623451957302 +mu 0.566423597484745 0.566863200605549 0.566730476062995 0.0391506564090822 0.497812293804711 0.663919046237306 +qGlc -5.33059443280429 -5.29095249924626 -5.28239349948049 0.598354168216332 -6.44429207491713 -4.14029242037748 +qAce 2.04297214219372 2.0341833425011 1.99875872209999 0.241245710777178 1.64615422948205 2.5122927511501 +res 5.11927718654217 30.7137600438551 29.2972446428811 7.93867131680922 18.6564507640508 48.3836974133471 + + +Goodness of fit (khi2 test) + +khi2 value 5.11927718654844 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.393790552811419 +p-value, i.e. P(X^2<=value) 0.0275273560489301 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ypfJ.txt b/validation/validation_results/Berges_2021/Berges_2021/ypfJ.txt new file mode 100644 index 0000000..99113b3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ypfJ.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.033264 NA NA +1.195 0.057456 NA NA +1.61361111111111 0.074088 NA NA +2.36138888888889 0.114912 NA NA +3.28638888888889 0.192024 NA NA +3.81944444444444 0.2646 NA NA +4.41083333333333 0.388584 NA NA +0.283333333333333 NA 14.3466597174658 0.038665767936653 +1.91666666666667 NA 13.7206063350575 0.419735403917205 +2.7 NA 13.415602918329 0.714170911965673 +3.61666666666667 NA 12.7879171362067 1.26209463585027 +4.05 NA 11.839731266931 1.53662485534771 +4.75 NA 10.4650225822839 2.13183434388804 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ypfJ_res/KEIO_ROBOT4_37.pdf b/validation/validation_results/Berges_2021/Berges_2021/ypfJ_res/KEIO_ROBOT4_37.pdf new file mode 100644 index 0000000..a1ae8bb Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ypfJ_res/KEIO_ROBOT4_37.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ypfJ_res/KEIO_ROBOT4_37_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ypfJ_res/KEIO_ROBOT4_37_log.txt new file mode 100644 index 0000000..89e7b5e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ypfJ_res/KEIO_ROBOT4_37_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.033264 NA NA + [2,] 0.057456 NA NA + [3,] 0.074088 NA NA + [4,] 0.114912 NA NA + [5,] 0.192024 NA NA + [6,] 0.264600 NA NA + [7,] 0.388584 NA NA + [8,] NA 14.34666 0.03866577 + [9,] NA 13.72061 0.41973540 +[10,] NA 13.41560 0.71417091 +[11,] NA 12.78792 1.26209464 +[12,] NA 11.83973 1.53662486 +[13,] NA 10.46502 2.13183434 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02867763 14.38734515 0.13195606 0.58716828 -5.17715603 2.82072166 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.798588e-09 6.326806e-09 -3.320414e-08 -1.662588e-08 7.025971e-08 5.654357e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.004592181 0.251822578 0.110597722 0.040299772 0.645395710 0.287116409 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.37786 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.798588e-09 6.326806e-09 -3.320414e-08 -1.662588e-08 7.025971e-08 5.654357e-08 + +$result$normp +[1] 9.775377e-08 + +$result$res + [1] -0.229318745 0.019497102 -0.006200058 -0.008708039 0.274214216 0.274751299 -0.317774107 -0.011048237 0.305280523 -0.020856406 -0.569279058 0.160361118 0.135542061 0.591131637 -0.005123628 -0.237718254 -0.580149321 -0.284087948 0.515947514 + +$result$prevres + [1] -0.229318834 0.019496978 -0.006200191 -0.008708174 0.274214137 0.274751309 -0.317773904 -0.011048246 0.305280544 -0.020856375 -0.569279035 0.160361121 0.135541991 0.591131793 -0.005123553 -0.237718234 -0.580149372 -0.284088030 0.515947397 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 100.855533 0.000000 0 3.45629489 0.00000000 0.00000000 + [3,] 128.957681 0.000000 0 5.96745630 0.00000000 0.00000000 + [4,] 200.047674 0.000000 0 13.54703261 0.00000000 0.00000000 + [5,] 344.359574 0.000000 0 32.45445129 0.00000000 0.00000000 + [6,] 470.915988 0.000000 0 51.58064736 0.00000000 0.00000000 + [7,] 666.422942 0.000000 0 84.29731527 0.00000000 0.00000000 + [8,] -3.469424 2.173913 0 -0.01448574 0.01921805 0.00000000 + [9,] -39.897018 2.173913 0 -1.29792815 0.22100003 0.00000000 +[10,] -74.390387 2.173913 0 -3.61089897 0.41206783 0.00000000 +[11,] -141.095948 2.173913 0 -9.73092951 0.78156740 0.00000000 +[12,] -187.530531 2.173913 0 -14.84774649 1.03878072 0.00000000 +[13,] -292.606054 2.173913 0 -28.17838286 1.62082155 0.00000000 +[14,] 4.347646 0.000000 5 0.01815255 0.00000000 0.04420151 +[15,] 49.996228 0.000000 5 1.62647522 0.00000000 0.50830007 +[16,] 93.220970 0.000000 5 4.52493284 0.00000000 0.94775601 +[17,] 176.811839 0.000000 5 12.19413860 0.00000000 1.79760503 +[18,] 235.000498 0.000000 5 18.60618538 0.00000000 2.38919565 +[19,] 366.673993 0.000000 5 35.31123163 0.00000000 3.72788957 + +$result$retres +$result$retres$res + [1] -0.229318834 0.019496978 -0.006200191 -0.008708174 0.274214137 0.274751309 -0.317773904 -0.011048246 0.305280544 -0.020856375 -0.569279035 0.160361121 0.135541991 0.591131793 -0.005123553 -0.237718234 -0.580149372 -0.284088030 0.515947397 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02867762 14.38735 0.1319561 + [2,] 0.05784594 14.13016 0.2720790 + [3,] 0.07396400 13.98805 0.3495091 + [4,] 0.11473784 13.62854 0.5453842 + [5,] 0.19750828 12.89874 0.9430085 + [6,] 0.27009503 12.25873 1.2917109 + [7,] 0.38222852 11.27003 1.8303936 + [8,] 0.03386837 14.34158 0.1568921 + [9,] 0.08836916 13.86104 0.4187107 + [10,] 0.13997608 13.40601 0.6666273 + [11,] 0.23977696 12.52605 1.1460648 + [12,] 0.30924961 11.91350 1.4798072 + [13,] 0.46645734 10.52737 2.2350238 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0045863767 NA NA + [2,] -0.0003899396 NA NA + [3,] 0.0001240038 NA NA + [4,] 0.0001741635 NA NA + [5,] -0.0054842827 NA NA + [6,] -0.0054950262 NA NA + [7,] 0.0063554781 NA NA + [8,] NA 0.005082193 -0.118226359 + [9,] NA -0.140429050 0.001024711 +[10,] NA 0.009593932 0.047543647 +[11,] NA 0.261868356 0.116029874 +[12,] NA -0.073766116 0.056817606 +[13,] NA -0.062349316 -0.103189479 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ypfJ_res/KEIO_ROBOT4_37_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ypfJ_res/KEIO_ROBOT4_37_res.txt new file mode 100644 index 0000000..4647fc1 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ypfJ_res/KEIO_ROBOT4_37_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0286776251089105 0.0278931610829535 0.0273450353646942 0.00350585181243164 0.0219976586710117 0.0354302794276125 +Glc 14.3873451543233 14.3520769355791 14.3599181269431 0.174131024378151 14.0180760350116 14.6420888548148 +Ace 0.131956062253453 0.152663752366172 0.156133838248655 0.0835139589340077 0.000604857467656721 0.296807205933463 +mu 0.587168283758178 0.59599001026977 0.596311419915741 0.0300617002186424 0.532530675817396 0.651912602437088 +qGlc -5.17715603034682 -5.13982191400204 -5.14655331796491 0.518059309985906 -6.15139592203692 -4.27646210243005 +qAce 2.82072165539981 2.80640555021532 2.81994694299986 0.274280995816256 2.29533607325769 3.45312626074637 +res 1.85611669152183 31.0217139275788 30.1638059852874 7.73960130370454 18.8806458590323 46.3947981610754 + + +Goodness of fit (khi2 test) + +khi2 value 1.85611669152201 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.142778207040155 +p-value, i.e. P(X^2<=value) 0.000148069136346256 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqcA.txt b/validation/validation_results/Berges_2021/Berges_2021/yqcA.txt new file mode 100644 index 0000000..2ed63b5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqcA.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.095256 NA NA NA +3.34194444444444 0.1512 NA NA NA +3.9975 0.213192 NA NA NA +4.52333333333333 0.320544 NA NA NA +1.95 NA 13.5203485781316 0.341063881450405 0 +3.25 NA 13.3429250811023 0.900928800571094 0 +4.08333333333333 NA 11.6913541408461 1.24235221966662 0 +4.76666666666667 NA 11.1524597923599 1.59200447581875 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqcA_res/KEIO_ROBOT2_14.pdf b/validation/validation_results/Berges_2021/Berges_2021/yqcA_res/KEIO_ROBOT2_14.pdf new file mode 100644 index 0000000..88e433d Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yqcA_res/KEIO_ROBOT2_14.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqcA_res/KEIO_ROBOT2_14_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yqcA_res/KEIO_ROBOT2_14_log.txt new file mode 100644 index 0000000..302e1c0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqcA_res/KEIO_ROBOT2_14_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.095256 NA NA NA +[2,] 0.151200 NA NA NA +[3,] 0.213192 NA NA NA +[4,] 0.320544 NA NA NA +[5,] NA 13.52035 0.3410639 0 +[6,] NA 13.34293 0.9009288 0 +[7,] NA 11.69135 1.2423522 0 +[8,] NA 11.15246 1.5920045 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 1.954653e-02 1.403556e+01 2.795120e-01 1.000000e-06 6.126452e-01 -5.396591e+00 2.480863e+00 -2.447328e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-1.604466e-09 -3.834132e-08 5.655551e-08 4.235165e-22 2.055434e-08 4.565102e-09 -1.326837e-07 3.710484e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.01050416 0.68990664 0.30126515 0.28865185 0.12895634 1.95551310 0.85291508 0.82704791 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6509312 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-1.604466e-09 -3.834132e-08 5.655551e-08 4.235165e-22 2.055434e-08 4.565102e-09 -1.326837e-07 3.710484e-13 + +$result$normp +[1] 1.507297e-07 + +$result$res + [1] -2.381994e-01 1.226039e-02 6.552337e-01 -4.117027e-01 2.582231e-01 -8.611926e-01 9.030111e-01 -3.000415e-01 6.034530e-01 -6.044620e-01 -3.807144e-01 3.817234e-01 4.101105e-06 2.531207e-06 6.264425e-07 -1.850319e-06 + +$result$prevres + [1] -2.381993e-01 1.226049e-02 6.552337e-01 -4.117028e-01 2.582231e-01 -8.611926e-01 9.030111e-01 -3.000415e-01 6.034528e-01 -6.044621e-01 -3.807144e-01 3.817236e-01 4.101105e-06 2.531206e-06 6.264417e-07 -1.850320e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.314785e+02 0.000000 0 0 1.131779e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.873967e+02 0.000000 0 0 2.530607e+01 0.0000000 0.0000000 0.0000000 + [3,] 5.788666e+02 0.000000 0 0 4.523105e+01 0.0000000 0.0000000 0.0000000 + [4,] 7.988884e+02 0.000000 0 0 7.063410e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.408987e+01 2.173913 0 0 -1.003713e+00 0.1596941 0.0000000 0.0000000 + [6,] -1.210917e+02 2.173913 0 0 -5.045533e+00 0.4385959 0.0000000 0.0000000 + [7,] -2.145184e+02 2.173913 0 0 -1.180595e+01 0.7769888 0.0000000 0.0000000 + [8,] -3.360010e+02 2.173913 0 0 -2.236983e+01 1.2170003 0.0000000 0.0000000 + [9,] 4.661761e+01 0.000000 5 0 1.061258e+00 0.0000000 0.3672965 0.0000000 +[10,] 1.280341e+02 0.000000 5 0 5.334801e+00 0.0000000 1.0087706 0.0000000 +[11,] 2.268171e+02 0.000000 5 0 1.248280e+01 0.0000000 1.7870742 0.0000000 +[12,] 3.552644e+02 0.000000 5 0 2.365232e+01 0.0000000 2.7991006 0.0000000 +[13,] -4.598746e-05 0.000000 0 5 -1.046913e-06 0.0000000 0.0000000 0.3672965 +[14,] -1.263034e-04 0.000000 0 5 -5.262689e-06 0.0000000 0.0000000 1.0087706 +[15,] -2.237511e-04 0.000000 0 5 -1.231407e-05 0.0000000 0.0000000 1.7870742 +[16,] -3.504622e-04 0.000000 0 5 -2.333261e-05 0.0000000 0.0000000 2.7991006 + +$result$retres +$result$retres$res + [1] -2.381993e-01 1.226049e-02 6.552337e-01 -4.117028e-01 2.582231e-01 -8.611926e-01 9.030111e-01 -3.000415e-01 6.034528e-01 -6.044621e-01 -3.807144e-01 3.817236e-01 4.101105e-06 2.531206e-06 6.264417e-07 -1.850320e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09049201 13.41063 0.5668007 7.165946e-07 + [2,] 0.15144521 12.87371 0.8136264 4.731054e-07 + [3,] 0.22629667 12.21437 1.1167321 1.740968e-07 + [4,] 0.31230994 11.45670 1.4650367 -1.694997e-07 + [5,] 0.06455102 13.63913 0.4617544 8.202209e-07 + [6,] 0.14315022 12.94678 0.7800364 5.062413e-07 + [7,] 0.23851501 12.10674 1.1662093 1.252883e-07 + [8,] 0.36251763 11.01444 1.6683492 -3.700639e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.0047639855 NA NA NA +[2,] -0.0002452099 NA NA NA +[3,] -0.0131046734 NA NA NA +[4,] 0.0082340565 NA NA NA +[5,] NA -0.1187826 -0.12069057 -8.202209e-07 +[6,] NA 0.3961486 0.12089241 -5.062413e-07 +[7,] NA -0.4153851 0.07614287 -1.252883e-07 +[8,] NA 0.1380191 -0.07634472 3.700639e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqcA_res/KEIO_ROBOT2_14_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yqcA_res/KEIO_ROBOT2_14_res.txt new file mode 100644 index 0000000..4f468d5 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqcA_res/KEIO_ROBOT2_14_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0195465286853215 0.0195283276987491 0.0193193511729653 0.00456330251195105 0.0130340610600617 0.0275231835026834 +Glc 14.035560979026 14.1212164942314 14.1415345654148 0.294075125651987 13.5471473266896 14.6272813677944 +Ace 0.279512014039047 0.288210317931931 0.28641270563924 0.161429569809349 1.00000000001488e-06 0.619148744183861 +Lac 1e-06 0.0875639506467995 0.0675969436564443 0.0805679355061623 9.99999999993885e-07 0.271849733302088 +mu 0.612645188913658 0.619076927577653 0.616180351936769 0.0523660473259895 0.53166875070422 0.708811871387596 +qGlc -5.39659114277361 -5.57241059842853 -5.68850870858183 0.90438352867847 -7.40018953875613 -4.15820202780516 +qAce 2.48086323089756 2.47042124332176 2.48458169821891 0.491772060111059 1.43858917334058 3.22362720925602 +qLac -2.44732848426008e-06 -0.017951007448056 -0.0292192927196026 0.231395899755764 -0.433007878381474 0.436454059032769 +res 3.38969152986101 19.6916436674 18.8682802461743 7.04199647989536 9.57043898251242 34.1742363896551 + + +Goodness of fit (khi2 test) + +khi2 value 3.38969152986114 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.423711441232642 +p-value, i.e. P(X^2<=value) 0.0924199464438536 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqcC.txt b/validation/validation_results/Berges_2021/Berges_2021/yqcC.txt new file mode 100644 index 0000000..fe61eb6 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqcC.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.084672 NA NA NA +3.34194444444444 0.134568 NA NA NA +3.9975 0.175392 NA NA NA +4.52333333333333 0.244944 NA NA NA +1.95 NA 13.5620335304768 0.386830376127548 0 +3.25 NA 12.8685611732892 0.953123096569092 0 +4.08333333333333 NA 11.9416118919371 1.52881634593299 0 +4.76666666666667 NA 10.5107246694968 2.1619972200826 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqcC_res/KEIO_ROBOT2_1.pdf b/validation/validation_results/Berges_2021/Berges_2021/yqcC_res/KEIO_ROBOT2_1.pdf new file mode 100644 index 0000000..ddae551 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yqcC_res/KEIO_ROBOT2_1.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqcC_res/KEIO_ROBOT2_1_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yqcC_res/KEIO_ROBOT2_1_log.txt new file mode 100644 index 0000000..06b3bfe --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqcC_res/KEIO_ROBOT2_1_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.084672 NA NA NA +[2,] 0.134568 NA NA NA +[3,] 0.175392 NA NA NA +[4,] 0.244944 NA NA NA +[5,] NA 13.56203 0.3868304 0 +[6,] NA 12.86856 0.9531231 0 +[7,] NA 11.94161 1.5288163 0 +[8,] NA 10.51072 2.1619972 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.257894e-02 1.425119e+01 8.038104e-02 1.000000e-06 5.240022e-01 -7.563616e+00 4.385574e+00 -2.835544e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac +-1.342813e-09 2.538359e-09 2.489641e-08 -2.117582e-22 1.452704e-08 -1.579822e-07 -6.633145e-09 2.284067e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.005422143 0.305845583 0.140186953 0.123095741 0.058274308 0.970933726 0.438566291 0.400063459 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.2608533 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac +-1.342813e-09 2.538359e-09 2.489641e-08 -2.117582e-22 1.452704e-08 -1.579822e-07 -6.633145e-09 2.284067e-13 + +$result$normp +[1] 1.607529e-07 + +$result$res + [1] -4.645723e-02 -2.240474e-01 4.008299e-01 -1.675525e-01 2.383062e-01 -1.757700e-01 -2.906005e-01 2.280642e-01 1.479036e-01 -1.208858e-01 -1.588724e-01 1.318545e-01 3.913679e-06 2.256752e-06 4.202064e-07 -1.814719e-06 + +$result$prevres + [1] -4.645713e-02 -2.240473e-01 4.008299e-01 -1.675526e-01 2.383062e-01 -1.757700e-01 -2.906005e-01 2.280643e-01 1.479036e-01 -1.208858e-01 -1.588723e-01 1.318545e-01 3.913679e-06 2.256752e-06 4.202060e-07 -1.814720e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 1.854446e+02 0.000000 0 0 1.047367e+01 0.0000000 0.0000000 0.0000000 + [2,] 2.880717e+02 0.000000 0 0 2.173719e+01 0.0000000 0.0000000 0.0000000 + [3,] 4.061497e+02 0.000000 0 0 3.665879e+01 0.0000000 0.0000000 0.0000000 + [4,] 5.349963e+02 0.000000 0 0 5.464027e+01 0.0000000 0.0000000 0.0000000 + [5,] -5.579815e+01 2.173913 0 0 -1.434006e+00 0.1665689 0.0000000 0.0000000 + [6,] -1.409051e+02 2.173913 0 0 -6.570956e+00 0.4206306 0.0000000 0.0000000 + [7,] -2.352381e+02 2.173913 0 0 -1.444511e+01 0.7022337 0.0000000 0.0000000 + [8,] -3.500335e+02 2.173913 0 0 -2.596727e+01 1.0449216 0.0000000 0.0000000 + [9,] 7.441229e+01 0.000000 5 0 1.912387e+00 0.0000000 0.3831085 0.0000000 +[10,] 1.879107e+02 0.000000 5 0 8.763011e+00 0.0000000 0.9674503 0.0000000 +[11,] 3.137129e+02 0.000000 5 0 1.926397e+01 0.0000000 1.6151375 0.0000000 +[12,] 4.668039e+02 0.000000 5 0 3.462989e+01 0.0000000 2.4033197 0.0000000 +[13,] -4.811214e-05 0.000000 0 5 -1.236477e-06 0.0000000 0.0000000 0.3831085 +[14,] -1.214959e-04 0.000000 0 5 -5.665828e-06 0.0000000 0.0000000 0.9674503 +[15,] -2.028348e-04 0.000000 0 5 -1.245534e-05 0.0000000 0.0000000 1.6151375 +[16,] -3.018175e-04 0.000000 0 5 -2.239036e-05 0.0000000 0.0000000 2.4033197 + +$result$retres +$result$retres$res + [1] -4.645713e-02 -2.240473e-01 4.008299e-01 -1.675526e-01 2.383062e-01 -1.757700e-01 -2.906005e-01 2.280643e-01 1.479036e-01 -1.208858e-01 -1.588723e-01 1.318545e-01 3.913679e-06 2.256752e-06 4.202060e-07 -1.814720e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.08374286 13.36833 0.5922851 6.690224e-07 + [2,] 0.13008705 12.69938 0.9801573 4.182390e-07 + [3,] 0.18340860 11.92972 1.4264255 1.296990e-07 + [4,] 0.24159295 11.08987 1.9133925 -1.851552e-07 + [5,] 0.06272888 13.67165 0.4164111 7.827358e-07 + [6,] 0.12396816 12.78771 0.9289459 4.513503e-07 + [7,] 0.19184606 11.80794 1.4970419 8.404120e-08 + [8,] 0.27444791 10.61563 2.1883681 -3.629439e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.0009291426 NA NA NA +[2,] 0.0044809469 NA NA NA +[3,] -0.0080165975 NA NA NA +[4,] 0.0033510524 NA NA NA +[5,] NA -0.10962083 -0.02958072 -7.827358e-07 +[6,] NA 0.08085421 0.02417716 -4.513503e-07 +[7,] NA 0.13367621 0.03177447 -8.404120e-08 +[8,] NA -0.10490958 -0.02637091 3.629439e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqcC_res/KEIO_ROBOT2_1_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yqcC_res/KEIO_ROBOT2_1_res.txt new file mode 100644 index 0000000..52f656a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqcC_res/KEIO_ROBOT2_1_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0225789368223568 0.0227777399806621 0.0228649636041822 0.00555616835368767 0.0138559618865094 0.0334399028789975 +Glc 14.2511913717608 14.2179769383142 14.2268771154757 0.33869489318047 13.5531652313488 14.9096664715308 +Ace 0.0803810389601655 0.132955492171123 0.10445131147232 0.129181646760911 9.99999999917039e-07 0.370130556105556 +Lac 1e-06 0.0877890238408141 0.0686717451158718 0.087721005578885 9.99999999986122e-07 0.273884902373849 +mu 0.524002242141629 0.528044738090465 0.524023649381263 0.0578890567141491 0.422801800684208 0.636281263948925 +qGlc -7.56361550175106 -7.57241739844697 -7.58982076079972 1.31192888518561 -10.2897104515071 -5.07313457376644 +qAce 4.38557368907834 4.2765406766186 4.20624522064771 0.528464315673444 3.28272395955431 5.3581629771268 +qLac -2.83554420279808e-06 -0.0266022007318714 0.024887063955514 0.315316460651675 -0.696570749808112 0.529883932143614 +res 0.544355694928562 19.4672339549621 19.2270515031997 5.3375068516271 11.0072426299834 29.869915024905 + + +Goodness of fit (khi2 test) + +khi2 value 0.544355694928594 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.0680444618660742 +p-value, i.e. P(X^2<=value) 0.000184107415100919 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqfE.txt b/validation/validation_results/Berges_2021/Berges_2021/yqfE.txt new file mode 100644 index 0000000..6d0a33f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqfE.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.058968 NA NA +1.61361111111111 0.074088 NA NA +2.36138888888889 0.114912 NA NA +3.28638888888889 0.199584 NA NA +3.81944444444444 0.300888 NA NA +4.41083333333333 0.421848 NA NA +0.283333333333333 NA 14.6361297722452 0.0470318676847792 +1.91666666666667 NA 13.5692365336593 0.425006626146467 +2.7 NA 13.2277206530934 0.809676875773931 +3.61666666666667 NA 12.6999793743425 1.53710160045397 +4.05 NA 11.6364492524126 1.75642328534372 +4.75 NA 9.97651301667975 2.46918315695956 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqfE_res/KEIO_ROBOT4_43.pdf b/validation/validation_results/Berges_2021/Berges_2021/yqfE_res/KEIO_ROBOT4_43.pdf new file mode 100644 index 0000000..8783c84 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yqfE_res/KEIO_ROBOT4_43.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqfE_res/KEIO_ROBOT4_43_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yqfE_res/KEIO_ROBOT4_43_log.txt new file mode 100644 index 0000000..553cb1d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqfE_res/KEIO_ROBOT4_43_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.058968 NA NA + [3,] 0.074088 NA NA + [4,] 0.114912 NA NA + [5,] 0.199584 NA NA + [6,] 0.300888 NA NA + [7,] 0.421848 NA NA + [8,] NA 14.636130 0.04703187 + [9,] NA 13.569237 0.42500663 +[10,] NA 13.227721 0.80967688 +[11,] NA 12.699979 1.53710160 +[12,] NA 11.636449 1.75642329 +[13,] NA 9.976513 2.46918316 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02887857 14.46229148 0.15266405 0.60654344 -5.51546970 3.06511404 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.298266e-09 2.084575e-08 6.457436e-08 -1.791664e-08 1.045539e-07 -2.866441e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.006756127 0.387483361 0.170608217 0.058629188 0.932653480 0.417090467 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5850465 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.298266e-09 2.084575e-08 6.457436e-08 -1.791664e-08 1.045539e-07 -2.866441e-07 + +$result$normp +[1] 3.130927e-07 + +$result$res + [1] -0.29487143 0.03238589 0.13798325 0.30194569 0.61922284 -0.40046067 -0.13001578 -0.48495029 0.68661875 0.31863821 -0.71760608 0.05540166 0.14189776 0.66497851 0.24215365 -0.26189854 -1.10810629 -0.23757767 0.70045033 + +$result$prevres + [1] -0.29487154 0.03238572 0.13798305 0.30194546 0.61922262 -0.40046083 -0.13001579 -0.48495033 0.68661876 0.31863824 -0.71760605 0.05540168 0.14189771 0.66497818 0.24215338 -0.26189873 -1.10810628 -0.23757749 0.70045093 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.0000000 0.00000000 + [2,] 103.217916 0.000000 0 3.56203893 0.0000000 0.00000000 + [3,] 133.053097 0.000000 0 6.20011199 0.0000000 0.00000000 + [4,] 209.412919 0.000000 0 14.28060666 0.0000000 0.00000000 + [5,] 366.999575 0.000000 0 34.83053834 0.0000000 0.00000000 + [6,] 507.086728 0.000000 0 55.93171210 0.0000000 0.00000000 + [7,] 725.880291 0.000000 0 92.46158303 0.0000000 0.00000000 + [8,] -3.706588 2.173913 0 -0.01559826 0.0194074 0.00000000 + [9,] -43.451079 2.173913 0 -1.43043342 0.2275065 0.00000000 +[10,] -81.901957 2.173913 0 -4.02793194 0.4288323 0.00000000 +[11,] -157.511933 2.173913 0 -11.01644163 0.8247202 0.00000000 +[12,] -210.804542 2.173913 0 -16.93058680 1.1037561 0.00000000 +[13,] -332.765605 2.173913 0 -32.51462580 1.7423347 0.00000000 +[14,] 4.737686 0.000000 5 0.01993738 0.0000000 0.04463703 +[15,] 55.538298 0.000000 5 1.82835132 0.0000000 0.52326485 +[16,] 104.685440 0.000000 5 5.14842187 0.0000000 0.98631418 +[17,] 201.328596 0.000000 5 14.08099489 0.0000000 1.89685642 +[18,] 269.446140 0.000000 5 21.64033671 0.0000000 2.53863907 +[19,] 425.334327 0.000000 5 41.55954301 0.0000000 4.00736986 + +$result$retres +$result$retres$res + [1] -0.29487154 0.03238572 0.13798305 0.30194546 0.61922262 -0.40046083 -0.13001579 -0.48495033 0.68661876 0.31863824 -0.71760605 0.05540168 0.14189771 0.66497818 0.24215338 -0.26189873 -1.10810628 -0.23757749 0.70045093 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02887857 14.46229 0.1526640 + [2,] 0.05961571 14.18279 0.3079915 + [3,] 0.07684766 14.02610 0.3950716 + [4,] 0.12095091 13.62505 0.6179435 + [5,] 0.21196845 12.79740 1.0778927 + [6,] 0.29287878 12.06166 1.4867660 + [7,] 0.41924768 10.91256 2.1253602 + [8,] 0.03429343 14.41305 0.1800275 + [9,] 0.09235514 13.88508 0.4734373 + [10,] 0.14852705 13.37429 0.7572971 + [11,] 0.25898374 12.36988 1.3154803 + [12,] 0.33683755 11.66193 1.7089078 + [13,] 0.51500736 10.04179 2.6092733 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0058974308 NA NA + [2,] -0.0006477144 NA NA + [3,] -0.0027596611 NA NA + [4,] -0.0060389092 NA NA + [5,] -0.0123844524 NA NA + [6,] 0.0080092166 NA NA + [7,] 0.0026003157 NA NA + [8,] NA 0.22307715 -0.13299564 + [9,] NA -0.31584463 -0.04843068 +[10,] NA -0.14657359 0.05237975 +[11,] NA 0.33009878 0.22162126 +[12,] NA -0.02548477 0.04751550 +[13,] NA -0.06527295 -0.14009019 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqfE_res/KEIO_ROBOT4_43_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yqfE_res/KEIO_ROBOT4_43_res.txt new file mode 100644 index 0000000..a3e7bdd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqfE_res/KEIO_ROBOT4_43_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0288785714919106 0.0294299871847321 0.0289820581291996 0.00369707796083511 0.0220976882897079 0.0378225895171221 +Glc 14.4622914760706 14.4457389470698 14.4436881795708 0.195721624771552 14.0640547329679 14.8196715943425 +Ace 0.152664050736553 0.149823300455033 0.150428825192523 0.069833901571546 0.0134135889090226 0.279649745476002 +mu 0.606543441184735 0.604422370152663 0.605030649353441 0.0305033832126538 0.547420840135247 0.669993567864067 +qGlc -5.51546970180024 -5.44523396424187 -5.40604903652227 0.437310011117801 -6.3519369918659 -4.56082321556301 +qAce 3.06511404358214 3.04582072430103 3.05626483597995 0.242705686729046 2.50856117880925 3.49185477474802 +res 4.44963256628058 31.5302041339359 31.387762554531 7.4444493050822 19.0799728357852 47.5224957732034 + + +Goodness of fit (khi2 test) + +khi2 value 4.44963256628136 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.342279428175489 +p-value, i.e. P(X^2<=value) 0.0145989141165674 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqiC.txt b/validation/validation_results/Berges_2021/Berges_2021/yqiC.txt new file mode 100644 index 0000000..f80a4d9 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqiC.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.163296 NA NA +3.67805555555556 0.254016 NA NA +4.09222222222222 0.33264 NA NA +4.565 0.436968 NA NA +0.05 NA 14.6724002421889 0.0228852259746376 +1.95 NA 14.4617426209444 0.52613976409905 +2.83333333333333 NA 13.5165632306445 0.921822999906298 +3.98333333333333 NA 11.7221346342511 1.82163697827604 +4.88333333333333 NA 9.44392442063239 2.84043236600983 +5.16666666666667 NA 8.55970967501807 3.334678675666 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqiC_res/KEIO_ROBOT3_42.pdf b/validation/validation_results/Berges_2021/Berges_2021/yqiC_res/KEIO_ROBOT3_42.pdf new file mode 100644 index 0000000..cf3a0cb Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yqiC_res/KEIO_ROBOT3_42.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqiC_res/KEIO_ROBOT3_42_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yqiC_res/KEIO_ROBOT3_42_log.txt new file mode 100644 index 0000000..58505c8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqiC_res/KEIO_ROBOT3_42_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.163296 NA NA + [2,] 0.254016 NA NA + [3,] 0.332640 NA NA + [4,] 0.436968 NA NA + [5,] NA 14.672400 0.02288523 + [6,] NA 14.461743 0.52613976 + [7,] NA 13.516563 0.92182300 + [8,] NA 11.722135 1.82163698 + [9,] NA 9.443924 2.84043237 +[10,] NA 8.559710 3.33467868 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03230397 14.90873015 0.13691579 0.56851689 -6.31111587 3.19552865 + +$result$lastp + X Glc Ace mu qGlc qAce + 7.166321e-10 4.755254e-09 -1.660075e-08 -5.671433e-09 1.623217e-08 2.325246e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.007084885 0.291697848 0.129229747 0.052217471 0.519374206 0.233067384 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4217291 + +$result$laststep + X Glc Ace mu qGlc qAce + 7.166321e-10 4.755254e-09 -1.660075e-08 -5.671433e-09 1.623217e-08 2.325246e-08 + +$result$normp +[1] 3.369031e-08 + +$result$res + [1] 0.12519618 0.37148982 -0.08912565 -0.20419806 0.49128247 -0.61094322 -0.09717628 0.20178667 0.14046097 -0.12541061 0.59633017 -0.10301217 -0.28686487 -0.59120157 0.15390878 0.23083966 + +$result$prevres + [1] 0.12519613 0.37148980 -0.08912564 -0.20419797 0.49128246 -0.61094321 -0.09717626 0.20178669 0.14046096 -0.12541064 0.59633026 -0.10301213 -0.28686486 -0.59120160 0.15390872 0.23083960 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 256.6246580 0.000000 0 2.384986e+01 0.000000000 0.000000000 + [2,] 404.6650743 0.000000 0 4.808061e+01 0.000000000 0.000000000 + [3,] 512.1002965 0.000000 0 6.769712e+01 0.000000000 0.000000000 + [4,] 670.0167111 0.000000 0 9.880578e+01 0.000000000 0.000000000 + [5,] -0.6958338 2.173913 0 -5.646173e-04 0.003561684 0.000000000 + [6,] -48.9925867 2.173913 0 -1.822528e+00 0.250772644 0.000000000 + [7,] -96.6947945 2.173913 0 -5.564743e+00 0.494940376 0.000000000 + [8,] -208.1971395 2.173913 0 -1.806554e+01 1.065674435 0.000000000 + [9,] -363.4089012 2.173913 0 -4.048566e+01 1.860138792 0.000000000 +[10,] -431.1429085 2.173913 0 -5.148907e+01 2.206840962 0.000000000 +[11,] 0.8103450 0.000000 5 6.575345e-04 0.000000000 0.008191872 +[12,] 57.0551383 0.000000 5 2.122455e+00 0.000000000 0.576777081 +[13,] 112.6075443 0.000000 5 6.480515e+00 0.000000000 1.138362865 +[14,] 242.4594699 0.000000 5 2.103853e+01 0.000000000 2.451051201 +[15,] 423.2139296 0.000000 5 4.714826e+01 0.000000000 4.278319223 +[16,] 502.0947036 0.000000 5 5.996246e+01 0.000000000 5.075734213 + +$result$retres +$result$retres$res + [1] 0.12519613 0.37148980 -0.08912564 -0.20419797 0.49128246 -0.61094321 -0.09717626 0.20178669 0.14046096 -0.12541064 0.59633026 -0.10301213 -0.28686486 -0.59120160 0.15390872 0.23083960 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.16579992 13.426789 0.8872719 + [2,] 0.26144580 12.365023 1.4248797 + [3,] 0.33085749 11.594482 1.8150300 + [4,] 0.43288404 10.461884 2.3885025 + [5,] 0.03323542 14.898390 0.1421513 + [6,] 0.09788548 14.180709 0.5055373 + [7,] 0.16173968 13.471862 0.8644500 + [8,] 0.31099678 11.814957 1.7033967 + [9,] 0.51876333 9.508536 2.8712141 + [10,] 0.60943211 8.502021 3.3808466 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.002503923 NA NA + [2,] -0.007429796 NA NA + [3,] 0.001782513 NA NA + [4,] 0.004083959 NA NA + [5,] NA -0.22598993 -0.11926605 + [6,] NA 0.28103388 0.02060243 + [7,] NA 0.04470108 0.05737297 + [8,] NA -0.09282188 0.11824032 + [9,] NA -0.06461204 -0.03078174 +[10,] NA 0.05768890 -0.04616792 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yqiC_res/KEIO_ROBOT3_42_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yqiC_res/KEIO_ROBOT3_42_res.txt new file mode 100644 index 0000000..d8cbd67 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yqiC_res/KEIO_ROBOT3_42_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0323039741343286 0.0322668652560374 0.0324467348974241 0.00375952027916315 0.025604182522056 0.0394373165000376 +Glc 14.908730149511 14.8952951493095 14.8940066611225 0.257513781816866 14.3848309832061 15.348435071678 +Ace 0.136915787955837 0.157324887206813 0.147016470885437 0.0967297283085611 1.000000000001e-06 0.342405235583282 +mu 0.568516894349986 0.570610761769087 0.567658788907018 0.0260410533307583 0.525799480093035 0.620962853218121 +qGlc -6.3111158694839 -6.32808036121423 -6.30971161116667 0.520101336853046 -7.19639568850235 -5.3455143896599 +qAce 3.19552864584512 3.16252962057414 3.16996732607443 0.176427152404156 2.81259105776307 3.50316158041359 +res 1.7785540659331 22.5305908961294 20.9783898582918 6.95539222272603 10.6632576680362 37.9403851275381 + + +Goodness of fit (khi2 test) + +khi2 value 1.77855406593312 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.177855406593312 +p-value, i.e. P(X^2<=value) 0.00222712624808121 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yrbA.txt b/validation/validation_results/Berges_2021/Berges_2021/yrbA.txt new file mode 100644 index 0000000..471c97d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yrbA.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.148176 NA NA +3.67805555555556 0.229824 NA NA +4.09222222222222 0.305424 NA NA +4.565 0.394632 NA NA +0.05 NA 14.6842861825266 0.0108073230091357 +1.95 NA 14.6543408789455 0.406952688144306 +2.83333333333333 NA 13.2849703928886 0.667512726115276 +3.98333333333333 NA 12.1021998140843 1.34709848500217 +4.88333333333333 NA 9.48499352025986 1.8666227539702 +5.16666666666667 NA 9.28007965013069 1.50224268487244 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yrbA_res/KEIO_ROBOT3_32.pdf b/validation/validation_results/Berges_2021/Berges_2021/yrbA_res/KEIO_ROBOT3_32.pdf new file mode 100644 index 0000000..40ab851 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yrbA_res/KEIO_ROBOT3_32.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yrbA_res/KEIO_ROBOT3_32_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yrbA_res/KEIO_ROBOT3_32_log.txt new file mode 100644 index 0000000..eea59fa --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yrbA_res/KEIO_ROBOT3_32_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.148176 NA NA + [2,] 0.229824 NA NA + [3,] 0.305424 NA NA + [4,] 0.394632 NA NA + [5,] NA 14.684286 0.01080732 + [6,] NA 14.654341 0.40695269 + [7,] NA 13.284970 0.66751273 + [8,] NA 12.102200 1.34709849 + [9,] NA 9.484994 1.86662275 +[10,] NA 9.280080 1.50224268 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03267104 14.91609989 0.22521580 0.54249507 -6.34713066 1.76464082 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.204649e-09 1.552644e-08 -9.790734e-08 -1.089777e-08 -1.851931e-08 2.278404e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.02108117 0.76532089 0.32033584 0.15419319 1.47131125 0.60123718 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.085323 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.204649e-09 1.552644e-08 -9.790734e-08 -1.089777e-08 -1.851931e-08 2.278404e-07 + +$result$normp +[1] 2.49402e-07 + +$result$res + [1] 0.37064442 0.52293351 -0.23039077 -0.29327303 0.48109443 -0.99336707 0.51210216 -0.26409879 0.88569658 -0.62142731 1.08665279 0.09039788 -0.27150051 -1.52890732 -1.22356324 1.84692039 + +$result$prevres + [1] 0.37064438 0.52293355 -0.23039065 -0.29327278 0.48109440 -0.99336706 0.51210219 -0.26409876 0.88569657 -0.62142734 1.08665328 0.09039822 -0.27150031 -1.52890738 -1.22356365 1.84691984 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 238.1143934 0.000000 0 2.238103e+01 0.000000000 0.000000000 + [2,] 367.7303909 0.000000 0 4.418865e+01 0.000000000 0.000000000 + [3,] 460.3713350 0.000000 0 6.155033e+01 0.000000000 0.000000000 + [4,] 594.9712176 0.000000 0 8.873596e+01 0.000000000 0.000000000 + [5,] -0.6993474 2.173913 0 -5.737927e-04 0.003599801 0.000000000 + [6,] -47.8224278 2.173913 0 -1.787051e+00 0.246159791 0.000000000 + [7,] -92.8599658 2.173913 0 -5.357912e+00 0.477984720 0.000000000 + [8,] -195.3189493 2.173913 0 -1.696596e+01 1.005379149 0.000000000 + [9,] -334.2733216 2.173913 0 -3.725791e+01 1.720628893 0.000000000 +[10,] -394.0384522 2.173913 0 -4.707676e+01 2.028262210 0.000000000 +[11,] 0.4471978 0.000000 5 3.669117e-04 0.000000000 0.008279542 +[12,] 30.5800565 0.000000 5 1.142730e+00 0.000000000 0.566167520 +[13,] 59.3793149 0.000000 5 3.426117e+00 0.000000000 1.099364857 +[14,] 124.8967227 0.000000 5 1.084888e+01 0.000000000 2.312372042 +[15,] 213.7511107 0.000000 5 2.382458e+01 0.000000000 3.957446454 +[16,] 251.9679298 0.000000 5 3.010324e+01 0.000000000 4.665003082 + +$result$retres +$result$retres$res + [1] 0.37064438 0.52293355 -0.23039065 -0.29327278 0.48109440 -0.99336706 0.51210219 -0.26409876 0.88569657 -0.62142734 1.08665328 0.09039822 -0.27150031 -1.52890738 -1.22356365 1.84691984 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15558889 13.477975 0.6250459 + [2,] 0.24028267 12.487067 0.9005398 + [3,] 0.30081619 11.778832 1.0974447 + [4,] 0.38876654 10.749823 1.3835316 + [5,] 0.03356936 14.905590 0.2281380 + [6,] 0.09409966 14.197392 0.4250323 + [7,] 0.15195104 13.520537 0.6132127 + [8,] 0.28356113 11.980714 1.0413170 + [9,] 0.46205008 9.892414 1.6219100 + [10,] 0.53881928 8.994223 1.8716267 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.007412888 NA NA + [2,] -0.010458671 NA NA + [3,] 0.004607813 NA NA + [4,] 0.005865456 NA NA + [5,] NA -0.2213034 -0.21733066 + [6,] NA 0.4569488 -0.01807964 + [7,] NA -0.2355670 0.05430006 + [8,] NA 0.1214854 0.30578148 + [9,] NA -0.4074204 0.24471273 +[10,] NA 0.2858566 -0.36938397 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yrbA_res/KEIO_ROBOT3_32_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yrbA_res/KEIO_ROBOT3_32_res.txt new file mode 100644 index 0000000..a4b23ce --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yrbA_res/KEIO_ROBOT3_32_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0326710391394502 0.0327265299125064 0.0325554294797546 0.00402685975869718 0.0263616211334718 0.0404344345846199 +Glc 14.9160998891664 14.9375285318387 14.89453543516 0.255132381004479 14.4629376203339 15.4515638632191 +Ace 0.22521579707008 0.234985385319828 0.235890778074797 0.105407437875119 0.0494162391392525 0.440616507647312 +mu 0.542495065816931 0.543612927068542 0.542296965027262 0.0269538965417632 0.498015758953128 0.590545518999157 +qGlc -6.34713065983469 -6.35010289527536 -6.27445896142337 0.517533301339722 -7.47955659679191 -5.52193333434819 +qAce 1.76464081804841 1.74037175637765 1.73042794667634 0.194556019612792 1.36861847446536 2.08754700662312 +res 11.7792609288844 23.8004430414568 22.3041015416833 7.02822313788334 13.740047244484 40.1324261388105 + + +Goodness of fit (khi2 test) + +khi2 value 11.7792609288854 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 1.17792609288854 +p-value, i.e. P(X^2<=value) 0.69989858929078 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/yrbL.txt b/validation/validation_results/Berges_2021/Berges_2021/yrbL.txt new file mode 100644 index 0000000..de6e4c8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yrbL.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.1134 NA NA NA +3.34194444444444 0.170856 NA NA NA +3.9975 0.223776 NA NA NA +4.52333333333333 0.337176 NA NA NA +1.95 NA 13.2654003484441 0.38055736473915 0 +3.25 NA 12.5945356044042 0.906498483324393 0 +4.08333333333333 NA 11.2768169017106 1.36032588491302 0 +4.76666666666667 NA 10.1970521611792 1.94288963151786 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/yrbL_res/KEIO_ROBOT2_45.pdf b/validation/validation_results/Berges_2021/Berges_2021/yrbL_res/KEIO_ROBOT2_45.pdf new file mode 100644 index 0000000..10af902 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/yrbL_res/KEIO_ROBOT2_45.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/yrbL_res/KEIO_ROBOT2_45_log.txt b/validation/validation_results/Berges_2021/Berges_2021/yrbL_res/KEIO_ROBOT2_45_log.txt new file mode 100644 index 0000000..427a873 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yrbL_res/KEIO_ROBOT2_45_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.113400 NA NA NA +[2,] 0.170856 NA NA NA +[3,] 0.223776 NA NA NA +[4,] 0.337176 NA NA NA +[5,] NA 13.26540 0.3805574 0 +[6,] NA 12.59454 0.9064985 0 +[7,] NA 11.27682 1.3603259 0 +[8,] NA 10.19705 1.9428896 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.592261e-02 1.386777e+01 1.573622e-01 1.000000e-06 5.600794e-01 -5.972868e+00 2.907295e+00 -2.197195e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 7.649986e-09 1.351685e-07 -1.024813e-07 -2.117582e-22 -7.250235e-08 1.544097e-07 3.255505e-08 -6.542202e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.008967531 0.524697836 0.230837695 0.217109801 0.083569954 1.312398370 0.575363409 0.551436616 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4722998 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 7.649986e-09 1.351685e-07 -1.024813e-07 -2.117582e-22 -7.250235e-08 1.544097e-07 3.255505e-08 -6.542202e-13 + +$result$normp +[1] 2.428791e-07 + +$result$res + [1] -4.087985e-01 -1.183580e-01 9.730059e-01 -5.319861e-01 1.191622e-01 -3.411957e-01 3.167522e-01 -9.471865e-02 2.166392e-01 -2.649659e-01 -6.369278e-02 1.120195e-01 3.992873e-06 2.369442e-06 5.024239e-07 -1.831740e-06 + +$result$prevres + [1] -4.087991e-01 -1.183585e-01 9.730059e-01 -5.319855e-01 1.191621e-01 -3.411957e-01 3.167522e-01 -9.471872e-02 2.166394e-01 -2.649660e-01 -6.369290e-02 1.120195e-01 3.992874e-06 2.369443e-06 5.024257e-07 -1.831738e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 2.029581e+02 0.000000 0 0 1.316031e+01 0.0000000 0.0000000 0.0000000 + [2,] 3.249845e+02 0.000000 0 0 2.815402e+01 0.0000000 0.0000000 0.0000000 + [3,] 4.691585e+02 0.000000 0 0 4.861682e+01 0.0000000 0.0000000 0.0000000 + [4,] 6.298294e+02 0.000000 0 0 7.385162e+01 0.0000000 0.0000000 0.0000000 + [5,] -4.591896e+01 2.173913 0 0 -1.367752e+00 0.1992910 0.0000000 0.0000000 + [6,] -1.199378e+02 2.173913 0 0 -6.506553e+00 0.5205369 0.0000000 0.0000000 + [7,] -2.050626e+02 2.173913 0 0 -1.466890e+01 0.8899838 0.0000000 0.0000000 + [8,] -3.114866e+02 2.173913 0 0 -2.693650e+01 1.3518700 0.0000000 0.0000000 + [9,] 5.140745e+01 0.000000 5 0 1.531233e+00 0.0000000 0.4583692 0.0000000 +[10,] 1.342734e+02 0.000000 5 0 7.284253e+00 0.0000000 1.1972348 0.0000000 +[11,] 2.295729e+02 0.000000 5 0 1.642220e+01 0.0000000 2.0469628 0.0000000 +[12,] 3.487172e+02 0.000000 5 0 3.015610e+01 0.0000000 3.1093011 0.0000000 +[13,] -3.885128e-05 0.000000 0 5 -1.157232e-06 0.0000000 0.0000000 0.4583692 +[14,] -1.014774e-04 0.000000 0 5 -5.505088e-06 0.0000000 0.0000000 1.1972348 +[15,] -1.735001e-04 0.000000 0 5 -1.241111e-05 0.0000000 0.0000000 2.0469628 +[16,] -2.635437e-04 0.000000 0 5 -2.279053e-05 0.0000000 0.0000000 3.1093011 + +$result$retres +$result$retres$res + [1] -4.087991e-01 -1.183585e-01 9.730059e-01 -5.319855e-01 1.191621e-01 -3.411957e-01 3.167522e-01 -9.471872e-02 2.166394e-01 -2.649660e-01 -6.369290e-02 1.120195e-01 3.992874e-06 2.369443e-06 5.024257e-07 -1.831738e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.10522402 13.02207 0.5690050 6.889002e-07 + [2,] 0.16848883 12.34740 0.8974040 4.407121e-07 + [3,] 0.24323612 11.55027 1.2854068 1.474782e-07 + [4,] 0.32653629 10.66193 1.7178065 -1.793088e-07 + [5,] 0.07726723 13.32021 0.4238852 7.985748e-07 + [6,] 0.16003192 12.43759 0.8535053 4.738886e-07 + [7,] 0.25521495 11.42252 1.3475873 1.004851e-07 + [8,] 0.37421372 10.15348 1.9652935 -3.663475e-07 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.008175983 NA NA NA +[2,] 0.002367169 NA NA NA +[3,] -0.019460118 NA NA NA +[4,] 0.010639711 NA NA NA +[5,] NA -0.05481458 -0.04332788 -7.985748e-07 +[6,] NA 0.15695000 0.05299319 -4.738886e-07 +[7,] NA -0.14570603 0.01273858 -1.004851e-07 +[8,] NA 0.04357061 -0.02240389 3.663475e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/yrbL_res/KEIO_ROBOT2_45_res.txt b/validation/validation_results/Berges_2021/Berges_2021/yrbL_res/KEIO_ROBOT2_45_res.txt new file mode 100644 index 0000000..0cbaccd --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/yrbL_res/KEIO_ROBOT2_45_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0259226054078775 0.0271505012617268 0.0270488624170366 0.00555379886197194 0.0179325645298129 0.0391433016489185 +Glc 13.8677708774965 13.9543642856663 13.9737150604313 0.334226938182628 13.2498676651689 14.5241521672568 +Ace 0.15736220953221 0.160966476065206 0.168329908770109 0.138215479888771 9.99999999965959e-07 0.446730453315895 +Lac 1e-06 0.0922913194246621 0.0764665529892733 0.0805285884351084 9.99999999993061e-07 0.292187127718257 +mu 0.560079367345419 0.553328774056021 0.549133985571718 0.0488797166728989 0.461107596667493 0.64977028778439 +qGlc -5.97286812262945 -6.02918947984125 -6.06692130806623 0.851183159358363 -7.6444376333532 -4.40812203709917 +qAce 2.90729518767898 2.85542952723296 2.85764685188098 0.378151456470907 2.08769234087452 3.53280334889551 +qLac -2.19719463878127e-06 -0.0450886234896021 -0.0444440121702125 0.228787319485355 -0.461766256796585 0.38655740421945 +res 1.78453697135774 19.4820429371018 18.4693116860546 5.53931464173535 10.6285267014431 30.8086115049376 + + +Goodness of fit (khi2 test) + +khi2 value 1.78453697135872 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.22306712141984 +p-value, i.e. P(X^2<=value) 0.0130802359665497 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ysgA.txt b/validation/validation_results/Berges_2021/Berges_2021/ysgA.txt new file mode 100644 index 0000000..fc89f4d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ysgA.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.033264 NA NA +1.195 0.058968 NA NA +1.61361111111111 0.074088 NA NA +2.36138888888889 0.116424 NA NA +3.28638888888889 0.187488 NA NA +3.81944444444444 0.273672 NA NA +4.41083333333333 0.394632 NA NA +0.283333333333333 NA 14.1234459218697 0.044320989757744 +1.91666666666667 NA 13.6156699580794 0.383178340317912 +2.7 NA 13.4869879553196 0.647958868942575 +3.61666666666667 NA 12.4508789555548 1.07599837738445 +4.05 NA 11.9256887290361 1.30013862777677 +4.75 NA 10.87929448291 1.88777361736879 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ysgA_res/KEIO_ROBOT4_31.pdf b/validation/validation_results/Berges_2021/Berges_2021/ysgA_res/KEIO_ROBOT4_31.pdf new file mode 100644 index 0000000..fbaa1f5 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ysgA_res/KEIO_ROBOT4_31.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ysgA_res/KEIO_ROBOT4_31_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ysgA_res/KEIO_ROBOT4_31_log.txt new file mode 100644 index 0000000..8a07094 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ysgA_res/KEIO_ROBOT4_31_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.033264 NA NA + [2,] 0.058968 NA NA + [3,] 0.074088 NA NA + [4,] 0.116424 NA NA + [5,] 0.187488 NA NA + [6,] 0.273672 NA NA + [7,] 0.394632 NA NA + [8,] NA 14.12345 0.04432099 + [9,] NA 13.61567 0.38317834 +[10,] NA 13.48699 0.64795887 +[11,] NA 12.45088 1.07599838 +[12,] NA 11.92569 1.30013863 +[13,] NA 10.87929 1.88777362 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02819894 14.14305101 0.12722117 0.59523156 -4.42552477 2.41768915 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.735756e-08 2.564313e-07 -3.115141e-07 -1.639140e-07 -7.261810e-08 5.830412e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.003977296 0.217900648 0.095479534 0.035451228 0.550653196 0.243650827 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3296012 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.735756e-08 2.564313e-07 -3.115141e-07 -1.639140e-07 -7.261810e-08 5.830412e-07 + +$result$normp +[1] 7.315583e-07 + +$result$res + [1] -0.25325305 -0.07684471 -0.02030708 -0.07162883 0.59693490 0.01105973 -0.25878701 -0.04110880 0.17591859 -0.39162536 0.21082885 0.19802032 -0.15203359 0.51970606 -0.06027188 -0.31955534 -0.38657743 -0.05661282 0.30331141 + +$result$prevres + [1] -0.25325392 -0.07684592 -0.02030837 -0.07163014 0.59693413 0.01105988 -0.25878492 -0.04110931 0.17591846 -0.39162528 0.21082911 0.19802059 -0.15203357 0.51970753 -0.06027114 -0.31955511 -0.38657789 -0.05661360 0.30331020 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.00000000 + [2,] 101.832053 0.000000 0 3.43150713 0.00000000 0.00000000 + [3,] 130.646543 0.000000 0 5.94469118 0.00000000 0.00000000 + [4,] 203.893252 0.000000 0 13.57697038 0.00000000 0.00000000 + [5,] 353.606930 0.000000 0 32.76968169 0.00000000 0.00000000 + [6,] 485.644807 0.000000 0 52.30599258 0.00000000 0.00000000 + [7,] 690.551763 0.000000 0 85.89134186 0.00000000 0.00000000 + [8,] -2.969209 2.173913 0 -0.01219479 0.01891945 0.00000000 + [9,] -34.418391 2.173913 0 -1.10325663 0.21930993 0.00000000 +[10,] -64.465187 2.173913 0 -3.08477367 0.41076457 0.00000000 +[11,] -122.976519 2.173913 0 -8.36431758 0.78359188 0.00000000 +[12,] -163.918737 2.173913 0 -12.80074381 1.04447087 0.00000000 +[13,] -257.001171 2.173913 0 -24.41358383 1.63758117 0.00000000 +[14,] 3.730820 0.000000 5 0.01532278 0.00000000 0.04351474 +[15,] 43.246802 0.000000 5 1.38624493 0.00000000 0.50441285 +[16,] 81.000681 0.000000 5 3.87602642 0.00000000 0.94475851 +[17,] 154.520327 0.000000 5 10.50978757 0.00000000 1.80226133 +[18,] 205.964335 0.000000 5 16.08416907 0.00000000 2.40228300 +[19,] 322.922663 0.000000 5 30.67573382 0.00000000 3.76643668 + +$result$retres +$result$retres$res + [1] -0.25325392 -0.07684592 -0.02030837 -0.07163014 0.59693413 0.01105988 -0.25878492 -0.04110931 0.17591846 -0.39162528 0.21082911 0.19802059 -0.15203357 0.51970753 -0.06027114 -0.31955511 -0.38657789 -0.05661360 0.30331020 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02819892 14.14305 0.1272215 + [2,] 0.05743108 13.92571 0.2459555 + [3,] 0.07368183 13.80489 0.3119622 + [4,] 0.11499140 13.49775 0.4797517 + [5,] 0.19942668 12.86998 0.8227076 + [6,] 0.27389320 12.31632 1.1251727 + [7,] 0.38945630 11.45712 1.5945623 + [8,] 0.03337919 14.10454 0.1482625 + [9,] 0.08824743 13.69659 0.3711241 + [10,] 0.14066897 13.30684 0.5840478 + [11,] 0.24275155 12.54786 0.9986828 + [12,] 0.31418193 12.01678 1.2888159 + [13,] 0.47657944 10.80936 1.9484357 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0050650783 NA NA + [2,] 0.0015369183 NA NA + [3,] 0.0004061675 NA NA + [4,] 0.0014326028 NA NA + [5,] -0.0119386826 NA NA + [6,] -0.0002211975 NA NA + [7,] 0.0051756984 NA NA + [8,] NA 0.01891028 -0.10394151 + [9,] NA -0.08092249 0.01205423 +[10,] NA 0.18014763 0.06391102 +[11,] NA -0.09698139 0.07731558 +[12,] NA -0.09108947 0.01132272 +[13,] NA 0.06993544 -0.06066204 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ysgA_res/KEIO_ROBOT4_31_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ysgA_res/KEIO_ROBOT4_31_res.txt new file mode 100644 index 0000000..f83b43c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ysgA_res/KEIO_ROBOT4_31_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0281989390504707 0.02806671193113 0.0280236323232151 0.00340510368621246 0.0219905756449708 0.0352437742038841 +Glc 14.1430510092498 14.1372198222063 14.1470647939411 0.173999290426271 13.8258809182589 14.4616611015218 +Ace 0.127221166074915 0.150100028853814 0.154013390328486 0.0733161251982601 0.00332746857652084 0.290339540168643 +mu 0.595231559968474 0.598703187197165 0.597928313678951 0.0287863396433432 0.543179303730034 0.656211112128693 +qGlc -4.42552477107723 -4.45277571539594 -4.51455694643897 0.48469122247374 -5.23833846850951 -3.40830339484669 +qAce 2.4176891485976 2.36611807511865 2.37336171920937 0.263440847556467 1.85329667122954 2.78277330355901 +res 1.41227999911164 32.7972154111346 32.8469655837784 7.32504763788171 21.1206690301826 47.3265550022755 + + +Goodness of fit (khi2 test) + +khi2 value 1.4122799991283 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.108636923009869 +p-value, i.e. P(X^2<=value) 3.02971286002385e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ytfB.txt b/validation/validation_results/Berges_2021/Berges_2021/ytfB.txt new file mode 100644 index 0000000..9a1e565 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ytfB.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.034776 NA NA +1.195 0.065016 NA NA +1.61361111111111 0.0756 NA NA +2.36138888888889 0.1134 NA NA +3.28638888888889 0.18144 NA NA +3.81944444444444 0.285768 NA NA +4.41083333333333 0.394632 NA NA +0.283333333333333 NA 14.3696169166362 0.0448059271617909 +1.91666666666667 NA 13.9511334748496 0.407114524819669 +2.7 NA 13.1604859736693 0.677041527551088 +3.61666666666667 NA 12.475923175511 1.1759440638624 +4.05 NA 11.7192992833029 1.45546170616062 +4.75 NA 10.1633403790114 1.98102579308719 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ytfB_res/KEIO_ROBOT4_3.pdf b/validation/validation_results/Berges_2021/Berges_2021/ytfB_res/KEIO_ROBOT4_3.pdf new file mode 100644 index 0000000..aa0499a Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ytfB_res/KEIO_ROBOT4_3.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ytfB_res/KEIO_ROBOT4_3_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ytfB_res/KEIO_ROBOT4_3_log.txt new file mode 100644 index 0000000..20f3d60 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ytfB_res/KEIO_ROBOT4_3_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.0000000 1.1950000 1.6136111 2.3613889 3.2863889 3.8194444 4.4108333 0.2833333 1.9166667 2.7000000 3.6166667 4.0500000 4.7500000 + +$sys$data_meas + X Glc Ace + [1,] 0.034776 NA NA + [2,] 0.065016 NA NA + [3,] 0.075600 NA NA + [4,] 0.113400 NA NA + [5,] 0.181440 NA NA + [6,] 0.285768 NA NA + [7,] 0.394632 NA NA + [8,] NA 14.36962 0.04480593 + [9,] NA 13.95113 0.40711452 +[10,] NA 13.16049 0.67704153 +[11,] NA 12.47592 1.17594406 +[12,] NA 11.71930 1.45546171 +[13,] NA 10.16334 1.98102579 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02896899 14.42098069 0.13917873 0.59032045 -5.56995044 2.55734126 + +$result$lastp + X Glc Ace mu qGlc qAce + 2.318543e-09 2.779835e-08 -3.840585e-08 -2.120489e-08 3.683184e-08 6.329224e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.00560972 0.30969067 0.13496836 0.04870564 0.78105005 0.34142037 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4639832 + +$result$laststep + X Glc Ace mu qGlc qAce + 2.318543e-09 2.779835e-08 -3.840585e-08 -2.120489e-08 3.683184e-08 6.329224e-08 + +$result$normp +[1] 8.980686e-08 + +$result$res + [1] -0.290350422 -0.318090726 -0.025176195 0.168476408 1.007627299 -0.481204327 -0.155707486 0.003479576 -0.226515071 0.409279652 -0.202617696 -0.022640294 0.039013833 0.586103247 -0.021869446 -0.227848682 -0.504673191 -0.355367725 0.523655796 + +$result$prevres + [1] -0.290350538 -0.318090886 -0.025176368 0.168476233 1.007627195 -0.481204314 -0.155707222 0.003479523 -0.226515070 0.409279679 -0.202617658 -0.022640268 0.039013792 0.586103428 -0.021869360 -0.227848659 -0.504673250 -0.355367820 0.523655662 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.00000000 0.00000000 0.0000000 + [2,] 101.236156 0.000000 0 3.50458739 0.00000000 0.0000000 + [3,] 129.615279 0.000000 0 6.05882513 0.00000000 0.0000000 + [4,] 201.542283 0.000000 0 13.78691290 0.00000000 0.0000000 + [5,] 347.945422 0.000000 0 33.12557482 0.00000000 0.0000000 + [6,] 476.619863 0.000000 0 52.73581686 0.00000000 0.0000000 + [7,] 675.753393 0.000000 0 86.34600039 0.00000000 0.0000000 + [8,] -3.734365 2.173913 0 -0.01575263 0.01942222 0.0000000 + [9,] -43.077857 2.173913 0 -1.41677670 0.22404544 0.0000000 +[10,] -80.462806 2.173913 0 -3.94928654 0.41848238 0.0000000 +[11,] -152.956786 2.173913 0 -10.66841906 0.79551937 0.0000000 +[12,] -203.523174 2.173913 0 -16.29722160 1.05851222 0.0000000 +[13,] -318.158354 2.173913 0 -30.98885066 1.65472314 0.0000000 +[14,] 3.943501 0.000000 5 0.01663483 0.00000000 0.0446711 +[15,] 45.490349 0.000000 5 1.49612053 0.00000000 0.5153045 +[16,] 84.968969 0.000000 5 4.17045867 0.00000000 0.9625095 +[17,] 161.522834 0.000000 5 11.26588317 0.00000000 1.8296945 +[18,] 214.921095 0.000000 5 17.20991588 0.00000000 2.4345781 +[19,] 335.976196 0.000000 5 32.72432113 0.00000000 3.8058632 + +$result$retres +$result$retres$res + [1] -0.290350538 -0.318090886 -0.025176368 0.168476233 1.007627195 -0.481204314 -0.155707222 0.003479523 -0.226515070 0.409279679 -0.202617658 -0.022640268 0.039013792 0.586103428 -0.021869360 -0.227848659 -0.504673250 -0.355367820 0.523655662 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02896899 14.42098 0.1391788 + [2,] 0.05865418 14.14089 0.2677787 + [3,] 0.07509647 13.98575 0.3390087 + [4,] 0.11676952 13.59254 0.5195415 + [5,] 0.20159254 12.79220 0.8870053 + [6,] 0.27614391 12.08877 1.2099711 + [7,] 0.39151786 11.00016 1.7097852 + [8,] 0.03424304 14.37122 0.1620266 + [9,] 0.08980795 13.84694 0.4027407 + [10,] 0.14260680 13.34875 0.6314718 + [11,] 0.24499022 12.38272 1.0750094 + [12,] 0.31640525 11.70888 1.3843881 + [13,] 0.47830478 10.18129 2.0857569 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0058070108 NA NA + [2,] 0.0063618177 NA NA + [3,] 0.0005035274 NA NA + [4,] -0.0033695247 NA NA + [5,] -0.0201525439 NA NA + [6,] 0.0096240863 NA NA + [7,] 0.0031141444 NA NA + [8,] NA -0.001600581 -0.117220686 + [9,] NA 0.104196932 0.004373872 +[10,] NA -0.188268652 0.045569732 +[11,] NA 0.093204123 0.100934650 +[12,] NA 0.010414523 0.071073564 +[13,] NA -0.017946344 -0.104731132 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ytfB_res/KEIO_ROBOT4_3_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ytfB_res/KEIO_ROBOT4_3_res.txt new file mode 100644 index 0000000..3837b5c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ytfB_res/KEIO_ROBOT4_3_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0289689915625648 0.0288984935886889 0.0288115696053231 0.00397525509793933 0.0211533188793502 0.037781797604344 +Glc 14.4209806852722 14.4351942341579 14.4224887394735 0.182167841862303 14.1245804379702 14.7238320079517 +Ace 0.139178726722176 0.149272183624745 0.152322875049805 0.0782337276241811 0.00408291896051815 0.326933576811919 +mu 0.590320447570168 0.59241490514962 0.589863558180981 0.0335950885789895 0.526308985895299 0.657993711538549 +qGlc -5.56995043696181 -5.64259637679289 -5.59455543575105 0.626204006464612 -6.90370606796247 -4.59984919913532 +qAce 2.55734125705697 2.55586289450031 2.55221788875063 0.212565448005126 2.13857890904601 2.91190486537666 +res 2.7986449827316 30.7484388390336 30.4033065900454 7.75355351813328 18.1775599463118 48.0691428027234 + + +Goodness of fit (khi2 test) + +khi2 value 2.79864498273187 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.215280383287067 +p-value, i.e. P(X^2<=value) 0.00143174053701186 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/ytfJ.txt b/validation/validation_results/Berges_2021/Berges_2021/ytfJ.txt new file mode 100644 index 0000000..87e7df3 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ytfJ.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.149688 NA NA +3.67805555555556 0.24948 NA NA +4.09222222222222 0.319032 NA NA +4.565 0.403704 NA NA +0.05 NA 14.2708408014489 0.0166480817716134 +1.95 NA 14.2580369827867 0.374827294809422 +2.83333333333333 NA 13.6222519775065 0.678396025441201 +3.98333333333333 NA 12.2591463944 1.20693556558721 +4.88333333333333 NA 9.7676810600686 1.42546091177408 +5.16666666666667 NA 9.28978451112512 1.96033050994901 diff --git a/validation/validation_results/Berges_2021/Berges_2021/ytfJ_res/KEIO_ROBOT3_16.pdf b/validation/validation_results/Berges_2021/Berges_2021/ytfJ_res/KEIO_ROBOT3_16.pdf new file mode 100644 index 0000000..2d3b9d9 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/ytfJ_res/KEIO_ROBOT3_16.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/ytfJ_res/KEIO_ROBOT3_16_log.txt b/validation/validation_results/Berges_2021/Berges_2021/ytfJ_res/KEIO_ROBOT3_16_log.txt new file mode 100644 index 0000000..a548ff0 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ytfJ_res/KEIO_ROBOT3_16_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.149688 NA NA + [2,] 0.249480 NA NA + [3,] 0.319032 NA NA + [4,] 0.403704 NA NA + [5,] NA 14.270841 0.01664808 + [6,] NA 14.258037 0.37482729 + [7,] NA 13.622252 0.67839603 + [8,] NA 12.259146 1.20693557 + [9,] NA 9.767681 1.42546091 +[10,] NA 9.289785 1.96033051 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.03021366 14.66800628 0.17614891 0.57051519 -5.70954462 1.80852425 + +$result$lastp + X Glc Ace mu qGlc qAce + 5.807710e-09 2.390355e-07 7.282581e-08 -4.627144e-08 -3.024650e-07 -2.541599e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.0128919 0.4958726 0.2103748 0.1016981 0.9274468 0.3877849 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7196605 + +$result$laststep + X Glc Ace mu qGlc qAce + 5.807710e-09 2.390355e-07 7.282581e-08 -4.627144e-08 -3.024650e-07 -2.541599e-07 + +$result$normp +[1] 4.697857e-07 + +$result$res + [1] 0.31387258 -0.15739561 -0.35213410 0.24396588 0.84438254 -0.45099755 -0.37907761 -0.48478839 0.65084801 -0.18036699 0.81136138 -0.01552601 -0.57882692 -0.98566107 1.04027573 -0.27162311 + +$result$prevres + [1] 0.31387212 -0.15739588 -0.35213414 0.24396627 0.84438202 -0.45099781 -0.37907770 -0.48478822 0.65084834 -0.18036664 0.81136101 -0.01552637 -0.57882722 -0.98566113 1.04027615 -0.27162244 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 258.1042678 0.000000 0 2.243520e+01 0.000000000 0.000000000 + [2,] 407.6503150 0.000000 0 4.530115e+01 0.000000000 0.000000000 + [3,] 516.3052339 0.000000 0 6.383648e+01 0.000000000 0.000000000 + [4,] 676.1568355 0.000000 0 9.325914e+01 0.000000000 0.000000000 + [5,] -0.6295390 2.173913 0 -4.777775e-04 0.003331382 0.000000000 + [6,] -44.4247839 2.173913 0 -1.546469e+00 0.235086168 0.000000000 + [7,] -87.7899909 2.173913 0 -4.728481e+00 0.464565287 0.000000000 + [8,] -189.3660495 2.173913 0 -1.538019e+01 1.002083408 0.000000000 + [9,] -331.0434822 2.173913 0 -3.452161e+01 1.751809163 0.000000000 +[10,] -392.9400254 2.173913 0 -4.392610e+01 2.079352031 0.000000000 +[11,] 0.4586416 0.000000 5 3.480779e-04 0.000000000 0.007662178 +[12,] 32.3650371 0.000000 5 1.126657e+00 0.000000000 0.540698186 +[13,] 63.9581346 0.000000 5 3.444867e+00 0.000000000 1.068500161 +[14,] 137.9599106 0.000000 5 1.120502e+01 0.000000000 2.304791838 +[15,] 241.1769655 0.000000 5 2.515022e+01 0.000000000 4.029161075 +[16,] 286.2708015 0.000000 5 3.200173e+01 0.000000000 4.782509671 + +$result$retres +$result$retres$res + [1] 0.31387212 -0.15739588 -0.35213414 0.24396627 0.84438202 -0.45099781 -0.37907770 -0.48478822 0.65084834 -0.18036664 0.81136101 -0.01552637 -0.57882722 -0.98566113 1.04027615 -0.27162244 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.15596544 13.409520 0.5747801 + [2,] 0.24633208 12.505158 0.8612409 + [3,] 0.31198932 11.848080 1.0693734 + [4,] 0.40858333 10.881397 1.3755749 + [5,] 0.03108793 14.659257 0.1789203 + [6,] 0.09190896 14.050578 0.3717220 + [7,] 0.15213277 13.447876 0.5626306 + [8,] 0.29319742 12.036144 1.0098033 + [9,] 0.48995321 10.067071 1.6335161 + [10,] 0.57591258 9.206816 1.9060060 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.006277442 NA NA + [2,] 0.003147918 NA NA + [3,] 0.007042683 NA NA + [4,] -0.004879325 NA NA + [5,] NA -0.38841573 -0.162272202 + [6,] NA 0.20745899 0.003105275 + [7,] NA 0.17437574 0.115765444 + [8,] NA 0.22300258 0.197132226 + [9,] NA -0.29939024 -0.208055231 +[10,] NA 0.08296865 0.054324488 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/ytfJ_res/KEIO_ROBOT3_16_res.txt b/validation/validation_results/Berges_2021/Berges_2021/ytfJ_res/KEIO_ROBOT3_16_res.txt new file mode 100644 index 0000000..f0e2e0a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/ytfJ_res/KEIO_ROBOT3_16_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0302136562426861 0.0301977802269615 0.0300336636376002 0.00417644764595762 0.0226853893194341 0.0386079672312869 +Glc 14.6680062794739 14.6755705071882 14.6299904775602 0.243258455996709 14.3036845612181 15.2859873143581 +Ace 0.176148909542794 0.194026399368408 0.206076367977771 0.11112780320697 1.00000000000008e-06 0.409265731729811 +mu 0.570515188963283 0.572482332063187 0.570401084137676 0.0308916500212174 0.515055272920194 0.634344094193929 +qGlc -5.70954461847408 -5.74798636844905 -5.66471570277255 0.490948356320044 -6.86478538931864 -5.00226599563937 +qAce 1.80852424878625 1.77605830058426 1.78539185473015 0.208407876056567 1.32171562800664 2.16184980602745 +res 5.17911220612652 24.7914258803322 23.7562132888494 6.66764858475829 13.7382474999758 36.0434506830136 + + +Goodness of fit (khi2 test) + +khi2 value 5.17911220612848 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.517911220612848 +p-value, i.e. P(X^2<=value) 0.121103677075235 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf1.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf1.txt new file mode 100644 index 0000000..ed9615c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf1.txt @@ -0,0 +1,14 @@ +time X Glc Ace +0 0.036288 NA NA +1.18888888888889 0.066528 NA NA +2.27694444444444 0.09828 NA NA +3.12833333333333 0.137592 NA NA +3.77138888888889 0.179928 NA NA +4.41555555555556 0.255528 NA NA +4.82277777777778 0.367416 NA NA +0.0666666666666667 NA 15.125933361165 0.0115510320274051 +1.71666666666667 NA 15.385713486263 0.373332829191045 +2.8 NA 13.8590491308855 0.844622675919923 +3.63333333333333 NA 12.6614900404757 1.34103319575272 +4.26666666666667 NA 11.9974638560879 1.96571033657265 +4.88333333333333 NA 10.5660230031028 2.68976739705958 diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf1_res/KEIO_ROBOT1_47.pdf b/validation/validation_results/Berges_2021/Berges_2021/zwf1_res/KEIO_ROBOT1_47.pdf new file mode 100644 index 0000000..d6615cc Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/zwf1_res/KEIO_ROBOT1_47.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf1_res/KEIO_ROBOT1_47_log.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf1_res/KEIO_ROBOT1_47_log.txt new file mode 100644 index 0000000..b69b0f6 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf1_res/KEIO_ROBOT1_47_log.txt @@ -0,0 +1,195 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 0.00000000 1.18888889 2.27694444 3.12833333 3.77138889 4.41555556 4.82277778 0.06666667 1.71666667 2.80000000 3.63333333 4.26666667 4.88333333 + +$sys$data_meas + X Glc Ace + [1,] 0.036288 NA NA + [2,] 0.066528 NA NA + [3,] 0.098280 NA NA + [4,] 0.137592 NA NA + [5,] 0.179928 NA NA + [6,] 0.255528 NA NA + [7,] 0.367416 NA NA + [8,] NA 15.12593 0.01155103 + [9,] NA 15.38571 0.37333283 +[10,] NA 13.85905 0.84462268 +[11,] NA 12.66149 1.34103320 +[12,] NA 11.99746 1.96571034 +[13,] NA 10.56602 2.68976740 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02763491 15.39029627 0.04677580 0.52213580 -7.88292072 4.29540979 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.940006e-08 3.035710e-07 -1.743019e-07 -1.659592e-07 8.021557e-07 -4.041185e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.009478703 0.506502205 0.223426194 0.078535683 1.607656898 0.738384273 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.7548199 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.940006e-08 3.035710e-07 -1.743019e-07 -1.659592e-07 8.021557e-07 -4.041185e-07 + +$result$normp +[1] 9.783766e-07 + +$result$res + [1] -0.43265437 -0.75587772 -0.37720026 0.19678001 0.90350148 1.08166376 -1.22946866 0.54257449 -1.30572203 0.32257443 0.79272097 -0.13348840 -0.21865947 0.21638832 0.01612532 -0.22161887 -0.03013837 -0.18358996 0.20283355 + +$result$prevres + [1] -0.43265534 -0.75587901 -0.37720173 0.19677872 0.90350073 1.08166418 -1.22946697 0.54257385 -1.30572211 0.32257471 0.79272139 -0.13348813 -0.21865971 0.21638917 0.01612546 -0.22161921 -0.03013889 -0.18359033 0.20283380 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 50.000000 0.000000 0 0.000000000 0.000000000 0.000000000 + [2,] 93.017222 0.000000 0 3.056063840 0.000000000 0.000000000 + [3,] 164.169198 0.000000 0 10.330037611 0.000000000 0.000000000 + [4,] 256.066801 0.000000 0 22.137271413 0.000000000 0.000000000 + [5,] 358.239152 0.000000 0 37.336375611 0.000000000 0.000000000 + [6,] 501.469793 0.000000 0 61.191052289 0.000000000 0.000000000 + [7,] 620.278605 0.000000 0 82.668840010 0.000000000 0.000000000 + [8,] -1.162569 2.173913 0 -0.001077129 0.004075579 0.000000000 + [9,] -47.609521 2.173913 0 -1.295783044 0.166903099 0.000000000 +[10,] -108.783585 2.173913 0 -5.199454138 0.381358961 0.000000000 +[11,] -185.977394 2.173913 0 -12.125640682 0.651974703 0.000000000 +[12,] -271.729297 2.173913 0 -21.527415907 0.952592271 0.000000000 +[13,] -387.416356 2.173913 0 -36.206496367 1.358152509 0.000000000 +[14,] 1.457015 0.000000 5 0.001349935 0.000000000 0.009373832 +[15,] 59.667672 0.000000 5 1.623968383 0.000000000 0.383877129 +[16,] 136.335403 0.000000 5 6.516329385 0.000000000 0.877125611 +[17,] 233.080228 0.000000 5 15.196723847 0.000000000 1.499541817 +[18,] 340.550672 0.000000 5 26.979703857 0.000000000 2.190962223 +[19,] 485.538004 0.000000 5 45.376581840 0.000000000 3.123750770 + +$result$retres +$result$retres$res + [1] -0.43265534 -0.75587901 -0.37720173 0.19677872 0.90350073 1.08166418 -1.22946697 0.54257385 -1.30572211 0.32257471 0.79272139 -0.13348813 -0.21865971 0.21638917 0.01612546 -0.22161921 -0.03013889 -0.18359033 0.20283380 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.02763489 15.39030 0.04677598 + [2,] 0.05141042 15.03135 0.24236802 + [3,] 0.09073597 14.43763 0.56588404 + [4,] 0.14152757 13.67081 0.98372691 + [5,] 0.19799801 12.81825 1.44828734 + [6,] 0.27716128 11.62308 2.09953286 + [7,] 0.34282666 10.63170 2.63973647 + [8,] 0.02861378 15.37552 0.05482887 + [9,] 0.06772210 14.78508 0.37655792 + [10,] 0.11923066 14.00743 0.80029883 + [11,] 0.18422784 13.02614 1.33500542 + [12,] 0.25643093 11.93606 1.92899227 + [13,] 0.35383942 10.46544 2.73033416 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.008653107 NA NA + [2,] 0.015117580 NA NA + [3,] 0.007544035 NA NA + [4,] -0.003935574 NA NA + [5,] -0.018070015 NA NA + [6,] -0.021633284 NA NA + [7,] 0.024589339 NA NA + [8,] NA -0.24958397 -0.043277834 + [9,] NA 0.60063217 -0.003225093 +[10,] NA -0.14838437 0.044323842 +[11,] NA -0.36465184 0.006027778 +[12,] NA 0.06140454 0.036718067 +[13,] NA 0.10058347 -0.040566760 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf1_res/KEIO_ROBOT1_47_res.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf1_res/KEIO_ROBOT1_47_res.txt new file mode 100644 index 0000000..8786d1a --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf1_res/KEIO_ROBOT1_47_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0276349126360326 0.0277482857196933 0.0273829464528642 0.00380391939717101 0.0212640228605678 0.0347695157884177 +Glc 15.3902962727631 15.3837480248393 15.3738853999518 0.212922963667416 14.9983580417277 15.7569279199095 +Ace 0.0467758012099349 0.0837544305310006 0.0641381545843853 0.0719124698966686 9.9999999999662e-07 0.230408549997326 +mu 0.522135800231532 0.52334208917848 0.527401305339661 0.0311722277692003 0.467626248778103 0.58605773575037 +qGlc -7.88292071691249 -7.81586316122407 -7.88801090115269 0.666239116697895 -8.89565915196523 -6.4574615541294 +qAce 4.29540979226341 4.21283967216076 4.23822798622448 0.339833602296763 3.61589187969615 4.8668191102854 +res 7.40679084331622 31.3917033242765 30.2672642311727 8.37939569701655 18.4801454625705 48.827142945281 + + +Goodness of fit (khi2 test) + +khi2 value 7.40679084332946 +data points 19 +fitted parameters 6 +degrees of freedom 13 +khi2 reduced value 0.569753141794574 +p-value, i.e. P(X^2<=value) 0.120010228540596 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf2.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf2.txt new file mode 100644 index 0000000..c886d5e --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf2.txt @@ -0,0 +1,9 @@ +time X Glc Ace Lac +2.50138888888889 0.09828 NA NA NA +3.34194444444444 0.137592 NA NA NA +3.9975 0.179928 NA NA NA +4.52333333333333 0.255528 NA NA NA +1.95 NA 14.0069524077463 0.409912010980321 0 +3.25 NA 12.8062115639112 0.977467367222399 0 +4.08333333333333 NA 11.5933174769701 1.52474443115104 0 +4.76666666666667 NA 10.8862911465424 2.25155623704185 0 diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf2_res/KEIO_ROBOT2_47.pdf b/validation/validation_results/Berges_2021/Berges_2021/zwf2_res/KEIO_ROBOT2_47.pdf new file mode 100644 index 0000000..e3f9c64 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/zwf2_res/KEIO_ROBOT2_47.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf2_res/KEIO_ROBOT2_47_log.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf2_res/KEIO_ROBOT2_47_log.txt new file mode 100644 index 0000000..49b533f --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf2_res/KEIO_ROBOT2_47_log.txt @@ -0,0 +1,176 @@ +$sys +$sys$params + X Glc Ace Lac mu qGlc qAce qLac + 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "Lac" "mu" "qGlc" "qAce" "qLac" + +$sys$nconc +[1] "X" "Glc" "Ace" "Lac" + +$sys$nflux +[1] "mu" "qGlc" "qAce" "qLac" + +$sys$metab +[1] "Glc" "Ace" "Lac" + +$sys$weight + col +row X Glc Ace Lac + [1,] 0.02 0.46 0.2 0.2 + [2,] 0.02 0.46 0.2 0.2 + [3,] 0.02 0.46 0.2 0.2 + [4,] 0.02 0.46 0.2 0.2 + [5,] 0.02 0.46 0.2 0.2 + [6,] 0.02 0.46 0.2 0.2 + [7,] 0.02 0.46 0.2 0.2 + [8,] 0.02 0.46 0.2 0.2 + +$sys$te_upc + X Glc Ace Lac mu qGlc qAce qLac + 50 50 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace Lac mu qGlc qAce qLac + 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$u + X Glc Ace Lac mu qGlc qAce qLac +X <= 50 -1 0 0 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 0 0 +Lac <= 50 0 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 0 -1 0 0 0 +qGlc <= 50 0 0 0 0 0 -1 0 0 +qAce <= 50 0 0 0 0 0 0 -1 0 +qLac <= 50 0 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 0 0 +Lac >= 1e-06 0 0 0 1 0 0 0 0 +mu >= 0 0 0 0 0 1 0 0 0 +qGlc >= -50 0 0 0 0 0 1 0 0 +qAce >= -50 0 0 0 0 0 0 1 0 +qLac >= -50 0 0 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 Lac <= 50 mu <= 50 qGlc <= 50 qAce <= 50 qLac <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 Lac >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 qLac >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 -5e+01 + +$sys$times +[1] 2.501389 3.341944 3.997500 4.523333 1.950000 3.250000 4.083333 4.766667 + +$sys$data_meas + X Glc Ace Lac +[1,] 0.098280 NA NA NA +[2,] 0.137592 NA NA NA +[3,] 0.179928 NA NA NA +[4,] 0.255528 NA NA NA +[5,] NA 14.00695 0.4099120 0 +[6,] NA 12.80621 0.9774674 0 +[7,] NA 11.59332 1.5247444 0 +[8,] NA 10.88629 2.2515562 0 + +$sys$nb_par +[1] 8 + +$sys$nb_conc +[1] 4 + + +$result +$result$par + X Glc Ace Lac mu qGlc qAce qLac + 2.791005e-02 1.450801e+01 2.462541e-02 1.000000e-06 4.820753e-01 -7.376273e+00 4.275210e+00 -2.620048e-06 + +$result$lastp + X Glc Ace Lac mu qGlc qAce qLac + 3.866318e-09 1.742140e-07 -4.246718e-08 0.000000e+00 -3.505685e-08 -2.587422e-07 -4.755447e-08 -3.273650e-13 + +$result$hci + X Glc Ace Lac mu qGlc qAce qLac +0.009826544 0.500199674 0.229383016 0.201122912 0.085974443 1.449298197 0.653883077 0.598173979 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.4127456 + +$result$laststep + X Glc Ace Lac mu qGlc qAce qLac + 3.866318e-09 1.742140e-07 -4.246718e-08 0.000000e+00 -3.505685e-08 -2.587422e-07 -4.755447e-08 -3.273650e-13 + +$result$normp +[1] 3.203231e-07 + +$result$res + [1] -2.535489e-01 1.093008e-01 5.900478e-01 -4.241077e-01 -3.591159e-01 1.800483e-01 6.177101e-01 -4.386426e-01 4.316445e-03 -7.251290e-02 1.225769e-01 -5.438045e-02 3.816747e-06 2.124709e-06 3.281645e-07 -1.790509e-06 + +$result$prevres + [1] -2.535492e-01 1.093006e-01 5.900478e-01 -4.241074e-01 -3.591160e-01 1.800483e-01 6.177102e-01 -4.386425e-01 4.316487e-03 -7.251295e-02 1.225769e-01 -5.438039e-02 3.816747e-06 2.124710e-06 3.281653e-07 -1.790508e-06 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] + [1,] 1.669811e+02 0.000000 0 0 1.165760e+01 0.0000000 0.0000000 0.0000000 + [2,] 2.504081e+02 0.000000 0 0 2.335652e+01 0.0000000 0.0000000 0.0000000 + [3,] 3.434766e+02 0.000000 0 0 3.832183e+01 0.0000000 0.0000000 0.0000000 + [4,] 4.425752e+02 0.000000 0 0 5.587354e+01 0.0000000 0.0000000 0.0000000 + [5,] -5.189399e+01 2.173913 0 0 -1.630212e+00 0.1963544 0.0000000 0.0000000 + [6,] -1.261018e+02 2.173913 0 0 -7.154883e+00 0.4771387 0.0000000 0.0000000 + [7,] -2.048929e+02 2.173913 0 0 -1.527930e+01 0.7752655 0.0000000 0.0000000 + [8,] -2.978116e+02 2.173913 0 0 -2.680351e+01 1.1268477 0.0000000 0.0000000 + [9,] 6.917758e+01 0.000000 5 0 2.173163e+00 0.0000000 0.4516151 0.0000000 +[10,] 1.681006e+02 0.000000 5 0 9.537857e+00 0.0000000 1.0974191 0.0000000 +[11,] 2.731336e+02 0.000000 5 0 2.036816e+01 0.0000000 1.7831106 0.0000000 +[12,] 3.969995e+02 0.000000 5 0 3.573057e+01 0.0000000 2.5917497 0.0000000 +[13,] -4.239524e-05 0.000000 0 5 -1.331815e-06 0.0000000 0.0000000 0.4516151 +[14,] -1.030199e-04 0.000000 0 5 -5.845243e-06 0.0000000 0.0000000 1.0974191 +[15,] -1.673890e-04 0.000000 0 5 -1.248256e-05 0.0000000 0.0000000 1.7831106 +[16,] -2.432998e-04 0.000000 0 5 -2.189736e-05 0.0000000 0.0000000 2.5917497 + +$result$retres +$result$retres$res + [1] -2.535492e-01 1.093006e-01 5.900478e-01 -4.241074e-01 -3.591160e-01 1.800483e-01 6.177102e-01 -4.386425e-01 4.316487e-03 -7.251295e-02 1.225769e-01 -5.438039e-02 3.816747e-06 2.124710e-06 3.281653e-07 -1.790508e-06 + +$result$retres$sim + col +row X Glc Ace Lac + [1,] 0.09320902 13.50886 0.6037192 6.451044e-07 + [2,] 0.13977801 12.79631 1.0167091 3.920049e-07 + [3,] 0.19172896 12.00140 1.4774279 1.096550e-07 + [4,] 0.24704585 11.15499 1.9679972 -1.909887e-07 + [5,] 0.07145254 13.84176 0.4107753 7.633494e-07 + [6,] 0.13371777 12.88903 0.9629648 4.249420e-07 + [7,] 0.19982876 11.87746 1.5492598 6.563306e-08 + [8,] 0.27779375 10.68452 2.2406802 -3.581015e-07 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace Lac +[1,] 0.005070983 NA NA NA +[2,] -0.002186013 NA NA NA +[3,] -0.011800956 NA NA NA +[4,] 0.008482149 NA NA NA +[5,] NA 0.16519338 -0.0008632975 -7.633494e-07 +[6,] NA -0.08282221 0.0145025903 -4.249420e-07 +[7,] NA -0.28414670 -0.0245153715 -6.563306e-08 +[8,] NA 0.20177553 0.0108760786 3.581015e-07 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf2_res/KEIO_ROBOT2_47_res.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf2_res/KEIO_ROBOT2_47_res.txt new file mode 100644 index 0000000..d0ce776 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf2_res/KEIO_ROBOT2_47_res.txt @@ -0,0 +1,23 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0279100484621791 0.0270463581609042 0.0255236228996247 0.00656918794596394 0.0171147335042118 0.0411205179727649 +Glc 14.5080064632486 14.4949985043066 14.5023559915871 0.400504797875113 13.7800028780728 15.2511687311347 +Ace 0.0246254084055752 0.0825939996822003 0.0404370241737414 0.103149864267329 9.99999999885814e-07 0.345649346482032 +Lac 1e-06 0.078104271435109 0.0561427113593425 0.0781581628450055 9.99999999989591e-07 0.236080972964002 +mu 0.482075272234544 0.495004141479817 0.498972773648981 0.0564028543994358 0.38388932990749 0.594017277227212 +qGlc -7.37627321427026 -7.49501286146345 -7.42805467900007 1.17314638175372 -9.63990723890488 -5.27693761420462 +qAce 4.27520964885811 4.2173568272737 4.16461788994062 0.473531696999949 3.39269761940614 5.20453321218915 +qLac -2.62004795000239e-06 0.00122532102323217 0.0219970400620464 0.256825235018802 -0.495232642973215 0.424576321950521 +res 1.36287123937104 20.2304562934044 20.8224545647757 5.2502639228922 9.73022775279533 29.1632730158028 + + +Goodness of fit (khi2 test) + +khi2 value 1.36287123937126 +data points 16 +fitted parameters 8 +degrees of freedom 8 +khi2 reduced value 0.170358904921407 +p-value, i.e. P(X^2<=value) 0.00524238013208473 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf3.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf3.txt new file mode 100644 index 0000000..599a9cc --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf3.txt @@ -0,0 +1,11 @@ +time X Glc Ace +2.87694444444444 0.130032 NA NA +3.67805555555556 0.21168 NA NA +4.09222222222222 0.296352 NA NA +4.565 0.373464 NA NA +0.05 NA 14.4102331959261 0.0216139118216424 +1.95 NA 14.2957428748693 0.481246963873198 +2.83333333333333 NA 13.4802244021032 0.845184093956694 +3.98333333333333 NA 12.2550358745751 1.79016454664031 +4.88333333333333 NA 9.70928392639294 2.60018284818064 +5.16666666666667 NA 9.15540772537103 3.25076701808274 diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf3_res/KEIO_ROBOT3_47.pdf b/validation/validation_results/Berges_2021/Berges_2021/zwf3_res/KEIO_ROBOT3_47.pdf new file mode 100644 index 0000000..799da44 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/zwf3_res/KEIO_ROBOT3_47.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf3_res/KEIO_ROBOT3_47_log.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf3_res/KEIO_ROBOT3_47_log.txt new file mode 100644 index 0000000..b141f4d --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf3_res/KEIO_ROBOT3_47_log.txt @@ -0,0 +1,180 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 2.876944 3.678056 4.092222 4.565000 0.050000 1.950000 2.833333 3.983333 4.883333 5.166667 + +$sys$data_meas + X Glc Ace + [1,] 0.130032 NA NA + [2,] 0.211680 NA NA + [3,] 0.296352 NA NA + [4,] 0.373464 NA NA + [5,] NA 14.410233 0.02161391 + [6,] NA 14.295743 0.48124696 + [7,] NA 13.480224 0.84518409 + [8,] NA 12.255036 1.79016455 + [9,] NA 9.709284 2.60018285 +[10,] NA 9.155408 3.25076702 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02447011 14.67506980 0.14443120 0.59825049 -6.54311535 3.60452779 + +$result$lastp + X Glc Ace mu qGlc qAce + 4.934526e-09 1.292857e-07 8.455612e-09 -4.689563e-08 -1.154723e-08 -2.057770e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.009126495 0.419520859 0.188193862 0.088510023 0.891390809 0.408713512 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.6135874 + +$result$laststep + X Glc Ace mu qGlc qAce + 4.934526e-09 1.292857e-07 8.455612e-09 -4.689563e-08 -1.154723e-08 -2.057770e-07 + +$result$normp +[1] 2.479664e-07 + +$result$res + [1] 0.33884954 0.46255451 -0.66506183 0.10569294 0.55806550 -0.46176467 0.01026007 -0.46270974 0.57380397 -0.21765513 0.63647034 -0.05416833 -0.22563077 -0.97654747 0.67218161 -0.05230538 + +$result$prevres + [1] 0.33884908 0.46255419 -0.66506197 0.10569317 0.55806523 -0.46176476 0.01026009 -0.46270959 0.57380410 -0.21765507 0.63647029 -0.05416852 -0.22563101 -0.97654764 0.67218182 -0.05230495 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 279.5431260 0.000000 0 1.967959e+01 0.000000000 0.00000000 + [2,] 451.4306373 0.000000 0 4.062984e+01 0.000000000 0.00000000 + [3,] 578.3603784 0.000000 0 5.791533e+01 0.000000000 0.00000000 + [4,] 767.4219098 0.000000 0 8.572565e+01 0.000000000 0.00000000 + [5,] -0.7219521 2.173913 0 -4.438578e-04 0.002699974 0.00000000 + [6,] -52.5697921 2.173913 0 -1.492732e+00 0.196601796 0.00000000 + [7,] -105.7302302 2.173913 0 -4.654280e+00 0.395412505 0.00000000 + [8,] -233.9039040 2.173913 0 -1.554943e+01 0.874759550 0.00000000 + [9,] -417.7090021 2.173913 0 -3.567012e+01 1.562158358 0.00000000 +[10,] -499.2590417 2.173913 0 -4.570568e+01 1.867141193 0.00000000 +[11,] 0.9147450 0.000000 5 5.623874e-04 0.000000000 0.00620994 +[12,] 66.6082344 0.000000 5 1.891357e+00 0.000000000 0.45218413 +[13,] 133.9648434 0.000000 5 5.897177e+00 0.000000000 0.90944876 +[14,] 296.3665151 0.000000 5 1.970181e+01 0.000000000 2.01194696 +[15,] 529.2556438 0.000000 5 4.519561e+01 0.000000000 3.59296422 +[16,] 632.5831240 0.000000 5 5.791111e+01 0.000000000 4.29442474 + +$result$retres +$result$retres$res + [1] 0.33884908 0.46255419 -0.66506197 0.10569317 0.55806523 -0.46176476 0.01026009 -0.46270959 0.57380410 -0.21765507 0.63647029 -0.05416852 -0.22563101 -0.97654764 0.67218182 -0.05230495 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.13680898 13.446410 0.8212858 + [2,] 0.22093108 12.526360 1.3281311 + [3,] 0.28305076 11.846952 1.7024092 + [4,] 0.37557786 10.834975 2.2598956 + [5,] 0.02521312 14.666943 0.1489080 + [6,] 0.07857398 14.083331 0.4704133 + [7,] 0.13328575 13.484944 0.8000579 + [8,] 0.26519978 12.042189 1.5948550 + [9,] 0.45436866 9.973234 2.7346192 + [10,] 0.53829849 9.055286 3.2403060 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.006776982 NA NA + [2,] -0.009251084 NA NA + [3,] 0.013301239 NA NA + [4,] -0.002113863 NA NA + [5,] NA -0.256710004 -0.12729406 + [6,] NA 0.212411788 0.01083370 + [7,] NA -0.004719642 0.04512620 + [8,] NA 0.212846410 0.19530953 + [9,] NA -0.263949885 -0.13443636 +[10,] NA 0.100121333 0.01046099 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf3_res/KEIO_ROBOT3_47_res.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf3_res/KEIO_ROBOT3_47_res.txt new file mode 100644 index 0000000..a435a74 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf3_res/KEIO_ROBOT3_47_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.024470107927589 0.0246451393444466 0.0247212061738458 0.00358508585121187 0.0173270906231219 0.0316960279415277 +Glc 14.6750698001357 14.6711693579076 14.7010961631001 0.269621019872365 14.1293069978804 15.1765227040126 +Ace 0.144431197720741 0.171223731551008 0.167938200381897 0.100879719919461 1.00000000000265e-06 0.371002914726568 +mu 0.598250494764439 0.598787004552039 0.593609221774355 0.0318968532535891 0.545710305978665 0.667865815931951 +qGlc -6.54311534512776 -6.64556325221245 -6.71772925863198 0.615230912839939 -7.72938318342856 -5.32598456026347 +qAce 3.60452778561764 3.56427009105699 3.58039293792474 0.227236092286851 3.12187208120882 3.95815888982152 +res 3.76489484768137 23.4008451503714 22.6353430459401 6.74815434143941 12.4421956081269 38.3342188689643 + + +Goodness of fit (khi2 test) + +khi2 value 3.7648948476822 +data points 16 +fitted parameters 6 +degrees of freedom 10 +khi2 reduced value 0.37648948476822 +p-value, i.e. P(X^2<=value) 0.0426696658551315 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1.txt new file mode 100644 index 0000000..2446dc6 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1.txt @@ -0,0 +1,17 @@ +time X Glc Ace +1.69472222222222 6.8040000000000003E-2 NA NA +2.3002777777777799 8.0135999999999999E-2 NA NA +2.6983333333333301 8.0135999999999999E-2 NA NA +3.43611111111111 0.10584000000000002 NA NA +3.8211111111111098 0.12398400000000001 NA NA +4.2011111111111097 0.13608000000000001 NA NA +4.5980555555555496 0.154224 NA NA +4.9950000000000001 0.189 NA NA +5.3752777777777796 0.23133599999999999 NA NA +1.35 NA 13.9962749760806 0.227238654210141 +1.91666666666667 NA 13.7668815652328 0.340786157030873 +2.86666666666667 NA 13.1362953668268 0.624680660668013 +4 NA 12.7460170755836 1.22435697262662 +4.8 NA 11.6368577386613 1.83627015047314 +5.18333333333333 NA 11.2214000038242 2.27529727862031 +5.58333333333333 NA 10.434112899185 2.76600358980824 diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1_res/KEIO_ROBOT6_7.pdf b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1_res/KEIO_ROBOT6_7.pdf new file mode 100644 index 0000000..9046d70 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1_res/KEIO_ROBOT6_7.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1_res/KEIO_ROBOT6_7_log.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1_res/KEIO_ROBOT6_7_log.txt new file mode 100644 index 0000000..3789845 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1_res/KEIO_ROBOT6_7_log.txt @@ -0,0 +1,211 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + [15,] 0.02 0.46 0.2 + [16,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.694722 2.300278 2.698333 3.436111 3.821111 4.201111 4.598056 4.995000 5.375278 1.350000 1.916667 2.866667 4.000000 4.800000 5.183333 5.583333 + +$sys$data_meas + X Glc Ace + [1,] 0.068040 NA NA + [2,] 0.080136 NA NA + [3,] 0.080136 NA NA + [4,] 0.105840 NA NA + [5,] 0.123984 NA NA + [6,] 0.136080 NA NA + [7,] 0.154224 NA NA + [8,] 0.189000 NA NA + [9,] 0.231336 NA NA +[10,] NA 13.99627 0.2272387 +[11,] NA 13.76688 0.3407862 +[12,] NA 13.13630 0.6246807 +[13,] NA 12.74602 1.2243570 +[14,] NA 11.63686 1.8362702 +[15,] NA 11.22140 2.2752973 +[16,] NA 10.43411 2.7660036 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.02743156 14.31201004 0.00000100 0.39107214 -6.82660156 4.86745821 + +$result$lastp + X Glc Ace mu qGlc qAce +-2.668867e-09 -2.773472e-08 5.551115e-17 2.016423e-08 -1.471065e-07 1.706891e-07 + +$result$hci + X Glc Ace mu qGlc qAce +0.005416128 0.273676808 0.127048291 0.042539900 0.849792169 0.409410778 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3920899 + +$result$laststep + X Glc Ace mu qGlc qAce +-2.668867e-09 -2.773472e-08 5.551115e-17 2.016423e-08 -1.471065e-07 1.706891e-07 + +$result$normp +[1] 2.279431e-07 + +$result$res + [1] -0.74095022 -0.63469694 -0.06670419 -0.03411228 -0.08696717 0.28751896 0.57120570 0.22327938 -0.34247358 -0.03756426 0.02327309 0.40301261 -0.52979781 0.05392771 -0.14309280 0.23024145 0.05103115 0.20132744 0.40719036 0.32992152 0.26731341 -0.12358764 -0.38263034 + +$result$prevres + [1] -0.74095005 -0.63469677 -0.06670402 -0.03411213 -0.08696704 0.28751905 0.57120574 0.22327935 -0.34247371 -0.03756424 0.02327309 0.40301258 -0.52979785 0.05392769 -0.14309278 0.23024151 0.05103121 0.20132751 0.40719046 0.32992160 0.26731340 -0.12358771 -0.38263052 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 97.00685 0.000000 0 4.5097405 0.0000000 0.0000000 + [2,] 122.92784 0.000000 0 7.7567741 0.0000000 0.0000000 + [3,] 143.63365 0.000000 0 10.6316923 0.0000000 0.0000000 + [4,] 191.67290 0.000000 0 18.0666869 0.0000000 0.0000000 + [5,] 222.81749 0.000000 0 23.3555213 0.0000000 0.0000000 + [6,] 258.51673 0.000000 0 29.7922595 0.0000000 0.0000000 + [7,] 301.92973 0.000000 0 38.0829617 0.0000000 0.0000000 + [8,] 352.63313 0.000000 0 48.3180304 0.0000000 0.0000000 + [9,] 409.17554 0.000000 0 60.3338717 0.0000000 0.0000000 +[10,] -26.39094 2.173913 0 -0.5314624 0.1060476 0.0000000 +[11,] -42.35226 2.173913 0 -1.2511858 0.1701855 0.0000000 +[12,] -78.48217 2.173913 0 -3.6506501 0.3153676 0.0000000 +[13,] -143.41618 2.173913 0 -9.8405643 0.5762941 0.0000000 +[14,] -210.03616 2.173913 0 -17.9195763 0.8439955 0.0000000 +[15,] -250.14285 2.173913 0 -23.4166220 1.0051576 0.0000000 +[16,] -298.92458 2.173913 0 -30.6273549 1.2011789 0.0000000 +[17,] 43.27932 0.000000 5 0.8715615 0.0000000 0.2439095 +[18,] 69.45477 0.000000 5 2.0518581 0.0000000 0.3914268 +[19,] 128.70533 0.000000 5 5.9868133 0.0000000 0.7253455 +[20,] 235.19260 0.000000 5 16.1378438 0.0000000 1.3254765 +[21,] 344.44475 0.000000 5 29.3868640 0.0000000 1.9411896 +[22,] 410.21695 0.000000 5 38.4016383 0.0000000 2.3118625 +[23,] 490.21561 0.000000 5 50.2267408 0.0000000 2.7627115 + +$result$retres +$result$retres$res + [1] -0.74095005 -0.63469677 -0.06670402 -0.03411213 -0.08696704 0.28751905 0.57120574 0.22327935 -0.34247371 -0.03756424 0.02327309 0.40301258 -0.52979785 0.05392769 -0.14309278 0.23024151 0.05103121 0.20132751 0.40719046 0.32992160 0.26731340 -0.12358771 -0.38263052 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05322100 13.86183 0.3209878 + [2,] 0.06744206 13.61358 0.4979895 + [3,] 0.07880192 13.41528 0.6393793 + [4,] 0.10515776 12.95521 0.9674158 + [5,] 0.12224466 12.65694 1.1800870 + [6,] 0.14183038 12.31505 1.4238597 + [7,] 0.16564811 11.89929 1.7203058 + [8,] 0.19346559 11.41370 2.0665345 + [9,] 0.22448653 10.87220 2.4526349 + [10,] 0.04650881 13.97900 0.2374449 + [11,] 0.05804678 13.77759 0.3810517 + [12,] 0.08416405 13.32168 0.7061188 + [13,] 0.13110295 12.50231 1.2903413 + [14,] 0.17926060 11.66166 1.8897328 + [15,] 0.20825256 11.15558 2.2505797 + [16,] 0.24351546 10.54002 2.6894775 + + +$result$it +[1] 9 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] 0.0148190010 NA NA + [2,] 0.0126939353 NA NA + [3,] 0.0013340804 NA NA + [4,] 0.0006822426 NA NA + [5,] 0.0017393409 NA NA + [6,] -0.0057503810 NA NA + [7,] -0.0114241147 NA NA + [8,] -0.0044655870 NA NA + [9,] 0.0068494741 NA NA +[10,] NA 0.01727955 -0.01020624 +[11,] NA -0.01070562 -0.04026550 +[12,] NA -0.18538579 -0.08143809 +[13,] NA 0.24370701 -0.06598432 +[14,] NA -0.02480674 -0.05346268 +[15,] NA 0.06582268 0.02471754 +[16,] NA -0.10591109 0.07652610 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1_res/KEIO_ROBOT6_7_res.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1_res/KEIO_ROBOT6_7_res.txt new file mode 100644 index 0000000..8a62cc8 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_1_res/KEIO_ROBOT6_7_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0274315642946867 0.0265265090155164 0.0260263142101923 0.00413315207079173 0.0194899944831248 0.0347029836648974 +Glc 14.3120100445898 14.2609886657634 14.2901106021554 0.232625424377406 13.8195398611113 14.6815142879572 +Ace 1.00000000001488e-06 0.0436266714195628 0.00593509934630962 0.0561183425202083 9.99999999931611e-07 0.174614289576992 +mu 0.391072136761987 0.401447175265292 0.402439115113405 0.0321793575225811 0.340799824322196 0.45920272339732 +qGlc -6.8266015568791 -6.74422896089054 -6.67735571079083 0.739489210639847 -8.18218540123175 -5.26018281029223 +qAce 4.86745821341705 4.81709172291219 4.8091274326796 0.354309912307567 4.18742452402102 5.55191595229834 +res 2.6134866822382 42.1800373507489 41.5421455102228 9.35857223270795 24.58205638473 60.8914998772651 + + +Goodness of fit (khi2 test) + +khi2 value 2.61348668223844 +data points 23 +fitted parameters 6 +degrees of freedom 17 +khi2 reduced value 0.153734510719908 +p-value, i.e. P(X^2<=value) 2.55132998489858e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2.txt new file mode 100644 index 0000000..2b82905 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2.txt @@ -0,0 +1,17 @@ +time X Glc Ace +1.69472222222222 4.8384000000000003E-2 NA NA +2.3002777777777799 8.0135999999999999E-2 NA NA +2.6983333333333301 8.769600000000001E-2 NA NA +3.43611111111111 0.12096 NA NA +3.8211111111111098 0.14363999999999999 NA NA +4.2011111111111097 0.17388000000000001 NA NA +4.5980555555555496 0.20260800000000001 NA NA +4.9950000000000001 0.24645600000000001 NA NA +5.3752777777777796 0.27367199999999997 NA NA +1.35 NA 13.6276306491593 0.231856815855635 +1.91666666666667 NA 13.451641041218 0.328802283722802 +2.86666666666667 NA 13.5252692833252 0.633879357086119 +4 NA 12.8505141021941 1.23321918088029 +4.8 NA 11.8114241397162 1.87169374639449 +5.18333333333333 NA 11.0806435749575 2.13908974913255 +5.58333333333333 NA 10.1818746170598 2.78956891142757 diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2_res/KEIO_ROBOT6_8.pdf b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2_res/KEIO_ROBOT6_8.pdf new file mode 100644 index 0000000..ad1aa91 Binary files /dev/null and b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2_res/KEIO_ROBOT6_8.pdf differ diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2_res/KEIO_ROBOT6_8_log.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2_res/KEIO_ROBOT6_8_log.txt new file mode 100644 index 0000000..82da71c --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2_res/KEIO_ROBOT6_8_log.txt @@ -0,0 +1,211 @@ +$sys +$sys$params + X Glc Ace mu qGlc qAce + 0.6 0.6 0.6 0.6 0.6 0.6 + +$sys$to_est +[1] "X" "Glc" "Ace" "mu" "qGlc" "qAce" + +$sys$nconc +[1] "X" "Glc" "Ace" + +$sys$nflux +[1] "mu" "qGlc" "qAce" + +$sys$metab +[1] "Glc" "Ace" + +$sys$weight + col +row X Glc Ace + [1,] 0.02 0.46 0.2 + [2,] 0.02 0.46 0.2 + [3,] 0.02 0.46 0.2 + [4,] 0.02 0.46 0.2 + [5,] 0.02 0.46 0.2 + [6,] 0.02 0.46 0.2 + [7,] 0.02 0.46 0.2 + [8,] 0.02 0.46 0.2 + [9,] 0.02 0.46 0.2 + [10,] 0.02 0.46 0.2 + [11,] 0.02 0.46 0.2 + [12,] 0.02 0.46 0.2 + [13,] 0.02 0.46 0.2 + [14,] 0.02 0.46 0.2 + [15,] 0.02 0.46 0.2 + [16,] 0.02 0.46 0.2 + +$sys$te_upc + X Glc Ace mu qGlc qAce + 50 50 50 50 50 50 + +$sys$te_loc + X Glc Ace mu qGlc qAce + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$u + X Glc Ace mu qGlc qAce +X <= 50 -1 0 0 0 0 0 +Glc <= 50 0 -1 0 0 0 0 +Ace <= 50 0 0 -1 0 0 0 +mu <= 50 0 0 0 -1 0 0 +qGlc <= 50 0 0 0 0 -1 0 +qAce <= 50 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 +Glc >= 1e-06 0 1 0 0 0 0 +Ace >= 1e-06 0 0 1 0 0 0 +mu >= 0 0 0 0 1 0 0 +qGlc >= -50 0 0 0 0 1 0 +qAce >= -50 0 0 0 0 0 1 + +$sys$co + X <= 50 Glc <= 50 Ace <= 50 mu <= 50 qGlc <= 50 qAce <= 50 X >= 1e-06 Glc >= 1e-06 Ace >= 1e-06 mu >= 0 qGlc >= -50 qAce >= -50 + -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 -5e+01 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 + +$sys$times + [1] 1.694722 2.300278 2.698333 3.436111 3.821111 4.201111 4.598056 4.995000 5.375278 1.350000 1.916667 2.866667 4.000000 4.800000 5.183333 5.583333 + +$sys$data_meas + X Glc Ace + [1,] 0.048384 NA NA + [2,] 0.080136 NA NA + [3,] 0.087696 NA NA + [4,] 0.120960 NA NA + [5,] 0.143640 NA NA + [6,] 0.173880 NA NA + [7,] 0.202608 NA NA + [8,] 0.246456 NA NA + [9,] 0.273672 NA NA +[10,] NA 13.62763 0.2318568 +[11,] NA 13.45164 0.3288023 +[12,] NA 13.52527 0.6338794 +[13,] NA 12.85051 1.2332192 +[14,] NA 11.81142 1.8716937 +[15,] NA 11.08064 2.1390897 +[16,] NA 10.18187 2.7895689 + +$sys$nb_par +[1] 6 + +$sys$nb_conc +[1] 3 + + +$result +$result$par + X Glc Ace mu qGlc qAce + 0.026368773 14.151836677 0.001807275 0.442192507 -5.739174212 4.219699930 + +$result$lastp + X Glc Ace mu qGlc qAce + 1.121769e-09 1.226487e-07 -1.947860e-08 -1.044672e-08 -3.373479e-07 2.152448e-08 + +$result$hci + X Glc Ace mu qGlc qAce +0.005056893 0.283176874 0.129535575 0.040792438 0.764206804 0.361463116 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.425325 + +$result$laststep + X Glc Ace mu qGlc qAce + 1.121769e-09 1.226487e-07 -1.947860e-08 -1.044672e-08 -3.373479e-07 2.152448e-08 + +$result$normp +[1] 3.602769e-07 + +$result$res + [1] 0.37024223 -0.36086157 -0.03716955 -0.02328137 -0.03912831 -0.24415544 -0.05926003 -0.31928212 0.51801581 0.53204097 0.52975804 -0.53685726 -0.78956018 -0.38214209 0.05865805 0.58810248 -0.12286328 0.04324749 0.05090263 -0.03790740 -0.09932101 0.50479209 -0.33885052 + +$result$prevres + [1] 0.37024216 -0.36086164 -0.03716961 -0.02328141 -0.03912833 -0.24415543 -0.05925998 -0.31928200 0.51801601 0.53204076 0.52975786 -0.53685737 -0.78956018 -0.38214199 0.05865821 0.58810271 -0.12286322 0.04324753 0.05090263 -0.03790743 -0.09932105 0.50479206 -0.33885053 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] + [1,] 105.78582 0.000000 0 4.7273296 0.0000000 0.0000000 + [2,] 138.26728 0.000000 0 8.3866710 0.0000000 0.0000000 + [3,] 164.87800 0.000000 0 11.7313560 0.0000000 0.0000000 + [4,] 228.47930 0.000000 0 20.7016025 0.0000000 0.0000000 + [5,] 270.88375 0.000000 0 27.2937063 0.0000000 0.0000000 + [6,] 320.44893 0.000000 0 35.4987359 0.0000000 0.0000000 + [7,] 381.93436 0.000000 0 46.3076613 0.0000000 0.0000000 + [8,] 455.21718 0.000000 0 59.9575724 0.0000000 0.0000000 + [9,] 538.57708 0.000000 0 76.3376309 0.0000000 0.0000000 +[10,] -23.04003 2.173913 0 -0.4506484 0.1058580 0.0000000 +[11,] -37.63567 2.173913 0 -1.0838170 0.1729180 0.0000000 +[12,] -72.01549 2.173913 0 -3.2820522 0.3308769 0.0000000 +[13,] -137.22755 2.173913 0 -9.2669313 0.6304953 0.0000000 +[14,] -207.44216 2.173913 0 -17.4569862 0.9530980 0.0000000 +[15,] -250.97294 2.173913 0 -23.1928992 1.1531012 0.0000000 +[16,] -304.99143 2.173913 0 -30.8693187 1.4012904 0.0000000 +[17,] 38.96216 0.000000 5 0.7620752 0.0000000 0.2434733 +[18,] 63.64432 0.000000 5 1.8328039 0.0000000 0.3977113 +[19,] 121.78280 0.000000 5 5.5501600 0.0000000 0.7610169 +[20,] 232.06056 0.000000 5 15.6709730 0.0000000 1.4501391 +[21,] 350.79796 0.000000 5 29.5208792 0.0000000 2.1921254 +[22,] 424.41129 0.000000 5 39.2206747 0.0000000 2.6521328 +[23,] 515.75999 0.000000 5 52.2019906 0.0000000 3.2229679 + +$result$retres +$result$retres$res + [1] 0.37024216 -0.36086164 -0.03716961 -0.02328141 -0.03912833 -0.24415543 -0.05925998 -0.31928200 0.51801601 0.53204076 0.52975786 -0.53685737 -0.78956018 -0.38214199 0.05865821 0.58810271 -0.12286322 0.04324753 0.05090263 -0.03790743 -0.09932105 0.50479206 -0.33885053 + +$result$retres$sim + col +row X Glc Ace + [1,] 0.05578884 13.77000 0.2825535 + [2,] 0.07291877 13.54767 0.4460188 + [3,] 0.08695261 13.36552 0.5799392 + [4,] 0.12049437 12.93019 0.9000174 + [5,] 0.14285743 12.63994 1.1134208 + [6,] 0.16899689 12.30068 1.3628612 + [7,] 0.20142280 11.87983 1.6722912 + [8,] 0.24007036 11.37822 2.0410923 + [9,] 0.28403232 10.80765 2.4606070 + [10,] 0.04790119 13.87237 0.2072842 + [11,] 0.06154177 13.69533 0.3374518 + [12,] 0.09367197 13.27831 0.6440599 + [13,] 0.15461691 12.48732 1.2256377 + [14,] 0.22023706 11.63564 1.8518295 + [15,] 0.26091942 11.10763 2.2400482 + [16,] 0.31140323 10.45240 2.7217988 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X Glc Ace + [1,] -0.0074048433 NA NA + [2,] 0.0072172328 NA NA + [3,] 0.0007433922 NA NA + [4,] 0.0004656282 NA NA + [5,] 0.0007825666 NA NA + [6,] 0.0048831086 NA NA + [7,] 0.0011851995 NA NA + [8,] 0.0063856400 NA NA + [9,] -0.0103603201 NA NA +[10,] NA -0.24473875 0.024572644 +[11,] NA -0.24368861 -0.008649506 +[12,] NA 0.24695439 -0.010180526 +[13,] NA 0.36319768 0.007581486 +[14,] NA 0.17578531 0.019864210 +[15,] NA -0.02698278 -0.100958413 +[16,] NA -0.27052725 0.067770105 + + diff --git a/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2_res/KEIO_ROBOT6_8_res.txt b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2_res/KEIO_ROBOT6_8_res.txt new file mode 100644 index 0000000..4544588 --- /dev/null +++ b/validation/validation_results/Berges_2021/Berges_2021/zwf_6_2_res/KEIO_ROBOT6_8_res.txt @@ -0,0 +1,21 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0263687728802841 0.0265223722729158 0.0266989242575723 0.00366789405019053 0.0195334817190118 0.0335146240235301 +Glc 14.1518366771248 14.133169615224 14.1050437410583 0.240591037987672 13.727227596276 14.6069189757725 +Ace 0.00180727471902704 0.0373187410617877 1.00000000001119e-06 0.0560399500805978 9.99999999941803e-07 0.174714033666324 +mu 0.442192507061362 0.444674033829012 0.442182602842389 0.0294622595184951 0.392149945537401 0.503094624002006 +qGlc -5.73917421219146 -5.64704723151416 -5.60538103937688 0.626774710049391 -6.75171100972078 -4.50744903329553 +qAce 4.21969992982707 4.10856704341597 4.11317107768157 0.269813505272207 3.63515204231491 4.61860791590803 +res 3.07532331607239 41.5137959721968 41.1085699254052 8.76635531685853 27.5583422393885 60.6096606990108 + + +Goodness of fit (khi2 test) + +khi2 value 3.07532331607262 +data points 23 +fitted parameters 6 +degrees of freedom 17 +khi2 reduced value 0.180901371533684 +p-value, i.e. P(X^2<=value) 8.30137648968507e-05 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset.txt b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset.txt new file mode 100644 index 0000000..61ff454 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset.txt @@ -0,0 +1,2287 @@ +experiments time X Glc Ace +artI 2.87694444444444 0.184464 +artI 3.67805555555556 0.297864 +artI 4.09222222222222 0.361368 +artI 4.565 0.47628 +artI 0.05 14.381245810333 0.0160850202994414 +artI 1.95 13.5621449331404 0.439526057291736 +artI 2.83333333333333 13.3766030275724 0.788742133512994 +artI 3.98333333333333 11.6425454396719 1.46200912027406 +artI 4.88333333333333 8.87425168742146 2.00766963832224 +artI 5.16666666666667 8.27929544860947 2.21451931058294 +hemX 2.87694444444444 0.16632 +hemX 3.67805555555556 0.260064 +hemX 4.09222222222222 0.328104 +hemX 4.565 0.44604 +hemX 0.05 14.1334758215365 0.0275345280503521 +hemX 1.95 13.9013951003329 0.447037313738487 +hemX 2.83333333333333 13.3975521580251 0.857935788195311 +hemX 3.98333333333333 11.7518002418634 1.43577373966348 +hemX 4.88333333333333 9.18584051118 2.25913839748539 +hemX 5.16666666666667 8.36932489281138 2.57909039828179 +modF 2.87694444444444 0.148176 +modF 3.67805555555556 0.24192 +modF 4.09222222222222 0.322056 +modF 4.565 0.382536 +modF 0.05 14.2532679913876 0.0179647286936219 +modF 1.95 14.0904825899408 0.416068258072687 +modF 2.83333333333333 13.5451913151602 0.738217696058503 +modF 3.98333333333333 11.8535655359681 1.41736843460368 +modF 4.88333333333333 9.44599723101056 1.93437059934784 +modF 5.16666666666667 8.90318490242077 2.43945209185069 +nanE 2.87694444444444 0.152712 +nanE 3.67805555555556 0.216216 +nanE 4.09222222222222 0.312984 +nanE 4.565 0.418824 +nanE 0.05 14.4771749259809 0.0189549416820499 +nanE 1.95 13.86609892062 0.43593225944473 +nanE 2.83333333333333 13.2572108454472 0.809168226761888 +nanE 3.98333333333333 12.0009505532612 1.52733310430626 +nanE 4.88333333333333 9.31889075322955 2.25252254345599 +nanE 5.16666666666667 8.91292399789472 2.68604141592259 +wbbJ 0.0 0.033264 +wbbJ 1.195 0.061992 +wbbJ 1.61361111111111 0.074088 +wbbJ 2.36138888888889 0.123984 +wbbJ 3.28638888888889 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growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT2/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT2/flux_results.tsv new file mode 100644 index 0000000..5027ded --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT2/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.021749314669834315 +growth_rate 0.6178219210748811 +Glc_q -6.7492950870510455 +Glc_M0 14.242581600855084 +Ace_q 2.67077912382109 +Ace_M0 0.2229762007464601 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT2/plots.pdf 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growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT4/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT4/flux_results.tsv new file mode 100644 index 0000000..e8b65c9 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT4/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.031032944177474667 +growth_rate 0.5855422525980092 +Glc_q -4.801066957722991 +Glc_M0 14.145874907016227 +Ace_q 2.2582947204709547 +Ace_M0 0.12106441485288312 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT4/plots.pdf 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bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT_BW/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT_BW/flux_results.tsv new file mode 100644 index 0000000..85f4807 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/WT_BW/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.02334982163887278 +growth_rate 0.5132025073632198 +Glc_q -8.136200527710868 +Glc_M0 13.512293281023538 +Ace_q 3.2356679461502487 +Ace_M0 0.27306146732079206 diff --git 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@@ -0,0 +1,24 @@ +iterations: 100 +mc: false +model: + args: null + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/hemX/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/hemX/flux_results.tsv new file mode 100644 index 0000000..424aaa1 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/hemX/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.02998214862058754 +growth_rate 0.5891639239255181 +Glc_q -6.002633649430653 +Glc_M0 14.472777335277407 +Ace_q 2.430392237402438 +Ace_M0 0.18148527201182707 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/hemX/plots.pdf b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/hemX/plots.pdf new file mode 100644 index 0000000..27b7eb5 Binary files /dev/null and b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/hemX/plots.pdf differ diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/hemX/stat_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/hemX/stat_results.tsv new file mode 100644 index 0000000..8e21d45 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/hemX/stat_results.tsv @@ -0,0 +1,18 @@ +================== +Khi² test results +================== + +khi2_value 2.718866 +number_of_measurements 16.000000 +number_of_params 6.000000 +Degrees_of_freedom 10.000000 +p_val 0.012712 + +At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.012711727248724644 + +================== +AIC test results +================== + +AIC 30.003438 +AICc 44.003438 \ No newline at end of file diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/log.txt b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/log.txt new file mode 100644 index 0000000..46e4f9c --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/log.txt @@ -0,0 +1,21749 @@ +2024-05-27 14:29:58,859 - physiofit - INFO - ============================================= +2024-05-27 14:29:58,860 - physiofit - INFO - Physiofit version: 3.3.7 +2024-05-27 14:29:58,860 - physiofit - INFO - Path to results: +C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\All_experiments_res +2024-05-27 14:29:58,860 - physiofit - INFO - ============================================= +2024-05-27 14:29:58,861 - physiofit - INFO - Running optimization for WT1 +2024-05-27 14:29:58,863 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:29:58,863 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:29:58,867 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +0 0.000000 0.031752 NaN NaN +1 0.066667 NaN 15.153739 0.004196 +2 1.188889 0.061992 NaN NaN +3 1.716667 NaN 14.334846 0.348769 +4 2.276944 0.111888 NaN NaN +5 2.800000 NaN 13.607064 0.760104 +6 3.128333 0.172368 NaN NaN +7 3.633333 NaN 12.588734 1.010550 +8 3.771389 0.234360 NaN NaN +9 4.266667 NaN 11.357240 1.674587 +10 4.415556 0.368928 NaN NaN +11 4.822778 0.545832 NaN NaN +12 4.883333 NaN 9.604400 2.029532 +Experimental matrix: +[[3.17520000e-02 nan nan] + [ nan 1.51537394e+01 4.19622433e-03] + [6.19920000e-02 nan nan] + [ nan 1.43348460e+01 3.48769380e-01] + [1.11888000e-01 nan nan] + [ nan 1.36070638e+01 7.60104476e-01] + [1.72368000e-01 nan nan] + [ nan 1.25887340e+01 1.01054974e+00] + [2.34360000e-01 nan nan] + [ nan 1.13572400e+01 1.67458664e+00] + [3.68928000e-01 nan nan] + [5.45832000e-01 nan nan] + [ nan 9.60439982e+00 2.02953207e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:29:58,868 - physiofit - INFO - mc : False +2024-05-27 14:29:58,868 - physiofit - INFO - iterations : 100 +2024-05-27 14:29:58,868 - physiofit - INFO - debug_mode : False +2024-05-27 14:29:58,869 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:29:59,242 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:29:59,243 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 9.912228724061507 + x: [ 2.183e-02 6.564e-01 -6.890e+00 1.493e+01 + 2.558e+00 1.718e-01] + nit: 81 + nfev: 7583 + population: [[ 2.143e-02 6.608e-01 ... 2.557e+00 1.696e-01] + [ 2.166e-02 6.579e-01 ... 2.543e+00 1.804e-01] + ... + [ 2.159e-02 6.591e-01 ... 2.598e+00 1.646e-01] + [ 2.215e-02 6.524e-01 ... 2.559e+00 1.743e-01]] + population_energies: [ 9.912e+00 9.965e+00 ... 9.954e+00 9.955e+00] + jac: [-1.585e-02 -1.441e-03 -7.463e-02 3.899e-02 + 5.789e-02 -1.817e-02] +2024-05-27 14:29:59,243 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02182761903840257 +2024-05-27 14:29:59,243 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6564026175468902 +2024-05-27 14:29:59,243 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.889636213821353 +2024-05-27 14:29:59,243 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.928367833515656 +2024-05-27 14:29:59,243 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.557714526865979 +2024-05-27 14:29:59,244 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.17182017820615572 +2024-05-27 14:29:59,248 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.021828 NaN NaN +0.066667 NaN 14.918120 0.175625 +1.188889 0.047635 NaN NaN +1.716667 NaN 14.450493 0.349227 +2.276944 0.097297 NaN NaN +2.800000 NaN 13.717897 0.621196 +3.128333 0.170140 NaN NaN +3.633333 NaN 12.669794 1.010295 +3.771389 0.259492 NaN NaN +4.266667 NaN 11.387486 1.486340 +4.415556 0.396057 NaN NaN +4.822778 0.517423 NaN NaN +4.883333 NaN 9.506357 2.184692 + +2024-05-27 14:29:59,251 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 9.912228724061507 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.2989044916155757 + +2024-05-27 14:29:59,252 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.2989044916155757 +2024-05-27 14:29:59,254 - physiofit - INFO - Results for WT1: + optimal +WT1 X_0 0.021828 +WT1 growth_rate 0.656403 +WT1 Glc_q -6.889636 +WT1 Glc_M0 14.928368 +WT1 Ace_q 2.557715 +WT1 Ace_M0 0.171820 +2024-05-27 14:29:59,261 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:00,232 - physiofit - INFO - Running optimization for WT2 +2024-05-27 14:30:00,234 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:00,234 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:00,238 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +13 1.950000 NaN 13.794850 0.388241 +14 2.501389 0.111888 NaN NaN +15 3.250000 NaN 12.682199 0.887038 +16 3.341944 0.172368 NaN NaN +17 3.997500 0.234360 NaN NaN +18 4.083333 NaN 11.303985 1.329107 +19 4.523333 0.368928 NaN NaN +20 4.766667 NaN 10.098951 1.884428 +Experimental matrix: +[[ nan 13.79484974 0.3882408 ] + [ 0.111888 nan nan] + [ nan 12.68219888 0.88703837] + [ 0.172368 nan nan] + [ 0.23436 nan nan] + [ nan 11.30398519 1.32910714] + [ 0.368928 nan nan] + [ nan 10.09895085 1.88442802]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:00,238 - physiofit - INFO - mc : False +2024-05-27 14:30:00,238 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:00,238 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:00,238 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:00,673 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:00,674 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.5362585990485016 + x: [ 2.175e-02 6.178e-01 -6.749e+00 1.424e+01 + 2.671e+00 2.230e-01] + nit: 96 + nfev: 9157 + population: [[ 2.199e-02 6.148e-01 ... 2.647e+00 2.266e-01] + [ 2.196e-02 6.144e-01 ... 2.720e+00 2.163e-01] + ... + [ 2.235e-02 6.116e-01 ... 2.659e+00 2.147e-01] + [ 2.155e-02 6.184e-01 ... 2.684e+00 2.403e-01]] + population_energies: [ 2.536e+00 2.580e+00 ... 2.552e+00 2.633e+00] + jac: [-3.750e-03 -1.286e-03 -1.394e-02 6.574e-03 + 3.478e-03 -1.231e-03] +2024-05-27 14:30:00,675 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.021749314669834315 +2024-05-27 14:30:00,675 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6178219210748811 +2024-05-27 14:30:00,675 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.7492950870510455 +2024-05-27 14:30:00,675 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.242581600855084 +2024-05-27 14:30:00,675 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.67077912382109 +2024-05-27 14:30:00,675 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.2229762007464601 +2024-05-27 14:30:00,679 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.687571 0.442601 +2.501389 0.102002 NaN NaN +3.250000 NaN 12.710600 0.829200 +3.341944 0.171453 NaN NaN +3.997500 0.257064 NaN NaN +4.083333 NaN 11.518983 1.300737 +4.523333 0.355739 NaN NaN +4.766667 NaN 9.963526 1.916251 + +2024-05-27 14:30:00,684 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.5362585990485016 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.1356121151893743 + +2024-05-27 14:30:00,684 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.1356121151893743 +2024-05-27 14:30:00,686 - physiofit - INFO - Results for WT2: + optimal +WT2 X_0 0.021749 +WT2 growth_rate 0.617822 +WT2 Glc_q -6.749295 +WT2 Glc_M0 14.242582 +WT2 Ace_q 2.670779 +WT2 Ace_M0 0.222976 +2024-05-27 14:30:00,692 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:01,655 - physiofit - INFO - Running optimization for WT3 +2024-05-27 14:30:01,658 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:01,658 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:01,662 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +21 0.050000 NaN 14.357892 0.020872 +22 1.950000 NaN 13.884627 0.404925 +23 2.833333 NaN 13.666652 0.798660 +24 2.876944 0.160272 NaN NaN +25 3.678056 0.254016 NaN NaN +26 3.983333 NaN 11.814446 1.436027 +27 4.092222 0.353808 NaN NaN +28 4.565000 0.482328 NaN NaN +29 4.883333 NaN 9.367698 2.062118 +30 5.166667 NaN 8.602129 2.444646 +Experimental matrix: +[[ nan 14.35789178 0.02087209] + [ nan 13.88462721 0.40492457] + [ nan 13.66665227 0.79865981] + [ 0.160272 nan nan] + [ 0.254016 nan nan] + [ nan 11.81444553 1.43602668] + [ 0.353808 nan nan] + [ 0.482328 nan nan] + [ nan 9.36769778 2.06211842] + [ nan 8.60212894 2.44464599]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:01,663 - physiofit - INFO - mc : False +2024-05-27 14:30:01,663 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:01,663 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:01,664 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:02,114 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:02,115 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.042940486681606 + x: [ 2.441e-02 6.513e-01 -5.740e+00 1.451e+01 + 2.196e+00 2.165e-01] + nit: 98 + nfev: 9281 + population: [[ 2.433e-02 6.518e-01 ... 2.210e+00 2.074e-01] + [ 2.450e-02 6.501e-01 ... 2.242e+00 1.972e-01] + ... + [ 2.465e-02 6.505e-01 ... 2.169e+00 2.079e-01] + [ 2.382e-02 6.564e-01 ... 2.214e+00 2.165e-01]] + population_energies: [ 4.043e+00 4.123e+00 ... 4.174e+00 4.075e+00] + jac: [-7.410e-03 -8.437e-04 -2.744e-05 -1.199e-05 + 2.018e-04 2.104e-04] +2024-05-27 14:30:02,115 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.024407088054807135 +2024-05-27 14:30:02,115 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6512949038792489 +2024-05-27 14:30:02,115 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.74030671017599 +2024-05-27 14:30:02,115 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.505368685481091 +2024-05-27 14:30:02,115 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.196157048185848 +2024-05-27 14:30:02,115 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.21647727125827196 +2024-05-27 14:30:02,119 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.498248 0.219201 +1.950000 NaN 13.954468 0.427244 +2.833333 NaN 13.358751 0.655157 +2.876944 0.158954 NaN NaN +3.678056 0.267835 NaN NaN +3.983333 NaN 11.840606 1.235976 +4.092222 0.350765 NaN NaN +4.565000 0.477247 NaN NaN +4.883333 NaN 9.545100 2.114203 +5.166667 NaN 8.496270 2.515470 + +2024-05-27 14:30:02,122 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.042940486681606 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.054610932751767226 + +2024-05-27 14:30:02,122 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.054610932751767226 +2024-05-27 14:30:02,124 - physiofit - INFO - Results for WT3: + optimal +WT3 X_0 0.024407 +WT3 growth_rate 0.651295 +WT3 Glc_q -5.740307 +WT3 Glc_M0 14.505369 +WT3 Ace_q 2.196157 +WT3 Ace_M0 0.216477 +2024-05-27 14:30:02,130 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:03,081 - physiofit - INFO - Running optimization for WT4 +2024-05-27 14:30:03,084 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:03,084 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:03,087 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +31 0.000000 0.034776 NaN NaN +32 0.283333 NaN 14.211683 0.042764 +33 1.195000 0.060480 NaN NaN +34 1.613611 0.077112 NaN NaN +35 1.916667 NaN 13.543060 0.339709 +36 2.361389 0.117936 NaN NaN +37 2.700000 NaN 13.003071 0.649267 +38 3.286389 0.208656 NaN NaN +39 3.616667 NaN 12.309991 1.097467 +40 3.819444 0.297864 NaN NaN +41 4.050000 NaN 11.846996 1.345863 +42 4.410833 0.409752 NaN NaN +43 4.750000 NaN 10.220731 1.832603 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.2116831 0.04276392] + [ 0.06048 nan nan] + [ 0.077112 nan nan] + [ nan 13.54305952 0.33970947] + [ 0.117936 nan nan] + [ nan 13.00307079 0.64926705] + [ 0.208656 nan nan] + [ nan 12.30999132 1.09746732] + [ 0.297864 nan nan] + [ nan 11.84699581 1.34586286] + [ 0.409752 nan nan] + [ nan 10.22073086 1.83260327]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:03,088 - physiofit - INFO - mc : False +2024-05-27 14:30:03,088 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:03,088 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:03,088 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:03,583 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:03,584 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.6871133659349988 + x: [ 3.103e-02 5.855e-01 -4.801e+00 1.415e+01 + 2.258e+00 1.211e-01] + nit: 107 + nfev: 10105 + population: [[ 3.086e-02 5.867e-01 ... 2.250e+00 1.266e-01] + [ 3.112e-02 5.847e-01 ... 2.223e+00 1.365e-01] + ... + [ 3.087e-02 5.867e-01 ... 2.274e+00 1.156e-01] + [ 3.115e-02 5.844e-01 ... 2.274e+00 1.102e-01]] + population_energies: [ 1.687e+00 1.710e+00 ... 1.691e+00 1.705e+00] + jac: [ 1.297e-02 4.163e-03 2.722e-04 4.411e-04 + 6.733e-04 -1.969e-04] +2024-05-27 14:30:03,584 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.031032944177474667 +2024-05-27 14:30:03,585 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5855422525980092 +2024-05-27 14:30:03,585 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.801066957722991 +2024-05-27 14:30:03,585 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.145874907016227 +2024-05-27 14:30:03,585 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.2582947204709547 +2024-05-27 14:30:03,585 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.12106441485288312 +2024-05-27 14:30:03,589 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.031033 NaN NaN +0.283333 NaN 14.099957 0.142663 +1.195000 0.062475 NaN NaN +1.613611 0.079829 NaN NaN +1.916667 NaN 13.618685 0.369040 +2.361389 0.123686 NaN NaN +2.700000 NaN 13.163790 0.583011 +3.286389 0.212591 NaN NaN +3.616667 NaN 12.285313 0.996223 +3.819444 0.290469 NaN NaN +4.050000 NaN 11.674434 1.283565 +4.410833 0.410665 NaN NaN +4.750000 NaN 10.293399 1.933167 + +2024-05-27 14:30:03,593 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.6871133659349988 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 8.556572048964745e-05 + +2024-05-27 14:30:03,594 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 8.556572048964745e-05 +2024-05-27 14:30:03,598 - physiofit - INFO - Results for WT4: + optimal +WT4 X_0 0.031033 +WT4 growth_rate 0.585542 +WT4 Glc_q -4.801067 +WT4 Glc_M0 14.145875 +WT4 Ace_q 2.258295 +WT4 Ace_M0 0.121064 +2024-05-27 14:30:03,605 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:04,553 - physiofit - INFO - Running optimization for WT_BW +2024-05-27 14:30:04,556 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:04,556 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:04,560 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +44 1.828889 0.063504 NaN NaN +45 2.261389 0.075600 NaN NaN +46 2.774167 0.096768 NaN NaN +47 2.800000 NaN 12.250388 0.682281 +48 3.208889 0.120960 NaN NaN +49 3.706389 0.158760 NaN NaN +50 3.733333 NaN 11.264776 1.131679 +51 4.225833 0.192024 NaN NaN +52 4.283333 NaN 10.762084 1.507763 +53 4.635556 0.257040 NaN NaN +54 4.750000 NaN 9.690208 1.864408 +55 4.967500 0.300888 NaN NaN +56 5.116667 NaN 8.807617 2.178490 +57 5.433333 NaN 7.742783 2.448553 +Experimental matrix: +[[ 0.063504 nan nan] + [ 0.0756 nan nan] + [ 0.096768 nan nan] + [ nan 12.25038764 0.68228059] + [ 0.12096 nan nan] + [ 0.15876 nan nan] + [ nan 11.2647757 1.13167881] + [ 0.192024 nan nan] + [ nan 10.76208395 1.50776307] + [ 0.25704 nan nan] + [ nan 9.69020796 1.86440782] + [ 0.300888 nan nan] + [ nan 8.80761667 2.17848992] + [ nan 7.74278267 2.44855281]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:04,560 - physiofit - INFO - mc : False +2024-05-27 14:30:04,560 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:04,560 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:04,561 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:05,083 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:05,085 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.261743304286648 + x: [ 2.335e-02 5.132e-01 -8.136e+00 1.351e+01 + 3.236e+00 2.731e-01] + nit: 111 + nfev: 10759 + population: [[ 2.330e-02 5.135e-01 ... 3.249e+00 2.691e-01] + [ 2.323e-02 5.142e-01 ... 3.251e+00 2.728e-01] + ... + [ 2.337e-02 5.136e-01 ... 3.258e+00 2.621e-01] + [ 2.319e-02 5.145e-01 ... 3.229e+00 2.785e-01]] + population_energies: [ 1.262e+00 1.269e+00 ... 1.273e+00 1.265e+00] + jac: [ 1.264e-01 1.335e-02 5.742e-05 4.466e-04 + 2.094e-04 5.172e-04] +2024-05-27 14:30:05,085 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02334982163887278 +2024-05-27 14:30:05,086 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5132025073632198 +2024-05-27 14:30:05,086 - physiofit.physiofit.base.fitter - INFO - Glc_q = -8.136200527710868 +2024-05-27 14:30:05,086 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.512293281023538 +2024-05-27 14:30:05,086 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.2356679461502487 +2024-05-27 14:30:05,086 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.27306146732079206 +2024-05-27 14:30:05,092 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.059691 NaN NaN +2.261389 0.074525 NaN NaN +2.774167 0.096960 NaN NaN +2.800000 NaN 12.324778 0.745322 +3.208889 0.121195 NaN NaN +3.706389 0.156447 NaN NaN +3.733333 NaN 11.367664 1.125954 +4.225833 0.204240 NaN NaN +4.283333 NaN 10.547520 1.452116 +4.635556 0.252035 NaN NaN +4.750000 NaN 9.645059 1.811014 +4.967500 0.298844 NaN NaN +5.116667 NaN 8.767727 2.159918 +5.433333 NaN 7.865154 2.518860 + +2024-05-27 14:30:05,097 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.261743304286648 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 4.555171806578333e-06 + +2024-05-27 14:30:05,098 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 4.555171806578333e-06 +2024-05-27 14:30:05,100 - physiofit - INFO - Results for WT_BW: + optimal +WT_BW X_0 0.023350 +WT_BW growth_rate 0.513203 +WT_BW Glc_q -8.136201 +WT_BW Glc_M0 13.512293 +WT_BW Ace_q 3.235668 +WT_BW Ace_M0 0.273061 +2024-05-27 14:30:05,107 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:06,049 - physiofit - INFO - Running optimization for WT_BW_6_1 +2024-05-27 14:30:06,051 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:06,051 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:06,055 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +58 1.350000 NaN 13.627681 0.216959 +59 1.694722 0.061992 NaN NaN +60 1.916667 NaN 13.579213 0.371914 +61 2.300278 0.086184 NaN NaN +62 2.698333 0.110376 NaN NaN +63 2.866667 NaN 12.620046 0.707538 +64 3.436111 0.178416 NaN NaN +65 3.821111 0.208656 NaN NaN +66 4.000000 NaN 11.249982 1.464368 +67 4.201111 0.302400 NaN NaN +68 4.598056 0.378000 NaN NaN +69 4.800000 NaN 9.365603 2.135749 +70 4.995000 0.545832 NaN NaN +71 5.183333 NaN 8.200209 2.546580 +72 5.375278 0.609336 NaN NaN +73 5.583333 NaN 6.551724 2.885181 +Experimental matrix: +[[ nan 13.62768138 0.21695885] + [ 0.061992 nan nan] + [ nan 13.57921333 0.37191422] + [ 0.086184 nan nan] + [ 0.110376 nan nan] + [ nan 12.62004575 0.70753768] + [ 0.178416 nan nan] + [ 0.208656 nan nan] + [ nan 11.24998175 1.46436775] + [ 0.3024 nan nan] + [ 0.378 nan nan] + [ nan 9.36560348 2.13574936] + [ 0.545832 nan nan] + [ nan 8.20020915 2.54657963] + [ 0.609336 nan nan] + [ nan 6.55172432 2.88518116]] +Time vector: [1.35 1.69472222 1.91666667 2.30027778 2.69833333 2.86666667 + 3.43611111 3.82111111 4. 4.20111111 4.59805556 4.8 + 4.995 5.18333333 5.37527778 5.58333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:06,055 - physiofit - INFO - mc : False +2024-05-27 14:30:06,055 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:06,055 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:06,056 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:06,453 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:06,454 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 14.195146746370312 + x: [ 2.071e-02 6.360e-01 -6.746e+00 1.390e+01 + 2.593e+00 2.609e-01] + nit: 88 + nfev: 8332 + population: [[ 2.094e-02 6.337e-01 ... 2.594e+00 2.495e-01] + [ 2.116e-02 6.314e-01 ... 2.598e+00 2.236e-01] + ... + [ 2.049e-02 6.388e-01 ... 2.581e+00 2.670e-01] + [ 1.998e-02 6.432e-01 ... 2.606e+00 2.560e-01]] + population_energies: [ 1.420e+01 1.439e+01 ... 1.423e+01 1.429e+01] + jac: [-1.655e-01 -1.019e-02 1.432e-02 -8.522e-03 + 1.684e-03 -3.130e-03] +2024-05-27 14:30:06,455 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02070952138835857 +2024-05-27 14:30:06,455 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6359665496678683 +2024-05-27 14:30:06,455 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.745613978937317 +2024-05-27 14:30:06,455 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.90169398307654 +2024-05-27 14:30:06,455 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5929970705205583 +2024-05-27 14:30:06,456 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.2608581297353596 +2024-05-27 14:30:06,460 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.350000 NaN 13.603007 0.375673 +1.694722 0.060848 NaN NaN +1.916667 NaN 13.378108 0.462123 +2.300278 0.089433 NaN NaN +2.698333 0.115197 NaN NaN +2.866667 NaN 12.761412 0.699180 +3.436111 0.184167 NaN NaN +3.821111 0.235260 NaN NaN +4.000000 NaN 11.325311 1.251213 +4.201111 0.299573 NaN NaN +4.598056 0.385601 NaN NaN +4.800000 NaN 9.470835 1.964069 +4.995000 0.496333 NaN NaN +5.183333 NaN 8.186952 2.457590 +5.375278 0.632127 NaN NaN +5.583333 NaN 6.467932 3.118378 + +2024-05-27 14:30:06,465 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 14.195146746370312 +Number of measurements: 23 +Number of parameters to fit: 6 +Degrees of freedom: 17 +p-value = 0.3467566984265852 + +2024-05-27 14:30:06,465 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.3467566984265852 +2024-05-27 14:30:06,467 - physiofit - INFO - Results for WT_BW_6_1: + optimal +WT_BW_6_1 X_0 0.020710 +WT_BW_6_1 growth_rate 0.635967 +WT_BW_6_1 Glc_q -6.745614 +WT_BW_6_1 Glc_M0 13.901694 +WT_BW_6_1 Ace_q 2.592997 +WT_BW_6_1 Ace_M0 0.260858 +2024-05-27 14:30:06,474 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:07,436 - physiofit - INFO - Running optimization for WT_BW_6_2 +2024-05-27 14:30:07,438 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:07,439 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:07,442 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +74 1.350000 NaN 13.631446 0.198784 +75 1.694722 0.092232 NaN NaN +76 1.916667 NaN 13.522748 0.337257 +77 2.300278 0.120960 NaN NaN +78 2.698333 0.146664 NaN NaN +79 2.866667 NaN 12.560951 0.621969 +80 3.436111 0.222264 NaN NaN +81 3.821111 0.266112 NaN NaN +82 4.000000 NaN 11.375063 1.308316 +83 4.201111 0.326592 NaN NaN +84 4.598056 0.414288 NaN NaN +85 4.800000 NaN 9.319926 1.971872 +86 4.995000 0.630504 NaN NaN +87 5.183333 NaN 7.533245 2.311215 +88 5.375278 0.795312 NaN NaN +89 5.583333 NaN 5.965173 2.733823 +Experimental matrix: +[[ nan 13.63144649 0.19878418] + [ 0.092232 nan nan] + [ nan 13.52274821 0.33725713] + [ 0.12096 nan nan] + [ 0.146664 nan nan] + [ nan 12.56095077 0.62196882] + [ 0.222264 nan nan] + [ 0.266112 nan nan] + [ nan 11.37506323 1.30831566] + [ 0.326592 nan nan] + [ 0.414288 nan nan] + [ nan 9.31992577 1.97187178] + [ 0.630504 nan nan] + [ nan 7.53324535 2.31121479] + [ 0.795312 nan nan] + [ nan 5.9651729 2.73382285]] +Time vector: [1.35 1.69472222 1.91666667 2.30027778 2.69833333 2.86666667 + 3.43611111 3.82111111 4. 4.20111111 4.59805556 4.8 + 4.995 5.18333333 5.37527778 5.58333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:07,443 - physiofit - INFO - mc : False +2024-05-27 14:30:07,443 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:07,443 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:07,443 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:07,820 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:07,822 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 18.202416682966156 + x: [ 2.104e-02 6.724e-01 -6.189e+00 1.391e+01 + 2.045e+00 2.468e-01] + nit: 83 + nfev: 7777 + population: [[ 2.101e-02 6.723e-01 ... 2.050e+00 2.564e-01] + [ 2.093e-02 6.741e-01 ... 2.069e+00 2.238e-01] + ... + [ 2.110e-02 6.710e-01 ... 2.086e+00 2.264e-01] + [ 2.154e-02 6.678e-01 ... 2.072e+00 2.458e-01]] + population_energies: [ 1.820e+01 1.828e+01 ... 1.834e+01 1.842e+01] + jac: [ 1.093e-01 2.950e-02 -2.888e-01 -3.753e-01 + -1.646e-01 8.876e-02] +2024-05-27 14:30:07,822 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02103809269928879 +2024-05-27 14:30:07,822 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6723675101009716 +2024-05-27 14:30:07,823 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.188878188224044 +2024-05-27 14:30:07,823 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.90653188200499 +2024-05-27 14:30:07,823 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.0449787516241145 +2024-05-27 14:30:07,823 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.24679867447542234 +2024-05-27 14:30:07,827 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.350000 NaN 13.620204 0.341409 +1.694722 0.065747 NaN NaN +1.916667 NaN 13.397611 0.414961 +2.300278 0.098787 NaN NaN +2.698333 0.129102 NaN NaN +2.866667 NaN 12.769437 0.622527 +3.436111 0.212017 NaN NaN +3.821111 0.274658 NaN NaN +4.000000 NaN 11.248941 1.124941 +4.201111 0.354612 NaN NaN +4.598056 0.463088 NaN NaN +4.800000 NaN 9.217727 1.796111 +4.995000 0.604747 NaN NaN +5.183333 NaN 7.782269 2.270427 +5.375278 0.780939 NaN NaN +5.583333 NaN 5.832652 2.914635 + +2024-05-27 14:30:07,831 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 18.202416682966156 +Number of measurements: 23 +Number of parameters to fit: 6 +Degrees of freedom: 17 +p-value = 0.6238200348037268 + +2024-05-27 14:30:07,832 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.6238200348037268 +2024-05-27 14:30:07,835 - physiofit - INFO - Results for WT_BW_6_2: + optimal +WT_BW_6_2 X_0 0.021038 +WT_BW_6_2 growth_rate 0.672368 +WT_BW_6_2 Glc_q -6.188878 +WT_BW_6_2 Glc_M0 13.906532 +WT_BW_6_2 Ace_q 2.044979 +WT_BW_6_2 Ace_M0 0.246799 +2024-05-27 14:30:07,841 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:08,867 - physiofit - INFO - Running optimization for WT_BW_6_3 +2024-05-27 14:30:08,871 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:08,871 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:08,874 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +90 1.350000 NaN 13.425509 0.198988 +91 1.694722 0.068040 NaN NaN +92 1.916667 NaN 13.579805 0.339571 +93 2.300278 0.105840 NaN NaN +94 2.698333 0.122472 NaN NaN +95 2.866667 NaN 12.867892 0.637954 +96 3.436111 0.181440 NaN NaN +97 3.821111 0.238896 NaN NaN +98 4.000000 NaN 11.068879 1.325591 +99 4.201111 0.281232 NaN NaN +100 4.598056 0.370440 NaN NaN +101 4.800000 NaN 9.276867 2.001093 +102 4.995000 0.606312 NaN NaN +103 5.183333 NaN 8.041652 2.412517 +104 5.375278 0.663768 NaN NaN +105 5.583333 NaN 6.250809 2.763018 +Experimental matrix: +[[ nan 13.42550931 0.19898751] + [ 0.06804 nan nan] + [ nan 13.57980534 0.33957081] + [ 0.10584 nan nan] + [ 0.122472 nan nan] + [ nan 12.86789202 0.6379541 ] + [ 0.18144 nan nan] + [ 0.238896 nan nan] + [ nan 11.06887928 1.32559135] + [ 0.281232 nan nan] + [ 0.37044 nan nan] + [ nan 9.27686657 2.00109344] + [ 0.606312 nan nan] + [ nan 8.04165234 2.41251681] + [ 0.663768 nan nan] + [ nan 6.2508087 2.7630178 ]] +Time vector: [1.35 1.69472222 1.91666667 2.30027778 2.69833333 2.86666667 + 3.43611111 3.82111111 4. 4.20111111 4.59805556 4.8 + 4.995 5.18333333 5.37527778 5.58333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:08,874 - physiofit - INFO - mc : False +2024-05-27 14:30:08,874 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:08,874 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:08,874 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:09,214 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:09,216 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 26.61503095006438 + x: [ 1.926e-02 6.642e-01 -6.669e+00 1.386e+01 + 2.371e+00 2.404e-01] + nit: 75 + nfev: 6994 + population: [[ 1.917e-02 6.652e-01 ... 2.364e+00 2.393e-01] + [ 1.968e-02 6.601e-01 ... 2.388e+00 2.287e-01] + ... + [ 1.925e-02 6.659e-01 ... 2.367e+00 2.256e-01] + [ 1.976e-02 6.584e-01 ... 2.375e+00 2.306e-01]] + population_energies: [ 2.662e+01 2.680e+01 ... 2.697e+01 2.685e+01] + jac: [-5.347e-02 -7.869e-03 -1.456e-01 1.369e-01 + 2.486e-02 -2.310e-02] +2024-05-27 14:30:09,216 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.01926382256772249 +2024-05-27 14:30:09,216 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6641916161917825 +2024-05-27 14:30:09,216 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.669383525826929 +2024-05-27 14:30:09,216 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.860049942593323 +2024-05-27 14:30:09,216 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3705453655737636 +2024-05-27 14:30:09,216 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.24041576539650392 +2024-05-27 14:30:09,222 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.350000 NaN 13.579299 0.340205 +1.694722 0.059374 NaN NaN +1.916667 NaN 13.362599 0.417228 +2.300278 0.088770 NaN NaN +2.698333 0.115635 NaN NaN +2.866667 NaN 12.754995 0.633193 +3.436111 0.188758 NaN NaN +3.821111 0.243759 NaN NaN +4.000000 NaN 11.297012 1.151414 +4.201111 0.313742 NaN NaN +4.598056 0.408388 NaN NaN +4.800000 NaN 9.364081 1.838449 +4.995000 0.531587 NaN NaN +5.183333 NaN 8.004369 2.321741 +5.375278 0.684332 NaN NaN +5.583333 NaN 6.163543 2.976039 + +2024-05-27 14:30:09,225 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 26.61503095006438 +Number of measurements: 23 +Number of parameters to fit: 6 +Degrees of freedom: 17 +p-value = 0.9360393443052187 + +2024-05-27 14:30:09,225 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.9360393443052187 +2024-05-27 14:30:09,227 - physiofit - INFO - Results for WT_BW_6_3: + optimal +WT_BW_6_3 X_0 0.019264 +WT_BW_6_3 growth_rate 0.664192 +WT_BW_6_3 Glc_q -6.669384 +WT_BW_6_3 Glc_M0 13.860050 +WT_BW_6_3 Ace_q 2.370545 +WT_BW_6_3 Ace_M0 0.240416 +2024-05-27 14:30:09,234 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:10,188 - physiofit - INFO - Running optimization for WT_BW_6_4 +2024-05-27 14:30:10,191 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:10,191 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:10,195 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +106 1.350000 NaN 13.658459 0.231295 +107 1.694722 0.072576 NaN NaN +108 1.916667 NaN 13.456913 0.381290 +109 2.300278 0.107352 NaN NaN +110 2.698333 0.145152 NaN NaN +111 2.866667 NaN 12.981707 0.751702 +112 3.436111 0.226800 NaN NaN +113 3.821111 0.293328 NaN NaN +114 4.000000 NaN 11.019453 1.512507 +115 4.201111 0.359856 NaN NaN +116 4.598056 0.477792 NaN NaN +117 4.800000 NaN 8.902288 2.200375 +118 4.995000 0.666792 NaN NaN +119 5.183333 NaN 7.467238 2.624928 +120 5.375278 0.807408 NaN NaN +121 5.583333 NaN 5.663558 3.013850 +Experimental matrix: +[[ nan 13.65845854 0.23129526] + [ 0.072576 nan nan] + [ nan 13.45691262 0.38129009] + [ 0.107352 nan nan] + [ 0.145152 nan nan] + [ nan 12.98170699 0.75170215] + [ 0.2268 nan nan] + [ 0.293328 nan nan] + [ nan 11.01945271 1.51250682] + [ 0.359856 nan nan] + [ 0.477792 nan nan] + [ nan 8.90228756 2.20037511] + [ 0.666792 nan nan] + [ nan 7.46723782 2.62492816] + [ 0.807408 nan nan] + [ nan 5.66355842 3.01384977]] +Time vector: [1.35 1.69472222 1.91666667 2.30027778 2.69833333 2.86666667 + 3.43611111 3.82111111 4. 4.20111111 4.59805556 4.8 + 4.995 5.18333333 5.37527778 5.58333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:10,195 - physiofit - INFO - mc : False +2024-05-27 14:30:10,195 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:10,195 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:10,196 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:10,638 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:10,639 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 8.850637299071447 + x: [ 2.414e-02 6.548e-01 -6.106e+00 1.401e+01 + 2.124e+00 2.907e-01] + nit: 94 + nfev: 8970 + population: [[ 2.440e-02 6.528e-01 ... 2.121e+00 2.908e-01] + [ 2.416e-02 6.542e-01 ... 2.126e+00 2.761e-01] + ... + [ 2.380e-02 6.580e-01 ... 2.131e+00 2.925e-01] + [ 2.380e-02 6.573e-01 ... 2.111e+00 3.127e-01]] + population_energies: [ 8.851e+00 8.944e+00 ... 8.955e+00 9.006e+00] + jac: [-2.973e-02 1.074e-03 2.149e-04 4.368e-04 + -1.712e-03 -9.702e-04] +2024-05-27 14:30:10,639 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.024142422974610746 +2024-05-27 14:30:10,640 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6547649256693445 +2024-05-27 14:30:10,640 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.106476745973377 +2024-05-27 14:30:10,640 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.014940008578504 +2024-05-27 14:30:10,640 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.1242420854956787 +2024-05-27 14:30:10,640 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.290704809935982 +2024-05-27 14:30:10,643 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.350000 NaN 13.695127 0.401957 +1.694722 0.073231 NaN NaN +1.916667 NaN 13.450309 0.487122 +2.300278 0.108865 NaN NaN +2.698333 0.141280 NaN NaN +2.866667 NaN 12.768958 0.724141 +3.436111 0.229021 NaN NaN +3.821111 0.294683 NaN NaN +4.000000 NaN 11.150305 1.287217 +4.201111 0.377931 NaN NaN +4.598056 0.490103 NaN NaN +4.800000 NaN 9.023132 2.027190 +4.995000 0.635569 NaN NaN +5.183333 NaN 7.534724 2.544958 +5.375278 0.815266 NaN NaN +5.583333 NaN 5.527107 3.243342 + +2024-05-27 14:30:10,647 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 8.850637299071447 +Number of measurements: 23 +Number of parameters to fit: 6 +Degrees of freedom: 17 +p-value = 0.055168670839424616 + +2024-05-27 14:30:10,647 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.055168670839424616 +2024-05-27 14:30:10,649 - physiofit - INFO - Results for WT_BW_6_4: + optimal +WT_BW_6_4 X_0 0.024142 +WT_BW_6_4 growth_rate 0.654765 +WT_BW_6_4 Glc_q -6.106477 +WT_BW_6_4 Glc_M0 14.014940 +WT_BW_6_4 Ace_q 2.124242 +WT_BW_6_4 Ace_M0 0.290705 +2024-05-27 14:30:10,658 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:11,612 - physiofit - INFO - Running optimization for WT_MG_6_1 +2024-05-27 14:30:11,614 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:11,615 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:11,618 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +122 1.350000 NaN 13.691968 0.217680 +123 1.694722 0.069552 NaN NaN +124 1.916667 NaN 13.433410 0.361662 +125 2.300278 0.101304 NaN NaN +126 2.698333 0.120960 NaN NaN +127 2.866667 NaN 13.213420 0.708646 +128 3.436111 0.204120 NaN NaN +129 3.821111 0.238896 NaN NaN +130 4.000000 NaN 11.029767 1.393978 +131 4.201111 0.302400 NaN NaN +132 4.598056 0.417312 NaN NaN +133 4.800000 NaN 9.276194 2.056157 +134 4.995000 0.612360 NaN NaN +135 5.183333 NaN 8.013711 2.531650 +136 5.375278 0.742392 NaN NaN +137 5.583333 NaN 6.154459 2.851306 +Experimental matrix: +[[ nan 13.6919677 0.21767955] + [ 0.069552 nan nan] + [ nan 13.43341015 0.36166183] + [ 0.101304 nan nan] + [ 0.12096 nan nan] + [ nan 13.21341966 0.70864597] + [ 0.20412 nan nan] + [ 0.238896 nan nan] + [ nan 11.02976726 1.39397786] + [ 0.3024 nan nan] + [ 0.417312 nan nan] + [ nan 9.27619411 2.05615746] + [ 0.61236 nan nan] + [ nan 8.01371108 2.53164955] + [ 0.742392 nan nan] + [ nan 6.15445855 2.85130556]] +Time vector: [1.35 1.69472222 1.91666667 2.30027778 2.69833333 2.86666667 + 3.43611111 3.82111111 4. 4.20111111 4.59805556 4.8 + 4.995 5.18333333 5.37527778 5.58333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:11,619 - physiofit - INFO - mc : False +2024-05-27 14:30:11,619 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:11,619 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:11,619 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:12,067 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:12,068 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 14.197511256813353 + x: [ 1.821e-02 6.909e-01 -6.465e+00 1.393e+01 + 2.289e+00 2.977e-01] + nit: 96 + nfev: 9388 + population: [[ 1.806e-02 6.924e-01 ... 2.301e+00 2.920e-01] + [ 1.846e-02 6.872e-01 ... 2.310e+00 2.930e-01] + ... + [ 1.774e-02 6.966e-01 ... 2.257e+00 2.976e-01] + [ 1.807e-02 6.916e-01 ... 2.352e+00 2.743e-01]] + population_energies: [ 1.420e+01 1.434e+01 ... 1.446e+01 1.438e+01] + jac: [-4.114e-04 3.045e-04 -1.208e-05 -4.814e-05 + -5.311e-05 5.151e-05] +2024-05-27 14:30:12,069 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.018210310264975552 +2024-05-27 14:30:12,069 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6909191204247087 +2024-05-27 14:30:12,069 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.464630956292189 +2024-05-27 14:30:12,069 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.930724409605814 +2024-05-27 14:30:12,069 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.288692573162123 +2024-05-27 14:30:12,069 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.29768140106235014 +2024-05-27 14:30:12,073 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.350000 NaN 13.668080 0.390666 +1.694722 0.058727 NaN NaN +1.916667 NaN 13.460560 0.464135 +2.300278 0.089237 NaN NaN +2.698333 0.117486 NaN NaN +2.866667 NaN 12.866265 0.674535 +3.436111 0.195598 NaN NaN +3.821111 0.255205 NaN NaN +4.000000 NaN 11.399123 1.193952 +4.201111 0.331828 NaN NaN +4.598056 0.436537 NaN NaN +4.800000 NaN 9.405055 1.899918 +4.995000 0.574287 NaN NaN +5.183333 NaN 7.981030 2.404069 +5.375278 0.746854 NaN NaN +5.583333 NaN 6.032810 3.093804 + +2024-05-27 14:30:12,077 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 14.197511256813353 +Number of measurements: 23 +Number of parameters to fit: 6 +Degrees of freedom: 17 +p-value = 0.34692512822790417 + +2024-05-27 14:30:12,077 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.34692512822790417 +2024-05-27 14:30:12,079 - physiofit - INFO - Results for WT_MG_6_1: + optimal +WT_MG_6_1 X_0 0.018210 +WT_MG_6_1 growth_rate 0.690919 +WT_MG_6_1 Glc_q -6.464631 +WT_MG_6_1 Glc_M0 13.930724 +WT_MG_6_1 Ace_q 2.288693 +WT_MG_6_1 Ace_M0 0.297681 +2024-05-27 14:30:12,085 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:13,057 - physiofit - INFO - Running optimization for WT_MG_6_2 +2024-05-27 14:30:13,059 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:13,059 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:13,063 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +138 1.350000 NaN 13.593843 0.211550 +139 1.694722 0.068040 NaN NaN +140 1.916667 NaN 13.512690 0.364579 +141 2.300278 0.107352 NaN NaN +142 2.698333 0.120960 NaN NaN +143 2.866667 NaN 12.640083 0.703182 +144 3.436111 0.207144 NaN NaN +145 3.821111 0.247968 NaN NaN +146 4.000000 NaN 11.269327 1.489067 +147 4.201111 0.332640 NaN NaN +148 4.598056 0.411264 NaN NaN +149 4.800000 NaN 8.985221 2.128773 +150 4.995000 0.654696 NaN NaN +151 5.183333 NaN 7.548224 2.531324 +152 5.375278 0.795312 NaN NaN +153 5.583333 NaN 5.862553 2.893368 +Experimental matrix: +[[ nan 13.59384335 0.21154954] + [ 0.06804 nan nan] + [ nan 13.51268988 0.36457868] + [ 0.107352 nan nan] + [ 0.12096 nan nan] + [ nan 12.64008271 0.70318191] + [ 0.207144 nan nan] + [ 0.247968 nan nan] + [ nan 11.26932737 1.48906738] + [ 0.33264 nan nan] + [ 0.411264 nan nan] + [ nan 8.98522135 2.12877346] + [ 0.654696 nan nan] + [ nan 7.54822371 2.53132428] + [ 0.795312 nan nan] + [ nan 5.86255275 2.89336821]] +Time vector: [1.35 1.69472222 1.91666667 2.30027778 2.69833333 2.86666667 + 3.43611111 3.82111111 4. 4.20111111 4.59805556 4.8 + 4.995 5.18333333 5.37527778 5.58333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:13,064 - physiofit - INFO - mc : False +2024-05-27 14:30:13,064 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:13,064 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:13,064 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:13,495 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:13,496 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 20.336380535706134 + x: [ 1.735e-02 7.122e-01 -6.407e+00 1.380e+01 + 2.215e+00 3.303e-01] + nit: 95 + nfev: 8927 + population: [[ 1.736e-02 7.123e-01 ... 2.235e+00 3.235e-01] + [ 1.682e-02 7.185e-01 ... 2.249e+00 3.314e-01] + ... + [ 1.755e-02 7.091e-01 ... 2.184e+00 3.497e-01] + [ 1.789e-02 7.048e-01 ... 2.160e+00 3.424e-01]] + population_energies: [ 2.034e+01 2.045e+01 ... 2.076e+01 2.076e+01] + jac: [-3.580e-02 -3.465e-03 -6.011e-02 1.061e-02 + 7.585e-03 -6.355e-03] +2024-05-27 14:30:13,496 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.017346589034926408 +2024-05-27 14:30:13,496 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.7121589870806185 +2024-05-27 14:30:13,496 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.406842821219588 +2024-05-27 14:30:13,497 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.796672869717584 +2024-05-27 14:30:13,497 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.2152948447472522 +2024-05-27 14:30:13,497 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.33034561252896993 +2024-05-27 14:30:13,501 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.350000 NaN 13.544581 0.417512 +1.694722 0.057992 NaN NaN +1.916667 NaN 13.341674 0.487671 +2.300278 0.089261 NaN NaN +2.698333 0.118515 NaN NaN +2.866667 NaN 12.750733 0.692000 +3.436111 0.200428 NaN NaN +3.821111 0.263653 NaN NaN +4.000000 NaN 11.258540 1.207956 +4.201111 0.345591 NaN NaN +4.598056 0.458492 NaN NaN +4.800000 NaN 9.189983 1.923201 +4.995000 0.608277 NaN NaN +5.183333 NaN 7.694991 2.440125 +5.375278 0.797473 NaN NaN +5.583333 NaN 5.632562 3.153251 + +2024-05-27 14:30:13,505 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 20.336380535706134 +Number of measurements: 23 +Number of parameters to fit: 6 +Degrees of freedom: 17 +p-value = 0.7426134741011544 + +2024-05-27 14:30:13,505 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.7426134741011544 +2024-05-27 14:30:13,507 - physiofit - INFO - Results for WT_MG_6_2: + optimal +WT_MG_6_2 X_0 0.017347 +WT_MG_6_2 growth_rate 0.712159 +WT_MG_6_2 Glc_q -6.406843 +WT_MG_6_2 Glc_M0 13.796673 +WT_MG_6_2 Ace_q 2.215295 +WT_MG_6_2 Ace_M0 0.330346 +2024-05-27 14:30:13,513 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:14,486 - physiofit - INFO - Running optimization for artI +2024-05-27 14:30:14,489 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:14,489 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:14,493 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +154 0.050000 NaN 14.381246 0.016085 +155 1.950000 NaN 13.562145 0.439526 +156 2.833333 NaN 13.376603 0.788742 +157 2.876944 0.184464 NaN NaN +158 3.678056 0.297864 NaN NaN +159 3.983333 NaN 11.642545 1.462009 +160 4.092222 0.361368 NaN NaN +161 4.565000 0.476280 NaN NaN +162 4.883333 NaN 8.874252 2.007670 +163 5.166667 NaN 8.279295 2.214519 +Experimental matrix: +[[ nan 14.38124581 0.01608502] + [ nan 13.56214493 0.43952606] + [ nan 13.37660303 0.78874213] + [ 0.184464 nan nan] + [ 0.297864 nan nan] + [ nan 11.64254544 1.46200912] + [ 0.361368 nan nan] + [ 0.47628 nan nan] + [ nan 8.87425169 2.00766964] + [ nan 8.27929545 2.21451931]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:14,493 - physiofit - INFO - mc : False +2024-05-27 14:30:14,493 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:14,493 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:14,494 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:14,905 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:14,906 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.202418375011267 + x: [ 4.006e-02 5.409e-01 -5.571e+00 1.454e+01 + 1.893e+00 1.842e-01] + nit: 91 + nfev: 8588 + population: [[ 4.003e-02 5.413e-01 ... 1.880e+00 1.907e-01] + [ 4.112e-02 5.338e-01 ... 1.854e+00 1.986e-01] + ... + [ 3.939e-02 5.446e-01 ... 1.865e+00 1.956e-01] + [ 4.003e-02 5.409e-01 ... 1.887e+00 1.990e-01]] + population_energies: [ 4.202e+00 4.310e+00 ... 4.271e+00 4.229e+00] + jac: [ 3.226e-02 3.824e-03 -2.948e-04 -3.721e-04 + -1.048e-04 4.982e-04] +2024-05-27 14:30:14,907 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.04005789525247605 +2024-05-27 14:30:14,907 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5409127545186931 +2024-05-27 14:30:14,907 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.570758684261088 +2024-05-27 14:30:14,907 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.542581992742319 +2024-05-27 14:30:14,907 - physiofit.physiofit.base.fitter - INFO - Ace_q = 1.8926722556303168 +2024-05-27 14:30:14,908 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.18423554335102177 +2024-05-27 14:30:14,911 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.531272 0.188078 +1.950000 NaN 13.770562 0.446530 +2.833333 NaN 13.044974 0.693050 +2.876944 0.189901 NaN NaN +3.678056 0.292900 NaN NaN +3.983333 NaN 11.397002 1.252950 +4.092222 0.366450 NaN NaN +4.565000 0.473235 NaN NaN +4.883333 NaN 9.165571 2.011082 +5.166667 NaN 8.206667 2.336871 + +2024-05-27 14:30:14,915 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.202418375011267 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.06224616974177757 + +2024-05-27 14:30:14,916 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.06224616974177757 +2024-05-27 14:30:14,917 - physiofit - INFO - Results for artI: + optimal +artI X_0 0.040058 +artI growth_rate 0.540913 +artI Glc_q -5.570759 +artI Glc_M0 14.542582 +artI Ace_q 1.892672 +artI Ace_M0 0.184236 +2024-05-27 14:30:14,925 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:15,927 - physiofit - INFO - Running optimization for hemX +2024-05-27 14:30:15,930 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:15,930 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:15,935 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +164 0.050000 NaN 14.133476 0.027535 +165 1.950000 NaN 13.901395 0.447037 +166 2.833333 NaN 13.397552 0.857936 +167 2.876944 0.166320 NaN NaN +168 3.678056 0.260064 NaN NaN +169 3.983333 NaN 11.751800 1.435774 +170 4.092222 0.328104 NaN NaN +171 4.565000 0.446040 NaN NaN +172 4.883333 NaN 9.185841 2.259138 +173 5.166667 NaN 8.369325 2.579090 +Experimental matrix: +[[ nan 14.13347582 0.02753453] + [ nan 13.9013951 0.44703731] + [ nan 13.39755216 0.85793579] + [ 0.16632 nan nan] + [ 0.260064 nan nan] + [ nan 11.75180024 1.43577374] + [ 0.328104 nan nan] + [ 0.44604 nan nan] + [ nan 9.18584051 2.2591384 ] + [ nan 8.36932489 2.5790904 ]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:15,935 - physiofit - INFO - mc : False +2024-05-27 14:30:15,935 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:15,935 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:15,936 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:16,434 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:16,435 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.71886593298556 + x: [ 2.998e-02 5.892e-01 -6.003e+00 1.447e+01 + 2.430e+00 1.815e-01] + nit: 108 + nfev: 10118 + population: [[ 2.984e-02 5.905e-01 ... 2.415e+00 1.905e-01] + [ 2.969e-02 5.916e-01 ... 2.432e+00 1.790e-01] + ... + [ 2.986e-02 5.910e-01 ... 2.397e+00 1.949e-01] + [ 2.938e-02 5.937e-01 ... 2.435e+00 1.861e-01]] + population_energies: [ 2.719e+00 2.731e+00 ... 2.751e+00 2.741e+00] + jac: [-2.302e-02 -7.005e-04 -2.434e-02 -1.052e-03 + 2.650e-03 1.727e-03] +2024-05-27 14:30:16,436 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02998214862058754 +2024-05-27 14:30:16,436 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5891639239255181 +2024-05-27 14:30:16,437 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.002633649430653 +2024-05-27 14:30:16,437 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.472777335277407 +2024-05-27 14:30:16,437 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.430392237402438 +2024-05-27 14:30:16,437 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.18148527201182707 +2024-05-27 14:30:16,440 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.463645 0.185183 +1.950000 NaN 13.814604 0.447971 +2.833333 NaN 13.156679 0.714357 +2.876944 0.163301 NaN NaN +3.678056 0.261800 NaN NaN +3.983333 NaN 11.585339 1.350574 +4.092222 0.334151 NaN NaN +4.565000 0.441481 NaN NaN +4.883333 NaN 9.352369 2.254676 +5.166667 NaN 8.366642 2.653784 + +2024-05-27 14:30:16,443 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.71886593298556 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.012711727248724644 + +2024-05-27 14:30:16,444 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.012711727248724644 +2024-05-27 14:30:16,447 - physiofit - INFO - Results for hemX: + optimal +hemX X_0 0.029982 +hemX growth_rate 0.589164 +hemX Glc_q -6.002634 +hemX Glc_M0 14.472777 +hemX Ace_q 2.430392 +hemX Ace_M0 0.181485 +2024-05-27 14:30:16,456 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:17,500 - physiofit - INFO - Running optimization for modF +2024-05-27 14:30:17,503 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:17,503 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:17,506 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +174 0.050000 NaN 14.253268 0.017965 +175 1.950000 NaN 14.090483 0.416068 +176 2.833333 NaN 13.545191 0.738218 +177 2.876944 0.148176 NaN NaN +178 3.678056 0.241920 NaN NaN +179 3.983333 NaN 11.853566 1.417368 +180 4.092222 0.322056 NaN NaN +181 4.565000 0.382536 NaN NaN +182 4.883333 NaN 9.445997 1.934371 +183 5.166667 NaN 8.903185 2.439452 +Experimental matrix: +[[ nan 14.25326799 0.01796473] + [ nan 14.09048259 0.41606826] + [ nan 13.54519132 0.7382177 ] + [ 0.148176 nan nan] + [ 0.24192 nan nan] + [ nan 11.85356554 1.41736843] + [ 0.322056 nan nan] + [ 0.382536 nan nan] + [ nan 9.44599723 1.9343706 ] + [ nan 8.9031849 2.43945209]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:17,507 - physiofit - INFO - mc : False +2024-05-27 14:30:17,507 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:17,507 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:17,507 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:17,876 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:17,877 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.349564710242008 + x: [ 3.307e-02 5.420e-01 -6.168e+00 1.463e+01 + 2.426e+00 1.301e-01] + nit: 80 + nfev: 7675 + population: [[ 3.278e-02 5.441e-01 ... 2.432e+00 1.346e-01] + [ 3.359e-02 5.377e-01 ... 2.410e+00 1.519e-01] + ... + [ 3.227e-02 5.477e-01 ... 2.415e+00 1.301e-01] + [ 3.326e-02 5.408e-01 ... 2.403e+00 1.433e-01]] + population_energies: [ 4.350e+00 4.473e+00 ... 4.431e+00 4.380e+00] + jac: [-3.402e-04 -4.530e-06 1.776e-06 4.885e-06 + 1.776e-07 -3.730e-06] +2024-05-27 14:30:17,878 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03306757094486952 +2024-05-27 14:30:17,878 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5419643549844086 +2024-05-27 14:30:17,878 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.167780567684359 +2024-05-27 14:30:17,878 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.634651281615142 +2024-05-27 14:30:17,878 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4263461657652092 +2024-05-27 14:30:17,879 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.13013854762109056 +2024-05-27 14:30:17,882 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.624314 0.134205 +1.950000 NaN 13.928204 0.408048 +2.833333 NaN 13.263349 0.669596 +2.876944 0.157237 NaN NaN +3.678056 0.242725 NaN NaN +3.983333 NaN 11.751661 1.264280 +4.092222 0.303807 NaN NaN +4.565000 0.392533 NaN NaN +4.883333 NaN 9.702606 2.070358 +5.166667 NaN 8.821556 2.416955 + +2024-05-27 14:30:17,886 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.349564710242008 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.06979716848676583 + +2024-05-27 14:30:17,887 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.06979716848676583 +2024-05-27 14:30:17,889 - physiofit - INFO - Results for modF: + optimal +modF X_0 0.033068 +modF growth_rate 0.541964 +modF Glc_q -6.167781 +modF Glc_M0 14.634651 +modF Ace_q 2.426346 +modF Ace_M0 0.130139 +2024-05-27 14:30:17,895 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:18,870 - physiofit - INFO - Running optimization for nanE +2024-05-27 14:30:18,873 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:18,873 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:18,876 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +184 0.050000 NaN 14.477175 0.018955 +185 1.950000 NaN 13.866099 0.435932 +186 2.833333 NaN 13.257211 0.809168 +187 2.876944 0.152712 NaN NaN +188 3.678056 0.216216 NaN NaN +189 3.983333 NaN 12.000951 1.527333 +190 4.092222 0.312984 NaN NaN +191 4.565000 0.418824 NaN NaN +192 4.883333 NaN 9.318891 2.252523 +193 5.166667 NaN 8.912924 2.686041 +Experimental matrix: +[[ nan 14.47717493 0.01895494] + [ nan 13.86609892 0.43593226] + [ nan 13.25721085 0.80916823] + [ 0.152712 nan nan] + [ 0.216216 nan nan] + [ nan 12.00095055 1.5273331 ] + [ 0.312984 nan nan] + [ 0.418824 nan nan] + [ nan 9.31889075 2.25252254] + [ nan 8.912924 2.68604142]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:18,877 - physiofit - INFO - mc : False +2024-05-27 14:30:18,877 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:18,877 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:18,877 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:19,323 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:19,324 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.3298402099194755 + x: [ 2.541e-02 6.098e-01 -6.204e+00 1.448e+01 + 2.748e+00 1.759e-01] + nit: 98 + nfev: 9351 + population: [[ 2.527e-02 6.107e-01 ... 2.743e+00 1.837e-01] + [ 2.421e-02 6.202e-01 ... 2.736e+00 2.066e-01] + ... + [ 2.516e-02 6.120e-01 ... 2.776e+00 1.647e-01] + [ 2.561e-02 6.076e-01 ... 2.751e+00 1.799e-01]] + population_energies: [ 4.330e+00 4.419e+00 ... 4.385e+00 4.344e+00] + jac: [-3.706e-02 -4.629e-03 1.620e-04 3.465e-04 + 4.121e-05 2.320e-04] +2024-05-27 14:30:19,324 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02541013219473964 +2024-05-27 14:30:19,325 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6097806784522677 +2024-05-27 14:30:19,325 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.204211294830914 +2024-05-27 14:30:19,325 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.483546793420851 +2024-05-27 14:30:19,325 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.748289276676329 +2024-05-27 14:30:19,325 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.17587732363439076 +2024-05-27 14:30:19,329 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.475543 0.179423 +1.950000 NaN 13.893044 0.437453 +2.833333 NaN 13.287107 0.705866 +2.876944 0.146856 NaN NaN +3.678056 0.239357 NaN NaN +3.983333 NaN 11.808464 1.360863 +4.092222 0.308125 NaN NaN +4.565000 0.411084 NaN NaN +4.883333 NaN 9.663464 2.311037 +5.166667 NaN 8.705666 2.735314 + +2024-05-27 14:30:19,333 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.3298402099194755 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.06875693711238814 + +2024-05-27 14:30:19,333 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.06875693711238814 +2024-05-27 14:30:19,335 - physiofit - INFO - Results for nanE: + optimal +nanE X_0 0.025410 +nanE growth_rate 0.609781 +nanE Glc_q -6.204211 +nanE Glc_M0 14.483547 +nanE Ace_q 2.748289 +nanE Ace_M0 0.175877 +2024-05-27 14:30:19,341 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:20,308 - physiofit - INFO - Running optimization for wbbJ +2024-05-27 14:30:20,310 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:20,310 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:20,314 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +194 0.000000 0.033264 NaN NaN +195 0.283333 NaN 14.271250 0.045464 +196 1.195000 0.061992 NaN NaN +197 1.613611 0.074088 NaN NaN +198 1.916667 NaN 13.735146 0.403737 +199 2.361389 0.123984 NaN NaN +200 2.700000 NaN 13.275729 0.704609 +201 3.286389 0.182952 NaN NaN +202 3.616667 NaN 12.504572 1.225938 +203 3.819444 0.264600 NaN NaN +204 4.050000 NaN 11.623355 1.457222 +205 4.410833 0.400680 NaN NaN +206 4.750000 NaN 10.125713 2.068403 +Experimental matrix: +[[ 0.033264 nan nan] + [ nan 14.27125047 0.04546423] + [ 0.061992 nan nan] + [ 0.074088 nan nan] + [ nan 13.73514621 0.40373685] + [ 0.123984 nan nan] + [ nan 13.27572937 0.70460929] + [ 0.182952 nan nan] + [ nan 12.50457156 1.2259376 ] + [ 0.2646 nan nan] + [ nan 11.62335539 1.45722163] + [ 0.40068 nan nan] + [ nan 10.12571307 2.06840276]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:20,314 - physiofit - INFO - mc : False +2024-05-27 14:30:20,314 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:20,314 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:20,315 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:20,703 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:20,704 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.7052307689483954 + x: [ 2.815e-02 5.957e-01 -5.545e+00 1.434e+01 + 2.683e+00 1.383e-01] + nit: 85 + nfev: 8160 + population: [[ 2.832e-02 5.942e-01 ... 2.670e+00 1.390e-01] + [ 2.885e-02 5.906e-01 ... 2.668e+00 1.510e-01] + ... + [ 2.803e-02 5.978e-01 ... 2.665e+00 1.394e-01] + [ 2.863e-02 5.922e-01 ... 2.649e+00 1.493e-01]] + population_energies: [ 2.705e+00 2.780e+00 ... 2.722e+00 2.734e+00] + jac: [ 2.448e-03 5.621e-04 -8.438e-07 5.675e-05 + 3.522e-05 1.386e-05] +2024-05-27 14:30:20,704 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.028151525538691262 +2024-05-27 14:30:20,705 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5956707080820606 +2024-05-27 14:30:20,706 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.544673776765851 +2024-05-27 14:30:20,706 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.337550699467299 +2024-05-27 14:30:20,706 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.6827731834043833 +2024-05-27 14:30:20,706 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.13834084406010308 +2024-05-27 14:30:20,710 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028152 NaN NaN +0.283333 NaN 14.289374 0.161651 +1.195000 0.057365 NaN NaN +1.613611 0.073610 NaN NaN +1.916667 NaN 13.778851 0.408666 +2.361389 0.114917 NaN NaN +2.700000 NaN 13.290857 0.644781 +3.286389 0.199379 NaN NaN +3.616667 NaN 12.340206 1.104750 +3.819444 0.273892 NaN NaN +4.050000 NaN 11.674818 1.426696 +4.410833 0.389555 NaN NaN +4.750000 NaN 10.161667 2.158829 + +2024-05-27 14:30:20,714 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.7052307689483954 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.001194507523499259 + +2024-05-27 14:30:20,714 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.001194507523499259 +2024-05-27 14:30:20,716 - physiofit - INFO - Results for wbbJ: + optimal +wbbJ X_0 0.028152 +wbbJ growth_rate 0.595671 +wbbJ Glc_q -5.544674 +wbbJ Glc_M0 14.337551 +wbbJ Ace_q 2.682773 +wbbJ Ace_M0 0.138341 +2024-05-27 14:30:20,721 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:21,678 - physiofit - INFO - Running optimization for yacC +2024-05-27 14:30:21,680 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:21,680 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:21,684 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +207 1.828889 0.068040 NaN NaN +208 2.261389 0.090720 NaN NaN +209 2.774167 0.128520 NaN NaN +210 2.800000 NaN 12.466636 0.613438 +211 3.208889 0.157248 NaN NaN +212 3.706389 0.235872 NaN NaN +213 3.733333 NaN 11.688367 1.049990 +214 4.225833 0.306936 NaN NaN +215 4.283333 NaN 10.064340 1.333976 +216 4.635556 0.399168 NaN NaN +217 4.750000 NaN 10.026009 1.717441 +218 4.967500 0.612360 NaN NaN +219 5.116667 NaN 9.238784 2.012674 +220 5.433333 NaN 8.470138 2.341990 +Experimental matrix: +[[ 0.06804 nan nan] + [ 0.09072 nan nan] + [ 0.12852 nan nan] + [ nan 12.46663564 0.61343769] + [ 0.157248 nan nan] + [ 0.235872 nan nan] + [ nan 11.68836698 1.04999023] + [ 0.306936 nan nan] + [ nan 10.06434047 1.33397593] + [ 0.399168 nan nan] + [ nan 10.02600878 1.71744125] + [ 0.61236 nan nan] + [ nan 9.23878389 2.01267428] + [ nan 8.47013841 2.34198962]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:21,684 - physiofit - INFO - mc : False +2024-05-27 14:30:21,684 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:21,685 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:21,685 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:22,111 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:22,112 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 17.53654496971041 + x: [ 1.493e-02 7.333e-01 -4.124e+00 1.270e+01 + 1.809e+00 4.721e-01] + nit: 93 + nfev: 8943 + population: [[ 1.495e-02 7.331e-01 ... 1.831e+00 4.524e-01] + [ 1.532e-02 7.263e-01 ... 1.863e+00 4.724e-01] + ... + [ 1.515e-02 7.304e-01 ... 1.781e+00 4.752e-01] + [ 1.426e-02 7.440e-01 ... 1.822e+00 4.700e-01]] + population_energies: [ 1.754e+01 1.784e+01 ... 1.782e+01 1.768e+01] + jac: [ 1.043e-02 6.469e-04 1.131e-03 -5.976e-04 + -5.329e-06 1.730e-04] +2024-05-27 14:30:22,112 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.014930789687192992 +2024-05-27 14:30:22,113 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.7333233837963405 +2024-05-27 14:30:22,113 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.1239455375005285 +2024-05-27 14:30:22,113 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 12.69501965267019 +2024-05-27 14:30:22,113 - physiofit.physiofit.base.fitter - INFO - Ace_q = 1.8092912513347998 +2024-05-27 14:30:22,113 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.472098827110952 +2024-05-27 14:30:22,117 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.057088 NaN NaN +2.261389 0.078395 NaN NaN +2.774167 0.114181 NaN NaN +2.800000 NaN 12.124591 0.722362 +3.208889 0.157052 NaN NaN +3.706389 0.226197 NaN NaN +3.733333 NaN 11.481549 1.004482 +4.225833 0.331069 NaN NaN +4.283333 NaN 10.836987 1.287270 +4.635556 0.447102 NaN NaN +4.750000 NaN 10.044522 1.634947 +4.967500 0.570327 NaN NaN +5.116667 NaN 9.200926 2.005056 +5.433333 NaN 8.265636 2.415394 + +2024-05-27 14:30:22,121 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 17.53654496971041 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.7712894177484444 + +2024-05-27 14:30:22,121 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.7712894177484444 +2024-05-27 14:30:22,123 - physiofit - INFO - Results for yacC: + optimal +yacC X_0 0.014931 +yacC growth_rate 0.733323 +yacC Glc_q -4.123946 +yacC Glc_M0 12.695020 +yacC Ace_q 1.809291 +yacC Ace_M0 0.472099 +2024-05-27 14:30:22,130 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:23,092 - physiofit - INFO - Running optimization for yadG +2024-05-27 14:30:23,094 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:23,094 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:23,098 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +221 0.050000 NaN 14.662311 0.017491 +222 1.950000 NaN 13.935465 0.401462 +223 2.833333 NaN 13.696149 0.681098 +224 2.876944 0.143640 NaN NaN +225 3.678056 0.210168 NaN NaN +226 3.983333 NaN 11.894771 1.342321 +227 4.092222 0.305424 NaN NaN +228 4.565000 0.379512 NaN NaN +229 4.883333 NaN 9.844090 2.103830 +230 5.166667 NaN 9.124959 2.292114 +Experimental matrix: +[[ nan 14.6623106 0.01749108] + [ nan 13.93546523 0.40146208] + [ nan 13.6961492 0.68109771] + [ 0.14364 nan nan] + [ 0.210168 nan nan] + [ nan 11.89477098 1.34232105] + [ 0.305424 nan nan] + [ 0.379512 nan nan] + [ nan 9.84409005 2.10382967] + [ nan 9.12495946 2.29211418]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:23,098 - physiofit - INFO - mc : False +2024-05-27 14:30:23,098 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:23,098 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:23,099 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:23,552 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:23,553 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.1039069755455833 + x: [ 2.798e-02 5.713e-01 -6.363e+00 1.470e+01 + 2.563e+00 1.299e-01] + nit: 99 + nfev: 9595 + population: [[ 2.819e-02 5.690e-01 ... 2.564e+00 1.351e-01] + [ 2.782e-02 5.721e-01 ... 2.564e+00 1.372e-01] + ... + [ 2.900e-02 5.623e-01 ... 2.579e+00 1.134e-01] + [ 2.857e-02 5.656e-01 ... 2.566e+00 1.189e-01]] + population_energies: [ 3.104e+00 3.124e+00 ... 3.141e+00 3.152e+00] + jac: [-1.406e-02 -4.290e-03 -1.481e-03 5.206e-04 + 7.284e-04 3.588e-03] +2024-05-27 14:30:23,553 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02798433889810636 +2024-05-27 14:30:23,553 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5712669267962659 +2024-05-27 14:30:23,554 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.362816600455657 +2024-05-27 14:30:23,554 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.70032176860767 +2024-05-27 14:30:23,554 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.562724119930549 +2024-05-27 14:30:23,554 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.12985471996519413 +2024-05-27 14:30:23,558 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.691290 0.133492 +1.950000 NaN 14.062466 0.386761 +2.833333 NaN 13.439227 0.637781 +2.876944 0.144770 NaN NaN +3.678056 0.228788 NaN NaN +3.983333 NaN 11.978243 1.226215 +4.092222 0.289859 NaN NaN +4.565000 0.379737 NaN NaN +4.883333 NaN 9.938942 2.047575 +5.166667 NaN 9.047632 2.406564 + +2024-05-27 14:30:23,562 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.1039069755455833 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.021128145756913554 + +2024-05-27 14:30:23,562 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.021128145756913554 +2024-05-27 14:30:23,564 - physiofit - INFO - Results for yadG: + optimal +yadG X_0 0.027984 +yadG growth_rate 0.571267 +yadG Glc_q -6.362817 +yadG Glc_M0 14.700322 +yadG Ace_q 2.562724 +yadG Ace_M0 0.129855 +2024-05-27 14:30:23,569 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:24,543 - physiofit - INFO - Running optimization for yaeR +2024-05-27 14:30:24,546 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:24,546 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:24,549 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +231 1.950000 NaN 13.510704 0.357960 +232 2.501389 0.113400 NaN NaN +233 3.250000 NaN 12.927054 0.983032 +234 3.341944 0.158760 NaN NaN +235 3.997500 0.219240 NaN NaN +236 4.083333 NaN 11.640036 1.417349 +237 4.523333 0.343224 NaN NaN +238 4.766667 NaN 10.387025 1.996362 +Experimental matrix: +[[ nan 13.51070391 0.35796 ] + [ 0.1134 nan nan] + [ nan 12.92705399 0.9830323 ] + [ 0.15876 nan nan] + [ 0.21924 nan nan] + [ nan 11.64003596 1.4173494 ] + [ 0.343224 nan nan] + [ nan 10.38702513 1.99636222]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:24,550 - physiofit - INFO - mc : False +2024-05-27 14:30:24,550 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:24,550 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:24,550 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:24,943 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:24,944 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.011700317958044 + x: [ 2.194e-02 5.994e-01 -6.194e+00 1.411e+01 + 3.069e+00 2.002e-01] + nit: 87 + nfev: 8256 + population: [[ 2.212e-02 5.975e-01 ... 3.052e+00 2.062e-01] + [ 2.071e-02 6.148e-01 ... 3.052e+00 2.280e-01] + ... + [ 2.209e-02 5.969e-01 ... 3.136e+00 1.879e-01] + [ 2.189e-02 6.001e-01 ... 3.151e+00 1.896e-01]] + population_energies: [ 3.012e+00 3.116e+00 ... 3.068e+00 3.074e+00] + jac: [ 7.423e-04 -5.684e-05 7.726e-03 -2.066e-03 + 7.276e-04 -4.205e-04] +2024-05-27 14:30:24,944 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.021936633817665536 +2024-05-27 14:30:24,944 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5993876561621357 +2024-05-27 14:30:24,944 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.193861977132481 +2024-05-27 14:30:24,945 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.111146871712618 +2024-05-27 14:30:24,945 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.0688945941282273 +2024-05-27 14:30:24,945 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.2002058032562901 +2024-05-27 14:30:24,949 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.608325 0.449341 +2.501389 0.098245 NaN NaN +3.250000 NaN 12.747699 0.875758 +3.341944 0.162598 NaN NaN +3.997500 0.240859 NaN NaN +4.083333 NaN 11.717482 1.386203 +4.523333 0.330098 NaN NaN +4.766667 NaN 10.391094 2.043393 + +2024-05-27 14:30:24,952 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.011700317958044 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.1926231100659054 + +2024-05-27 14:30:24,952 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.1926231100659054 +2024-05-27 14:30:24,955 - physiofit - INFO - Results for yaeR: + optimal +yaeR X_0 0.021937 +yaeR growth_rate 0.599388 +yaeR Glc_q -6.193862 +yaeR Glc_M0 14.111147 +yaeR Ace_q 3.068895 +yaeR Ace_M0 0.200206 +2024-05-27 14:30:24,961 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:26,014 - physiofit - INFO - Running optimization for yafJ +2024-05-27 14:30:26,016 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:26,017 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:26,020 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +239 1.950000 NaN 13.469154 0.320140 +240 2.501389 0.111888 NaN NaN +241 3.250000 NaN 12.571858 0.996182 +242 3.341944 0.173880 NaN NaN +243 3.997500 0.252504 NaN NaN +244 4.083333 NaN 11.995377 1.255511 +245 4.523333 0.359856 NaN NaN +246 4.766667 NaN 11.159571 1.718026 +Experimental matrix: +[[ nan 13.46915405 0.32014026] + [ 0.111888 nan nan] + [ nan 12.57185811 0.99618221] + [ 0.17388 nan nan] + [ 0.252504 nan nan] + [ nan 11.99537705 1.25551098] + [ 0.359856 nan nan] + [ nan 11.15957089 1.71802568]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:26,020 - physiofit - INFO - mc : False +2024-05-27 14:30:26,020 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:26,020 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:26,021 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:26,431 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:26,432 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.8919161663790778 + x: [ 2.509e-02 5.850e-01 -3.978e+00 1.371e+01 + 2.343e+00 2.442e-01] + nit: 90 + nfev: 8715 + population: [[ 2.571e-02 5.790e-01 ... 2.366e+00 2.299e-01] + [ 2.484e-02 5.880e-01 ... 2.360e+00 2.264e-01] + ... + [ 2.578e-02 5.791e-01 ... 2.340e+00 2.284e-01] + [ 2.606e-02 5.766e-01 ... 2.376e+00 2.215e-01]] + population_energies: [ 1.892e+00 1.919e+00 ... 1.924e+00 1.925e+00] + jac: [-2.657e-02 -1.961e-03 6.768e-05 1.946e-04 + 4.441e-06 -7.530e-05] +2024-05-27 14:30:26,432 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02508624622839086 +2024-05-27 14:30:26,432 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5850031389297311 +2024-05-27 14:30:26,432 - physiofit.physiofit.base.fitter - INFO - Glc_q = -3.977962187481271 +2024-05-27 14:30:26,433 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.705473335073652 +2024-05-27 14:30:26,433 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3426107625533206 +2024-05-27 14:30:26,433 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.2441933581387525 +2024-05-27 14:30:26,436 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.342277 0.458078 +2.501389 0.108380 NaN NaN +3.250000 NaN 12.734113 0.816225 +3.341944 0.177216 NaN NaN +3.997500 0.260049 NaN NaN +4.083333 NaN 12.016692 1.238712 +4.523333 0.353712 NaN NaN +4.766667 NaN 11.102898 1.776843 + +2024-05-27 14:30:26,439 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.8919161663790778 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.07063431220567276 + +2024-05-27 14:30:26,440 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.07063431220567276 +2024-05-27 14:30:26,442 - physiofit - INFO - Results for yafJ: + optimal +yafJ X_0 0.025086 +yafJ growth_rate 0.585003 +yafJ Glc_q -3.977962 +yafJ Glc_M0 13.705473 +yafJ Ace_q 2.342611 +yafJ Ace_M0 0.244193 +2024-05-27 14:30:26,449 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:27,392 - physiofit - INFO - Running optimization for yahJ +2024-05-27 14:30:27,394 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:27,394 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:27,398 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +247 0.050000 NaN 14.218150 0.015991 +248 1.950000 NaN 13.786019 0.422845 +249 2.833333 NaN 13.467323 0.792222 +250 2.876944 0.161784 NaN NaN +251 3.678056 0.258552 NaN NaN +252 3.983333 NaN 11.818017 1.456673 +253 4.092222 0.378000 NaN NaN +254 4.565000 0.585144 NaN NaN +255 4.883333 NaN 9.245831 2.285966 +256 5.166667 NaN 8.481888 2.504717 +Experimental matrix: +[[ nan 14.21815042 0.01599123] + [ nan 13.78601945 0.42284502] + [ nan 13.4673227 0.79222229] + [ 0.161784 nan nan] + [ 0.258552 nan nan] + [ nan 11.8180172 1.4566733 ] + [ 0.378 nan nan] + [ 0.585144 nan nan] + [ nan 9.24583068 2.28596594] + [ nan 8.48188793 2.50471696]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:27,398 - physiofit - INFO - mc : False +2024-05-27 14:30:27,398 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:27,398 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:27,399 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:27,800 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:27,800 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 8.601913770986306 + x: [ 1.510e-02 7.949e-01 -5.210e+00 1.418e+01 + 2.106e+00 2.976e-01] + nit: 85 + nfev: 8167 + population: [[ 1.500e-02 7.963e-01 ... 2.109e+00 2.983e-01] + [ 1.557e-02 7.878e-01 ... 2.111e+00 2.928e-01] + ... + [ 1.520e-02 7.948e-01 ... 2.118e+00 2.880e-01] + [ 1.476e-02 7.998e-01 ... 2.104e+00 2.985e-01]] + population_energies: [ 8.602e+00 8.676e+00 ... 8.679e+00 8.647e+00] + jac: [ 9.821e-02 5.322e-03 -5.285e-04 -1.902e-04 + 8.130e-04 -1.400e-04] +2024-05-27 14:30:27,801 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.015100250926870548 +2024-05-27 14:30:27,802 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.7949229499198881 +2024-05-27 14:30:27,802 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.210089654094659 +2024-05-27 14:30:27,802 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.18295285071596 +2024-05-27 14:30:27,802 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.1064604924380497 +2024-05-27 14:30:27,802 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.29760079279234103 +2024-05-27 14:30:27,806 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.178940 0.299223 +1.950000 NaN 13.815581 0.446131 +2.833333 NaN 13.340775 0.638097 +2.876944 0.148660 NaN NaN +3.678056 0.281036 NaN NaN +3.983333 NaN 11.934058 1.206838 +4.092222 0.390611 NaN NaN +4.565000 0.568803 NaN NaN +4.883333 NaN 9.480382 2.198869 +5.166667 NaN 8.267472 2.689254 + +2024-05-27 14:30:27,810 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 8.601913770986306 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.4297468372538977 + +2024-05-27 14:30:27,810 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.4297468372538977 +2024-05-27 14:30:27,812 - physiofit - INFO - Results for yahJ: + optimal +yahJ X_0 0.015100 +yahJ growth_rate 0.794923 +yahJ Glc_q -5.210090 +yahJ Glc_M0 14.182953 +yahJ Ace_q 2.106460 +yahJ Ace_M0 0.297601 +2024-05-27 14:30:27,818 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:28,794 - physiofit - INFO - Running optimization for yahO +2024-05-27 14:30:28,797 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:28,797 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:28,800 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +257 0.000000 0.034776 NaN NaN +258 0.066667 NaN 14.621430 0.008012 +259 1.188889 0.057456 NaN NaN +260 1.716667 NaN 14.796643 0.343938 +261 2.276944 0.099792 NaN NaN +262 2.800000 NaN 13.368497 0.744428 +263 3.128333 0.151200 NaN NaN +264 3.633333 NaN 13.061815 1.231642 +265 3.771389 0.216216 NaN NaN +266 4.266667 NaN 12.301721 1.770858 +267 4.415556 0.300888 NaN NaN +268 4.822778 0.397656 NaN NaN +269 4.883333 NaN 10.443631 2.193268 +Experimental matrix: +[[3.47760000e-02 nan nan] + [ nan 1.46214297e+01 8.01209304e-03] + [5.74560000e-02 nan nan] + [ nan 1.47966435e+01 3.43938318e-01] + [9.97920000e-02 nan nan] + [ nan 1.33684971e+01 7.44427522e-01] + [1.51200000e-01 nan nan] + [ nan 1.30618155e+01 1.23164212e+00] + [2.16216000e-01 nan nan] + [ nan 1.23017208e+01 1.77085778e+00] + [3.00888000e-01 nan nan] + [3.97656000e-01 nan nan] + [ nan 1.04436305e+01 2.19326810e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:28,801 - physiofit - INFO - mc : False +2024-05-27 14:30:28,801 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:28,801 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:28,801 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:29,182 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:29,183 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.639400963134042 + x: [ 2.860e-02 5.405e-01 -6.111e+00 1.489e+01 + 3.240e+00 9.810e-02] + nit: 83 + nfev: 7966 + population: [[ 2.854e-02 5.411e-01 ... 3.220e+00 1.045e-01] + [ 2.696e-02 5.532e-01 ... 3.282e+00 1.074e-01] + ... + [ 2.867e-02 5.393e-01 ... 3.178e+00 1.158e-01] + [ 2.839e-02 5.423e-01 ... 3.179e+00 1.177e-01]] + population_energies: [ 4.639e+00 4.807e+00 ... 4.693e+00 4.694e+00] + jac: [ 3.706e-03 -3.793e-05 4.228e-05 9.699e-05 + 2.229e-04 8.663e-04] +2024-05-27 14:30:29,184 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02859601353806398 +2024-05-27 14:30:29,184 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5404503848102283 +2024-05-27 14:30:29,184 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.111054257341435 +2024-05-27 14:30:29,184 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.891779223235378 +2024-05-27 14:30:29,184 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.240212125373008 +2024-05-27 14:30:29,184 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.09810152556862434 +2024-05-27 14:30:29,189 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028596 NaN NaN +0.066667 NaN 14.879917 0.104391 +1.188889 0.054369 NaN NaN +1.716667 NaN 14.397427 0.360218 +2.276944 0.097890 NaN NaN +2.800000 NaN 13.746648 0.705274 +3.128333 0.155085 NaN NaN +3.633333 NaN 12.911231 1.148231 +3.771389 0.219536 NaN NaN +4.266667 NaN 11.970870 1.646830 +4.415556 0.310957 NaN NaN +4.822778 0.387509 NaN NaN +4.883333 NaN 10.687654 2.327219 + +2024-05-27 14:30:29,192 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.639400963134042 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.017702170986345543 + +2024-05-27 14:30:29,193 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.017702170986345543 +2024-05-27 14:30:29,194 - physiofit - INFO - Results for yahO: + optimal +yahO X_0 0.028596 +yahO growth_rate 0.540450 +yahO Glc_q -6.111054 +yahO Glc_M0 14.891779 +yahO Ace_q 3.240212 +yahO Ace_M0 0.098102 +2024-05-27 14:30:29,201 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:30,164 - physiofit - INFO - Running optimization for yaiA +2024-05-27 14:30:30,167 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:30,167 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:30,171 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +270 0.000000 0.036288 NaN NaN +271 0.066667 NaN 15.870975 0.009760 +272 1.188889 0.069552 NaN NaN +273 1.716667 NaN 15.277379 0.356494 +274 2.276944 0.110376 NaN NaN +275 2.800000 NaN 13.188496 0.707464 +276 3.128333 0.161784 NaN NaN +277 3.633333 NaN 12.658575 1.152771 +278 3.771389 0.217728 NaN NaN +279 4.266667 NaN 11.771417 1.636080 +280 4.415556 0.337176 NaN NaN +281 4.822778 0.443016 NaN NaN +282 4.883333 NaN 10.133616 2.079033 +Experimental matrix: +[[3.62880000e-02 nan nan] + [ nan 1.58709755e+01 9.75994940e-03] + [6.95520000e-02 nan nan] + [ nan 1.52773787e+01 3.56493539e-01] + [1.10376000e-01 nan nan] + [ nan 1.31884963e+01 7.07464103e-01] + [1.61784000e-01 nan nan] + [ nan 1.26585746e+01 1.15277135e+00] + [2.17728000e-01 nan nan] + [ nan 1.17714168e+01 1.63608003e+00] + [3.37176000e-01 nan nan] + [4.43016000e-01 nan nan] + [ nan 1.01336156e+01 2.07903295e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:30,172 - physiofit - INFO - mc : False +2024-05-27 14:30:30,172 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:30,172 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:30,172 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:30,586 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:30,587 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 8.608794749139262 + x: [ 3.144e-02 5.402e-01 -7.409e+00 1.554e+01 + 2.752e+00 1.032e-01] + nit: 88 + nfev: 8339 + population: [[ 3.131e-02 5.409e-01 ... 2.783e+00 9.346e-02] + [ 3.071e-02 5.440e-01 ... 2.750e+00 1.173e-01] + ... + [ 3.177e-02 5.363e-01 ... 2.771e+00 9.370e-02] + [ 3.113e-02 5.430e-01 ... 2.722e+00 1.061e-01]] + population_energies: [ 8.609e+00 8.674e+00 ... 8.694e+00 8.644e+00] + jac: [-5.080e-02 -2.036e-02 6.298e-02 -2.212e-02 + -1.958e-02 9.190e-03] +2024-05-27 14:30:30,587 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.031441674011833225 +2024-05-27 14:30:30,587 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5401843649841053 +2024-05-27 14:30:30,587 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.408683908889539 +2024-05-27 14:30:30,587 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.537719632382252 +2024-05-27 14:30:30,587 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.7521831110301673 +2024-05-27 14:30:30,587 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1031892963062206 +2024-05-27 14:30:30,591 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.031442 NaN NaN +0.066667 NaN 15.521907 0.109063 +1.188889 0.059761 NaN NaN +1.716667 NaN 14.878929 0.347917 +2.276944 0.107566 NaN NaN +2.800000 NaN 14.011984 0.669970 +3.128333 0.170377 NaN NaN +3.633333 NaN 12.899348 1.083293 +3.771389 0.241140 NaN NaN +4.266667 NaN 11.647184 1.548448 +4.415556 0.341500 NaN NaN +4.822778 0.425525 NaN NaN +4.883333 NaN 9.938766 2.183093 + +2024-05-27 14:30:30,595 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 8.608794749139262 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.19819394161484316 + +2024-05-27 14:30:30,595 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.19819394161484316 +2024-05-27 14:30:30,598 - physiofit - INFO - Results for yaiA: + optimal +yaiA X_0 0.031442 +yaiA growth_rate 0.540184 +yaiA Glc_q -7.408684 +yaiA Glc_M0 15.537720 +yaiA Ace_q 2.752183 +yaiA Ace_M0 0.103189 +2024-05-27 14:30:30,603 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:31,603 - physiofit - INFO - Running optimization for yaiL +2024-05-27 14:30:31,606 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:31,606 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:31,609 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +283 0.000000 0.034776 NaN NaN +284 0.283333 NaN 14.387343 0.039590 +285 1.195000 0.065016 NaN NaN +286 1.613611 0.080136 NaN NaN +287 1.916667 NaN 14.132181 0.419289 +288 2.361389 0.111888 NaN NaN +289 2.700000 NaN 13.162101 0.631246 +290 3.286389 0.190512 NaN NaN +291 3.616667 NaN 12.310651 1.102419 +292 3.819444 0.294840 NaN NaN +293 4.050000 NaN 11.916114 1.348943 +294 4.410833 0.418824 NaN NaN +295 4.750000 NaN 10.353005 1.971408 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.38734289 0.03958953] + [ 0.065016 nan nan] + [ 0.080136 nan nan] + [ nan 14.13218137 0.4192892 ] + [ 0.111888 nan nan] + [ nan 13.16210066 0.63124606] + [ 0.190512 nan nan] + [ nan 12.31065053 1.10241934] + [ 0.29484 nan nan] + [ nan 11.9161138 1.34894298] + [ 0.418824 nan nan] + [ nan 10.35300474 1.97140838]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:31,609 - physiofit - INFO - mc : False +2024-05-27 14:30:31,610 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:31,610 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:31,610 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:32,079 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:32,081 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.7647879758601484 + x: [ 2.810e-02 6.101e-01 -5.201e+00 1.441e+01 + 2.408e+00 1.304e-01] + nit: 95 + nfev: 9354 + population: [[ 2.812e-02 6.100e-01 ... 2.401e+00 1.308e-01] + [ 2.872e-02 6.050e-01 ... 2.386e+00 1.371e-01] + ... + [ 2.847e-02 6.058e-01 ... 2.431e+00 1.217e-01] + [ 2.784e-02 6.125e-01 ... 2.437e+00 1.297e-01]] + population_energies: [ 2.765e+00 2.854e+00 ... 2.787e+00 2.786e+00] + jac: [-1.418e-01 -2.131e-02 1.683e-05 -5.782e-04 + -7.137e-05 5.823e-04] +2024-05-27 14:30:32,081 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.028097201254568018 +2024-05-27 14:30:32,081 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6100550434611618 +2024-05-27 14:30:32,082 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.200712881705896 +2024-05-27 14:30:32,082 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.412775273069995 +2024-05-27 14:30:32,082 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4084870494010295 +2024-05-27 14:30:32,082 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.13035340821466407 +2024-05-27 14:30:32,086 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028097 NaN NaN +0.283333 NaN 14.367580 0.151284 +1.195000 0.058247 NaN NaN +1.613611 0.075193 NaN NaN +1.916667 NaN 13.881107 0.376573 +2.361389 0.118658 NaN NaN +2.700000 NaN 13.408636 0.595378 +3.286389 0.208627 NaN NaN +3.616667 NaN 12.476752 1.026940 +3.819444 0.288802 NaN NaN +4.050000 NaN 11.818445 1.331806 +4.410833 0.414271 NaN NaN +4.750000 NaN 10.308815 2.030927 + +2024-05-27 14:30:32,090 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.7647879758601484 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0013419059983172785 + +2024-05-27 14:30:32,090 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0013419059983172785 +2024-05-27 14:30:32,092 - physiofit - INFO - Results for yaiL: + optimal +yaiL X_0 0.028097 +yaiL growth_rate 0.610055 +yaiL Glc_q -5.200713 +yaiL Glc_M0 14.412775 +yaiL Ace_q 2.408487 +yaiL Ace_M0 0.130353 +2024-05-27 14:30:32,099 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:33,071 - physiofit - INFO - Running optimization for yajD +2024-05-27 14:30:33,074 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:33,074 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:33,077 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +296 0.000000 0.033264 NaN NaN +297 0.066667 NaN 15.656662 0.012247 +298 1.188889 0.065016 NaN NaN +299 1.716667 NaN 15.544161 0.377293 +300 2.276944 0.116424 NaN NaN +301 2.800000 NaN 13.490683 0.834704 +302 3.128333 0.182952 NaN NaN +303 3.633333 NaN 12.601478 1.369990 +304 3.771389 0.261576 NaN NaN +305 4.266667 NaN 11.613583 1.947445 +306 4.415556 0.409752 NaN NaN +307 4.822778 0.577584 NaN NaN +308 4.883333 NaN 9.755441 2.425128 +Experimental matrix: +[[3.32640000e-02 nan nan] + [ nan 1.56566619e+01 1.22465083e-02] + [6.50160000e-02 nan nan] + [ nan 1.55441606e+01 3.77292507e-01] + [1.16424000e-01 nan nan] + [ nan 1.34906826e+01 8.34703868e-01] + [1.82952000e-01 nan nan] + [ nan 1.26014777e+01 1.36998976e+00] + [2.61576000e-01 nan nan] + [ nan 1.16135827e+01 1.94744532e+00] + [4.09752000e-01 nan nan] + [5.77584000e-01 nan nan] + [ nan 9.75544126e+00 2.42512764e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:33,078 - physiofit - INFO - mc : False +2024-05-27 14:30:33,078 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:33,078 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:33,078 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:33,510 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:33,511 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 11.64753666356364 + x: [ 2.588e-02 6.350e-01 -6.912e+00 1.551e+01 + 2.806e+00 1.850e-01] + nit: 91 + nfev: 8924 + population: [[ 2.601e-02 6.336e-01 ... 2.802e+00 1.914e-01] + [ 2.706e-02 6.254e-01 ... 2.824e+00 1.665e-01] + ... + [ 2.605e-02 6.340e-01 ... 2.812e+00 1.616e-01] + [ 2.629e-02 6.308e-01 ... 2.807e+00 1.777e-01]] + population_energies: [ 1.165e+01 1.180e+01 ... 1.173e+01 1.174e+01] + jac: [-6.001e-02 -2.035e-02 4.311e-04 -6.395e-04 + 2.036e-03 3.475e-03] +2024-05-27 14:30:33,511 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025876567875853723 +2024-05-27 14:30:33,511 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6350393897819422 +2024-05-27 14:30:33,512 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.911664683875421 +2024-05-27 14:30:33,512 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.514950747964527 +2024-05-27 14:30:33,512 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.80589343596242 +2024-05-27 14:30:33,512 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.18495138685309015 +2024-05-27 14:30:33,515 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.025877 NaN NaN +0.066667 NaN 15.502771 0.189896 +1.188889 0.055055 NaN NaN +1.716667 NaN 14.958797 0.410730 +2.276944 0.109869 NaN NaN +2.800000 NaN 14.129677 0.747324 +3.128333 0.188661 NaN NaN +3.633333 NaN 12.966886 1.219376 +3.771389 0.283814 NaN NaN +4.266667 NaN 11.565907 1.788125 +4.415556 0.427259 NaN NaN +4.822778 0.553351 NaN NaN +4.883333 NaN 9.537900 2.611424 + +2024-05-27 14:30:33,519 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 11.64753666356364 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.44326420674515593 + +2024-05-27 14:30:33,519 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.44326420674515593 +2024-05-27 14:30:33,522 - physiofit - INFO - Results for yajD: + optimal +yajD X_0 0.025877 +yajD growth_rate 0.635039 +yajD Glc_q -6.911665 +yajD Glc_M0 15.514951 +yajD Ace_q 2.805893 +yajD Ace_M0 0.184951 +2024-05-27 14:30:33,528 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:34,507 - physiofit - INFO - Running optimization for yajG +2024-05-27 14:30:34,509 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:34,509 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:34,513 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +309 1.950000 NaN 13.549026 0.352071 +310 2.501389 0.119448 NaN NaN +311 3.250000 NaN 12.798163 0.885313 +312 3.341944 0.189000 NaN NaN +313 3.997500 0.276696 NaN NaN +314 4.083333 NaN 11.816590 1.284468 +315 4.523333 0.412776 NaN NaN +316 4.766667 NaN 10.646501 1.716918 +Experimental matrix: +[[ nan 13.54902646 0.35207137] + [ 0.119448 nan nan] + [ nan 12.79816333 0.8853128 ] + [ 0.189 nan nan] + [ 0.276696 nan nan] + [ nan 11.81659029 1.28446765] + [ 0.412776 nan nan] + [ nan 10.6465013 1.7169176 ]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:34,513 - physiofit - INFO - mc : False +2024-05-27 14:30:34,513 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:34,513 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:34,513 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:35,010 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:35,011 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.4159258580505911 + x: [ 2.275e-02 6.364e-01 -4.707e+00 1.395e+01 + 2.149e+00 2.610e-01] + nit: 109 + nfev: 10369 + population: [[ 2.271e-02 6.369e-01 ... 2.163e+00 2.543e-01] + [ 2.279e-02 6.363e-01 ... 2.163e+00 2.591e-01] + ... + [ 2.305e-02 6.336e-01 ... 2.171e+00 2.470e-01] + [ 2.321e-02 6.316e-01 ... 2.168e+00 2.512e-01]] + population_energies: [ 1.416e+00 1.423e+00 ... 1.430e+00 1.435e+00] + jac: [-1.744e-04 -1.847e-05 -2.509e-06 -7.772e-07 + 2.041e-05 4.219e-05] +2024-05-27 14:30:35,011 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.022753337787356772 +2024-05-27 14:30:35,012 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6363832126164681 +2024-05-27 14:30:35,012 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.707311416768262 +2024-05-27 14:30:35,012 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.95221630964235 +2024-05-27 14:30:35,012 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.1488348948668046 +2024-05-27 14:30:35,012 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.26099877950898465 +2024-05-27 14:30:35,016 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.538371 0.449915 +2.501389 0.111782 NaN NaN +3.250000 NaN 12.789066 0.791964 +3.341944 0.190846 NaN NaN +3.997500 0.289644 NaN NaN +4.083333 NaN 11.857746 1.217101 +4.523333 0.404756 NaN NaN +4.766667 NaN 10.625099 1.779791 + +2024-05-27 14:30:35,018 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.4159258580505911 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.03511753799713332 + +2024-05-27 14:30:35,019 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.03511753799713332 +2024-05-27 14:30:35,021 - physiofit - INFO - Results for yajG: + optimal +yajG X_0 0.022753 +yajG growth_rate 0.636383 +yajG Glc_q -4.707311 +yajG Glc_M0 13.952216 +yajG Ace_q 2.148835 +yajG Ace_M0 0.260999 +2024-05-27 14:30:35,029 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:36,108 - physiofit - INFO - Running optimization for yajO +2024-05-27 14:30:36,112 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:36,112 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:36,116 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +317 1.828889 0.058968 NaN NaN +318 2.261389 0.072576 NaN NaN +319 2.774167 0.096768 NaN NaN +320 2.800000 NaN 12.313719 0.621801 +321 3.208889 0.111888 NaN NaN +322 3.706389 0.167832 NaN NaN +323 3.733333 NaN 11.756639 1.076347 +324 4.225833 0.204120 NaN NaN +325 4.283333 NaN 11.055539 1.403817 +326 4.635556 0.290304 NaN NaN +327 4.750000 NaN 10.407189 1.792746 +328 4.967500 0.334152 NaN NaN +329 5.116667 NaN 9.455774 2.085068 +330 5.433333 NaN 8.625268 2.404388 +Experimental matrix: +[[ 0.058968 nan nan] + [ 0.072576 nan nan] + [ 0.096768 nan nan] + [ nan 12.31371928 0.62180107] + [ 0.111888 nan nan] + [ 0.167832 nan nan] + [ nan 11.75663932 1.07634678] + [ 0.20412 nan nan] + [ nan 11.05553902 1.40381688] + [ 0.290304 nan nan] + [ nan 10.40718865 1.7927459 ] + [ 0.334152 nan nan] + [ nan 9.45577446 2.08506798] + [ nan 8.62526786 2.40438796]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:36,116 - physiofit - INFO - mc : False +2024-05-27 14:30:36,116 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:36,116 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:36,116 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:36,615 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:36,616 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.9849791298360842 + x: [ 1.886e-02 5.801e-01 -6.280e+00 1.327e+01 + 2.970e+00 3.031e-01] + nit: 110 + nfev: 10522 + population: [[ 1.888e-02 5.801e-01 ... 2.963e+00 3.032e-01] + [ 1.839e-02 5.861e-01 ... 2.932e+00 3.234e-01] + ... + [ 1.862e-02 5.832e-01 ... 2.959e+00 3.095e-01] + [ 1.870e-02 5.819e-01 ... 2.967e+00 3.085e-01]] + population_energies: [ 1.985e+00 2.010e+00 ... 1.997e+00 1.992e+00] + jac: [ 4.446e-02 -2.561e-03 -2.867e-04 -5.620e-04 + 6.533e-04 2.626e-03] +2024-05-27 14:30:36,616 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.018857197100288874 +2024-05-27 14:30:36,617 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5801107431298129 +2024-05-27 14:30:36,617 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.279690076668272 +2024-05-27 14:30:36,617 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.268367717312785 +2024-05-27 14:30:36,618 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.9701197802482766 +2024-05-27 14:30:36,618 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.30308140809204653 +2024-05-27 14:30:36,621 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.054481 NaN NaN +2.261389 0.070018 NaN NaN +2.774167 0.094275 NaN NaN +2.800000 NaN 12.436560 0.696504 +3.208889 0.121317 NaN NaN +3.706389 0.161905 NaN NaN +3.733333 NaN 11.692266 1.048534 +4.225833 0.218841 NaN NaN +4.283333 NaN 11.023193 1.364987 +4.635556 0.277558 NaN NaN +4.750000 NaN 10.261690 1.725157 +4.967500 0.336499 NaN NaN +5.116667 NaN 9.500656 2.085105 +5.433333 NaN 8.699705 2.463932 + +2024-05-27 14:30:36,626 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.9849791298360842 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 7.94751093073337e-05 + +2024-05-27 14:30:36,626 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 7.94751093073337e-05 +2024-05-27 14:30:36,628 - physiofit - INFO - Results for yajO: + optimal +yajO X_0 0.018857 +yajO growth_rate 0.580111 +yajO Glc_q -6.279690 +yajO Glc_M0 13.268368 +yajO Ace_q 2.970120 +yajO Ace_M0 0.303081 +2024-05-27 14:30:36,635 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:37,618 - physiofit - INFO - Running optimization for ybaQ +2024-05-27 14:30:37,620 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:37,620 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:37,624 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +331 1.950000 NaN 13.806808 0.380479 +332 2.501389 0.113400 NaN NaN +333 3.250000 NaN 12.674232 0.923825 +334 3.341944 0.178416 NaN NaN +335 3.997500 0.240408 NaN NaN +336 4.083333 NaN 11.804915 1.320145 +337 4.523333 0.403704 NaN NaN +338 4.766667 NaN 10.699770 1.842321 +Experimental matrix: +[[ nan 13.80680752 0.38047881] + [ 0.1134 nan nan] + [ nan 12.67423156 0.92382524] + [ 0.178416 nan nan] + [ 0.240408 nan nan] + [ nan 11.80491549 1.32014537] + [ 0.403704 nan nan] + [ nan 10.69976984 1.84232097]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:37,624 - physiofit - INFO - mc : False +2024-05-27 14:30:37,624 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:37,624 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:37,624 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:37,979 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:37,980 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.696439182598395 + x: [ 1.861e-02 6.708e-01 -5.246e+00 1.401e+01 + 2.461e+00 2.893e-01] + nit: 77 + nfev: 7489 + population: [[ 1.861e-02 6.710e-01 ... 2.449e+00 2.930e-01] + [ 1.838e-02 6.733e-01 ... 2.473e+00 2.743e-01] + ... + [ 1.847e-02 6.721e-01 ... 2.469e+00 3.018e-01] + [ 1.840e-02 6.728e-01 ... 2.498e+00 2.814e-01]] + population_energies: [ 4.696e+00 4.736e+00 ... 4.715e+00 4.710e+00] + jac: [-1.908e-02 7.904e-03 1.868e-03 6.143e-03 + 5.240e-04 1.836e-03] +2024-05-27 14:30:37,981 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.01860798053172678 +2024-05-27 14:30:37,981 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6707680004846418 +2024-05-27 14:30:37,981 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.2460160466720245 +2024-05-27 14:30:37,981 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.010546770925561 +2024-05-27 14:30:37,982 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.460689372302847 +2024-05-27 14:30:37,982 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.2893042174268645 +2024-05-27 14:30:37,986 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.617793 0.473529 +2.501389 0.099628 NaN NaN +3.250000 NaN 12.868668 0.824912 +3.341944 0.175083 NaN NaN +3.997500 0.271778 NaN NaN +4.083333 NaN 11.904558 1.277136 +4.523333 0.386719 NaN NaN +4.766667 NaN 10.595355 1.891230 + +2024-05-27 14:30:37,989 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.696439182598395 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.4167062958897137 + +2024-05-27 14:30:37,990 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.4167062958897137 +2024-05-27 14:30:37,992 - physiofit - INFO - Results for ybaQ: + optimal +ybaQ X_0 0.018608 +ybaQ growth_rate 0.670768 +ybaQ Glc_q -5.246016 +ybaQ Glc_M0 14.010547 +ybaQ Ace_q 2.460689 +ybaQ Ace_M0 0.289304 +2024-05-27 14:30:37,999 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:38,938 - physiofit - INFO - Running optimization for ybaY +2024-05-27 14:30:38,940 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:38,940 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:38,943 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +339 1.950000 NaN 13.870783 0.393298 +340 2.501389 0.128520 NaN NaN +341 3.250000 NaN 12.773739 0.906011 +342 3.341944 0.198072 NaN NaN +343 3.997500 0.267624 NaN NaN +344 4.083333 NaN 11.576351 1.435758 +345 4.523333 0.385560 NaN NaN +346 4.766667 NaN 10.428133 1.980915 +Experimental matrix: +[[ nan 13.87078257 0.39329829] + [ 0.12852 nan nan] + [ nan 12.77373853 0.90601051] + [ 0.198072 nan nan] + [ 0.267624 nan nan] + [ nan 11.57635056 1.43575758] + [ 0.38556 nan nan] + [ nan 10.42813257 1.98091493]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:38,944 - physiofit - INFO - mc : False +2024-05-27 14:30:38,944 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:38,944 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:38,944 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:39,414 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:39,415 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.091777197511719 + x: [ 3.128e-02 5.503e-01 -5.595e+00 1.440e+01 + 2.571e+00 1.511e-01] + nit: 102 + nfev: 9823 + population: [[ 3.128e-02 5.501e-01 ... 2.572e+00 1.525e-01] + [ 3.142e-02 5.490e-01 ... 2.579e+00 1.420e-01] + ... + [ 3.046e-02 5.567e-01 ... 2.586e+00 1.558e-01] + [ 3.165e-02 5.473e-01 ... 2.558e+00 1.563e-01]] + population_energies: [ 1.092e+00 1.099e+00 ... 1.106e+00 1.101e+00] + jac: [-3.094e-02 -3.294e-03 3.034e-04 3.574e-04 + 3.291e-05 -5.439e-04] +2024-05-27 14:30:39,415 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.031276057151891946 +2024-05-27 14:30:39,415 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5502744980065314 +2024-05-27 14:30:39,416 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.595443852005262 +2024-05-27 14:30:39,416 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.399565218333434 +2024-05-27 14:30:39,416 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5707019147312273 +2024-05-27 14:30:39,417 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15111283991060762 +2024-05-27 14:30:39,420 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.787600 0.432267 +2.501389 0.123879 NaN NaN +3.250000 NaN 12.815833 0.878723 +3.341944 0.196731 NaN NaN +3.997500 0.282188 NaN NaN +4.083333 NaN 11.709393 1.387053 +4.523333 0.376880 NaN NaN +4.766667 NaN 10.336216 2.017928 + +2024-05-27 14:30:39,423 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.091777197511719 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.018107303234684808 + +2024-05-27 14:30:39,424 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.018107303234684808 +2024-05-27 14:30:39,426 - physiofit - INFO - Results for ybaY: + optimal +ybaY X_0 0.031276 +ybaY growth_rate 0.550274 +ybaY Glc_q -5.595444 +ybaY Glc_M0 14.399565 +ybaY Ace_q 2.570702 +ybaY Ace_M0 0.151113 +2024-05-27 14:30:39,433 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:40,394 - physiofit - INFO - Running optimization for ybbA +2024-05-27 14:30:40,399 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:40,399 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:40,404 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +347 0.050000 NaN 14.370148 0.026307 +348 1.950000 NaN 13.920316 0.419364 +349 2.833333 NaN 13.237528 0.793831 +350 2.876944 0.157248 NaN NaN +351 3.678056 0.258552 NaN NaN +352 3.983333 NaN 11.893028 1.449930 +353 4.092222 0.350784 NaN NaN +354 4.565000 0.433944 NaN NaN +355 4.883333 NaN 9.243458 2.058784 +356 5.166667 NaN 8.419989 2.557508 +Experimental matrix: +[[ nan 14.37014824 0.02630661] + [ nan 13.92031568 0.41936425] + [ nan 13.23752807 0.79383147] + [ 0.157248 nan nan] + [ 0.258552 nan nan] + [ nan 11.8930283 1.4499296 ] + [ 0.350784 nan nan] + [ 0.433944 nan nan] + [ nan 9.24345757 2.05878355] + [ nan 8.41998868 2.55750801]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:40,404 - physiofit - INFO - mc : False +2024-05-27 14:30:40,404 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:40,404 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:40,405 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:40,845 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:40,846 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.2058554083140267 + x: [ 3.114e-02 5.803e-01 -5.996e+00 1.455e+01 + 2.342e+00 1.609e-01] + nit: 93 + nfev: 8831 + population: [[ 3.094e-02 5.819e-01 ... 2.351e+00 1.572e-01] + [ 3.194e-02 5.746e-01 ... 2.329e+00 1.483e-01] + ... + [ 3.089e-02 5.821e-01 ... 2.328e+00 1.530e-01] + [ 3.104e-02 5.809e-01 ... 2.355e+00 1.506e-01]] + population_energies: [ 3.206e+00 3.235e+00 ... 3.264e+00 3.215e+00] + jac: [ 6.739e-03 7.233e-04 -6.350e-06 -2.887e-06 + 3.233e-05 8.926e-05] +2024-05-27 14:30:40,846 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03114362283876591 +2024-05-27 14:30:40,847 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5802773741500807 +2024-05-27 14:30:40,847 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.9958813763620675 +2024-05-27 14:30:40,847 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.553254146728882 +2024-05-27 14:30:40,847 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3416339208052235 +2024-05-27 14:30:40,847 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.16087981732623574 +2024-05-27 14:30:40,851 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.543781 0.164580 +1.950000 NaN 13.877335 0.424854 +2.833333 NaN 13.209271 0.685759 +2.876944 0.165345 NaN NaN +3.678056 0.263197 NaN NaN +3.983333 NaN 11.628435 1.303140 +4.092222 0.334700 NaN NaN +4.565000 0.440353 NaN NaN +4.883333 NaN 9.401852 2.172710 +5.166667 NaN 8.423792 2.554682 + +2024-05-27 14:30:40,854 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.2058554083140267 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.023844040493718476 + +2024-05-27 14:30:40,855 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.023844040493718476 +2024-05-27 14:30:40,857 - physiofit - INFO - Results for ybbA: + optimal +ybbA X_0 0.031144 +ybbA growth_rate 0.580277 +ybbA Glc_q -5.995881 +ybbA Glc_M0 14.553254 +ybbA Ace_q 2.341634 +ybbA Ace_M0 0.160880 +2024-05-27 14:30:40,863 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:41,836 - physiofit - INFO - Running optimization for ybcJ +2024-05-27 14:30:41,838 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:41,839 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:41,842 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +357 0.000000 0.039312 NaN NaN +358 0.283333 NaN 14.160867 0.048784 +359 1.195000 0.066528 NaN NaN +360 1.613611 0.081648 NaN NaN +361 1.916667 NaN 13.601640 0.389211 +362 2.361389 0.127008 NaN NaN +363 2.700000 NaN 13.521505 0.638015 +364 3.286389 0.201096 NaN NaN +365 3.616667 NaN 12.498055 1.042734 +366 3.819444 0.288792 NaN NaN +367 4.050000 NaN 11.719328 1.425779 +368 4.410833 0.397656 NaN NaN +369 4.750000 NaN 10.168275 1.910714 +Experimental matrix: +[[ 0.039312 nan nan] + [ nan 14.16086699 0.04878427] + [ 0.066528 nan nan] + [ 0.081648 nan nan] + [ nan 13.60164042 0.38921139] + [ 0.127008 nan nan] + [ nan 13.52150515 0.63801524] + [ 0.201096 nan nan] + [ nan 12.49805497 1.04273353] + [ 0.288792 nan nan] + [ nan 11.71932765 1.4257789 ] + [ 0.397656 nan nan] + [ nan 10.16827506 1.91071447]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:41,842 - physiofit - INFO - mc : False +2024-05-27 14:30:41,842 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:41,843 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:41,843 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:42,211 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:42,212 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.650745546442297 + x: [ 3.323e-02 5.622e-01 -5.097e+00 1.434e+01 + 2.373e+00 1.026e-01] + nit: 81 + nfev: 7541 + population: [[ 3.306e-02 5.636e-01 ... 2.368e+00 1.057e-01] + [ 3.350e-02 5.601e-01 ... 2.369e+00 9.845e-02] + ... + [ 3.313e-02 5.635e-01 ... 2.375e+00 9.249e-02] + [ 3.341e-02 5.606e-01 ... 2.371e+00 1.007e-01]] + population_energies: [ 1.651e+00 1.664e+00 ... 1.671e+00 1.658e+00] + jac: [-2.394e-03 -8.650e-04 3.193e-03 5.145e-03 + 2.995e-03 -2.017e-03] +2024-05-27 14:30:42,212 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03323055558576712 +2024-05-27 14:30:42,212 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.562190026067161 +2024-05-27 14:30:42,213 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.0973221633148 +2024-05-27 14:30:42,214 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.344347679424011 +2024-05-27 14:30:42,214 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.372891072550647 +2024-05-27 14:30:42,214 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.10262342601736457 +2024-05-27 14:30:42,217 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.033231 NaN NaN +0.283333 NaN 14.292321 0.126843 +1.195000 0.065059 NaN NaN +1.613611 0.082321 NaN NaN +1.916667 NaN 13.760607 0.374365 +2.361389 0.125339 NaN NaN +2.700000 NaN 13.270915 0.602325 +3.286389 0.210828 NaN NaN +3.616667 NaN 12.344058 1.033793 +3.819444 0.284497 NaN NaN +4.050000 NaN 11.709156 1.329350 +4.410833 0.396706 NaN NaN +4.750000 NaN 10.293157 1.988522 + +2024-05-27 14:30:42,221 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.650745546442297 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 7.542781924883756e-05 + +2024-05-27 14:30:42,222 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 7.542781924883756e-05 +2024-05-27 14:30:42,224 - physiofit - INFO - Results for ybcJ: + optimal +ybcJ X_0 0.033231 +ybcJ growth_rate 0.562190 +ybcJ Glc_q -5.097322 +ybcJ Glc_M0 14.344348 +ybcJ Ace_q 2.372891 +ybcJ Ace_M0 0.102623 +2024-05-27 14:30:42,230 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:43,198 - physiofit - INFO - Running optimization for ybdH +2024-05-27 14:30:43,200 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:43,200 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:43,204 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +370 1.950000 NaN 13.497249 0.409502 +371 2.501389 0.099792 NaN NaN +372 3.250000 NaN 12.897693 1.128827 +373 3.341944 0.154224 NaN NaN +374 3.997500 0.205632 NaN NaN +375 4.083333 NaN 11.350397 1.855671 +376 4.523333 0.311472 NaN NaN +377 4.766667 NaN 9.836863 2.602835 +Experimental matrix: +[[ nan 13.49724862 0.40950193] + [ 0.099792 nan nan] + [ nan 12.8976928 1.12882703] + [ 0.154224 nan nan] + [ 0.205632 nan nan] + [ nan 11.35039747 1.85567123] + [ 0.311472 nan nan] + [ nan 9.8368634 2.60283547]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:43,204 - physiofit - INFO - mc : False +2024-05-27 14:30:43,204 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:43,204 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:43,205 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:43,670 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:43,671 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.9988204569642825 + x: [ 2.191e-02 5.800e-01 -7.863e+00 1.429e+01 + 4.527e+00 1.211e-01] + nit: 101 + nfev: 9712 + population: [[ 2.186e-02 5.802e-01 ... 4.557e+00 1.125e-01] + [ 2.211e-02 5.785e-01 ... 4.455e+00 1.295e-01] + ... + [ 2.209e-02 5.766e-01 ... 4.562e+00 1.104e-01] + [ 2.230e-02 5.756e-01 ... 4.550e+00 1.157e-01]] + population_energies: [ 1.999e+00 2.046e+00 ... 2.021e+00 2.028e+00] + jac: [-1.023e-04 2.248e-04 7.978e-05 7.594e-05 + 4.304e-04 9.602e-04] +2024-05-27 14:30:43,672 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.021908477661879176 +2024-05-27 14:30:43,672 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5799730675895703 +2024-05-27 14:30:43,672 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.862811204923339 +2024-05-27 14:30:43,672 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.289104968853078 +2024-05-27 14:30:43,672 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.52711984498779 +2024-05-27 14:30:43,673 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.12109356481047026 +2024-05-27 14:30:43,676 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.665786 0.479978 +2.501389 0.093467 NaN NaN +3.250000 NaN 12.630030 1.076328 +3.341944 0.152187 NaN NaN +3.997500 0.222587 NaN NaN +4.083333 NaN 11.414448 1.776216 +4.523333 0.301957 NaN NaN +4.766667 NaN 9.871945 2.664333 + +2024-05-27 14:30:43,680 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.9988204569642825 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.08019294665939507 + +2024-05-27 14:30:43,680 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.08019294665939507 +2024-05-27 14:30:43,682 - physiofit - INFO - Results for ybdH: + optimal +ybdH X_0 0.021908 +ybdH growth_rate 0.579973 +ybdH Glc_q -7.862811 +ybdH Glc_M0 14.289105 +ybdH Ace_q 4.527120 +ybdH Ace_M0 0.121094 +2024-05-27 14:30:43,688 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:44,641 - physiofit - INFO - Running optimization for ybeL +2024-05-27 14:30:44,643 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:44,643 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:44,648 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +378 0.000000 0.046872 NaN NaN +379 0.066667 NaN 14.615328 0.015355 +380 1.188889 0.078624 NaN NaN +381 1.716667 NaN 14.565905 0.346112 +382 2.276944 0.120960 NaN NaN +383 2.800000 NaN 13.501458 0.736482 +384 3.128333 0.187488 NaN NaN +385 3.633333 NaN 12.678857 1.161011 +386 3.771389 0.273672 NaN NaN +387 4.266667 NaN 11.712701 1.661202 +388 4.415556 0.394632 NaN NaN +389 4.822778 0.589680 NaN NaN +390 4.883333 NaN 9.664264 2.084358 +Experimental matrix: +[[ 0.046872 nan nan] + [ nan 14.61532775 0.01535506] + [ 0.078624 nan nan] + [ nan 14.56590478 0.34611172] + [ 0.12096 nan nan] + [ nan 13.50145752 0.73648239] + [ 0.187488 nan nan] + [ nan 12.67885667 1.16101061] + [ 0.273672 nan nan] + [ nan 11.7127014 1.66120233] + [ 0.394632 nan nan] + [ 0.58968 nan nan] + [ nan 9.66426364 2.08435778]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:44,648 - physiofit - INFO - mc : False +2024-05-27 14:30:44,648 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:44,648 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:44,649 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:45,063 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:45,064 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 11.7680520138299 + x: [ 2.642e-02 6.326e-01 -5.729e+00 1.481e+01 + 2.360e+00 1.686e-01] + nit: 89 + nfev: 8583 + population: [[ 2.640e-02 6.318e-01 ... 2.352e+00 1.744e-01] + [ 2.652e-02 6.306e-01 ... 2.376e+00 1.396e-01] + ... + [ 2.640e-02 6.323e-01 ... 2.320e+00 2.003e-01] + [ 2.676e-02 6.295e-01 ... 2.267e+00 2.147e-01]] + population_energies: [ 1.177e+01 1.191e+01 ... 1.205e+01 1.198e+01] + jac: [ 2.009e-02 2.824e-03 -4.552e-02 1.326e-02 + 2.913e-02 -8.400e-03] +2024-05-27 14:30:45,065 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.026415033341002418 +2024-05-27 14:30:45,065 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6325622746318373 +2024-05-27 14:30:45,065 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.728658823053663 +2024-05-27 14:30:45,065 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.809795673624594 +2024-05-27 14:30:45,065 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.360141366512223 +2024-05-27 14:30:45,066 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.16858694558181328 +2024-05-27 14:30:45,069 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.026415 NaN NaN +0.066667 NaN 14.799492 0.172832 +1.188889 0.056035 NaN NaN +1.716667 NaN 14.340418 0.361965 +2.276944 0.111524 NaN NaN +2.800000 NaN 13.642931 0.649322 +3.128333 0.191100 NaN NaN +3.633333 NaN 12.667005 1.051392 +3.771389 0.287026 NaN NaN +4.266667 NaN 11.493259 1.534962 +4.415556 0.431405 NaN NaN +4.822778 0.558157 NaN NaN +4.883333 NaN 9.796810 2.233879 + +2024-05-27 14:30:45,073 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 11.7680520138299 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.4532507540346215 + +2024-05-27 14:30:45,074 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.4532507540346215 +2024-05-27 14:30:45,076 - physiofit - INFO - Results for ybeL: + optimal +ybeL X_0 0.026415 +ybeL growth_rate 0.632562 +ybeL Glc_q -5.728659 +ybeL Glc_M0 14.809796 +ybeL Ace_q 2.360141 +ybeL Ace_M0 0.168587 +2024-05-27 14:30:45,083 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:46,119 - physiofit - INFO - Running optimization for ybfE +2024-05-27 14:30:46,122 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:46,122 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:46,126 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +391 0.000000 0.031752 NaN NaN +392 0.283333 NaN 14.141696 0.035195 +393 1.195000 0.058968 NaN NaN +394 1.613611 0.068040 NaN NaN +395 1.916667 NaN 13.985063 0.403903 +396 2.361389 0.105840 NaN NaN +397 2.700000 NaN 13.337938 0.651222 +398 3.286389 0.190512 NaN NaN +399 3.616667 NaN 12.834666 1.185256 +400 3.819444 0.270648 NaN NaN +401 4.050000 NaN 12.011189 1.452809 +402 4.410833 0.349272 NaN NaN +403 4.750000 NaN 10.600166 2.070068 +Experimental matrix: +[[ 0.031752 nan nan] + [ nan 14.14169567 0.03519542] + [ 0.058968 nan nan] + [ 0.06804 nan nan] + [ nan 13.9850633 0.40390307] + [ 0.10584 nan nan] + [ nan 13.33793796 0.65122218] + [ 0.190512 nan nan] + [ nan 12.83466592 1.18525592] + [ 0.270648 nan nan] + [ nan 12.01118917 1.45280922] + [ 0.349272 nan nan] + [ nan 10.60016564 2.07006839]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:46,126 - physiofit - INFO - mc : False +2024-05-27 14:30:46,126 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:46,126 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:46,127 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:46,558 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:46,559 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.075491657134591 + x: [ 3.008e-02 5.607e-01 -5.103e+00 1.438e+01 + 2.859e+00 9.026e-02] + nit: 92 + nfev: 8881 + population: [[ 2.997e-02 5.612e-01 ... 2.848e+00 9.475e-02] + [ 3.019e-02 5.597e-01 ... 2.850e+00 1.003e-01] + ... + [ 2.995e-02 5.622e-01 ... 2.882e+00 9.247e-02] + [ 3.008e-02 5.611e-01 ... 2.859e+00 1.002e-01]] + population_energies: [ 2.075e+00 2.099e+00 ... 2.099e+00 2.098e+00] + jac: [-2.557e-02 -3.022e-03 -1.234e-04 -5.633e-04 + -7.535e-04 -7.468e-04] +2024-05-27 14:30:46,559 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.030078364051008392 +2024-05-27 14:30:46,559 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5606743956405482 +2024-05-27 14:30:46,560 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.10329348015108 +2024-05-27 14:30:46,560 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.38219709732088 +2024-05-27 14:30:46,560 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.8592919449495398 +2024-05-27 14:30:46,560 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.0902606754577239 +2024-05-27 14:30:46,563 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.030078 NaN NaN +0.283333 NaN 14.335061 0.116670 +1.195000 0.058781 NaN NaN +1.613611 0.074330 NaN NaN +1.916667 NaN 13.854113 0.386138 +2.361389 0.113044 NaN NaN +2.700000 NaN 13.411922 0.633890 +3.286389 0.189882 NaN NaN +3.616667 NaN 12.576063 1.102208 +3.819444 0.256024 NaN NaN +4.050000 NaN 12.004054 1.422695 +4.410833 0.356683 NaN NaN +4.750000 NaN 10.729445 2.136838 + +2024-05-27 14:30:46,567 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.075491657134591 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0002787526684014371 + +2024-05-27 14:30:46,568 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0002787526684014371 +2024-05-27 14:30:46,571 - physiofit - INFO - Results for ybfE: + optimal +ybfE X_0 0.030078 +ybfE growth_rate 0.560674 +ybfE Glc_q -5.103293 +ybfE Glc_M0 14.382197 +ybfE Ace_q 2.859292 +ybfE Ace_M0 0.090261 +2024-05-27 14:30:46,577 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:47,672 - physiofit - INFO - Running optimization for ybgJ +2024-05-27 14:30:47,675 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:47,675 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:47,679 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +404 1.828889 0.081648 NaN NaN +405 2.261389 0.101304 NaN NaN +406 2.774167 0.127008 NaN NaN +407 2.800000 NaN 12.079645 0.717704 +408 3.208889 0.167832 NaN NaN +409 3.706389 0.228312 NaN NaN +410 3.733333 NaN 11.622231 1.341690 +411 4.225833 0.316008 NaN NaN +412 4.283333 NaN 10.938145 1.869419 +413 4.635556 0.417312 NaN NaN +414 4.750000 NaN 9.805253 2.415903 +415 4.967500 0.557928 NaN NaN +416 5.116667 NaN 9.024668 2.952651 +417 5.433333 NaN 8.077891 3.471272 +Experimental matrix: +[[ 0.081648 nan nan] + [ 0.101304 nan nan] + [ 0.127008 nan nan] + [ nan 12.07964528 0.71770375] + [ 0.167832 nan nan] + [ 0.228312 nan nan] + [ nan 11.62223075 1.34168994] + [ 0.316008 nan nan] + [ nan 10.9381454 1.86941898] + [ 0.417312 nan nan] + [ nan 9.80525271 2.41590323] + [ 0.557928 nan nan] + [ nan 9.02466761 2.95265094] + [ nan 8.07789106 3.47127197]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:47,679 - physiofit - INFO - mc : False +2024-05-27 14:30:47,679 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:47,679 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:47,679 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:48,237 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:48,238 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.023566748602037 + x: [ 2.005e-02 6.626e-01 -4.554e+00 1.299e+01 + 2.991e+00 3.350e-01] + nit: 122 + nfev: 11357 + population: [[ 2.004e-02 6.629e-01 ... 2.989e+00 3.348e-01] + [ 1.998e-02 6.637e-01 ... 2.989e+00 3.188e-01] + ... + [ 2.015e-02 6.624e-01 ... 2.991e+00 3.309e-01] + [ 1.989e-02 6.643e-01 ... 3.002e+00 3.385e-01]] + population_energies: [ 4.024e+00 4.095e+00 ... 4.067e+00 4.039e+00] + jac: [ 1.198e-01 1.587e-02 -9.584e-03 4.165e-02 + -4.264e-02 8.349e-03] +2024-05-27 14:30:48,239 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02005152706524463 +2024-05-27 14:30:48,239 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.662558982121915 +2024-05-27 14:30:48,239 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.553720327117258 +2024-05-27 14:30:48,239 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 12.989038107070156 +2024-05-27 14:30:48,239 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.9906879251110707 +2024-05-27 14:30:48,240 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.3349698127099261 +2024-05-27 14:30:48,246 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.067360 NaN NaN +2.261389 0.089712 NaN NaN +2.774167 0.126009 NaN NaN +2.800000 NaN 12.245848 0.823065 +3.208889 0.168070 NaN NaN +3.706389 0.233693 NaN NaN +3.733333 NaN 11.491767 1.318313 +4.225833 0.329695 NaN NaN +4.283333 NaN 10.772886 1.790444 +4.635556 0.432522 NaN NaN +4.750000 NaN 9.919981 2.350595 +4.967500 0.538920 NaN NaN +5.116667 NaN 9.038124 2.929761 +5.433333 NaN 8.083634 3.556628 + +2024-05-27 14:30:48,252 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.023566748602037 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.004677235715777846 + +2024-05-27 14:30:48,252 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.004677235715777846 +2024-05-27 14:30:48,255 - physiofit - INFO - Results for ybgJ: + optimal +ybgJ X_0 0.020052 +ybgJ growth_rate 0.662559 +ybgJ Glc_q -4.553720 +ybgJ Glc_M0 12.989038 +ybgJ Ace_q 2.990688 +ybgJ Ace_M0 0.334970 +2024-05-27 14:30:48,262 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:49,198 - physiofit - INFO - Running optimization for ybgK +2024-05-27 14:30:49,200 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:49,201 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:49,204 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +418 1.950000 NaN 13.416501 0.353440 +419 2.501389 0.114912 NaN NaN +420 3.250000 NaN 12.683259 0.885792 +421 3.341944 0.166320 NaN NaN +422 3.997500 0.229824 NaN NaN +423 4.083333 NaN 12.136843 1.414585 +424 4.523333 0.337176 NaN NaN +425 4.766667 NaN 10.669075 1.917539 +Experimental matrix: +[[ nan 13.41650127 0.35343995] + [ 0.114912 nan nan] + [ nan 12.68325892 0.88579212] + [ 0.16632 nan nan] + [ 0.229824 nan nan] + [ nan 12.13684268 1.41458478] + [ 0.337176 nan nan] + [ nan 10.66907533 1.91753895]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:49,204 - physiofit - INFO - mc : False +2024-05-27 14:30:49,204 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:49,204 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:49,205 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:49,765 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:49,767 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.717521402660276 + x: [ 2.561e-02 5.641e-01 -5.028e+00 1.394e+01 + 2.934e+00 1.447e-01] + nit: 120 + nfev: 11422 + population: [[ 2.554e-02 5.646e-01 ... 2.938e+00 1.461e-01] + [ 2.618e-02 5.588e-01 ... 2.955e+00 1.262e-01] + ... + [ 2.546e-02 5.651e-01 ... 2.905e+00 1.654e-01] + [ 2.648e-02 5.557e-01 ... 2.913e+00 1.458e-01]] + population_energies: [ 1.718e+00 1.734e+00 ... 1.731e+00 1.736e+00] + jac: [-1.681e-03 4.594e-04 7.541e-05 2.700e-04 + 1.267e-04 1.450e-04] +2024-05-27 14:30:49,767 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025608600387959618 +2024-05-27 14:30:49,768 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5640796282669304 +2024-05-27 14:30:49,768 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.028101913475757 +2024-05-27 14:30:49,768 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.93727741611054 +2024-05-27 14:30:49,768 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.9335552217219605 +2024-05-27 14:30:49,768 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.14467472346543755 +2024-05-27 14:30:49,772 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.479816 0.411572 +2.501389 0.104995 NaN NaN +3.250000 NaN 12.737891 0.844435 +3.341944 0.168688 NaN NaN +3.997500 0.244163 NaN NaN +4.083333 NaN 11.881154 1.344283 +4.523333 0.328471 NaN NaN +4.766667 NaN 10.806845 1.971069 + +2024-05-27 14:30:49,776 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.717521402660276 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.05623941611853047 + +2024-05-27 14:30:49,776 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.05623941611853047 +2024-05-27 14:30:49,779 - physiofit - INFO - Results for ybgK: + optimal +ybgK X_0 0.025609 +ybgK growth_rate 0.564080 +ybgK Glc_q -5.028102 +ybgK Glc_M0 13.937277 +ybgK Ace_q 2.933555 +ybgK Ace_M0 0.144675 +2024-05-27 14:30:49,786 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:50,707 - physiofit - INFO - Running optimization for ybgS +2024-05-27 14:30:50,710 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:50,711 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:50,714 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +426 0.000000 0.033264 NaN NaN +427 0.066667 NaN 15.788973 0.014019 +428 1.188889 0.061992 NaN NaN +429 1.716667 NaN 15.250680 0.340831 +430 2.276944 0.101304 NaN NaN +431 2.800000 NaN 13.450039 0.717139 +432 3.128333 0.152712 NaN NaN +433 3.633333 NaN 12.896727 1.197765 +434 3.771389 0.201096 NaN NaN +435 4.266667 NaN 11.691864 1.664620 +436 4.415556 0.294840 NaN NaN +437 4.822778 0.364392 NaN NaN +438 4.883333 NaN 10.622843 2.310195 +Experimental matrix: +[[3.32640000e-02 nan nan] + [ nan 1.57889726e+01 1.40193309e-02] + [6.19920000e-02 nan nan] + [ nan 1.52506804e+01 3.40831112e-01] + [1.01304000e-01 nan nan] + [ nan 1.34500392e+01 7.17139080e-01] + [1.52712000e-01 nan nan] + [ nan 1.28967271e+01 1.19776473e+00] + [2.01096000e-01 nan nan] + [ nan 1.16918642e+01 1.66462047e+00] + [2.94840000e-01 nan nan] + [3.64392000e-01 nan nan] + [ nan 1.06228426e+01 2.31019502e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:50,714 - physiofit - INFO - mc : False +2024-05-27 14:30:50,714 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:50,714 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:50,715 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:51,108 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:51,109 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.574390852993806 + x: [ 3.351e-02 4.909e-01 -7.716e+00 1.560e+01 + 3.365e+00 3.116e-02] + nit: 83 + nfev: 7952 + population: [[ 3.401e-02 4.874e-01 ... 3.359e+00 2.945e-02] + [ 3.410e-02 4.873e-01 ... 3.388e+00 3.926e-02] + ... + [ 3.317e-02 4.930e-01 ... 3.351e+00 4.254e-02] + [ 3.379e-02 4.877e-01 ... 3.378e+00 5.257e-03]] + population_energies: [ 3.574e+00 3.689e+00 ... 3.586e+00 3.688e+00] + jac: [ 1.218e-01 2.124e-02 -1.747e-03 9.321e-04 + 4.814e-04 6.967e-04] +2024-05-27 14:30:51,109 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03350841470002522 +2024-05-27 14:30:51,109 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.4908643292995073 +2024-05-27 14:30:51,109 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.716042021035626 +2024-05-27 14:30:51,110 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.598510482541965 +2024-05-27 14:30:51,110 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.365100888320436 +2024-05-27 14:30:51,110 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.031163710924088144 +2024-05-27 14:30:51,114 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.033508 NaN NaN +0.066667 NaN 15.580989 0.038805 +1.188889 0.060062 NaN NaN +1.716667 NaN 14.901904 0.334966 +2.276944 0.102459 NaN NaN +2.800000 NaN 14.043194 0.709464 +3.128333 0.155615 NaN NaN +3.633333 NaN 12.990945 1.168369 +3.771389 0.213372 NaN NaN +4.266667 NaN 11.848098 1.666784 +4.415556 0.292725 NaN NaN +4.822778 0.357497 NaN NaN +4.883333 NaN 10.336095 2.326195 + +2024-05-27 14:30:51,118 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.574390852993806 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0050659962409180725 + +2024-05-27 14:30:51,118 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0050659962409180725 +2024-05-27 14:30:51,119 - physiofit - INFO - Results for ybgS: + optimal +ybgS X_0 0.033508 +ybgS growth_rate 0.490864 +ybgS Glc_q -7.716042 +ybgS Glc_M0 15.598510 +ybgS Ace_q 3.365101 +ybgS Ace_M0 0.031164 +2024-05-27 14:30:51,124 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:52,106 - physiofit - INFO - Running optimization for ybhC +2024-05-27 14:30:52,108 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:52,109 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:52,112 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +439 0.000000 0.031752 NaN NaN +440 0.066667 NaN 15.172454 0.009248 +441 1.188889 0.061992 NaN NaN +442 1.716667 NaN 15.178301 0.369840 +443 2.276944 0.108864 NaN NaN +444 2.800000 NaN 14.054941 0.759689 +445 3.128333 0.163296 NaN NaN +446 3.633333 NaN 12.549203 1.161811 +447 3.771389 0.229824 NaN NaN +448 4.266667 NaN 11.523398 1.618054 +449 4.415556 0.314496 NaN NaN +450 4.822778 0.452088 NaN NaN +451 4.883333 NaN 9.992493 2.048487 +Experimental matrix: +[[3.17520000e-02 nan nan] + [ nan 1.51724538e+01 9.24842802e-03] + [6.19920000e-02 nan nan] + [ nan 1.51783014e+01 3.69839593e-01] + [1.08864000e-01 nan nan] + [ nan 1.40549410e+01 7.59688519e-01] + [1.63296000e-01 nan nan] + [ nan 1.25492026e+01 1.16181059e+00] + [2.29824000e-01 nan nan] + [ nan 1.15233978e+01 1.61805402e+00] + [3.14496000e-01 nan nan] + [4.52088000e-01 nan nan] + [ nan 9.99249339e+00 2.04848664e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:52,113 - physiofit - INFO - mc : False +2024-05-27 14:30:52,113 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:52,113 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:52,113 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:52,475 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:52,477 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 6.429004068643701 + x: [ 2.838e-02 5.630e-01 -7.512e+00 1.541e+01 + 2.747e+00 1.424e-01] + nit: 79 + nfev: 7599 + population: [[ 2.866e-02 5.607e-01 ... 2.737e+00 1.374e-01] + [ 2.877e-02 5.590e-01 ... 2.763e+00 1.348e-01] + ... + [ 2.809e-02 5.651e-01 ... 2.759e+00 1.380e-01] + [ 2.862e-02 5.626e-01 ... 2.773e+00 1.241e-01]] + population_energies: [ 6.429e+00 6.462e+00 ... 6.444e+00 6.494e+00] + jac: [ 6.256e-02 7.548e-03 2.296e-02 -6.103e-03 + 5.371e-03 -1.924e-03] +2024-05-27 14:30:52,477 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.028383829934278914 +2024-05-27 14:30:52,477 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5630245781064286 +2024-05-27 14:30:52,477 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.511587457311129 +2024-05-27 14:30:52,477 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.408569143121218 +2024-05-27 14:30:52,477 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.7467869246434473 +2024-05-27 14:30:52,477 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.14241866128642602 +2024-05-27 14:30:52,481 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028384 NaN NaN +0.066667 NaN 15.394085 0.147715 +1.188889 0.055434 NaN NaN +1.716667 NaN 14.791773 0.367965 +2.276944 0.102288 NaN NaN +2.800000 NaN 13.955245 0.673860 +3.128333 0.165199 NaN NaN +3.633333 NaN 12.858433 1.074935 +3.771389 0.237271 NaN NaN +4.266667 NaN 11.603613 1.533789 +4.415556 0.341001 NaN NaN +4.822778 0.428874 NaN NaN +4.883333 NaN 9.866995 2.168824 + +2024-05-27 14:30:52,485 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 6.429004068643701 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.07086232897759558 + +2024-05-27 14:30:52,485 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.07086232897759558 +2024-05-27 14:30:52,488 - physiofit - INFO - Results for ybhC: + optimal +ybhC X_0 0.028384 +ybhC growth_rate 0.563025 +ybhC Glc_q -7.511587 +ybhC Glc_M0 15.408569 +ybhC Ace_q 2.746787 +ybhC Ace_M0 0.142419 +2024-05-27 14:30:52,493 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:53,457 - physiofit - INFO - Running optimization for ybiB +2024-05-27 14:30:53,459 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:53,459 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:53,462 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +452 1.950000 NaN 13.635294 0.390395 +453 2.501389 0.107352 NaN NaN +454 3.250000 NaN 12.577467 0.973753 +455 3.341944 0.161784 NaN NaN +456 3.997500 0.214704 NaN NaN +457 4.083333 NaN 11.586131 1.452341 +458 4.523333 0.314496 NaN NaN +459 4.766667 NaN 10.719210 2.082724 +Experimental matrix: +[[ nan 13.63529438 0.39039523] + [ 0.107352 nan nan] + [ nan 12.57746654 0.97375285] + [ 0.161784 nan nan] + [ 0.214704 nan nan] + [ nan 11.58613064 1.45234115] + [ 0.314496 nan nan] + [ nan 10.71920982 2.08272417]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:53,463 - physiofit - INFO - mc : False +2024-05-27 14:30:53,463 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:53,463 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:53,463 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:53,887 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:53,888 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.3253848884691717 + x: [ 2.664e-02 5.390e-01 -5.770e+00 1.403e+01 + 3.309e+00 1.328e-01] + nit: 93 + nfev: 8985 + population: [[ 2.660e-02 5.396e-01 ... 3.326e+00 1.271e-01] + [ 2.630e-02 5.409e-01 ... 3.307e+00 1.510e-01] + ... + [ 2.665e-02 5.380e-01 ... 3.310e+00 1.424e-01] + [ 2.719e-02 5.335e-01 ... 3.312e+00 1.252e-01]] + population_energies: [ 1.325e+00 1.360e+00 ... 1.344e+00 1.347e+00] + jac: [-3.093e-02 -3.052e-03 -4.738e-05 -7.550e-07 + -1.361e-04 -5.457e-04] +2024-05-27 14:30:53,888 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.026637367002784098 +2024-05-27 14:30:53,889 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5389899939373712 +2024-05-27 14:30:53,889 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.770147449732734 +2024-05-27 14:30:53,889 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.03394847512862 +2024-05-27 14:30:53,889 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.308634141925069 +2024-05-27 14:30:53,889 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.13279395340163097 +2024-05-27 14:30:53,892 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.503370 0.437031 +2.501389 0.102569 NaN NaN +3.250000 NaN 12.675277 0.911863 +3.341944 0.161352 NaN NaN +3.997500 0.229735 NaN NaN +4.083333 NaN 11.743234 1.446302 +4.523333 0.305011 NaN NaN +4.766667 NaN 10.596221 2.104006 + +2024-05-27 14:30:53,895 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.3253848884691717 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.02976048137457897 + +2024-05-27 14:30:53,896 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.02976048137457897 +2024-05-27 14:30:53,899 - physiofit - INFO - Results for ybiB: + optimal +ybiB X_0 0.026637 +ybiB growth_rate 0.538990 +ybiB Glc_q -5.770147 +ybiB Glc_M0 14.033948 +ybiB Ace_q 3.308634 +ybiB Ace_M0 0.132794 +2024-05-27 14:30:53,904 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:54,853 - physiofit - INFO - Running optimization for ybiC +2024-05-27 14:30:54,855 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:54,855 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:54,858 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +460 1.950000 NaN 13.549637 0.414172 +461 2.501389 0.099792 NaN NaN +462 3.250000 NaN 12.660838 0.979888 +463 3.341944 0.151200 NaN NaN +464 3.997500 0.216216 NaN NaN +465 4.083333 NaN 11.460534 1.505459 +466 4.523333 0.300888 NaN NaN +467 4.766667 NaN 10.137964 2.060289 +Experimental matrix: +[[ nan 13.5496372 0.41417238] + [ 0.099792 nan nan] + [ nan 12.66083836 0.97988793] + [ 0.1512 nan nan] + [ 0.216216 nan nan] + [ nan 11.46053386 1.50545903] + [ 0.300888 nan nan] + [ nan 10.13796351 2.06028905]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:54,858 - physiofit - INFO - mc : False +2024-05-27 14:30:54,858 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:54,858 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:54,859 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:55,319 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:55,320 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.45230516507313245 + x: [ 2.406e-02 5.553e-01 -7.123e+00 1.417e+01 + 3.381e+00 1.854e-01] + nit: 101 + nfev: 9537 + population: [[ 2.388e-02 5.571e-01 ... 3.370e+00 1.935e-01] + [ 2.363e-02 5.596e-01 ... 3.381e+00 1.965e-01] + ... + [ 2.408e-02 5.550e-01 ... 3.366e+00 1.918e-01] + [ 2.432e-02 5.525e-01 ... 3.329e+00 2.003e-01]] + population_energies: [ 4.523e-01 4.628e-01 ... 4.548e-01 4.646e-01] + jac: [ 6.828e-02 6.607e-03 6.128e-06 3.194e-05 + 1.303e-04 3.344e-04] +2024-05-27 14:30:55,321 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.024064951166279908 +2024-05-27 14:30:55,321 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5552614028981602 +2024-05-27 14:30:55,321 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.12341633176565 +2024-05-27 14:30:55,322 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.174458022112326 +2024-05-27 14:30:55,322 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.3805553505662105 +2024-05-27 14:30:55,322 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.18535904505777395 +2024-05-27 14:30:55,326 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.571569 0.471472 +2.501389 0.096513 NaN NaN +3.250000 NaN 12.606881 0.929283 +3.341944 0.153916 NaN NaN +3.997500 0.221498 NaN NaN +4.083333 NaN 11.502891 1.453203 +4.523333 0.296601 NaN NaN +4.766667 NaN 10.127636 2.105857 + +2024-05-27 14:30:55,331 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.45230516507313245 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.0016285927697976602 + +2024-05-27 14:30:55,331 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0016285927697976602 +2024-05-27 14:30:55,333 - physiofit - INFO - Results for ybiC: + optimal +ybiC X_0 0.024065 +ybiC growth_rate 0.555261 +ybiC Glc_q -7.123416 +ybiC Glc_M0 14.174458 +ybiC Ace_q 3.380555 +ybiC Ace_M0 0.185359 +2024-05-27 14:30:55,340 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:56,302 - physiofit - INFO - Running optimization for ybiH +2024-05-27 14:30:56,304 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:56,304 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:56,307 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +468 0.050000 NaN 14.326979 0.020144 +469 1.950000 NaN 14.115697 0.444940 +470 2.833333 NaN 13.705296 0.784315 +471 2.876944 0.176904 NaN NaN +472 3.678056 0.282744 NaN NaN +473 3.983333 NaN 11.840712 1.446174 +474 4.092222 0.355320 NaN NaN +475 4.565000 0.461160 NaN NaN +476 4.883333 NaN 9.160270 2.226954 +477 5.166667 NaN 8.312693 2.462174 +Experimental matrix: +[[ nan 14.32697938 0.02014449] + [ nan 14.11569669 0.44493988] + [ nan 13.70529618 0.78431483] + [ 0.176904 nan nan] + [ 0.282744 nan nan] + [ nan 11.84071199 1.44617383] + [ 0.35532 nan nan] + [ 0.46116 nan nan] + [ nan 9.16027038 2.22695418] + [ nan 8.312693 2.46217363]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:56,308 - physiofit - INFO - mc : False +2024-05-27 14:30:56,308 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:56,308 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:56,308 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:56,699 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:56,700 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.3308825624012988 + x: [ 3.503e-02 5.654e-01 -5.908e+00 1.477e+01 + 2.217e+00 1.571e-01] + nit: 86 + nfev: 8131 + population: [[ 3.464e-02 5.681e-01 ... 2.218e+00 1.572e-01] + [ 3.584e-02 5.596e-01 ... 2.212e+00 1.652e-01] + ... + [ 3.612e-02 5.582e-01 ... 2.215e+00 1.592e-01] + [ 3.518e-02 5.651e-01 ... 2.184e+00 1.727e-01]] + population_energies: [ 3.331e+00 3.375e+00 ... 3.365e+00 3.375e+00] + jac: [-1.460e-02 -2.822e-03 1.469e-02 -3.949e-03 + 3.624e-02 -2.135e-02] +2024-05-27 14:30:56,701 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03503195010302243 +2024-05-27 14:30:56,701 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5654398003636838 +2024-05-27 14:30:56,701 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.907940088516112 +2024-05-27 14:30:56,702 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.771397429555432 +2024-05-27 14:30:56,702 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.2168418210908998 +2024-05-27 14:30:56,702 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15710439249298494 +2024-05-27 14:30:56,705 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.760901 0.161043 +1.950000 NaN 14.034946 0.433444 +2.833333 NaN 13.320704 0.701449 +2.876944 0.178217 NaN NaN +3.678056 0.280333 NaN NaN +3.983333 NaN 11.656531 1.325898 +4.092222 0.354308 NaN NaN +4.565000 0.462892 NaN NaN +4.883333 NaN 9.347120 2.192461 +5.166667 NaN 8.341027 2.569978 + +2024-05-27 14:30:56,710 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.3308825624012988 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.027468910428336046 + +2024-05-27 14:30:56,710 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.027468910428336046 +2024-05-27 14:30:56,713 - physiofit - INFO - Results for ybiH: + optimal +ybiH X_0 0.035032 +ybiH growth_rate 0.565440 +ybiH Glc_q -5.907940 +ybiH Glc_M0 14.771397 +ybiH Ace_q 2.216842 +ybiH Ace_M0 0.157104 +2024-05-27 14:30:56,719 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:57,735 - physiofit - INFO - Running optimization for ybiJ +2024-05-27 14:30:57,737 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:57,738 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:57,741 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +478 0.000000 0.045360 NaN NaN +479 0.066667 NaN 15.963894 0.010169 +480 1.188889 0.069552 NaN NaN +481 1.716667 NaN 15.332360 0.383111 +482 2.276944 0.108864 NaN NaN +483 2.800000 NaN 13.731101 0.833394 +484 3.128333 0.166320 NaN NaN +485 3.633333 NaN 12.385925 1.235329 +486 3.771389 0.226800 NaN NaN +487 4.266667 NaN 11.527866 1.808874 +488 4.415556 0.353808 NaN NaN +489 4.822778 0.464184 NaN NaN +490 4.883333 NaN 9.781636 2.366281 +Experimental matrix: +[[4.53600000e-02 nan nan] + [ nan 1.59638944e+01 1.01694966e-02] + [6.95520000e-02 nan nan] + [ nan 1.53323602e+01 3.83110525e-01] + [1.08864000e-01 nan nan] + [ nan 1.37311012e+01 8.33394488e-01] + [1.66320000e-01 nan nan] + [ nan 1.23859249e+01 1.23532899e+00] + [2.26800000e-01 nan nan] + [ nan 1.15278665e+01 1.80887426e+00] + [3.53808000e-01 nan nan] + [4.64184000e-01 nan nan] + [ nan 9.78163642e+00 2.36628122e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:57,742 - physiofit - INFO - mc : False +2024-05-27 14:30:57,742 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:57,742 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:57,742 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:58,084 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:58,085 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 6.583857289419729 + x: [ 3.119e-02 5.521e-01 -7.938e+00 1.575e+01 + 3.001e+00 1.142e-01] + nit: 76 + nfev: 7063 + population: [[ 3.116e-02 5.527e-01 ... 3.000e+00 1.109e-01] + [ 3.100e-02 5.539e-01 ... 2.974e+00 1.195e-01] + ... + [ 3.058e-02 5.579e-01 ... 3.087e+00 9.548e-02] + [ 3.042e-02 5.583e-01 ... 3.063e+00 7.918e-02]] + population_energies: [ 6.584e+00 6.618e+00 ... 6.718e+00 6.742e+00] + jac: [ 7.119e-02 1.136e-02 3.094e-02 4.281e-02 + -2.997e-02 -4.179e-04] +2024-05-27 14:30:58,085 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.031186253204796614 +2024-05-27 14:30:58,085 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5521364887401427 +2024-05-27 14:30:58,085 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.937918852212927 +2024-05-27 14:30:58,085 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.74523110309255 +2024-05-27 14:30:58,085 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.0008118640025216 +2024-05-27 14:30:58,085 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.11422302427700616 +2024-05-27 14:30:58,089 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.031186 NaN NaN +0.066667 NaN 15.728420 0.120578 +1.188889 0.060124 NaN NaN +1.716667 NaN 15.036776 0.382044 +2.276944 0.109636 NaN NaN +2.800000 NaN 14.089640 0.740095 +3.128333 0.175431 NaN NaN +3.633333 NaN 12.860400 1.204791 +3.771389 0.250210 NaN NaN +4.266667 NaN 11.465052 1.732281 +4.415556 0.357082 NaN NaN +4.822778 0.447112 NaN NaN +4.883333 NaN 9.547025 2.457362 + +2024-05-27 14:30:58,093 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 6.583857289419729 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.07769409763931323 + +2024-05-27 14:30:58,093 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.07769409763931323 +2024-05-27 14:30:58,095 - physiofit - INFO - Results for ybiJ: + optimal +ybiJ X_0 0.031186 +ybiJ growth_rate 0.552136 +ybiJ Glc_q -7.937919 +ybiJ Glc_M0 15.745231 +ybiJ Ace_q 3.000812 +ybiJ Ace_M0 0.114223 +2024-05-27 14:30:58,099 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:30:59,100 - physiofit - INFO - Running optimization for ybiT +2024-05-27 14:30:59,102 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:30:59,102 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:30:59,106 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +491 0.050000 NaN 14.318944 0.024037 +492 1.950000 NaN 14.207185 0.431867 +493 2.833333 NaN 13.340516 0.680914 +494 2.876944 0.173880 NaN NaN +495 3.678056 0.285768 NaN NaN +496 3.983333 NaN 11.690373 1.374661 +497 4.092222 0.390096 NaN NaN +498 4.565000 0.541296 NaN NaN +499 4.883333 NaN 9.118293 2.103496 +500 5.166667 NaN 8.467255 2.531664 +Experimental matrix: +[[ nan 14.31894447 0.02403657] + [ nan 14.20718539 0.43186682] + [ nan 13.3405155 0.68091389] + [ 0.17388 nan nan] + [ 0.285768 nan nan] + [ nan 11.69037252 1.37466139] + [ 0.390096 nan nan] + [ 0.541296 nan nan] + [ nan 9.11829288 2.1034963 ] + [ nan 8.4672554 2.5316641 ]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:30:59,106 - physiofit - INFO - mc : False +2024-05-27 14:30:59,106 - physiofit - INFO - iterations : 100 +2024-05-27 14:30:59,106 - physiofit - INFO - debug_mode : False +2024-05-27 14:30:59,107 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:30:59,559 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:30:59,560 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.768895686716343 + x: [ 2.522e-02 6.695e-01 -5.373e+00 1.448e+01 + 2.063e+00 1.828e-01] + nit: 98 + nfev: 9393 + population: [[ 2.501e-02 6.712e-01 ... 2.064e+00 1.835e-01] + [ 2.512e-02 6.702e-01 ... 2.076e+00 1.793e-01] + ... + [ 2.520e-02 6.699e-01 ... 2.073e+00 1.802e-01] + [ 2.473e-02 6.745e-01 ... 2.065e+00 1.872e-01]] + population_energies: [ 2.769e+00 2.779e+00 ... 2.781e+00 2.783e+00] + jac: [-3.349e-03 -1.801e-04 -2.038e-05 -8.513e-05 + -7.816e-06 -1.893e-04] +2024-05-27 14:30:59,561 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.0252181154069821 +2024-05-27 14:30:59,561 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6694695022885362 +2024-05-27 14:30:59,561 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.372979689806582 +2024-05-27 14:30:59,561 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.4833235916498 +2024-05-27 14:30:59,562 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.0628265220808166 +2024-05-27 14:30:59,562 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.18282765123198488 +2024-05-27 14:30:59,566 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.476434 0.185473 +1.950000 NaN 13.939005 0.391806 +2.833333 NaN 13.336817 0.623001 +2.876944 0.173051 NaN NaN +3.678056 0.295867 NaN NaN +3.983333 NaN 11.772728 1.223496 +4.092222 0.390403 NaN NaN +4.565000 0.535762 NaN NaN +4.883333 NaN 9.364499 2.148078 +5.166667 NaN 8.253075 2.574782 + +2024-05-27 14:30:59,570 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.768895686716343 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.013648252416198468 + +2024-05-27 14:30:59,571 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.013648252416198468 +2024-05-27 14:30:59,573 - physiofit - INFO - Results for ybiT: + optimal +ybiT X_0 0.025218 +ybiT growth_rate 0.669470 +ybiT Glc_q -5.372980 +ybiT Glc_M0 14.483324 +ybiT Ace_q 2.062827 +ybiT Ace_M0 0.182828 +2024-05-27 14:30:59,579 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:00,733 - physiofit - INFO - Running optimization for ybiU +2024-05-27 14:31:00,736 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:00,737 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:00,740 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +501 0.000000 0.030240 NaN NaN +502 0.066667 NaN 16.147746 0.013641 +503 1.188889 0.054432 NaN NaN +504 1.716667 NaN 15.184501 0.336394 +505 2.276944 0.092232 NaN NaN +506 2.800000 NaN 13.507280 0.739542 +507 3.128333 0.133056 NaN NaN +508 3.633333 NaN 12.955724 1.162593 +509 3.771389 0.175392 NaN NaN +510 4.266667 NaN 11.938308 1.701159 +511 4.415556 0.261576 NaN NaN +512 4.822778 0.379512 NaN NaN +513 4.883333 NaN 10.610869 2.239107 +Experimental matrix: +[[3.02400000e-02 nan nan] + [ nan 1.61477461e+01 1.36413682e-02] + [5.44320000e-02 nan nan] + [ nan 1.51845014e+01 3.36393965e-01] + [9.22320000e-02 nan nan] + [ nan 1.35072803e+01 7.39541940e-01] + [1.33056000e-01 nan nan] + [ nan 1.29557239e+01 1.16259305e+00] + [1.75392000e-01 nan nan] + [ nan 1.19383083e+01 1.70115941e+00] + [2.61576000e-01 nan nan] + [3.79512000e-01 nan nan] + [ nan 1.06108691e+01 2.23910681e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:00,741 - physiofit - INFO - mc : False +2024-05-27 14:31:00,741 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:00,741 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:00,742 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:01,165 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:01,166 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 9.329290852753159 + x: [ 2.502e-02 5.479e-01 -8.626e+00 1.565e+01 + 3.616e+00 8.410e-02] + nit: 87 + nfev: 8109 + population: [[ 2.477e-02 5.497e-01 ... 3.614e+00 9.172e-02] + [ 2.495e-02 5.493e-01 ... 3.621e+00 8.747e-02] + ... + [ 2.567e-02 5.422e-01 ... 3.575e+00 7.813e-02] + [ 2.437e-02 5.507e-01 ... 3.618e+00 8.620e-02]] + population_energies: [ 9.329e+00 9.362e+00 ... 9.371e+00 9.556e+00] + jac: [ 1.772e-03 -1.686e-03 1.111e-02 1.373e-02 + -3.037e-02 3.540e-03] +2024-05-27 14:31:01,166 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025024968209125656 +2024-05-27 14:31:01,166 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5479308471185746 +2024-05-27 14:31:01,166 - physiofit.physiofit.base.fitter - INFO - Glc_q = -8.626219694298719 +2024-05-27 14:31:01,167 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.652372243335185 +2024-05-27 14:31:01,167 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.6161468233004364 +2024-05-27 14:31:01,167 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.08409969620563781 +2024-05-27 14:31:01,170 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.025025 NaN NaN +0.066667 NaN 15.637715 0.090244 +1.188889 0.048005 NaN NaN +1.716667 NaN 15.037159 0.342000 +2.276944 0.087137 NaN NaN +2.800000 NaN 14.219233 0.684878 +3.128333 0.138932 NaN NaN +3.633333 NaN 13.161861 1.128132 +3.771389 0.197618 NaN NaN +4.266667 NaN 11.965234 1.629763 +4.415556 0.281264 NaN NaN +4.822778 0.351575 NaN NaN +4.883333 NaN 10.324679 2.317491 + +2024-05-27 14:31:01,174 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 9.329290852753159 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.252356147610064 + +2024-05-27 14:31:01,174 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.252356147610064 +2024-05-27 14:31:01,176 - physiofit - INFO - Results for ybiU: + optimal +ybiU X_0 0.025025 +ybiU growth_rate 0.547931 +ybiU Glc_q -8.626220 +ybiU Glc_M0 15.652372 +ybiU Ace_q 3.616147 +ybiU Ace_M0 0.084100 +2024-05-27 14:31:01,181 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:02,162 - physiofit - INFO - Running optimization for ybjP +2024-05-27 14:31:02,164 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:02,164 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:02,168 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +514 1.950000 NaN 14.114474 0.361378 +515 2.501389 0.074088 NaN NaN +516 3.250000 NaN 12.978494 0.921221 +517 3.341944 0.108864 NaN NaN +518 3.997500 0.139104 NaN NaN +519 4.083333 NaN 12.090740 1.461154 +520 4.523333 0.175392 NaN NaN +521 4.766667 NaN 11.380862 2.246503 +Experimental matrix: +[[ nan 14.11447355 0.36137821] + [ 0.074088 nan nan] + [ nan 12.97849406 0.92122107] + [ 0.108864 nan nan] + [ 0.139104 nan nan] + [ nan 12.09074034 1.46115414] + [ 0.175392 nan nan] + [ nan 11.38086199 2.24650261]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:02,168 - physiofit - INFO - mc : False +2024-05-27 14:31:02,168 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:02,168 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:02,169 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:02,753 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:02,754 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.7836900827885784 + x: [ 2.305e-02 4.519e-01 -8.628e+00 1.459e+01 + 5.608e+00 1.000e-06] + nit: 127 + nfev: 11905 + population: [[ 2.315e-02 4.509e-01 ... 5.593e+00 1.338e-04] + [ 2.289e-02 4.543e-01 ... 5.621e+00 1.579e-04] + ... + [ 2.315e-02 4.498e-01 ... 5.597e+00 2.728e-04] + [ 2.304e-02 4.520e-01 ... 5.611e+00 2.723e-04]] + population_energies: [ 7.837e-01 7.919e-01 ... 7.941e-01 7.856e-01] + jac: [ 6.435e-03 1.165e-03 -1.441e-02 3.044e-04 + 9.502e-03 3.710e+00] +2024-05-27 14:31:02,754 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.023045811143293196 +2024-05-27 14:31:02,754 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.45190431052767194 +2024-05-27 14:31:02,755 - physiofit.physiofit.base.fitter - INFO - Glc_q = -8.628053713034431 +2024-05-27 14:31:02,755 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.588961647642334 +2024-05-27 14:31:02,756 - physiofit.physiofit.base.fitter - INFO - Ace_q = 5.608387273546603 +2024-05-27 14:31:02,756 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 1e-06 +2024-05-27 14:31:02,759 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.966870 0.404372 +2.501389 0.071370 NaN NaN +3.250000 NaN 13.117786 0.956291 +3.341944 0.104347 NaN NaN +3.997500 0.140326 NaN NaN +4.083333 NaN 12.243799 1.524398 +4.523333 0.177967 NaN NaN +4.766667 NaN 11.236148 2.179389 + +2024-05-27 14:31:02,762 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.7836900827885784 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.00749613265543099 + +2024-05-27 14:31:02,763 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00749613265543099 +2024-05-27 14:31:02,766 - physiofit - INFO - Results for ybjP: + optimal +ybjP X_0 0.023046 +ybjP growth_rate 0.451904 +ybjP Glc_q -8.628054 +ybjP Glc_M0 14.588962 +ybjP Ace_q 5.608387 +ybjP Ace_M0 0.000001 +2024-05-27 14:31:02,771 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:03,724 - physiofit - INFO - Running optimization for ybjP_2 +2024-05-27 14:31:03,727 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:03,727 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:03,730 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +522 1.828889 0.055944 NaN NaN +523 2.261389 0.074088 NaN NaN +524 2.774167 0.092232 NaN NaN +525 2.800000 NaN 12.610544 0.627527 +526 3.208889 0.111888 NaN NaN +527 3.706389 0.152712 NaN NaN +528 3.733333 NaN 11.972180 1.222331 +529 4.225833 0.192024 NaN NaN +530 4.283333 NaN 11.077209 1.730353 +531 4.635556 0.260064 NaN NaN +532 4.750000 NaN 10.475251 2.381445 +533 4.967500 0.278208 NaN NaN +534 5.116667 NaN 9.670630 2.979979 +535 5.433333 NaN 8.973995 3.639334 +Experimental matrix: +[[ 0.055944 nan nan] + [ 0.074088 nan nan] + [ 0.092232 nan nan] + [ nan 12.61054446 0.62752743] + [ 0.111888 nan nan] + [ 0.152712 nan nan] + [ nan 11.97217995 1.22233059] + [ 0.192024 nan nan] + [ nan 11.0772091 1.73035277] + [ 0.260064 nan nan] + [ nan 10.47525131 2.3814454 ] + [ 0.278208 nan nan] + [ nan 9.67062966 2.9799787 ] + [ nan 8.97399527 3.63933447]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:03,731 - physiofit - INFO - mc : False +2024-05-27 14:31:03,731 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:03,731 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:03,731 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:04,302 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:04,304 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.1518231338415594 + x: [ 1.959e-02 5.450e-01 -6.974e+00 1.353e+01 + 5.409e+00 1.000e-06] + nit: 126 + nfev: 11801 + population: [[ 1.962e-02 5.446e-01 ... 5.416e+00 5.184e-04] + [ 1.967e-02 5.443e-01 ... 5.393e+00 1.789e-03] + ... + [ 1.966e-02 5.445e-01 ... 5.410e+00 8.038e-04] + [ 2.040e-02 5.362e-01 ... 5.343e+00 2.732e-04]] + population_energies: [ 2.152e+00 2.176e+00 ... 2.167e+00 2.200e+00] + jac: [ 7.067e-02 5.882e-03 7.194e-06 1.036e-04 + 1.774e-04 7.239e+00] +2024-05-27 14:31:04,304 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.01958665058133162 +2024-05-27 14:31:04,304 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5449971828516074 +2024-05-27 14:31:04,304 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.973608279302498 +2024-05-27 14:31:04,304 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.531096743657715 +2024-05-27 14:31:04,305 - physiofit.physiofit.base.fitter - INFO - Ace_q = 5.409010591208966 +2024-05-27 14:31:04,305 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 1e-06 +2024-05-27 14:31:04,310 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.053069 NaN NaN +2.261389 0.067175 NaN NaN +2.774167 0.088833 NaN NaN +2.800000 NaN 12.628923 0.699763 +3.208889 0.112582 NaN NaN +3.706389 0.147646 NaN NaN +3.733333 NaN 11.864539 1.292650 +4.225833 0.195961 NaN NaN +4.283333 NaN 11.194447 1.812401 +4.635556 0.244989 NaN NaN +4.750000 NaN 10.445172 2.393568 +4.967500 0.293572 NaN NaN +5.116667 NaN 9.707135 2.966020 +5.433333 NaN 8.939606 3.561346 + +2024-05-27 14:31:04,313 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.1518231338415594 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.00013012993522121835 + +2024-05-27 14:31:04,314 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00013012993522121835 +2024-05-27 14:31:04,316 - physiofit - INFO - Results for ybjP_2: + optimal +ybjP_2 X_0 0.019587 +ybjP_2 growth_rate 0.544997 +ybjP_2 Glc_q -6.973608 +ybjP_2 Glc_M0 13.531097 +ybjP_2 Ace_q 5.409011 +ybjP_2 Ace_M0 0.000001 +2024-05-27 14:31:04,322 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:05,267 - physiofit - INFO - Running optimization for ybjS +2024-05-27 14:31:05,269 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:05,270 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:05,273 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +536 0.000000 0.034776 NaN NaN +537 0.283333 NaN 14.133004 0.039715 +538 1.195000 0.066528 NaN NaN +539 1.613611 0.081648 NaN NaN +540 1.916667 NaN 13.888698 0.454876 +541 2.361389 0.133056 NaN NaN +542 2.700000 NaN 13.017628 0.740965 +543 3.286389 0.223776 NaN NaN +544 3.616667 NaN 12.418733 1.377443 +545 3.819444 0.322056 NaN NaN +546 4.050000 NaN 11.420610 1.673696 +547 4.410833 0.482328 NaN NaN +548 4.750000 NaN 9.767928 2.386325 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.13300416 0.03971517] + [ 0.066528 nan nan] + [ 0.081648 nan nan] + [ nan 13.88869845 0.45487637] + [ 0.133056 nan nan] + [ nan 13.01762831 0.74096509] + [ 0.223776 nan nan] + [ nan 12.41873271 1.37744277] + [ 0.322056 nan nan] + [ nan 11.42060956 1.6736963 ] + [ 0.482328 nan nan] + [ nan 9.76792841 2.38632487]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:05,273 - physiofit - INFO - mc : False +2024-05-27 14:31:05,274 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:05,274 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:05,274 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:05,723 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:05,724 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.559909385910098 + x: [ 2.973e-02 6.281e-01 -5.033e+00 1.427e+01 + 2.641e+00 1.504e-01] + nit: 97 + nfev: 9324 + population: [[ 2.951e-02 6.302e-01 ... 2.629e+00 1.556e-01] + [ 2.952e-02 6.301e-01 ... 2.687e+00 1.340e-01] + ... + [ 2.938e-02 6.300e-01 ... 2.643e+00 1.520e-01] + [ 3.011e-02 6.256e-01 ... 2.642e+00 1.467e-01]] + population_energies: [ 2.560e+00 2.602e+00 ... 2.591e+00 2.584e+00] + jac: [-7.620e-03 -4.172e-03 2.560e-03 8.344e-03 + 9.820e-03 7.995e-03] +2024-05-27 14:31:05,724 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02972874211187718 +2024-05-27 14:31:05,724 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6281465714551401 +2024-05-27 14:31:05,724 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.033441586099609 +2024-05-27 14:31:05,724 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.27428305345491 +2024-05-27 14:31:05,725 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.641043929821793 +2024-05-27 14:31:05,725 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1504039724555197 +2024-05-27 14:31:05,728 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.029729 NaN NaN +0.283333 NaN 14.227879 0.174752 +1.195000 0.062976 NaN NaN +1.613611 0.081916 NaN NaN +1.916667 NaN 13.718453 0.442047 +2.361389 0.131028 NaN NaN +2.700000 NaN 13.213705 0.706889 +3.286389 0.234264 NaN NaN +3.616667 NaN 12.202518 1.237458 +3.819444 0.327434 NaN NaN +4.050000 NaN 11.479850 1.616642 +4.410833 0.474739 NaN NaN +4.750000 NaN 9.805080 2.495392 + +2024-05-27 14:31:05,732 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.559909385910098 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0008872441789321705 + +2024-05-27 14:31:05,732 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0008872441789321705 +2024-05-27 14:31:05,735 - physiofit - INFO - Results for ybjS: + optimal +ybjS X_0 0.029729 +ybjS growth_rate 0.628147 +ybjS Glc_q -5.033442 +ybjS Glc_M0 14.274283 +ybjS Ace_q 2.641044 +ybjS Ace_M0 0.150404 +2024-05-27 14:31:05,740 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:06,704 - physiofit - INFO - Running optimization for ybjX +2024-05-27 14:31:06,707 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:06,707 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:06,711 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +549 1.950000 NaN 13.907092 0.442019 +550 2.501389 0.123984 NaN NaN +551 3.250000 NaN 13.080425 1.137392 +552 3.341944 0.179928 NaN NaN +553 3.997500 0.250992 NaN NaN +554 4.083333 NaN 11.898245 1.830666 +555 4.523333 0.374976 NaN NaN +556 4.766667 NaN 10.197008 2.613406 +Experimental matrix: +[[ nan 13.9070916 0.44201872] + [ 0.123984 nan nan] + [ nan 13.08042497 1.13739169] + [ 0.179928 nan nan] + [ 0.250992 nan nan] + [ nan 11.89824482 1.83066558] + [ 0.374976 nan nan] + [ nan 10.19700807 2.61340578]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:06,711 - physiofit - INFO - mc : False +2024-05-27 14:31:06,711 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:06,711 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:06,711 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:07,194 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:07,195 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.8216090419629833 + x: [ 2.590e-02 5.847e-01 -6.421e+00 1.461e+01 + 3.715e+00 1.510e-01] + nit: 108 + nfev: 10174 + population: [[ 2.572e-02 5.863e-01 ... 3.721e+00 1.535e-01] + [ 2.583e-02 5.845e-01 ... 3.719e+00 1.573e-01] + ... + [ 2.601e-02 5.849e-01 ... 3.699e+00 1.441e-01] + [ 2.653e-02 5.791e-01 ... 3.749e+00 1.326e-01]] + population_energies: [ 1.822e+00 1.834e+00 ... 1.842e+00 1.840e+00] + jac: [-3.138e-02 -1.779e-02 8.518e-03 -2.519e-03 + -1.425e-02 1.139e-02] +2024-05-27 14:31:07,195 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025898080873602448 +2024-05-27 14:31:07,195 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5847281421360807 +2024-05-27 14:31:07,195 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.420860389734121 +2024-05-27 14:31:07,195 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.612475209129645 +2024-05-27 14:31:07,195 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.7149344078536473 +2024-05-27 14:31:07,195 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15099727695470863 +2024-05-27 14:31:07,199 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 14.007458 0.501043 +2.501389 0.111810 NaN NaN +3.250000 NaN 12.994795 1.086943 +3.341944 0.182783 NaN NaN +3.997500 0.268170 NaN NaN +4.083333 NaN 11.800542 1.777905 +4.523333 0.364705 NaN NaN +4.766667 NaN 10.279708 2.657818 + +2024-05-27 14:31:07,202 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.8216090419629833 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.06464772734076196 + +2024-05-27 14:31:07,203 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.06464772734076196 +2024-05-27 14:31:07,204 - physiofit - INFO - Results for ybjX: + optimal +ybjX X_0 0.025898 +ybjX growth_rate 0.584728 +ybjX Glc_q -6.420860 +ybjX Glc_M0 14.612475 +ybjX Ace_q 3.714934 +ybjX Ace_M0 0.150997 +2024-05-27 14:31:07,211 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:08,169 - physiofit - INFO - Running optimization for ycaC +2024-05-27 14:31:08,172 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:08,172 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:08,176 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +557 1.950000 NaN 13.903795 0.477895 +558 2.501389 0.107352 NaN NaN +559 3.250000 NaN 12.493386 1.296228 +560 3.341944 0.173880 NaN NaN +561 3.997500 0.235872 NaN NaN +562 4.083333 NaN 11.358871 2.012807 +563 4.523333 0.337176 NaN NaN +564 4.766667 NaN 9.368425 2.716976 +Experimental matrix: +[[ nan 13.90379453 0.47789547] + [ 0.107352 nan nan] + [ nan 12.49338573 1.29622841] + [ 0.17388 nan nan] + [ 0.235872 nan nan] + [ nan 11.35887063 2.01280725] + [ 0.337176 nan nan] + [ nan 9.36842481 2.71697605]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:08,176 - physiofit - INFO - mc : False +2024-05-27 14:31:08,176 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:08,177 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:08,177 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:08,660 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:08,661 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.5462287144452207 + x: [ 2.714e-02 5.522e-01 -8.247e+00 1.466e+01 + 4.116e+00 1.902e-01] + nit: 107 + nfev: 10196 + population: [[ 2.744e-02 5.497e-01 ... 4.091e+00 1.935e-01] + [ 2.754e-02 5.494e-01 ... 4.155e+00 1.684e-01] + ... + [ 2.767e-02 5.478e-01 ... 4.166e+00 1.556e-01] + [ 2.768e-02 5.470e-01 ... 4.162e+00 1.586e-01]] + population_energies: [ 1.546e+00 1.567e+00 ... 1.572e+00 1.575e+00] + jac: [ 1.953e-02 1.571e-03 -8.249e-05 -2.780e-05 + -1.141e-04 -4.974e-05] +2024-05-27 14:31:08,662 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.027140262912598 +2024-05-27 14:31:08,662 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5521920987485301 +2024-05-27 14:31:08,662 - physiofit.physiofit.base.fitter - INFO - Glc_q = -8.246777386024771 +2024-05-27 14:31:08,662 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.657822376353709 +2024-05-27 14:31:08,662 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.115886527449588 +2024-05-27 14:31:08,662 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.19024140707630724 +2024-05-27 14:31:08,665 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.873430 0.581724 +2.501389 0.108015 NaN NaN +3.250000 NaN 12.624198 1.205204 +3.341944 0.171814 NaN NaN +3.997500 0.246758 NaN NaN +4.083333 NaN 11.199050 1.916481 +4.523333 0.329893 NaN NaN +4.766667 NaN 9.427795 2.800497 + +2024-05-27 14:31:08,669 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.5462287144452207 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.04363518511386525 + +2024-05-27 14:31:08,669 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.04363518511386525 +2024-05-27 14:31:08,671 - physiofit - INFO - Results for ycaC: + optimal +ycaC X_0 0.027140 +ycaC growth_rate 0.552192 +ycaC Glc_q -8.246777 +ycaC Glc_M0 14.657822 +ycaC Ace_q 4.115887 +ycaC Ace_M0 0.190241 +2024-05-27 14:31:08,676 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:09,620 - physiofit - INFO - Running optimization for ycbZ +2024-05-27 14:31:09,623 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:09,623 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:09,626 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +565 1.950000 NaN 13.990758 0.254203 +566 2.501389 0.105840 NaN NaN +567 3.250000 NaN 13.592563 0.674860 +568 3.341944 0.167832 NaN NaN +569 3.997500 0.223776 NaN NaN +570 4.083333 NaN 12.825052 1.061487 +571 4.523333 0.317520 NaN NaN +572 4.766667 NaN 12.378334 1.551367 +Experimental matrix: +[[ nan 13.99075763 0.25420268] + [ 0.10584 nan nan] + [ nan 13.59256325 0.67485996] + [ 0.167832 nan nan] + [ 0.223776 nan nan] + [ nan 12.8250523 1.06148657] + [ 0.31752 nan nan] + [ nan 12.37833376 1.55136705]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:09,626 - physiofit - INFO - mc : False +2024-05-27 14:31:09,626 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:09,626 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:09,627 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:10,171 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:10,172 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.6058643803421251 + x: [ 2.668e-02 5.437e-01 -3.268e+00 1.429e+01 + 2.502e+00 4.750e-02] + nit: 118 + nfev: 11284 + population: [[ 2.672e-02 5.432e-01 ... 2.497e+00 4.856e-02] + [ 2.660e-02 5.437e-01 ... 2.525e+00 3.657e-02] + ... + [ 2.681e-02 5.419e-01 ... 2.498e+00 5.301e-02] + [ 2.685e-02 5.423e-01 ... 2.514e+00 4.136e-02]] + population_energies: [ 6.059e-01 6.199e-01 ... 6.130e-01 6.082e-01] + jac: [ 2.608e-02 3.780e-03 -5.675e-05 -1.099e-04 + -3.851e-04 -1.154e-03] +2024-05-27 14:31:10,172 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.026677904720387387 +2024-05-27 14:31:10,172 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5437020755988893 +2024-05-27 14:31:10,172 - physiofit.physiofit.base.fitter - INFO - Glc_q = -3.2681821218649616 +2024-05-27 14:31:10,173 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.29115724552967 +2024-05-27 14:31:10,173 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.502219514795052 +2024-05-27 14:31:10,173 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.04750353578487222 +2024-05-27 14:31:10,177 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.988557 0.279184 +2.501389 0.103943 NaN NaN +3.250000 NaN 13.512856 0.643395 +3.341944 0.164163 NaN NaN +3.997500 0.234460 NaN NaN +4.083333 NaN 12.974854 1.055305 +4.523333 0.312056 NaN NaN +4.766667 NaN 12.310428 1.564010 + +2024-05-27 14:31:10,180 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.6058643803421251 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.003698056552723408 + +2024-05-27 14:31:10,180 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.003698056552723408 +2024-05-27 14:31:10,182 - physiofit - INFO - Results for ycbZ: + optimal +ycbZ X_0 0.026678 +ycbZ growth_rate 0.543702 +ycbZ Glc_q -3.268182 +ycbZ Glc_M0 14.291157 +ycbZ Ace_q 2.502220 +ycbZ Ace_M0 0.047504 +2024-05-27 14:31:10,188 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:11,155 - physiofit - INFO - Running optimization for yccJ +2024-05-27 14:31:11,157 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:11,157 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:11,164 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +573 0.000000 0.031752 NaN NaN +574 0.066667 NaN 16.034303 0.000000 +575 1.188889 0.058968 NaN NaN +576 1.716667 NaN 14.813259 0.378859 +577 2.276944 0.101304 NaN NaN +578 2.800000 NaN 13.559898 0.879546 +579 3.128333 0.158760 NaN NaN +580 3.633333 NaN 12.614042 1.434846 +581 3.771389 0.216216 NaN NaN +582 4.266667 NaN 11.439368 2.046900 +583 4.415556 0.340200 NaN NaN +584 4.822778 0.433944 NaN NaN +585 4.883333 NaN 9.822831 2.824449 +Experimental matrix: +[[ 0.031752 nan nan] + [ nan 16.03430286 0. ] + [ 0.058968 nan nan] + [ nan 14.81325896 0.37885937] + [ 0.101304 nan nan] + [ nan 13.55989768 0.879546 ] + [ 0.15876 nan nan] + [ nan 12.6140416 1.43484606] + [ 0.216216 nan nan] + [ nan 11.43936791 2.04689958] + [ 0.3402 nan nan] + [ 0.433944 nan nan] + [ nan 9.82283072 2.82444866]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:11,165 - physiofit - INFO - mc : False +2024-05-27 14:31:11,165 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:11,165 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:11,166 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:11,545 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:11,546 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.258513807595346 + x: [ 2.875e-02 5.578e-01 -8.121e+00 1.556e+01 + 3.842e+00 7.153e-02] + nit: 82 + nfev: 7974 + population: [[ 2.871e-02 5.577e-01 ... 3.840e+00 6.870e-02] + [ 2.876e-02 5.568e-01 ... 3.852e+00 6.586e-02] + ... + [ 2.890e-02 5.562e-01 ... 3.853e+00 6.766e-02] + [ 2.786e-02 5.649e-01 ... 3.790e+00 9.090e-02]] + population_energies: [ 4.259e+00 4.281e+00 ... 4.282e+00 4.404e+00] + jac: [-7.914e-05 -3.819e-06 0.000e+00 -6.217e-07 + -5.684e-06 -1.323e-05] +2024-05-27 14:31:11,546 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.028745289402477628 +2024-05-27 14:31:11,547 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5577766438847787 +2024-05-27 14:31:11,547 - physiofit.physiofit.base.fitter - INFO - Glc_q = -8.120853793310612 +2024-05-27 14:31:11,547 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.5611490026588 +2024-05-27 14:31:11,547 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.8417471717306646 +2024-05-27 14:31:11,547 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.07152749910117516 +2024-05-27 14:31:11,551 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028745 NaN NaN +0.066667 NaN 15.545294 0.079028 +1.188889 0.055791 NaN NaN +1.716667 NaN 14.889346 0.389339 +2.276944 0.102360 NaN NaN +2.800000 NaN 13.984499 0.817396 +3.128333 0.164578 NaN NaN +3.633333 NaN 12.803926 1.375892 +3.771389 0.235584 NaN NaN +4.266667 NaN 11.458370 2.012437 +4.415556 0.337433 NaN NaN +4.822778 0.423480 NaN NaN +4.883333 NaN 9.602265 2.890508 + +2024-05-27 14:31:11,554 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.258513807595346 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.011882265028890187 + +2024-05-27 14:31:11,554 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.011882265028890187 +2024-05-27 14:31:11,556 - physiofit - INFO - Results for yccJ: + optimal +yccJ X_0 0.028745 +yccJ growth_rate 0.557777 +yccJ Glc_q -8.120854 +yccJ Glc_M0 15.561149 +yccJ Ace_q 3.841747 +yccJ Ace_M0 0.071527 +2024-05-27 14:31:11,562 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:12,539 - physiofit - INFO - Running optimization for yccU +2024-05-27 14:31:12,542 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:12,542 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:12,546 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +586 0.000000 0.036288 NaN NaN +587 0.283333 NaN 14.099294 0.045284 +588 1.195000 0.065016 NaN NaN +589 1.613611 0.084672 NaN NaN +590 1.916667 NaN 13.460995 0.408009 +591 2.361389 0.116424 NaN NaN +592 2.700000 NaN 12.834316 0.689164 +593 3.286389 0.214704 NaN NaN +594 3.616667 NaN 12.065473 1.139790 +595 3.819444 0.328104 NaN NaN +596 4.050000 NaN 11.652711 1.532426 +597 4.410833 0.412776 NaN NaN +598 4.750000 NaN 10.280734 2.170703 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 14.0992939 0.04528375] + [ 0.065016 nan nan] + [ 0.084672 nan nan] + [ nan 13.46099511 0.408009 ] + [ 0.116424 nan nan] + [ nan 12.83431554 0.68916402] + [ 0.214704 nan nan] + [ nan 12.06547338 1.13979049] + [ 0.328104 nan nan] + [ nan 11.65271057 1.53242614] + [ 0.412776 nan nan] + [ nan 10.28073392 2.17070311]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:12,547 - physiofit - INFO - mc : False +2024-05-27 14:31:12,547 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:12,547 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:12,547 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:12,981 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:12,982 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.4161929749105435 + x: [ 3.407e-02 5.709e-01 -4.467e+00 1.399e+01 + 2.546e+00 8.915e-02] + nit: 94 + nfev: 9012 + population: [[ 3.413e-02 5.702e-01 ... 2.540e+00 9.097e-02] + [ 3.389e-02 5.724e-01 ... 2.522e+00 9.399e-02] + ... + [ 3.349e-02 5.754e-01 ... 2.525e+00 9.238e-02] + [ 3.380e-02 5.725e-01 ... 2.563e+00 9.570e-02]] + population_energies: [ 3.416e+00 3.430e+00 ... 3.473e+00 3.446e+00] + jac: [-2.357e-03 -4.774e-05 -7.061e-06 2.398e-06 + -5.032e-05 -1.180e-04] +2024-05-27 14:31:12,983 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03406844591364639 +2024-05-27 14:31:12,983 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5709212387283735 +2024-05-27 14:31:12,983 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.467263724464792 +2024-05-27 14:31:12,983 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.992699210385616 +2024-05-27 14:31:12,983 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5462366938756316 +2024-05-27 14:31:12,983 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.08914542752847723 +2024-05-27 14:31:12,986 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.034068 NaN NaN +0.283333 NaN 13.945894 0.115823 +1.195000 0.067398 NaN NaN +1.613611 0.085594 NaN NaN +1.916667 NaN 13.463020 0.391050 +2.361389 0.131176 NaN NaN +2.700000 NaN 13.013964 0.647002 +3.286389 0.222436 NaN NaN +3.616667 NaN 12.157612 1.135103 +3.819444 0.301561 NaN NaN +4.050000 NaN 11.567696 1.471341 +4.410833 0.422678 NaN NaN +4.750000 NaN 10.245337 2.225055 + +2024-05-27 14:31:12,991 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.4161929749105435 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.00403378135942479 + +2024-05-27 14:31:12,991 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00403378135942479 +2024-05-27 14:31:12,993 - physiofit - INFO - Results for yccU: + optimal +yccU X_0 0.034068 +yccU growth_rate 0.570921 +yccU Glc_q -4.467264 +yccU Glc_M0 13.992699 +yccU Ace_q 2.546237 +yccU Ace_M0 0.089145 +2024-05-27 14:31:12,998 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:13,957 - physiofit - INFO - Running optimization for ycdX +2024-05-27 14:31:13,961 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:13,961 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:13,965 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +599 1.950000 NaN 13.435660 0.390107 +600 2.501389 0.107352 NaN NaN +601 3.250000 NaN 12.962971 1.036419 +602 3.341944 0.157248 NaN NaN +603 3.997500 0.246456 NaN NaN +604 4.083333 NaN 12.265648 1.693309 +605 4.523333 0.374976 NaN NaN +606 4.766667 NaN 10.774621 2.334462 +Experimental matrix: +[[ nan 13.43566042 0.39010676] + [ 0.107352 nan nan] + [ nan 12.96297132 1.03641884] + [ 0.157248 nan nan] + [ 0.246456 nan nan] + [ nan 12.26564849 1.6933095 ] + [ 0.374976 nan nan] + [ nan 10.77462077 2.33446166]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:13,965 - physiofit - INFO - mc : False +2024-05-27 14:31:13,965 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:13,966 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:13,966 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:14,461 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:14,462 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.3238333400435374 + x: [ 1.744e-02 6.734e-01 -4.903e+00 1.392e+01 + 3.540e+00 2.344e-01] + nit: 107 + nfev: 10490 + population: [[ 1.744e-02 6.734e-01 ... 3.540e+00 2.344e-01] + [ 1.773e-02 6.693e-01 ... 3.532e+00 2.256e-01] + ... + [ 1.811e-02 6.642e-01 ... 3.458e+00 2.557e-01] + [ 1.778e-02 6.683e-01 ... 3.526e+00 2.340e-01]] + population_energies: [ 2.324e+00 2.344e+00 ... 2.390e+00 2.362e+00] +2024-05-27 14:31:14,462 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.01744155773851208 +2024-05-27 14:31:14,463 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6733576436864608 +2024-05-27 14:31:14,463 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.903107425228509 +2024-05-27 14:31:14,463 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.916709829102617 +2024-05-27 14:31:14,463 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.539816140939034 +2024-05-27 14:31:14,464 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.23443399327009473 +2024-05-27 14:31:14,467 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.571584 0.483599 +2.501389 0.093990 NaN NaN +3.250000 NaN 12.910721 0.960711 +3.341944 0.165534 NaN NaN +3.997500 0.257393 NaN NaN +4.083333 NaN 12.057971 1.576357 +4.523333 0.366749 NaN NaN +4.766667 NaN 10.897750 2.413983 + +2024-05-27 14:31:14,471 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.3238333400435374 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.11236087868220508 + +2024-05-27 14:31:14,472 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.11236087868220508 +2024-05-27 14:31:14,475 - physiofit - INFO - Results for ycdX: + optimal +ycdX X_0 0.017442 +ycdX growth_rate 0.673358 +ycdX Glc_q -4.903107 +ycdX Glc_M0 13.916710 +ycdX Ace_q 3.539816 +ycdX Ace_M0 0.234434 +2024-05-27 14:31:14,481 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:15,442 - physiofit - INFO - Running optimization for ycdY +2024-05-27 14:31:15,444 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:15,445 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:15,448 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +607 0.000000 0.039312 NaN NaN +608 0.066667 NaN 15.527803 0.010367 +609 1.188889 0.068040 NaN NaN +610 1.716667 NaN 14.804167 0.350114 +611 2.276944 0.114912 NaN NaN +612 2.800000 NaN 13.350898 0.707163 +613 3.128333 0.166320 NaN NaN +614 3.633333 NaN 12.477015 1.081216 +615 3.771389 0.240408 NaN NaN +616 4.266667 NaN 11.503713 1.529007 +617 4.415556 0.349272 NaN NaN +618 4.822778 0.473256 NaN NaN +619 4.883333 NaN 9.943683 1.980509 +Experimental matrix: +[[3.93120000e-02 nan nan] + [ nan 1.55278028e+01 1.03674128e-02] + [6.80400000e-02 nan nan] + [ nan 1.48041665e+01 3.50113898e-01] + [1.14912000e-01 nan nan] + [ nan 1.33508981e+01 7.07163298e-01] + [1.66320000e-01 nan nan] + [ nan 1.24770146e+01 1.08121604e+00] + [2.40408000e-01 nan nan] + [ nan 1.15037134e+01 1.52900691e+00] + [3.49272000e-01 nan nan] + [4.73256000e-01 nan nan] + [ nan 9.94368260e+00 1.98050933e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:15,449 - physiofit - INFO - mc : False +2024-05-27 14:31:15,449 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:15,449 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:15,449 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:15,903 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:15,903 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.119278840416351 + x: [ 3.105e-02 5.564e-01 -6.961e+00 1.525e+01 + 2.476e+00 1.183e-01] + nit: 91 + nfev: 8721 + population: [[ 3.089e-02 5.576e-01 ... 2.472e+00 1.267e-01] + [ 3.115e-02 5.557e-01 ... 2.465e+00 1.333e-01] + ... + [ 3.029e-02 5.621e-01 ... 2.479e+00 1.384e-01] + [ 3.089e-02 5.576e-01 ... 2.444e+00 1.379e-01]] + population_energies: [ 5.119e+00 5.158e+00 ... 5.204e+00 5.153e+00] + jac: [-6.140e-04 -1.481e-04 -8.882e-08 1.057e-05 + -2.025e-05 -4.698e-05] +2024-05-27 14:31:15,904 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.031048349219594245 +2024-05-27 14:31:15,904 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.556402793993694 +2024-05-27 14:31:15,904 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.961181997368279 +2024-05-27 14:31:15,904 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.253104193786738 +2024-05-27 14:31:15,904 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.476260301061626 +2024-05-27 14:31:15,904 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.11829577817658121 +2024-05-27 14:31:15,908 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.031048 NaN NaN +0.066667 NaN 15.238425 0.123518 +1.188889 0.060162 NaN NaN +1.716667 NaN 14.631945 0.339257 +2.276944 0.110216 NaN NaN +2.800000 NaN 13.796826 0.636329 +3.128333 0.177002 NaN NaN +3.633333 NaN 12.708629 1.023427 +3.771389 0.253144 NaN NaN +4.266667 NaN 11.469584 1.464185 +4.415556 0.362264 NaN NaN +4.822778 0.454389 NaN NaN +4.883333 NaN 9.761869 2.071661 + +2024-05-27 14:31:15,912 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.119278840416351 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.027527395096789618 + +2024-05-27 14:31:15,912 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.027527395096789618 +2024-05-27 14:31:15,915 - physiofit - INFO - Results for ycdY: + optimal +ycdY X_0 0.031048 +ycdY growth_rate 0.556403 +ycdY Glc_q -6.961182 +ycdY Glc_M0 15.253104 +ycdY Ace_q 2.476260 +ycdY Ace_M0 0.118296 +2024-05-27 14:31:15,919 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:17,076 - physiofit - INFO - Running optimization for yceB +2024-05-27 14:31:17,079 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:17,080 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:17,084 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +620 0.000000 0.036288 NaN NaN +621 0.066667 NaN 15.559624 0.021532 +622 1.188889 0.065016 NaN NaN +623 1.716667 NaN 14.717046 0.344988 +624 2.276944 0.099792 NaN NaN +625 2.800000 NaN 13.277032 0.754813 +626 3.128333 0.154224 NaN NaN +627 3.633333 NaN 12.357437 1.268876 +628 3.771389 0.205632 NaN NaN +629 4.266667 NaN 11.729404 2.021080 +630 4.415556 0.311472 NaN NaN +631 4.822778 0.367416 NaN NaN +632 4.883333 NaN 10.094382 2.824329 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 15.55962423 0.02153173] + [ 0.065016 nan nan] + [ nan 14.71704581 0.3449884 ] + [ 0.099792 nan nan] + [ nan 13.27703236 0.75481299] + [ 0.154224 nan nan] + [ nan 12.35743679 1.26887551] + [ 0.205632 nan nan] + [ nan 11.72940439 2.0210801 ] + [ 0.311472 nan nan] + [ 0.367416 nan nan] + [ nan 10.0943825 2.82432936]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:17,085 - physiofit - INFO - mc : False +2024-05-27 14:31:17,085 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:17,085 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:17,086 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:17,532 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:17,532 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.477108775984 + x: [ 3.248e-02 5.038e-01 -7.664e+00 1.526e+01 + 4.043e+00 1.000e-06] + nit: 97 + nfev: 9310 + population: [[ 3.246e-02 5.039e-01 ... 4.033e+00 1.694e-03] + [ 3.271e-02 5.021e-01 ... 3.997e+00 8.979e-05] + ... + [ 3.239e-02 5.049e-01 ... 4.027e+00 2.699e-04] + [ 3.242e-02 5.052e-01 ... 4.053e+00 1.236e-03]] + population_energies: [ 3.477e+00 3.548e+00 ... 3.508e+00 3.506e+00] + jac: [-4.828e-03 -3.631e-04 -4.619e-06 -3.548e-05 + -8.660e-05 3.650e+00] +2024-05-27 14:31:17,533 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.032480246556144024 +2024-05-27 14:31:17,533 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5038465071438611 +2024-05-27 14:31:17,533 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.663533469727407 +2024-05-27 14:31:17,533 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.264469333633823 +2024-05-27 14:31:17,533 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.0434778401771645 +2024-05-27 14:31:17,533 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 1e-06 +2024-05-27 14:31:17,536 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.032480 NaN NaN +0.066667 NaN 15.247593 0.008905 +1.188889 0.059125 NaN NaN +1.716667 NaN 14.585255 0.358372 +2.276944 0.102295 NaN NaN +2.800000 NaN 13.733427 0.807819 +3.128333 0.157092 NaN NaN +3.633333 NaN 12.676813 1.365315 +3.771389 0.217203 NaN NaN +4.266667 NaN 11.518430 1.976508 +4.415556 0.300484 NaN NaN +4.822778 0.368917 NaN NaN +4.883333 NaN 9.973405 2.791703 + +2024-05-27 14:31:17,540 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.477108775984 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.004410588785012129 + +2024-05-27 14:31:17,540 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.004410588785012129 +2024-05-27 14:31:17,542 - physiofit - INFO - Results for yceB: + optimal +yceB X_0 0.032480 +yceB growth_rate 0.503847 +yceB Glc_q -7.663533 +yceB Glc_M0 15.264469 +yceB Ace_q 4.043478 +yceB Ace_M0 0.000001 +2024-05-27 14:31:17,547 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:18,532 - physiofit - INFO - Running optimization for yceD +2024-05-27 14:31:18,536 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:18,536 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:18,542 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +633 0.000000 0.036288 NaN NaN +634 0.066667 NaN 14.587987 0.012235 +635 1.188889 0.063504 NaN NaN +636 1.716667 NaN 15.049885 0.339762 +637 2.276944 0.105840 NaN NaN +638 2.800000 NaN 13.311669 0.663343 +639 3.128333 0.160272 NaN NaN +640 3.633333 NaN 12.863669 1.065667 +641 3.771389 0.208656 NaN NaN +642 4.266667 NaN 11.825105 1.441465 +643 4.415556 0.303912 NaN NaN +644 4.822778 0.403704 NaN NaN +645 4.883333 NaN 10.417625 1.880671 +Experimental matrix: +[[3.62880000e-02 nan nan] + [ nan 1.45879871e+01 1.22345490e-02] + [6.35040000e-02 nan nan] + [ nan 1.50498855e+01 3.39761539e-01] + [1.05840000e-01 nan nan] + [ nan 1.33116691e+01 6.63342501e-01] + [1.60272000e-01 nan nan] + [ nan 1.28636686e+01 1.06566686e+00] + [2.08656000e-01 nan nan] + [ nan 1.18251049e+01 1.44146469e+00] + [3.03912000e-01 nan nan] + [4.03704000e-01 nan nan] + [ nan 1.04176249e+01 1.88067072e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:18,543 - physiofit - INFO - mc : False +2024-05-27 14:31:18,543 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:18,543 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:18,544 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:18,903 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:18,904 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.451938907964098 + x: [ 3.027e-02 5.300e-01 -6.405e+00 1.494e+01 + 2.641e+00 1.037e-01] + nit: 71 + nfev: 7068 + population: [[ 3.057e-02 5.279e-01 ... 2.609e+00 1.093e-01] + [ 3.065e-02 5.272e-01 ... 2.579e+00 1.111e-01] + ... + [ 3.036e-02 5.298e-01 ... 2.675e+00 9.364e-02] + [ 3.114e-02 5.241e-01 ... 2.620e+00 9.719e-02]] + population_energies: [ 5.452e+00 5.514e+00 ... 5.488e+00 5.502e+00] + jac: [-2.137e-03 -1.887e-04 6.750e-06 5.240e-06 + -6.484e-06 4.796e-06] +2024-05-27 14:31:18,904 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.030267018008706424 +2024-05-27 14:31:18,904 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5300359871562113 +2024-05-27 14:31:18,904 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.404717357581801 +2024-05-27 14:31:18,904 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.941411259570167 +2024-05-27 14:31:18,904 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.6414503623411485 +2024-05-27 14:31:18,905 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.10368674237283369 +2024-05-27 14:31:18,908 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.030267 NaN NaN +0.066667 NaN 14.928257 0.109112 +1.188889 0.056838 NaN NaN +1.716667 NaN 14.398641 0.327538 +2.276944 0.101182 NaN NaN +2.800000 NaN 13.693897 0.618190 +3.128333 0.158886 NaN NaN +3.633333 NaN 12.797990 0.987682 +3.771389 0.223415 NaN NaN +4.266667 NaN 11.797076 1.400482 +4.415556 0.314336 NaN NaN +4.822778 0.390061 NaN NaN +4.883333 NaN 10.440080 1.960138 + +2024-05-27 14:31:18,912 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.451938907964098 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.036148130074980224 + +2024-05-27 14:31:18,912 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.036148130074980224 +2024-05-27 14:31:18,914 - physiofit - INFO - Results for yceD: + optimal +yceD X_0 0.030267 +yceD growth_rate 0.530036 +yceD Glc_q -6.404717 +yceD Glc_M0 14.941411 +yceD Ace_q 2.641450 +yceD Ace_M0 0.103687 +2024-05-27 14:31:18,920 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:19,914 - physiofit - INFO - Running optimization for ycfH +2024-05-27 14:31:19,917 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:19,917 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:19,922 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +646 1.950000 NaN 13.790091 0.430034 +647 2.501389 0.114912 NaN NaN +648 3.250000 NaN 12.660774 1.100993 +649 3.341944 0.181440 NaN NaN +650 3.997500 0.276696 NaN NaN +651 4.083333 NaN 11.780806 1.816834 +652 4.523333 0.379512 NaN NaN +653 4.766667 NaN 10.704208 2.660274 +Experimental matrix: +[[ nan 13.79009126 0.43003372] + [ 0.114912 nan nan] + [ nan 12.66077381 1.1009928 ] + [ 0.18144 nan nan] + [ 0.276696 nan nan] + [ nan 11.78080579 1.81683425] + [ 0.379512 nan nan] + [ nan 10.70420836 2.66027364]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:19,923 - physiofit - INFO - mc : False +2024-05-27 14:31:19,923 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:19,923 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:19,924 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:20,466 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:20,467 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.5248987326723864 + x: [ 2.565e-02 5.945e-01 -5.074e+00 1.412e+01 + 3.724e+00 1.192e-01] + nit: 121 + nfev: 11190 + population: [[ 2.553e-02 5.956e-01 ... 3.724e+00 1.204e-01] + [ 2.562e-02 5.950e-01 ... 3.710e+00 1.277e-01] + ... + [ 2.568e-02 5.945e-01 ... 3.697e+00 1.270e-01] + [ 2.586e-02 5.928e-01 ... 3.740e+00 1.033e-01]] + population_energies: [ 5.249e-01 5.321e-01 ... 5.349e-01 5.323e-01] + jac: [ 4.242e-02 4.419e-03 -2.486e-02 -4.507e-02 + -1.819e-02 -3.666e-03] +2024-05-27 14:31:20,468 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025645509885650977 +2024-05-27 14:31:20,468 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5945349193830762 +2024-05-27 14:31:20,468 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.074284285617821 +2024-05-27 14:31:20,468 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.117232301385569 +2024-05-27 14:31:20,468 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.72354685978771 +2024-05-27 14:31:20,468 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.11918868177008947 +2024-05-27 14:31:20,472 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.638355 0.470592 +2.501389 0.113469 NaN NaN +3.250000 NaN 12.824749 1.067622 +3.341944 0.187030 NaN NaN +3.997500 0.276171 NaN NaN +4.083333 NaN 11.855617 1.778778 +4.523333 0.377529 NaN NaN +4.766667 NaN 10.612389 2.691068 + +2024-05-27 14:31:20,475 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.5248987326723864 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.002477816705450384 + +2024-05-27 14:31:20,476 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.002477816705450384 +2024-05-27 14:31:20,478 - physiofit - INFO - Results for ycfH: + optimal +ycfH X_0 0.025646 +ycfH growth_rate 0.594535 +ycfH Glc_q -5.074284 +ycfH Glc_M0 14.117232 +ycfH Ace_q 3.723547 +ycfH Ace_M0 0.119189 +2024-05-27 14:31:20,483 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:21,436 - physiofit - INFO - Running optimization for ycgJ +2024-05-27 14:31:21,439 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:21,439 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:21,444 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +654 0.000000 0.031752 NaN NaN +655 0.283333 NaN 13.807190 0.038717 +656 1.195000 0.054432 NaN NaN +657 1.613611 0.066528 NaN NaN +658 1.916667 NaN 14.119199 0.377329 +659 2.361389 0.093744 NaN NaN +660 2.700000 NaN 13.547468 0.662051 +661 3.286389 0.148176 NaN NaN +662 3.616667 NaN 12.879564 1.215558 +663 3.819444 0.211680 NaN NaN +664 4.050000 NaN 12.278271 1.566236 +665 4.410833 0.291816 NaN NaN +666 4.750000 NaN 11.381162 2.360172 +Experimental matrix: +[[ 0.031752 nan nan] + [ nan 13.80718955 0.03871738] + [ 0.054432 nan nan] + [ 0.066528 nan nan] + [ nan 14.11919863 0.37732893] + [ 0.093744 nan nan] + [ nan 13.54746843 0.66205078] + [ 0.148176 nan nan] + [ nan 12.87956381 1.21555757] + [ 0.21168 nan nan] + [ nan 12.27827091 1.56623628] + [ 0.291816 nan nan] + [ nan 11.3811616 2.36017182]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:21,444 - physiofit - INFO - mc : False +2024-05-27 14:31:21,445 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:21,445 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:21,446 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:21,934 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:21,935 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.6357191151878379 + x: [ 2.609e-02 5.460e-01 -4.703e+00 1.420e+01 + 3.972e+00 2.147e-02] + nit: 102 + nfev: 10089 + population: [[ 2.604e-02 5.464e-01 ... 3.961e+00 2.749e-02] + [ 2.565e-02 5.508e-01 ... 3.966e+00 3.250e-02] + ... + [ 2.624e-02 5.443e-01 ... 3.969e+00 2.028e-02] + [ 2.547e-02 5.520e-01 ... 3.967e+00 3.856e-02]] + population_energies: [ 1.636e+00 1.655e+00 ... 1.643e+00 1.661e+00] + jac: [-6.860e-03 -9.546e-04 -2.462e-05 -6.672e-05 + -1.941e-05 1.100e-04] +2024-05-27 14:31:21,936 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.026089005218516828 +2024-05-27 14:31:21,936 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5460203172018443 +2024-05-27 14:31:21,936 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.703238687070096 +2024-05-27 14:31:21,936 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.204178740164302 +2024-05-27 14:31:21,936 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.97224058625859 +2024-05-27 14:31:21,936 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.021465733059906643 +2024-05-27 14:31:21,940 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.026089 NaN NaN +0.283333 NaN 14.166579 0.053221 +1.195000 0.050099 NaN NaN +1.613611 0.062965 NaN NaN +1.916667 NaN 13.788942 0.372164 +2.361389 0.094716 NaN NaN +2.700000 NaN 13.447364 0.660653 +3.286389 0.156953 NaN NaN +3.616667 NaN 12.809781 1.199140 +3.819444 0.209979 NaN NaN +4.050000 NaN 12.377565 1.564179 +4.410833 0.290011 NaN NaN +4.750000 NaN 11.422614 2.370707 + +2024-05-27 14:31:21,944 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.6357191151878379 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 7.153300104329506e-05 + +2024-05-27 14:31:21,944 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 7.153300104329506e-05 +2024-05-27 14:31:21,947 - physiofit - INFO - Results for ycgJ: + optimal +ycgJ X_0 0.026089 +ycgJ growth_rate 0.546020 +ycgJ Glc_q -4.703239 +ycgJ Glc_M0 14.204179 +ycgJ Ace_q 3.972241 +ycgJ Ace_M0 0.021466 +2024-05-27 14:31:21,952 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:22,890 - physiofit - INFO - Running optimization for ycgM +2024-05-27 14:31:22,893 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:22,893 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:22,896 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +667 1.950000 NaN 13.960988 0.385402 +668 2.501389 0.114912 NaN NaN +669 3.250000 NaN 12.547714 0.872064 +670 3.341944 0.179928 NaN NaN +671 3.997500 0.257040 NaN NaN +672 4.083333 NaN 11.783373 1.373752 +673 4.523333 0.356832 NaN NaN +674 4.766667 NaN 10.578638 1.928477 +Experimental matrix: +[[ nan 13.96098762 0.38540161] + [ 0.114912 nan nan] + [ nan 12.54771384 0.87206424] + [ 0.179928 nan nan] + [ 0.25704 nan nan] + [ nan 11.78337327 1.37375163] + [ 0.356832 nan nan] + [ nan 10.57863767 1.92847715]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:22,897 - physiofit - INFO - mc : False +2024-05-27 14:31:22,897 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:22,897 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:22,898 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:23,292 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:23,293 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.8837293727137872 + x: [ 2.794e-02 5.603e-01 -5.692e+00 1.431e+01 + 2.690e+00 1.518e-01] + nit: 86 + nfev: 8194 + population: [[ 2.801e-02 5.597e-01 ... 2.705e+00 1.451e-01] + [ 2.807e-02 5.604e-01 ... 2.666e+00 1.487e-01] + ... + [ 2.813e-02 5.586e-01 ... 2.690e+00 1.517e-01] + [ 2.838e-02 5.562e-01 ... 2.707e+00 1.378e-01]] + population_energies: [ 8.837e-01 9.065e-01 ... 8.859e-01 8.918e-01] + jac: [ 1.626e-03 -7.359e-04 2.368e-04 5.771e-04 + 6.990e-04 1.804e-03] +2024-05-27 14:31:23,293 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02794156111754594 +2024-05-27 14:31:23,293 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5603122958125423 +2024-05-27 14:31:23,293 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.692208632681834 +2024-05-27 14:31:23,294 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.308780154005628 +2024-05-27 14:31:23,294 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.6897968642961216 +2024-05-27 14:31:23,294 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1518103008067933 +2024-05-27 14:31:23,297 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.746161 0.417670 +2.501389 0.113485 NaN NaN +3.250000 NaN 12.838927 0.846375 +3.341944 0.181753 NaN NaN +3.997500 0.262425 NaN NaN +4.083333 NaN 11.795320 1.339521 +4.523333 0.352339 NaN NaN +4.766667 NaN 10.490365 1.956164 + +2024-05-27 14:31:23,301 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.8837293727137872 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.01036146213203189 + +2024-05-27 14:31:23,301 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.01036146213203189 +2024-05-27 14:31:23,303 - physiofit - INFO - Results for ycgM: + optimal +ycgM X_0 0.027942 +ycgM growth_rate 0.560312 +ycgM Glc_q -5.692209 +ycgM Glc_M0 14.308780 +ycgM Ace_q 2.689797 +ycgM Ace_M0 0.151810 +2024-05-27 14:31:23,308 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:24,263 - physiofit - INFO - Running optimization for yciK +2024-05-27 14:31:24,266 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:24,266 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:24,269 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +675 0.050000 NaN 14.860241 0.019317 +676 1.950000 NaN 14.425443 0.428954 +677 2.833333 NaN 13.110801 0.729345 +678 2.876944 0.158760 NaN NaN +679 3.678056 0.244944 NaN NaN +680 3.983333 NaN 12.101287 1.391001 +681 4.092222 0.322056 NaN NaN +682 4.565000 0.400680 NaN NaN +683 4.883333 NaN 9.834603 2.117932 +684 5.166667 NaN 8.899848 2.294341 +Experimental matrix: +[[ nan 14.86024063 0.01931686] + [ nan 14.42544292 0.42895399] + [ nan 13.11080115 0.72934451] + [ 0.15876 nan nan] + [ 0.244944 nan nan] + [ nan 12.10128671 1.39100131] + [ 0.322056 nan nan] + [ 0.40068 nan nan] + [ nan 9.83460274 2.11793203] + [ nan 8.8998484 2.29434127]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:24,271 - physiofit - INFO - mc : False +2024-05-27 14:31:24,271 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:24,271 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:24,271 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:24,710 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:24,711 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.6268027394550795 + x: [ 3.639e-02 5.257e-01 -6.120e+00 1.492e+01 + 2.333e+00 1.271e-01] + nit: 95 + nfev: 9039 + population: [[ 3.622e-02 5.267e-01 ... 2.328e+00 1.328e-01] + [ 3.602e-02 5.283e-01 ... 2.311e+00 1.369e-01] + ... + [ 3.717e-02 5.202e-01 ... 2.337e+00 1.269e-01] + [ 3.618e-02 5.266e-01 ... 2.351e+00 1.273e-01]] + population_energies: [ 2.627e+00 2.641e+00 ... 2.646e+00 2.644e+00] + jac: [ 9.357e-03 1.118e-02 -4.947e-02 -4.498e-02 + 7.914e-03 1.466e-02] +2024-05-27 14:31:24,711 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.036388919796229324 +2024-05-27 14:31:24,711 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5256731161060252 +2024-05-27 14:31:24,712 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.119870949432911 +2024-05-27 14:31:24,712 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.923750725576092 +2024-05-27 14:31:24,713 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3325668656428986 +2024-05-27 14:31:24,713 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1271273091595539 +2024-05-27 14:31:24,716 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.912468 0.131428 +1.950000 NaN 14.166594 0.415715 +2.833333 NaN 13.468778 0.681685 +2.876944 0.165107 NaN NaN +3.678056 0.251569 NaN NaN +3.983333 NaN 11.908815 1.276259 +4.092222 0.312760 NaN NaN +4.565000 0.401000 NaN NaN +4.883333 NaN 9.828576 2.069135 +5.166667 NaN 8.942232 2.406962 + +2024-05-27 14:31:24,720 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.6268027394550795 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.011103746626836476 + +2024-05-27 14:31:24,721 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.011103746626836476 +2024-05-27 14:31:24,723 - physiofit - INFO - Results for yciK: + optimal +yciK X_0 0.036389 +yciK growth_rate 0.525673 +yciK Glc_q -6.119871 +yciK Glc_M0 14.923751 +yciK Ace_q 2.332567 +yciK Ace_M0 0.127127 +2024-05-27 14:31:24,729 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:25,724 - physiofit - INFO - Running optimization for yciO +2024-05-27 14:31:25,727 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:25,727 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:25,731 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +685 0.000000 0.034776 NaN NaN +686 0.283333 NaN 14.136707 0.045075 +687 1.195000 0.065016 NaN NaN +688 1.613611 0.074088 NaN NaN +689 1.916667 NaN 13.816014 0.386908 +690 2.361389 0.104328 NaN NaN +691 2.700000 NaN 13.426640 0.684847 +692 3.286389 0.176904 NaN NaN +693 3.616667 NaN 13.006238 1.192698 +694 3.819444 0.222264 NaN NaN +695 4.050000 NaN 12.226709 1.450679 +696 4.410833 0.340200 NaN NaN +697 4.750000 NaN 10.696446 1.830198 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.13670702 0.04507487] + [ 0.065016 nan nan] + [ 0.074088 nan nan] + [ nan 13.81601437 0.3869083 ] + [ 0.104328 nan nan] + [ nan 13.42663984 0.68484724] + [ 0.176904 nan nan] + [ nan 13.00623841 1.19269822] + [ 0.222264 nan nan] + [ nan 12.2267086 1.45067914] + [ 0.3402 nan nan] + [ nan 10.69644622 1.83019754]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:25,731 - physiofit - INFO - mc : False +2024-05-27 14:31:25,731 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:25,731 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:25,732 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:26,161 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:26,162 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.007922013475275 + x: [ 2.986e-02 5.439e-01 -5.097e+00 1.437e+01 + 2.734e+00 1.366e-01] + nit: 92 + nfev: 8671 + population: [[ 3.011e-02 5.426e-01 ... 2.724e+00 1.355e-01] + [ 2.997e-02 5.438e-01 ... 2.741e+00 1.417e-01] + ... + [ 2.999e-02 5.427e-01 ... 2.725e+00 1.313e-01] + [ 2.988e-02 5.437e-01 ... 2.685e+00 1.485e-01]] + population_energies: [ 4.008e+00 4.054e+00 ... 4.019e+00 4.046e+00] + jac: [ 3.030e-02 4.052e-03 -1.226e-05 -1.298e-04 + 9.068e-05 4.816e-04] +2024-05-27 14:31:26,162 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.029855160394644056 +2024-05-27 14:31:26,162 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5439430690309456 +2024-05-27 14:31:26,163 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.097279992721445 +2024-05-27 14:31:26,163 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.367386794856593 +2024-05-27 14:31:26,163 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.733644589051317 +2024-05-27 14:31:26,163 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.13662697973112434 +2024-05-27 14:31:26,167 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.029855 NaN NaN +0.283333 NaN 14.320769 0.161628 +1.195000 0.057189 NaN NaN +1.613611 0.071813 NaN NaN +1.916667 NaN 13.853596 0.412170 +2.361389 0.107858 NaN NaN +2.700000 NaN 13.432010 0.638265 +3.286389 0.178389 NaN NaN +3.616667 NaN 12.646491 1.059534 +3.819444 0.238392 NaN NaN +4.050000 NaN 12.114703 1.344730 +4.410833 0.328849 NaN NaN +4.750000 NaN 10.941171 1.974088 + +2024-05-27 14:31:26,170 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.007922013475275 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.008893173886319638 + +2024-05-27 14:31:26,170 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.008893173886319638 +2024-05-27 14:31:26,174 - physiofit - INFO - Results for yciO: + optimal +yciO X_0 0.029855 +yciO growth_rate 0.543943 +yciO Glc_q -5.097280 +yciO Glc_M0 14.367387 +yciO Ace_q 2.733645 +yciO Ace_M0 0.136627 +2024-05-27 14:31:26,179 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:27,122 - physiofit - INFO - Running optimization for yciW +2024-05-27 14:31:27,124 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:27,124 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:27,128 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +698 0.000000 0.036288 NaN NaN +699 0.283333 NaN 14.116410 0.043911 +700 1.195000 0.068040 NaN NaN +701 1.613611 0.084672 NaN NaN +702 1.916667 NaN 13.950861 0.423600 +703 2.361389 0.130032 NaN NaN +704 2.700000 NaN 13.304273 0.689358 +705 3.286389 0.222264 NaN NaN +706 3.616667 NaN 12.003423 1.223054 +707 3.819444 0.306936 NaN NaN +708 4.050000 NaN 11.624179 1.501887 +709 4.410833 0.427896 NaN NaN +710 4.750000 NaN 10.180000 2.032279 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 14.11641043 0.04391132] + [ 0.06804 nan nan] + [ 0.084672 nan nan] + [ nan 13.95086083 0.42359999] + [ 0.130032 nan nan] + [ nan 13.30427294 0.68935755] + [ 0.222264 nan nan] + [ nan 12.00342279 1.22305398] + [ 0.306936 nan nan] + [ nan 11.62417949 1.50188702] + [ 0.427896 nan nan] + [ nan 10.17999982 2.03227924]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:27,129 - physiofit - INFO - mc : False +2024-05-27 14:31:27,129 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:27,129 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:27,129 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:27,603 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:27,604 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.823845859197431 + x: [ 3.489e-02 5.675e-01 -4.933e+00 1.432e+01 + 2.365e+00 1.295e-01] + nit: 102 + nfev: 9865 + population: [[ 3.489e-02 5.673e-01 ... 2.354e+00 1.348e-01] + [ 3.486e-02 5.680e-01 ... 2.385e+00 1.227e-01] + ... + [ 3.507e-02 5.665e-01 ... 2.354e+00 1.292e-01] + [ 3.481e-02 5.675e-01 ... 2.381e+00 1.252e-01]] + population_energies: [ 1.824e+00 1.837e+00 ... 1.838e+00 1.836e+00] + jac: [-3.904e-03 -6.268e-04 -1.934e-05 -6.719e-05 + -2.645e-04 -5.462e-04] +2024-05-27 14:31:27,605 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03489006206405041 +2024-05-27 14:31:27,605 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.567474933043333 +2024-05-27 14:31:27,605 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.932887599915082 +2024-05-27 14:31:27,605 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.315535880934158 +2024-05-27 14:31:27,605 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3652827077827596 +2024-05-27 14:31:27,605 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.12945979831589247 +2024-05-27 14:31:27,609 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.034890 NaN NaN +0.283333 NaN 14.262633 0.154827 +1.195000 0.068740 NaN NaN +1.613611 0.087172 NaN NaN +1.916667 NaN 13.718869 0.415557 +2.361389 0.133251 NaN NaN +2.700000 NaN 13.215124 0.657099 +3.286389 0.225235 NaN NaN +3.616667 NaN 12.257323 1.116357 +3.819444 0.304795 NaN NaN +4.050000 NaN 11.598986 1.432025 +4.410833 0.426341 NaN NaN +4.750000 NaN 10.126205 2.138213 + +2024-05-27 14:31:27,612 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.823845859197431 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0001339467288483447 + +2024-05-27 14:31:27,612 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0001339467288483447 +2024-05-27 14:31:27,615 - physiofit - INFO - Results for yciW: + optimal +yciW X_0 0.034890 +yciW growth_rate 0.567475 +yciW Glc_q -4.932888 +yciW Glc_M0 14.315536 +yciW Ace_q 2.365283 +yciW Ace_M0 0.129460 +2024-05-27 14:31:27,620 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:28,561 - physiofit - INFO - Running optimization for ycjW +2024-05-27 14:31:28,563 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:28,563 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:28,567 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +711 0.050000 NaN 14.557227 0.015139 +712 1.950000 NaN 13.947454 0.429547 +713 2.833333 NaN 12.872134 0.754823 +714 2.876944 0.151200 NaN NaN +715 3.678056 0.231336 NaN NaN +716 3.983333 NaN 12.216810 1.483292 +717 4.092222 0.309960 NaN NaN +718 4.565000 0.388584 NaN NaN +719 4.883333 NaN 9.851687 2.011741 +720 5.166667 NaN 9.153583 2.654592 +Experimental matrix: +[[ nan 14.55722704 0.01513905] + [ nan 13.94745446 0.42954713] + [ nan 12.87213384 0.75482252] + [ 0.1512 nan nan] + [ 0.231336 nan nan] + [ nan 12.2168097 1.48329243] + [ 0.30996 nan nan] + [ 0.388584 nan nan] + [ nan 9.8516869 2.01174092] + [ nan 9.15358277 2.65459164]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:28,567 - physiofit - INFO - mc : False +2024-05-27 14:31:28,568 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:28,568 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:28,569 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:28,985 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:28,987 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.838215572019102 + x: [ 3.231e-02 5.450e-01 -5.758e+00 1.451e+01 + 2.645e+00 1.166e-01] + nit: 90 + nfev: 8477 + population: [[ 3.238e-02 5.441e-01 ... 2.651e+00 1.168e-01] + [ 3.284e-02 5.400e-01 ... 2.630e+00 1.345e-01] + ... + [ 3.218e-02 5.459e-01 ... 2.675e+00 1.139e-01] + [ 3.164e-02 5.500e-01 ... 2.623e+00 1.216e-01]] + population_energies: [ 3.838e+00 3.900e+00 ... 3.880e+00 3.875e+00] + jac: [-1.326e-01 -1.899e-02 -2.053e-02 2.164e-02 + 5.023e-03 -2.712e-03] +2024-05-27 14:31:28,987 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03231468172314421 +2024-05-27 14:31:28,987 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.545007256221699 +2024-05-27 14:31:28,987 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.757613234531189 +2024-05-27 14:31:28,987 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.512484982343837 +2024-05-27 14:31:28,987 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.645028116777193 +2024-05-27 14:31:28,987 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1166497601302422 +2024-05-27 14:31:28,991 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.503054 0.120982 +1.950000 NaN 13.865785 0.413741 +2.833333 NaN 13.254780 0.694435 +2.876944 0.155008 NaN NaN +3.678056 0.239868 NaN NaN +3.983333 NaN 11.861121 1.334677 +4.092222 0.300610 NaN NaN +4.565000 0.388961 NaN NaN +4.883333 NaN 9.966285 2.205159 +5.166667 NaN 9.150159 2.580084 + +2024-05-27 14:31:28,994 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.838215572019102 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.04564966574491684 + +2024-05-27 14:31:28,995 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.04564966574491684 +2024-05-27 14:31:28,996 - physiofit - INFO - Results for ycjW: + optimal +ycjW X_0 0.032315 +ycjW growth_rate 0.545007 +ycjW Glc_q -5.757613 +ycjW Glc_M0 14.512485 +ycjW Ace_q 2.645028 +ycjW Ace_M0 0.116650 +2024-05-27 14:31:29,002 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:29,984 - physiofit - INFO - Running optimization for ycjX +2024-05-27 14:31:29,987 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:29,988 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:29,992 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +721 1.828889 0.051408 NaN NaN +722 2.261389 0.061992 NaN NaN +723 2.774167 0.083160 NaN NaN +724 2.800000 NaN 12.713187 0.581184 +725 3.208889 0.096768 NaN NaN +726 3.706389 0.125496 NaN NaN +727 3.733333 NaN 11.707873 1.013202 +728 4.225833 0.160272 NaN NaN +729 4.283333 NaN 11.478143 1.397176 +730 4.750000 NaN 10.711727 1.785125 +731 4.967500 0.258552 NaN NaN +732 5.116667 NaN 9.834471 2.099509 +733 5.433333 NaN 9.086004 2.446821 +Experimental matrix: +[[ 0.051408 nan nan] + [ 0.061992 nan nan] + [ 0.08316 nan nan] + [ nan 12.71318666 0.5811839 ] + [ 0.096768 nan nan] + [ 0.125496 nan nan] + [ nan 11.70787254 1.01320244] + [ 0.160272 nan nan] + [ nan 11.47814336 1.39717623] + [ nan 10.71172659 1.78512511] + [ 0.258552 nan nan] + [ nan 9.83447124 2.09950873] + [ nan 9.08600448 2.44682069]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.75 4.9675 5.11666667 + 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:29,992 - physiofit - INFO - mc : False +2024-05-27 14:31:29,992 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:29,992 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:29,993 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:30,551 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:30,552 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.2068014822669182 + x: [ 1.783e-02 5.335e-01 -7.708e+00 1.357e+01 + 4.073e+00 1.539e-01] + nit: 119 + nfev: 11290 + population: [[ 1.789e-02 5.323e-01 ... 4.056e+00 1.601e-01] + [ 1.768e-02 5.362e-01 ... 4.052e+00 1.575e-01] + ... + [ 1.793e-02 5.326e-01 ... 4.055e+00 1.454e-01] + [ 1.781e-02 5.332e-01 ... 4.060e+00 1.554e-01]] + population_energies: [ 1.207e+00 1.220e+00 ... 1.230e+00 1.222e+00] + jac: [ 4.487e-02 2.866e-03 7.974e-03 -3.236e-03 + 6.118e-04 -3.294e-04] +2024-05-27 14:31:30,552 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.0178308404636435 +2024-05-27 14:31:30,553 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5335164332915815 +2024-05-27 14:31:30,553 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.707693571385821 +2024-05-27 14:31:30,553 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.570814052451821 +2024-05-27 14:31:30,553 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.0733019570232285 +2024-05-27 14:31:30,553 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15392785399169687 +2024-05-27 14:31:30,556 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.047308 NaN NaN +2.261389 0.059586 NaN NaN +2.774167 0.078335 NaN NaN +2.800000 NaN 12.681008 0.624165 +3.208889 0.098783 NaN NaN +3.706389 0.128811 NaN NaN +3.733333 NaN 11.940538 1.015484 +4.225833 0.169946 NaN NaN +4.283333 NaN 11.296725 1.355721 +4.750000 NaN 10.580993 1.733965 +4.967500 0.252440 NaN NaN +5.116667 NaN 9.879328 2.104775 +5.433333 NaN 9.152470 2.488900 + +2024-05-27 14:31:30,560 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.2068014822669182 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 1.1906963475158231e-05 + +2024-05-27 14:31:30,561 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 1.1906963475158231e-05 +2024-05-27 14:31:30,563 - physiofit - INFO - Results for ycjX: + optimal +ycjX X_0 0.017831 +ycjX growth_rate 0.533516 +ycjX Glc_q -7.707694 +ycjX Glc_M0 13.570814 +ycjX Ace_q 4.073302 +ycjX Ace_M0 0.153928 +2024-05-27 14:31:30,568 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:31,613 - physiofit - INFO - Running optimization for ydbC +2024-05-27 14:31:31,616 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:31,616 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:31,621 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +734 1.950000 NaN 13.665901 0.392663 +735 2.501389 0.108864 NaN NaN +736 3.250000 NaN 12.862947 0.961475 +737 3.341944 0.167832 NaN NaN +738 3.997500 0.247968 NaN NaN +739 4.083333 NaN 11.349803 1.410825 +740 4.523333 0.374976 NaN NaN +741 4.766667 NaN 10.132233 1.943943 +Experimental matrix: +[[ nan 13.66590057 0.39266252] + [ 0.108864 nan nan] + [ nan 12.8629474 0.96147515] + [ 0.167832 nan nan] + [ 0.247968 nan nan] + [ nan 11.34980254 1.41082498] + [ 0.374976 nan nan] + [ nan 10.13223298 1.9439429 ]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:31,621 - physiofit - INFO - mc : False +2024-05-27 14:31:31,622 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:31,622 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:31,623 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:32,100 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:32,101 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.7937687251362733 + x: [ 2.014e-02 6.412e-01 -6.508e+00 1.417e+01 + 2.719e+00 2.701e-01] + nit: 97 + nfev: 9233 + population: [[ 2.021e-02 6.404e-01 ... 2.716e+00 2.697e-01] + [ 1.978e-02 6.447e-01 ... 2.737e+00 2.692e-01] + ... + [ 2.011e-02 6.416e-01 ... 2.712e+00 2.809e-01] + [ 2.047e-02 6.377e-01 ... 2.708e+00 2.660e-01]] + population_energies: [ 1.794e+00 1.825e+00 ... 1.802e+00 1.803e+00] + jac: [ 1.522e-02 -6.494e-03 -1.321e-04 -4.997e-03 + 1.067e-02 -1.020e-02] +2024-05-27 14:31:32,101 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02013839129811845 +2024-05-27 14:31:32,101 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6411558913144022 +2024-05-27 14:31:32,102 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.507989514857879 +2024-05-27 14:31:32,102 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.17350318542841 +2024-05-27 14:31:32,102 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.7192257863224776 +2024-05-27 14:31:32,102 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.2701046730336295 +2024-05-27 14:31:32,106 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.664264 0.482879 +2.501389 0.100124 NaN NaN +3.250000 NaN 12.735542 0.870926 +3.341944 0.171629 NaN NaN +3.997500 0.261295 NaN NaN +4.083333 NaN 11.575620 1.355575 +4.523333 0.366057 NaN NaN +4.766667 NaN 10.034929 1.999320 + +2024-05-27 14:31:32,110 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.7937687251362733 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.06234488882410411 + +2024-05-27 14:31:32,110 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.06234488882410411 +2024-05-27 14:31:32,112 - physiofit - INFO - Results for ydbC: + optimal +ydbC X_0 0.020138 +ydbC growth_rate 0.641156 +ydbC Glc_q -6.507990 +ydbC Glc_M0 14.173503 +ydbC Ace_q 2.719226 +ydbC Ace_M0 0.270105 +2024-05-27 14:31:32,118 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:33,075 - physiofit - INFO - Running optimization for ydbL +2024-05-27 14:31:33,078 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:33,078 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:33,082 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +742 0.000000 0.036288 NaN NaN +743 0.283333 NaN 14.542461 0.042451 +744 1.195000 0.065016 NaN NaN +745 1.613611 0.081648 NaN NaN +746 1.916667 NaN 13.488601 0.398847 +747 2.361389 0.127008 NaN NaN +748 2.700000 NaN 13.493234 0.667101 +749 3.286389 0.199584 NaN NaN +750 3.616667 NaN 12.597758 1.126142 +751 3.819444 0.309960 NaN NaN +752 4.050000 NaN 11.771462 1.404212 +753 4.410833 0.397656 NaN NaN +754 4.750000 NaN 10.598185 2.102185 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 14.54246138 0.04245148] + [ 0.065016 nan nan] + [ 0.081648 nan nan] + [ nan 13.48860142 0.39884663] + [ 0.127008 nan nan] + [ nan 13.49323392 0.66710124] + [ 0.199584 nan nan] + [ nan 12.59775826 1.12614209] + [ 0.30996 nan nan] + [ nan 11.7714619 1.40421196] + [ 0.397656 nan nan] + [ nan 10.59818508 2.10218548]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:33,082 - physiofit - INFO - mc : False +2024-05-27 14:31:33,082 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:33,082 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:33,082 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:33,541 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:33,543 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.90305526251652 + x: [ 3.410e-02 5.600e-01 -4.742e+00 1.439e+01 + 2.527e+00 8.045e-02] + nit: 101 + nfev: 9558 + population: [[ 3.420e-02 5.593e-01 ... 2.523e+00 7.973e-02] + [ 3.379e-02 5.621e-01 ... 2.506e+00 9.422e-02] + ... + [ 3.414e-02 5.602e-01 ... 2.535e+00 8.111e-02] + [ 3.453e-02 5.567e-01 ... 2.527e+00 7.675e-02]] + population_energies: [ 2.903e+00 2.916e+00 ... 2.913e+00 2.926e+00] + jac: [ 1.419e-01 1.606e-02 -1.196e-02 8.931e-03 + 1.013e-02 2.556e-03] +2024-05-27 14:31:33,543 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.034102004442595334 +2024-05-27 14:31:33,544 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.560025372801832 +2024-05-27 14:31:33,544 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.741509998509303 +2024-05-27 14:31:33,544 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.39316280148254 +2024-05-27 14:31:33,544 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5269955971702482 +2024-05-27 14:31:33,545 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.08045217847217576 +2024-05-27 14:31:33,548 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.034102 NaN NaN +0.283333 NaN 14.343514 0.106912 +1.195000 0.066592 NaN NaN +1.613611 0.084185 NaN NaN +1.916667 NaN 13.837288 0.376707 +2.361389 0.127970 NaN NaN +2.700000 NaN 13.372191 0.624581 +3.286389 0.214824 NaN NaN +3.616667 NaN 12.493525 1.092867 +3.819444 0.289554 NaN NaN +4.050000 NaN 11.892474 1.413198 +4.410833 0.403241 NaN NaN +4.750000 NaN 10.553655 2.126724 + +2024-05-27 14:31:33,552 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.90305526251652 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.001738221209643274 + +2024-05-27 14:31:33,553 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.001738221209643274 +2024-05-27 14:31:33,555 - physiofit - INFO - Results for ydbL: + optimal +ydbL X_0 0.034102 +ydbL growth_rate 0.560025 +ydbL Glc_q -4.741510 +ydbL Glc_M0 14.393163 +ydbL Ace_q 2.526996 +ydbL Ace_M0 0.080452 +2024-05-27 14:31:33,562 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:34,730 - physiofit - INFO - Running optimization for ydcH +2024-05-27 14:31:34,732 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:34,732 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:34,737 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +755 0.000000 0.034776 NaN NaN +756 0.283333 NaN 13.990427 0.039937 +757 1.195000 0.061992 NaN NaN +758 1.613611 0.080136 NaN NaN +759 1.916667 NaN 13.753480 0.415458 +760 2.361389 0.128520 NaN NaN +761 2.700000 NaN 13.418613 0.722866 +762 3.286389 0.216216 NaN NaN +763 3.616667 NaN 12.428274 1.172139 +764 3.819444 0.319032 NaN NaN +765 4.050000 NaN 11.216332 1.464085 +766 4.410833 0.449064 NaN NaN +767 4.750000 NaN 9.857109 2.039357 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 13.99042747 0.03993671] + [ 0.061992 nan nan] + [ 0.080136 nan nan] + [ nan 13.75348029 0.4154585 ] + [ 0.12852 nan nan] + [ nan 13.41861283 0.72286641] + [ 0.216216 nan nan] + [ nan 12.42827394 1.17213879] + [ 0.319032 nan nan] + [ nan 11.21633221 1.46408492] + [ 0.449064 nan nan] + [ nan 9.85710882 2.03935744]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:34,737 - physiofit - INFO - mc : False +2024-05-27 14:31:34,737 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:34,737 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:34,738 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:35,195 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:35,196 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.6287146807331774 + x: [ 3.029e-02 6.112e-01 -5.171e+00 1.427e+01 + 2.321e+00 1.541e-01] + nit: 98 + nfev: 9204 + population: [[ 3.029e-02 6.112e-01 ... 2.321e+00 1.505e-01] + [ 3.089e-02 6.074e-01 ... 2.268e+00 1.658e-01] + ... + [ 3.068e-02 6.078e-01 ... 2.302e+00 1.626e-01] + [ 3.020e-02 6.113e-01 ... 2.307e+00 1.617e-01]] + population_energies: [ 2.629e+00 2.731e+00 ... 2.656e+00 2.656e+00] + jac: [ 1.059e-02 1.176e-03 2.230e-02 -1.058e-02 + 3.771e-03 -1.207e-03] +2024-05-27 14:31:35,196 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.030289566845094682 +2024-05-27 14:31:35,196 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6111774668513943 +2024-05-27 14:31:35,196 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.170625098923169 +2024-05-27 14:31:35,196 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.274288411095982 +2024-05-27 14:31:35,196 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3205480533886464 +2024-05-27 14:31:35,196 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15414698353901762 +2024-05-27 14:31:35,200 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.030290 NaN NaN +0.283333 NaN 14.225840 0.175890 +1.195000 0.062876 NaN NaN +1.613611 0.081207 NaN NaN +1.916667 NaN 13.703720 0.410215 +2.361389 0.128256 NaN NaN +2.700000 NaN 13.195999 0.638078 +3.286389 0.225737 NaN NaN +3.616667 NaN 12.193619 1.087940 +3.819444 0.312674 NaN NaN +4.050000 NaN 11.485001 1.405964 +4.410833 0.448813 NaN NaN +4.750000 NaN 9.858937 2.135732 + +2024-05-27 14:31:35,205 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.6287146807331774 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.001023902689512556 + +2024-05-27 14:31:35,205 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.001023902689512556 +2024-05-27 14:31:35,207 - physiofit - INFO - Results for ydcH: + optimal +ydcH X_0 0.030290 +ydcH growth_rate 0.611177 +ydcH Glc_q -5.170625 +ydcH Glc_M0 14.274288 +ydcH Ace_q 2.320548 +ydcH Ace_M0 0.154147 +2024-05-27 14:31:35,212 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:36,193 - physiofit - INFO - Running optimization for ydcI +2024-05-27 14:31:36,196 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:36,196 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:36,199 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +768 0.000000 0.031752 NaN NaN +769 0.283333 NaN 14.207543 0.036250 +770 1.195000 0.058968 NaN NaN +771 1.613611 0.074088 NaN NaN +772 1.916667 NaN 14.254115 0.349005 +773 2.361389 0.111888 NaN NaN +774 2.700000 NaN 13.506506 0.622281 +775 3.286389 0.190512 NaN NaN +776 3.616667 NaN 12.802610 1.041374 +777 3.819444 0.264600 NaN NaN +778 4.050000 NaN 12.322164 1.253128 +779 4.410833 0.370440 NaN NaN +780 4.750000 NaN 10.656248 1.691936 +Experimental matrix: +[[ 0.031752 nan nan] + [ nan 14.2075432 0.03625039] + [ 0.058968 nan nan] + [ 0.074088 nan nan] + [ nan 14.25411546 0.34900478] + [ 0.111888 nan nan] + [ nan 13.5065055 0.62228059] + [ 0.190512 nan nan] + [ nan 12.80261002 1.04137355] + [ 0.2646 nan nan] + [ nan 12.32216415 1.25312752] + [ 0.37044 nan nan] + [ nan 10.6562476 1.6919356 ]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:36,200 - physiofit - INFO - mc : False +2024-05-27 14:31:36,200 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:36,200 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:36,200 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:36,685 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:36,686 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.031670292219289 + x: [ 2.930e-02 5.747e-01 -5.064e+00 1.453e+01 + 2.277e+00 1.266e-01] + nit: 101 + nfev: 9572 + population: [[ 2.925e-02 5.753e-01 ... 2.287e+00 1.219e-01] + [ 2.908e-02 5.759e-01 ... 2.294e+00 1.271e-01] + ... + [ 2.928e-02 5.749e-01 ... 2.277e+00 1.194e-01] + [ 2.915e-02 5.762e-01 ... 2.316e+00 1.201e-01]] + population_energies: [ 2.032e+00 2.064e+00 ... 2.062e+00 2.061e+00] + jac: [ 6.292e-03 1.060e-03 4.157e-05 2.753e-05 + 1.639e-05 3.772e-04] +2024-05-27 14:31:36,687 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.029295081101182882 +2024-05-27 14:31:36,687 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5747133580758487 +2024-05-27 14:31:36,687 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.063916168867397 +2024-05-27 14:31:36,688 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.52770271465131 +2024-05-27 14:31:36,688 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.276892720411388 +2024-05-27 14:31:36,688 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1266323750197039 +2024-05-27 14:31:36,692 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.029295 NaN NaN +0.283333 NaN 14.482055 0.147157 +1.195000 0.058218 NaN NaN +1.613611 0.074053 NaN NaN +1.916667 NaN 14.009187 0.359773 +2.361389 0.113811 NaN NaN +2.700000 NaN 13.567579 0.558334 +3.286389 0.193669 NaN NaN +3.616667 NaN 12.722675 0.938228 +3.819444 0.263092 NaN NaN +4.050000 NaN 12.139223 1.200566 +4.410833 0.369586 NaN NaN +4.750000 NaN 10.828469 1.789922 + +2024-05-27 14:31:36,696 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.031670292219289 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0002472188437962271 + +2024-05-27 14:31:36,697 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0002472188437962271 +2024-05-27 14:31:36,700 - physiofit - INFO - Results for ydcI: + optimal +ydcI X_0 0.029295 +ydcI growth_rate 0.574713 +ydcI Glc_q -5.063916 +ydcI Glc_M0 14.527703 +ydcI Ace_q 2.276893 +ydcI Ace_M0 0.126632 +2024-05-27 14:31:36,707 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:37,648 - physiofit - INFO - Running optimization for ydcJ +2024-05-27 14:31:37,650 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:37,651 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:37,654 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +781 1.828889 0.061992 NaN NaN +782 2.261389 0.080136 NaN NaN +783 2.774167 0.108864 NaN NaN +784 2.800000 NaN 12.334048 0.720140 +785 3.208889 0.139104 NaN NaN +786 3.706389 0.185976 NaN NaN +787 3.733333 NaN 11.715592 1.375492 +788 4.225833 0.285768 NaN NaN +789 4.283333 NaN 10.834395 1.884128 +790 4.635556 0.368928 NaN NaN +791 4.750000 NaN 9.932735 2.489223 +792 4.967500 0.503496 NaN NaN +793 5.116667 NaN 8.625342 2.918415 +794 5.433333 NaN 8.147713 3.552857 +Experimental matrix: +[[ 0.061992 nan nan] + [ 0.080136 nan nan] + [ 0.108864 nan nan] + [ nan 12.33404768 0.72013989] + [ 0.139104 nan nan] + [ 0.185976 nan nan] + [ nan 11.71559227 1.37549177] + [ 0.285768 nan nan] + [ nan 10.83439457 1.88412768] + [ 0.368928 nan nan] + [ nan 9.93273494 2.48922348] + [ 0.503496 nan nan] + [ nan 8.6253417 2.91841503] + [ nan 8.14771335 3.55285729]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:37,655 - physiofit - INFO - mc : False +2024-05-27 14:31:37,655 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:37,655 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:37,656 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:38,105 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:38,106 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.402821708384564 + x: [ 1.453e-02 7.069e-01 -5.499e+00 1.306e+01 + 3.417e+00 4.193e-01] + nit: 96 + nfev: 8863 + population: [[ 1.461e-02 7.057e-01 ... 3.418e+00 4.213e-01] + [ 1.428e-02 7.108e-01 ... 3.369e+00 4.597e-01] + ... + [ 1.480e-02 7.030e-01 ... 3.456e+00 3.759e-01] + [ 1.434e-02 7.095e-01 ... 3.424e+00 4.098e-01]] + population_energies: [ 4.403e+00 4.454e+00 ... 4.472e+00 4.441e+00] + jac: [-3.100e-02 2.031e-02 2.574e-02 5.989e-02 + -4.092e-02 2.613e-02] +2024-05-27 14:31:38,106 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.014534128042810963 +2024-05-27 14:31:38,106 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.7068826490773048 +2024-05-27 14:31:38,107 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.4988128338735 +2024-05-27 14:31:38,107 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.062250567277271 +2024-05-27 14:31:38,107 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.4168583758182716 +2024-05-27 14:31:38,107 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.41927569481249527 +2024-05-27 14:31:38,110 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.052948 NaN NaN +2.261389 0.071883 NaN NaN +2.774167 0.103287 NaN NaN +2.800000 NaN 12.357040 0.857480 +3.208889 0.140444 NaN NaN +3.706389 0.199633 NaN NaN +3.733333 NaN 11.592511 1.332544 +4.225833 0.288204 NaN NaN +4.283333 NaN 10.840383 1.799902 +4.635556 0.385019 NaN NaN +4.750000 NaN 9.927895 2.366905 +4.967500 0.486842 NaN NaN +5.116667 NaN 8.967048 2.963957 +5.433333 NaN 7.911285 3.619988 + +2024-05-27 14:31:38,113 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.402821708384564 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.007485992666344273 + +2024-05-27 14:31:38,114 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.007485992666344273 +2024-05-27 14:31:38,116 - physiofit - INFO - Results for ydcJ: + optimal +ydcJ X_0 0.014534 +ydcJ growth_rate 0.706883 +ydcJ Glc_q -5.498813 +ydcJ Glc_M0 13.062251 +ydcJ Ace_q 3.416858 +ydcJ Ace_M0 0.419276 +2024-05-27 14:31:38,122 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:39,101 - physiofit - INFO - Running optimization for ydcL +2024-05-27 14:31:39,104 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:39,104 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:39,109 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +795 0.000000 0.034776 NaN NaN +796 0.066667 NaN 15.477895 0.018158 +797 1.188889 0.061992 NaN NaN +798 1.716667 NaN 15.258090 0.344190 +799 2.276944 0.096768 NaN NaN +800 2.800000 NaN 13.626225 0.734696 +801 3.128333 0.134568 NaN NaN +802 3.633333 NaN 12.996758 1.188668 +803 3.771389 0.190512 NaN NaN +804 4.266667 NaN 11.955261 1.652134 +805 4.415556 0.269136 NaN NaN +806 4.822778 0.346248 NaN NaN +807 4.883333 NaN 11.048864 2.223442 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 15.47789475 0.01815814] + [ 0.061992 nan nan] + [ nan 15.25809036 0.34418979] + [ 0.096768 nan nan] + [ nan 13.62622494 0.7346961 ] + [ 0.134568 nan nan] + [ nan 12.99675774 1.1886683 ] + [ 0.190512 nan nan] + [ nan 11.95526115 1.65213376] + [ 0.269136 nan nan] + [ 0.346248 nan nan] + [ nan 11.04886374 2.22344201]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:39,110 - physiofit - INFO - mc : False +2024-05-27 14:31:39,110 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:39,110 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:39,112 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:39,526 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:39,527 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.5466986020748825 + x: [ 3.100e-02 4.933e-01 -7.314e+00 1.544e+01 + 3.477e+00 5.550e-02] + nit: 91 + nfev: 8441 + population: [[ 3.084e-02 4.947e-01 ... 3.480e+00 4.985e-02] + [ 3.156e-02 4.881e-01 ... 3.524e+00 3.351e-02] + ... + [ 3.033e-02 4.986e-01 ... 3.458e+00 6.972e-02] + [ 3.048e-02 4.949e-01 ... 3.487e+00 6.068e-02]] + population_energies: [ 3.547e+00 3.610e+00 ... 3.584e+00 3.625e+00] + jac: [ 1.113e-03 -6.120e-03 1.541e-05 3.495e-04 + 6.266e-04 2.098e-03] +2024-05-27 14:31:39,527 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.030998578053795384 +2024-05-27 14:31:39,527 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.4932830358104354 +2024-05-27 14:31:39,528 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.314424157888542 +2024-05-27 14:31:39,528 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.437301156514662 +2024-05-27 14:31:39,528 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.47704892074066 +2024-05-27 14:31:39,529 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.05549779155970432 +2024-05-27 14:31:39,531 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.030999 NaN NaN +0.066667 NaN 15.421934 0.062803 +1.188889 0.055723 NaN NaN +1.716667 NaN 14.824968 0.346582 +2.276944 0.095309 NaN NaN +2.800000 NaN 14.067712 0.706558 +3.128333 0.145052 NaN NaN +3.633333 NaN 13.137674 1.148669 +3.771389 0.199199 NaN NaN +4.266667 NaN 12.125796 1.629684 +4.415556 0.273707 NaN NaN +4.822778 0.334600 NaN NaN +4.883333 NaN 10.785045 2.267035 + +2024-05-27 14:31:39,536 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.5466986020748825 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0048725185289519865 + +2024-05-27 14:31:39,536 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0048725185289519865 +2024-05-27 14:31:39,538 - physiofit - INFO - Results for ydcL: + optimal +ydcL X_0 0.030999 +ydcL growth_rate 0.493283 +ydcL Glc_q -7.314424 +ydcL Glc_M0 15.437301 +ydcL Ace_q 3.477049 +ydcL Ace_M0 0.055498 +2024-05-27 14:31:39,544 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:40,523 - physiofit - INFO - Running optimization for ydcP +2024-05-27 14:31:40,527 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:40,527 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:40,533 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +808 0.000000 0.037800 NaN NaN +809 0.066667 NaN 15.502781 0.022261 +810 1.188889 0.072576 NaN NaN +811 1.716667 NaN 13.703507 0.331146 +812 2.276944 0.123984 NaN NaN +813 2.800000 NaN 13.480907 0.749274 +814 3.128333 0.179928 NaN NaN +815 3.633333 NaN 12.384738 1.137404 +816 3.771389 0.250992 NaN NaN +817 4.266667 NaN 11.326938 1.590179 +818 4.415556 0.374976 NaN NaN +819 4.822778 0.517104 NaN NaN +820 4.883333 NaN 9.984199 2.046148 +Experimental matrix: +[[ 0.0378 nan nan] + [ nan 15.50278078 0.02226149] + [ 0.072576 nan nan] + [ nan 13.70350661 0.33114564] + [ 0.123984 nan nan] + [ nan 13.4809075 0.74927448] + [ 0.179928 nan nan] + [ nan 12.38473825 1.13740429] + [ 0.250992 nan nan] + [ nan 11.32693839 1.59017919] + [ 0.374976 nan nan] + [ 0.517104 nan nan] + [ nan 9.98419906 2.04614778]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:40,534 - physiofit - INFO - mc : False +2024-05-27 14:31:40,534 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:40,534 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:40,535 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:40,896 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:40,897 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 8.991315286764594 + x: [ 3.126e-02 5.724e-01 -6.025e+00 1.484e+01 + 2.409e+00 1.342e-01] + nit: 78 + nfev: 7383 + population: [[ 3.115e-02 5.729e-01 ... 2.410e+00 1.307e-01] + [ 3.141e-02 5.713e-01 ... 2.434e+00 1.407e-01] + ... + [ 3.093e-02 5.740e-01 ... 2.412e+00 1.410e-01] + [ 3.097e-02 5.748e-01 ... 2.424e+00 1.358e-01]] + population_energies: [ 8.991e+00 9.053e+00 ... 9.018e+00 9.007e+00] + jac: [ 3.586e-01 2.148e-02 -4.030e-02 -9.790e-03 + 1.302e-02 4.192e-03] +2024-05-27 14:31:40,898 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03125925020978347 +2024-05-27 14:31:40,898 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5724066772161047 +2024-05-27 14:31:40,898 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.025018939908933 +2024-05-27 14:31:40,898 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.844081975832147 +2024-05-27 14:31:40,898 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4093464370548405 +2024-05-27 14:31:40,898 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1341509270301196 +2024-05-27 14:31:40,901 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.031259 NaN NaN +0.066667 NaN 14.831283 0.139269 +1.188889 0.061735 NaN NaN +1.716667 NaN 14.294120 0.354075 +2.276944 0.115083 NaN NaN +2.800000 NaN 13.538956 0.656058 +3.128333 0.187353 NaN NaN +3.633333 NaN 12.540092 1.055494 +3.771389 0.270720 NaN NaN +4.266667 NaN 11.389590 1.515569 +4.415556 0.391431 NaN NaN +4.822778 0.494183 NaN NaN +4.883333 NaN 9.787994 2.156031 + +2024-05-27 14:31:40,905 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 8.991315286764594 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.22640085995433595 + +2024-05-27 14:31:40,905 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.22640085995433595 +2024-05-27 14:31:40,907 - physiofit - INFO - Results for ydcP: + optimal +ydcP X_0 0.031259 +ydcP growth_rate 0.572407 +ydcP Glc_q -6.025019 +ydcP Glc_M0 14.844082 +ydcP Ace_q 2.409346 +ydcP Ace_M0 0.134151 +2024-05-27 14:31:40,913 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:41,885 - physiofit - INFO - Running optimization for ydcS +2024-05-27 14:31:41,888 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:41,888 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:41,891 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +821 1.950000 NaN 13.384290 0.402156 +822 2.501389 0.099792 NaN NaN +823 3.250000 NaN 13.142857 0.848562 +824 3.341944 0.157248 NaN NaN +825 3.997500 0.211680 NaN NaN +826 4.083333 NaN 11.992066 1.468762 +827 4.523333 0.320544 NaN NaN +828 4.766667 NaN 11.027021 2.063266 +Experimental matrix: +[[ nan 13.38428956 0.40215646] + [ 0.099792 nan nan] + [ nan 13.14285665 0.8485618 ] + [ 0.157248 nan nan] + [ 0.21168 nan nan] + [ nan 11.99206625 1.46876204] + [ 0.320544 nan nan] + [ nan 11.02702099 2.06326575]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:41,891 - physiofit - INFO - mc : False +2024-05-27 14:31:41,891 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:41,892 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:41,892 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:42,369 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:42,370 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.6096483906298649 + x: [ 2.069e-02 6.003e-01 -5.072e+00 1.393e+01 + 3.420e+00 1.544e-01] + nit: 100 + nfev: 9531 + population: [[ 2.066e-02 6.005e-01 ... 3.386e+00 1.674e-01] + [ 2.137e-02 5.925e-01 ... 3.390e+00 1.574e-01] + ... + [ 2.006e-02 6.076e-01 ... 3.398e+00 1.600e-01] + [ 2.093e-02 5.975e-01 ... 3.415e+00 1.563e-01]] + population_energies: [ 1.610e+00 1.626e+00 ... 1.634e+00 1.648e+00] + jac: [ 2.759e-01 2.597e-02 8.613e-03 -1.700e-03 + 8.358e-04 2.856e-04] +2024-05-27 14:31:42,371 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.020685376552069777 +2024-05-27 14:31:42,371 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6002641966717046 +2024-05-27 14:31:42,371 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.072268537397441 +2024-05-27 14:31:42,371 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.930927460353237 +2024-05-27 14:31:42,371 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.4197722324919946 +2024-05-27 14:31:42,372 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15442911709893373 +2024-05-27 14:31:42,375 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.542249 0.416480 +2.501389 0.092844 NaN NaN +3.250000 NaN 12.876102 0.865603 +3.341944 0.153773 NaN NaN +3.997500 0.227917 NaN NaN +4.083333 NaN 12.077976 1.403707 +4.523333 0.312505 NaN NaN +4.766667 NaN 11.049727 2.096962 + +2024-05-27 14:31:42,380 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.6096483906298649 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.04811875164758187 + +2024-05-27 14:31:42,380 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.04811875164758187 +2024-05-27 14:31:42,383 - physiofit - INFO - Results for ydcS: + optimal +ydcS X_0 0.020685 +ydcS growth_rate 0.600264 +ydcS Glc_q -5.072269 +ydcS Glc_M0 13.930927 +ydcS Ace_q 3.419772 +ydcS Ace_M0 0.154429 +2024-05-27 14:31:42,389 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:43,349 - physiofit - INFO - Running optimization for ydcS_2 +2024-05-27 14:31:43,352 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:43,352 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:43,355 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +829 1.828889 0.054432 NaN NaN +830 2.261389 0.069552 NaN NaN +831 2.774167 0.084672 NaN NaN +832 2.800000 NaN 12.480761 0.617587 +833 3.208889 0.113400 NaN NaN +834 3.706389 0.157248 NaN NaN +835 3.733333 NaN 11.817746 1.035772 +836 4.225833 0.192024 NaN NaN +837 4.283333 NaN 11.368584 1.392182 +838 4.635556 0.260064 NaN NaN +839 4.750000 NaN 10.713928 1.801012 +840 4.967500 0.337176 NaN NaN +841 5.116667 NaN 10.176200 2.170108 +842 5.433333 NaN 9.420776 2.530418 +Experimental matrix: +[[ 0.054432 nan nan] + [ 0.069552 nan nan] + [ 0.084672 nan nan] + [ nan 12.48076149 0.61758698] + [ 0.1134 nan nan] + [ 0.157248 nan nan] + [ nan 11.81774631 1.03577228] + [ 0.192024 nan nan] + [ nan 11.3685837 1.39218183] + [ 0.260064 nan nan] + [ nan 10.71392809 1.80101188] + [ 0.337176 nan nan] + [ nan 10.17620001 2.17010759] + [ nan 9.4207765 2.53041799]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:43,357 - physiofit - INFO - mc : False +2024-05-27 14:31:43,357 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:43,357 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:43,358 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:43,841 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:43,842 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.5229709242495286 + x: [ 1.623e-02 6.038e-01 -5.246e+00 1.307e+01 + 3.374e+00 2.552e-01] + nit: 104 + nfev: 9681 + population: [[ 1.608e-02 6.057e-01 ... 3.377e+00 2.572e-01] + [ 1.596e-02 6.073e-01 ... 3.374e+00 2.558e-01] + ... + [ 1.619e-02 6.040e-01 ... 3.391e+00 2.464e-01] + [ 1.603e-02 6.062e-01 ... 3.384e+00 2.549e-01]] + population_energies: [ 1.523e+00 1.538e+00 ... 1.531e+00 1.542e+00] + jac: [-5.232e-01 -3.012e-02 4.875e-02 -8.294e-03 + 3.448e-02 -3.731e-02] +2024-05-27 14:31:43,843 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.016228556823625062 +2024-05-27 14:31:43,843 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6037888545816221 +2024-05-27 14:31:43,843 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.245778804106029 +2024-05-27 14:31:43,844 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.07319361198276 +2024-05-27 14:31:43,844 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.373955698330036 +2024-05-27 14:31:43,844 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.25517553945618826 +2024-05-27 14:31:43,847 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.048962 NaN NaN +2.261389 0.063572 NaN NaN +2.774167 0.086642 NaN NaN +2.800000 NaN 12.449602 0.656254 +3.208889 0.112648 NaN NaN +3.706389 0.152117 NaN NaN +3.733333 NaN 11.870906 1.028457 +4.225833 0.208155 NaN NaN +4.283333 NaN 11.341827 1.368748 +4.635556 0.266579 NaN NaN +4.750000 NaN 10.732427 1.760699 +4.967500 0.325738 NaN NaN +5.116667 NaN 10.117424 2.156254 +5.433333 NaN 9.464932 2.575921 + +2024-05-27 14:31:43,851 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.5229709242495286 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 1.518520796922298e-05 + +2024-05-27 14:31:43,851 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 1.518520796922298e-05 +2024-05-27 14:31:43,853 - physiofit - INFO - Results for ydcS_2: + optimal +ydcS_2 X_0 0.016229 +ydcS_2 growth_rate 0.603789 +ydcS_2 Glc_q -5.245779 +ydcS_2 Glc_M0 13.073194 +ydcS_2 Ace_q 3.373956 +ydcS_2 Ace_M0 0.255176 +2024-05-27 14:31:43,858 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:44,832 - physiofit - INFO - Running optimization for ydcY +2024-05-27 14:31:44,835 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:44,835 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:44,842 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +843 0.000000 0.052920 NaN NaN +844 0.066667 NaN 15.453465 0.006173 +845 1.188889 0.075600 NaN NaN +846 1.716667 NaN 15.212696 0.339056 +847 2.276944 0.110376 NaN NaN +848 2.800000 NaN 13.604500 0.718336 +849 3.128333 0.167832 NaN NaN +850 3.633333 NaN 12.948014 1.194867 +851 3.771389 0.219240 NaN NaN +852 4.266667 NaN 11.412168 1.652799 +853 4.415556 0.346248 NaN NaN +854 4.822778 0.430920 NaN NaN +855 4.883333 NaN 10.133040 2.263159 +Experimental matrix: +[[5.29200000e-02 nan nan] + [ nan 1.54534654e+01 6.17280415e-03] + [7.56000000e-02 nan nan] + [ nan 1.52126958e+01 3.39055520e-01] + [1.10376000e-01 nan nan] + [ nan 1.36044998e+01 7.18336054e-01] + [1.67832000e-01 nan nan] + [ nan 1.29480135e+01 1.19486736e+00] + [2.19240000e-01 nan nan] + [ nan 1.14121675e+01 1.65279945e+00] + [3.46248000e-01 nan nan] + [4.30920000e-01 nan nan] + [ nan 1.01330399e+01 2.26315931e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:44,843 - physiofit - INFO - mc : False +2024-05-27 14:31:44,843 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:44,843 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:44,844 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:45,316 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:45,317 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.046220045253309 + x: [ 3.417e-02 5.209e-01 -7.218e+00 1.552e+01 + 2.927e+00 5.695e-02] + nit: 100 + nfev: 9524 + population: [[ 3.484e-02 5.171e-01 ... 2.906e+00 5.474e-02] + [ 3.477e-02 5.181e-01 ... 2.890e+00 6.296e-02] + ... + [ 3.395e-02 5.232e-01 ... 2.967e+00 3.743e-02] + [ 3.524e-02 5.143e-01 ... 2.919e+00 4.872e-02]] + population_energies: [ 5.046e+00 5.108e+00 ... 5.096e+00 5.101e+00] + jac: [ 2.934e-03 5.596e-04 -4.352e-06 -1.776e-07 + -3.837e-05 3.784e-05] +2024-05-27 14:31:45,318 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.034171342928148635 +2024-05-27 14:31:45,318 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5209017992502631 +2024-05-27 14:31:45,318 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.217568213439672 +2024-05-27 14:31:45,318 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.524256330578119 +2024-05-27 14:31:45,318 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.9271975762442555 +2024-05-27 14:31:45,318 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.05694764516068989 +2024-05-27 14:31:45,321 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.034171 NaN NaN +0.066667 NaN 15.507525 0.063733 +1.188889 0.063477 NaN NaN +1.716667 NaN 14.839889 0.334504 +2.276944 0.111883 NaN NaN +2.800000 NaN 13.961972 0.690557 +3.128333 0.174329 NaN NaN +3.633333 NaN 12.855435 1.139330 +3.771389 0.243693 NaN NaN +4.266667 NaN 11.627315 1.637413 +4.415556 0.340855 NaN NaN +4.822778 0.421399 NaN NaN +4.883333 NaN 9.971746 2.308855 + +2024-05-27 14:31:45,325 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.046220045253309 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.025838478975565817 + +2024-05-27 14:31:45,325 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.025838478975565817 +2024-05-27 14:31:45,327 - physiofit - INFO - Results for ydcY: + optimal +ydcY X_0 0.034171 +ydcY growth_rate 0.520902 +ydcY Glc_q -7.217568 +ydcY Glc_M0 15.524256 +ydcY Ace_q 2.927198 +ydcY Ace_M0 0.056948 +2024-05-27 14:31:45,332 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:46,440 - physiofit - INFO - Running optimization for yddE +2024-05-27 14:31:46,443 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:46,443 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:46,448 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +856 1.828889 0.063504 NaN NaN +857 2.261389 0.092232 NaN NaN +858 2.774167 0.119448 NaN NaN +859 2.800000 NaN 12.001083 0.659970 +860 3.208889 0.146664 NaN NaN +861 3.706389 0.192024 NaN NaN +862 3.733333 NaN 11.245216 1.115286 +863 4.225833 0.279720 NaN NaN +864 4.283333 NaN 10.881907 1.525100 +865 4.635556 0.347760 NaN NaN +866 4.750000 NaN 9.580004 1.842727 +867 4.967500 0.409752 NaN NaN +868 5.116667 NaN 8.842438 2.206641 +869 5.433333 NaN 7.858293 2.528854 +Experimental matrix: +[[ 0.063504 nan nan] + [ 0.092232 nan nan] + [ 0.119448 nan nan] + [ nan 12.00108308 0.65996953] + [ 0.146664 nan nan] + [ 0.192024 nan nan] + [ nan 11.24521604 1.1152861 ] + [ 0.27972 nan nan] + [ nan 10.88190699 1.52510021] + [ 0.34776 nan nan] + [ nan 9.58000442 1.8427266 ] + [ 0.409752 nan nan] + [ nan 8.84243765 2.20664139] + [ nan 7.85829331 2.52885355]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:46,448 - physiofit - INFO - mc : False +2024-05-27 14:31:46,448 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:46,448 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:46,449 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:46,910 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:46,912 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.8552001338148032 + x: [ 2.375e-02 5.759e-01 -5.718e+00 1.308e+01 + 2.522e+00 3.173e-01] + nit: 94 + nfev: 9089 + population: [[ 2.363e-02 5.771e-01 ... 2.536e+00 3.093e-01] + [ 2.337e-02 5.794e-01 ... 2.506e+00 3.219e-01] + ... + [ 2.372e-02 5.764e-01 ... 2.500e+00 3.283e-01] + [ 2.354e-02 5.781e-01 ... 2.497e+00 3.284e-01]] + population_energies: [ 1.855e+00 1.880e+00 ... 1.868e+00 1.873e+00] + jac: [-2.695e-03 -1.312e-04 -1.077e-05 -1.157e-05 + -2.998e-05 -3.235e-05] +2024-05-27 14:31:46,912 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.0237490518491824 +2024-05-27 14:31:46,912 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5758679317910653 +2024-05-27 14:31:46,912 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.717815469751613 +2024-05-27 14:31:46,912 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.081958218242368 +2024-05-27 14:31:46,912 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5215644594843587 +2024-05-27 14:31:46,912 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.31733885328356065 +2024-05-27 14:31:46,916 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.068084 NaN NaN +2.261389 0.087340 NaN NaN +2.774167 0.117342 NaN NaN +2.800000 NaN 12.135204 0.734859 +3.208889 0.150722 NaN NaN +3.706389 0.200724 NaN NaN +3.733333 NaN 11.293597 1.106009 +4.225833 0.270714 NaN NaN +4.283333 NaN 10.539335 1.438639 +4.635556 0.342753 NaN NaN +4.750000 NaN 9.682710 1.816412 +4.967500 0.414954 NaN NaN +5.116667 NaN 8.828111 2.193291 +5.433333 NaN 7.929983 2.589367 + +2024-05-27 14:31:46,920 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.8552001338148032 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 5.2357593091150465e-05 + +2024-05-27 14:31:46,920 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 5.2357593091150465e-05 +2024-05-27 14:31:46,922 - physiofit - INFO - Results for yddE: + optimal +yddE X_0 0.023749 +yddE growth_rate 0.575868 +yddE Glc_q -5.717815 +yddE Glc_M0 13.081958 +yddE Ace_q 2.521564 +yddE Ace_M0 0.317339 +2024-05-27 14:31:46,927 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:47,914 - physiofit - INFO - Running optimization for yddM +2024-05-27 14:31:47,917 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:47,917 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:47,921 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +870 0.000000 0.036288 NaN NaN +871 0.283333 NaN 14.231162 0.043839 +872 1.195000 0.063504 NaN NaN +873 1.613611 0.080136 NaN NaN +874 1.916667 NaN 13.563719 0.365103 +875 2.361389 0.123984 NaN NaN +876 2.700000 NaN 13.421034 0.716624 +877 3.286389 0.207144 NaN NaN +878 3.616667 NaN 12.261480 1.213941 +879 3.819444 0.306936 NaN NaN +880 4.050000 NaN 11.840900 1.537403 +881 4.410833 0.406728 NaN NaN +882 4.750000 NaN 9.907831 2.006439 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 14.23116234 0.04383869] + [ 0.063504 nan nan] + [ 0.080136 nan nan] + [ nan 13.56371889 0.36510338] + [ 0.123984 nan nan] + [ nan 13.42103431 0.71662378] + [ 0.207144 nan nan] + [ nan 12.26148023 1.21394115] + [ 0.306936 nan nan] + [ nan 11.84090048 1.5374026 ] + [ 0.406728 nan nan] + [ nan 9.90783137 2.00643939]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:47,922 - physiofit - INFO - mc : False +2024-05-27 14:31:47,922 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:47,922 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:47,922 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:48,337 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:48,338 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.0406143297269264 + x: [ 3.302e-02 5.714e-01 -5.232e+00 1.435e+01 + 2.474e+00 1.241e-01] + nit: 87 + nfev: 8396 + population: [[ 3.298e-02 5.717e-01 ... 2.464e+00 1.319e-01] + [ 3.324e-02 5.703e-01 ... 2.490e+00 1.148e-01] + ... + [ 3.270e-02 5.740e-01 ... 2.423e+00 1.403e-01] + [ 3.288e-02 5.723e-01 ... 2.509e+00 9.818e-02]] + population_energies: [ 3.041e+00 3.064e+00 ... 3.079e+00 3.114e+00] + jac: [-1.503e-03 3.758e-04 -3.801e-05 -4.072e-05 + 6.773e-04 2.880e-03] +2024-05-27 14:31:48,338 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03301648186973496 +2024-05-27 14:31:48,338 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5714277916392163 +2024-05-27 14:31:48,338 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.232462938869538 +2024-05-27 14:31:48,338 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.349296772796153 +2024-05-27 14:31:48,338 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4737514263624933 +2024-05-27 14:31:48,338 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.12409313333966647 +2024-05-27 14:31:48,341 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.033016 NaN NaN +0.283333 NaN 14.296164 0.149213 +1.195000 0.065357 NaN NaN +1.613611 0.083019 NaN NaN +1.916667 NaN 13.747701 0.408509 +2.361389 0.127278 NaN NaN +2.700000 NaN 13.237364 0.649782 +3.286389 0.215927 NaN NaN +3.616667 NaN 12.263722 1.110090 +3.819444 0.292816 NaN NaN +4.050000 NaN 11.592790 1.427287 +4.410833 0.410543 NaN NaN +4.750000 NaN 10.088383 2.138525 + +2024-05-27 14:31:48,346 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.0406143297269264 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.002216076005596454 + +2024-05-27 14:31:48,347 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.002216076005596454 +2024-05-27 14:31:48,349 - physiofit - INFO - Results for yddM: + optimal +yddM X_0 0.033016 +yddM growth_rate 0.571428 +yddM Glc_q -5.232463 +yddM Glc_M0 14.349297 +yddM Ace_q 2.473751 +yddM Ace_M0 0.124093 +2024-05-27 14:31:48,354 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:49,340 - physiofit - INFO - Running optimization for ydeI +2024-05-27 14:31:49,342 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:49,342 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:49,346 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +883 1.950000 NaN 14.234405 0.387889 +884 2.501389 0.105840 NaN NaN +885 3.250000 NaN 12.538437 0.894036 +886 3.341944 0.157248 NaN NaN +887 3.997500 0.214704 NaN NaN +888 4.083333 NaN 12.130659 1.371928 +889 4.523333 0.297864 NaN NaN +890 4.766667 NaN 11.096264 1.896035 +Experimental matrix: +[[ nan 14.23440501 0.38788851] + [ 0.10584 nan nan] + [ nan 12.53843666 0.89403631] + [ 0.157248 nan nan] + [ 0.214704 nan nan] + [ nan 12.13065949 1.37192765] + [ 0.297864 nan nan] + [ nan 11.0962636 1.89603465]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:49,347 - physiofit - INFO - mc : False +2024-05-27 14:31:49,347 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:49,347 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:49,347 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:49,759 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:49,760 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.1829901103697433 + x: [ 2.920e-02 5.083e-01 -5.933e+00 1.447e+01 + 3.045e+00 1.247e-01] + nit: 83 + nfev: 8148 + population: [[ 2.943e-02 5.065e-01 ... 3.036e+00 1.242e-01] + [ 3.017e-02 5.004e-01 ... 3.044e+00 1.021e-01] + ... + [ 2.970e-02 5.038e-01 ... 3.059e+00 1.095e-01] + [ 2.824e-02 5.170e-01 ... 2.972e+00 1.733e-01]] + population_energies: [ 2.183e+00 2.214e+00 ... 2.198e+00 2.343e+00] + jac: [ 3.548e-02 3.729e-03 -2.209e-04 -7.397e-04 + -1.743e-04 -1.118e-03] +2024-05-27 14:31:49,761 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02919897078119934 +2024-05-27 14:31:49,761 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5083022843962759 +2024-05-27 14:31:49,761 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.932988160167847 +2024-05-27 14:31:49,761 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.473192566952237 +2024-05-27 14:31:49,761 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.0451071266955885 +2024-05-27 14:31:49,762 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1246845554254861 +2024-05-27 14:31:49,765 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.895703 0.421081 +2.501389 0.104125 NaN NaN +3.250000 NaN 13.035868 0.862391 +3.341944 0.159629 NaN NaN +3.997500 0.222755 NaN NaN +4.083333 NaN 12.098028 1.343738 +4.523333 0.291009 NaN NaN +4.766667 NaN 10.970088 1.922654 + +2024-05-27 14:31:49,768 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.1829901103697433 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.09787691279896066 + +2024-05-27 14:31:49,768 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.09787691279896066 +2024-05-27 14:31:49,771 - physiofit - INFO - Results for ydeI: + optimal +ydeI X_0 0.029199 +ydeI growth_rate 0.508302 +ydeI Glc_q -5.932988 +ydeI Glc_M0 14.473193 +ydeI Ace_q 3.045107 +ydeI Ace_M0 0.124685 +2024-05-27 14:31:49,777 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:50,741 - physiofit - INFO - Running optimization for ydeN +2024-05-27 14:31:50,743 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:50,744 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:50,747 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +891 0.000000 0.034776 NaN NaN +892 0.283333 NaN 14.416645 0.049048 +893 1.195000 0.063504 NaN NaN +894 1.613611 0.078624 NaN NaN +895 1.916667 NaN 14.266055 0.443907 +896 2.361389 0.123984 NaN NaN +897 2.700000 NaN 13.386659 0.716981 +898 3.286389 0.216216 NaN NaN +899 3.616667 NaN 11.995486 1.172722 +900 3.819444 0.276696 NaN NaN +901 4.050000 NaN 11.562760 1.552911 +902 4.410833 0.446040 NaN NaN +903 4.750000 NaN 10.236498 2.194531 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.4166449 0.04904762] + [ 0.063504 nan nan] + [ 0.078624 nan nan] + [ nan 14.26605494 0.44390735] + [ 0.123984 nan nan] + [ nan 13.38665856 0.71698142] + [ 0.216216 nan nan] + [ nan 11.99548631 1.17272203] + [ 0.276696 nan nan] + [ nan 11.56276036 1.55291085] + [ 0.44604 nan nan] + [ nan 10.23649772 2.19453087]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:50,748 - physiofit - INFO - mc : False +2024-05-27 14:31:50,748 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:50,748 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:50,748 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:51,141 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:51,143 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.343870515819501 + x: [ 2.910e-02 6.110e-01 -5.466e+00 1.450e+01 + 2.597e+00 1.390e-01] + nit: 85 + nfev: 8076 + population: [[ 2.899e-02 6.119e-01 ... 2.598e+00 1.387e-01] + [ 2.874e-02 6.142e-01 ... 2.618e+00 1.307e-01] + ... + [ 2.894e-02 6.118e-01 ... 2.607e+00 1.439e-01] + [ 2.925e-02 6.098e-01 ... 2.638e+00 1.184e-01]] + population_energies: [ 4.344e+00 4.390e+00 ... 4.394e+00 4.371e+00] + jac: [-9.110e-03 -1.833e-03 1.753e-03 1.266e-03 + -4.281e-02 9.012e-03] +2024-05-27 14:31:51,143 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.029095959573211504 +2024-05-27 14:31:51,144 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6109651324400748 +2024-05-27 14:31:51,144 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.465620253883222 +2024-05-27 14:31:51,144 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.501571241175427 +2024-05-27 14:31:51,144 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5972467744699244 +2024-05-27 14:31:51,144 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.13901970895202753 +2024-05-27 14:31:51,147 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.029096 NaN NaN +0.283333 NaN 14.452378 0.162396 +1.195000 0.060383 NaN NaN +1.613611 0.077981 NaN NaN +1.916667 NaN 13.922358 0.414260 +2.361389 0.123140 NaN NaN +2.700000 NaN 13.407075 0.659121 +3.286389 0.216690 NaN NaN +3.616667 NaN 12.389953 1.142454 +3.819444 0.300109 NaN NaN +4.050000 NaN 11.671011 1.484094 +4.410833 0.430723 NaN NaN +4.750000 NaN 10.021461 2.267955 + +2024-05-27 14:31:51,151 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.343870515819501 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.013046687613104048 + +2024-05-27 14:31:51,152 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.013046687613104048 +2024-05-27 14:31:51,154 - physiofit - INFO - Results for ydeN: + optimal +ydeN X_0 0.029096 +ydeN growth_rate 0.610965 +ydeN Glc_q -5.465620 +ydeN Glc_M0 14.501571 +ydeN Ace_q 2.597247 +ydeN Ace_M0 0.139020 +2024-05-27 14:31:51,159 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:52,174 - physiofit - INFO - Running optimization for ydfH +2024-05-27 14:31:52,176 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:52,176 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:52,180 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +904 1.828889 0.061992 NaN NaN +905 2.261389 0.081648 NaN NaN +906 2.774167 0.110376 NaN NaN +907 2.800000 NaN 12.386925 0.543952 +908 3.208889 0.134568 NaN NaN +909 3.706389 0.184464 NaN NaN +910 3.733333 NaN 12.053501 0.947805 +911 4.225833 0.270648 NaN NaN +912 4.283333 NaN 11.381361 1.254701 +913 4.635556 0.335664 NaN NaN +914 4.750000 NaN 10.652594 1.613413 +915 4.967500 0.412776 NaN NaN +916 5.116667 NaN 9.898042 1.846434 +917 5.433333 NaN 9.199727 2.147132 +Experimental matrix: +[[ 0.061992 nan nan] + [ 0.081648 nan nan] + [ 0.110376 nan nan] + [ nan 12.38692475 0.54395161] + [ 0.134568 nan nan] + [ 0.184464 nan nan] + [ nan 12.05350133 0.94780509] + [ 0.270648 nan nan] + [ nan 11.38136129 1.25470117] + [ 0.335664 nan nan] + [ nan 10.65259423 1.61341325] + [ 0.412776 nan nan] + [ nan 9.89804228 1.84643437] + [ nan 9.19972748 2.14713174]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:52,180 - physiofit - INFO - mc : False +2024-05-27 14:31:52,180 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:52,181 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:52,181 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:52,733 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:52,734 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.1615306395492189 + x: [ 1.982e-02 6.113e-01 -4.625e+00 1.322e+01 + 2.204e+00 2.987e-01] + nit: 114 + nfev: 10945 + population: [[ 1.989e-02 6.105e-01 ... 2.201e+00 2.996e-01] + [ 2.010e-02 6.088e-01 ... 2.147e+00 3.270e-01] + ... + [ 1.973e-02 6.130e-01 ... 2.169e+00 3.165e-01] + [ 1.976e-02 6.124e-01 ... 2.202e+00 2.970e-01]] + population_energies: [ 1.162e+00 1.206e+00 ... 1.181e+00 1.167e+00] + jac: [-3.419e-05 1.700e-03 1.524e-04 3.066e-04 + 2.610e-03 4.433e-03] +2024-05-27 14:31:52,734 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.019820755390192967 +2024-05-27 14:31:52,735 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6112890391090695 +2024-05-27 14:31:52,735 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.625367025063214 +2024-05-27 14:31:52,735 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.223544879713337 +2024-05-27 14:31:52,735 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.204109861573064 +2024-05-27 14:31:52,735 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.29869867088503776 +2024-05-27 14:31:52,740 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.060625 NaN NaN +2.261389 0.078972 NaN NaN +2.774167 0.108045 NaN NaN +2.800000 NaN 12.542977 0.623007 +3.208889 0.140934 NaN NaN +3.706389 0.191025 NaN NaN +3.733333 NaN 11.904110 0.927444 +4.225833 0.262417 NaN NaN +4.283333 NaN 11.316887 1.207272 +4.635556 0.337105 NaN NaN +4.750000 NaN 10.637954 1.530801 +4.967500 0.412942 NaN NaN +5.116667 NaN 9.950656 1.858317 +5.433333 NaN 9.219600 2.206685 + +2024-05-27 14:31:52,744 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.1615306395492189 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 2.665602879537297e-06 + +2024-05-27 14:31:52,745 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 2.665602879537297e-06 +2024-05-27 14:31:52,748 - physiofit - INFO - Results for ydfH: + optimal +ydfH X_0 0.019821 +ydfH growth_rate 0.611289 +ydfH Glc_q -4.625367 +ydfH Glc_M0 13.223545 +ydfH Ace_q 2.204110 +ydfH Ace_M0 0.298699 +2024-05-27 14:31:52,754 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:53,975 - physiofit - INFO - Running optimization for ydfW +2024-05-27 14:31:53,977 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:53,978 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:53,982 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +918 0.000000 0.033264 NaN NaN +919 0.283333 NaN 13.972384 0.044768 +920 1.195000 0.063504 NaN NaN +921 1.613611 0.080136 NaN NaN +922 1.916667 NaN 13.864617 0.430102 +923 2.361389 0.127008 NaN NaN +924 2.700000 NaN 13.418219 0.790786 +925 3.286389 0.211680 NaN NaN +926 3.616667 NaN 12.160260 1.421238 +927 3.819444 0.322056 NaN NaN +928 4.050000 NaN 11.515052 1.791202 +929 4.410833 0.430920 NaN NaN +930 4.750000 NaN 9.558428 2.328818 +Experimental matrix: +[[ 0.033264 nan nan] + [ nan 13.97238394 0.04476776] + [ 0.063504 nan nan] + [ 0.080136 nan nan] + [ nan 13.86461665 0.43010174] + [ 0.127008 nan nan] + [ nan 13.41821908 0.79078575] + [ 0.21168 nan nan] + [ nan 12.16025999 1.42123775] + [ 0.322056 nan nan] + [ nan 11.51505168 1.79120214] + [ 0.43092 nan nan] + [ nan 9.55842795 2.32881778]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:53,982 - physiofit - INFO - mc : False +2024-05-27 14:31:53,983 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:53,983 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:53,983 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:54,438 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:54,439 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.351485028736641 + x: [ 3.191e-02 5.922e-01 -5.509e+00 1.436e+01 + 2.779e+00 1.507e-01] + nit: 92 + nfev: 8853 + population: [[ 3.230e-02 5.890e-01 ... 2.772e+00 1.514e-01] + [ 3.165e-02 5.945e-01 ... 2.785e+00 1.686e-01] + ... + [ 3.230e-02 5.883e-01 ... 2.812e+00 1.537e-01] + [ 3.086e-02 6.010e-01 ... 2.788e+00 1.487e-01]] + population_energies: [ 4.351e+00 4.410e+00 ... 4.434e+00 4.453e+00] + jac: [-5.357e-03 -6.238e-04 -3.908e-06 -2.780e-05 + 2.442e-05 4.379e-05] +2024-05-27 14:31:54,439 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03190828641186182 +2024-05-27 14:31:54,439 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5921512030791395 +2024-05-27 14:31:54,440 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.509440686118986 +2024-05-27 14:31:54,440 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.364951147420221 +2024-05-27 14:31:54,440 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.7793523040602035 +2024-05-27 14:31:54,440 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15070433453533 +2024-05-27 14:31:54,443 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.031908 NaN NaN +0.283333 NaN 14.310720 0.178062 +1.195000 0.064747 NaN NaN +1.613611 0.082961 NaN NaN +1.916667 NaN 13.738230 0.466867 +2.361389 0.129175 NaN NaN +2.700000 NaN 13.193133 0.741852 +3.286389 0.223387 NaN NaN +3.616667 NaN 12.134457 1.275924 +3.819444 0.306297 NaN NaN +4.050000 NaN 11.395133 1.648891 +4.410833 0.434739 NaN NaN +4.750000 NaN 9.717284 2.495317 + +2024-05-27 14:31:54,446 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.351485028736641 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.013154348312035583 + +2024-05-27 14:31:54,447 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.013154348312035583 +2024-05-27 14:31:54,449 - physiofit - INFO - Results for ydfW: + optimal +ydfW X_0 0.031908 +ydfW growth_rate 0.592151 +ydfW Glc_q -5.509441 +ydfW Glc_M0 14.364951 +ydfW Ace_q 2.779352 +ydfW Ace_M0 0.150704 +2024-05-27 14:31:54,454 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:55,502 - physiofit - INFO - Running optimization for ydfZ +2024-05-27 14:31:55,505 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:55,505 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:55,509 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +931 0.000000 0.030240 NaN NaN +932 0.066667 NaN 15.102633 0.013934 +933 1.188889 0.058968 NaN NaN +934 1.716667 NaN 14.656345 0.348436 +935 2.276944 0.105840 NaN NaN +936 2.800000 NaN 13.561505 0.717521 +937 3.128333 0.148176 NaN NaN +938 3.633333 NaN 12.707683 1.223618 +939 3.771389 0.225288 NaN NaN +940 4.266667 NaN 12.184378 1.782995 +941 4.415556 0.326592 NaN NaN +942 4.822778 0.439992 NaN NaN +943 4.883333 NaN 9.876726 2.292870 +Experimental matrix: +[[3.02400000e-02 nan nan] + [ nan 1.51026327e+01 1.39344647e-02] + [5.89680000e-02 nan nan] + [ nan 1.46563449e+01 3.48435934e-01] + [1.05840000e-01 nan nan] + [ nan 1.35615053e+01 7.17520501e-01] + [1.48176000e-01 nan nan] + [ nan 1.27076833e+01 1.22361777e+00] + [2.25288000e-01 nan nan] + [ nan 1.21843780e+01 1.78299539e+00] + [3.26592000e-01 nan nan] + [4.39992000e-01 nan nan] + [ nan 9.87672630e+00 2.29287044e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:55,509 - physiofit - INFO - mc : False +2024-05-27 14:31:55,509 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:55,509 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:55,510 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:55,934 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:55,935 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.339272020216088 + x: [ 2.572e-02 5.827e-01 -6.978e+00 1.509e+01 + 3.220e+00 1.060e-01] + nit: 91 + nfev: 8588 + population: [[ 2.574e-02 5.827e-01 ... 3.205e+00 1.072e-01] + [ 2.591e-02 5.811e-01 ... 3.240e+00 1.064e-01] + ... + [ 2.528e-02 5.873e-01 ... 3.176e+00 1.178e-01] + [ 2.598e-02 5.803e-01 ... 3.205e+00 1.018e-01]] + population_energies: [ 4.339e+00 4.374e+00 ... 4.419e+00 4.350e+00] + jac: [ 3.521e-03 -2.497e-03 1.263e-02 -6.188e-04 + 1.077e-03 -3.914e-04] +2024-05-27 14:31:55,935 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025721336142552776 +2024-05-27 14:31:55,935 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5827320488854137 +2024-05-27 14:31:55,935 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.97772938624351 +2024-05-27 14:31:55,935 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.08917439960993 +2024-05-27 14:31:55,935 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.220134072525797 +2024-05-27 14:31:55,936 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.10596130667507876 +2024-05-27 14:31:55,939 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.025721 NaN NaN +0.066667 NaN 15.076974 0.111592 +1.188889 0.051425 NaN NaN +1.716667 NaN 14.559660 0.350326 +2.276944 0.096947 NaN NaN +2.800000 NaN 13.822620 0.690460 +3.128333 0.159222 NaN NaN +3.633333 NaN 12.838268 1.144726 +3.771389 0.231604 NaN NaN +4.266667 NaN 11.696028 1.671856 +4.415556 0.337109 NaN NaN +4.822778 0.427395 NaN NaN +4.883333 NaN 10.095655 2.410407 + +2024-05-27 14:31:55,942 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.339272020216088 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.012981973444144628 + +2024-05-27 14:31:55,943 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.012981973444144628 +2024-05-27 14:31:55,945 - physiofit - INFO - Results for ydfZ: + optimal +ydfZ X_0 0.025721 +ydfZ growth_rate 0.582732 +ydfZ Glc_q -6.977729 +ydfZ Glc_M0 15.089174 +ydfZ Ace_q 3.220134 +ydfZ Ace_M0 0.105961 +2024-05-27 14:31:55,950 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:56,935 - physiofit - INFO - Running optimization for ydgJ +2024-05-27 14:31:56,938 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:56,938 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:56,942 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +944 0.000000 0.034776 NaN NaN +945 0.283333 NaN 13.908720 0.041206 +946 1.195000 0.061992 NaN NaN +947 1.613611 0.077112 NaN NaN +948 1.916667 NaN 13.553123 0.383574 +949 2.361389 0.113400 NaN NaN +950 2.700000 NaN 13.651676 0.674101 +951 3.286389 0.192024 NaN NaN +952 3.616667 NaN 12.428535 1.139200 +953 3.819444 0.282744 NaN NaN +954 4.050000 NaN 11.983584 1.314883 +955 4.410833 0.394632 NaN NaN +956 4.750000 NaN 10.154021 1.942966 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 13.90871954 0.04120571] + [ 0.061992 nan nan] + [ 0.077112 nan nan] + [ nan 13.55312272 0.38357431] + [ 0.1134 nan nan] + [ nan 13.65167648 0.6741012 ] + [ 0.192024 nan nan] + [ nan 12.42853517 1.13920039] + [ 0.282744 nan nan] + [ nan 11.98358423 1.31488259] + [ 0.394632 nan nan] + [ nan 10.15402059 1.94296564]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:56,942 - physiofit - INFO - mc : False +2024-05-27 14:31:56,942 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:56,942 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:56,943 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:57,394 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:57,395 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.9938636968473546 + x: [ 2.847e-02 5.959e-01 -5.019e+00 1.421e+01 + 2.459e+00 1.314e-01] + nit: 92 + nfev: 8643 + population: [[ 2.873e-02 5.937e-01 ... 2.471e+00 1.251e-01] + [ 2.830e-02 5.965e-01 ... 2.494e+00 1.209e-01] + ... + [ 2.911e-02 5.904e-01 ... 2.426e+00 1.348e-01] + [ 2.875e-02 5.931e-01 ... 2.444e+00 1.364e-01]] + population_energies: [ 2.994e+00 3.015e+00 ... 3.164e+00 3.003e+00] + jac: [ 1.886e-01 4.917e-02 4.496e-02 7.920e-03 + -1.500e-02 -1.700e-03] +2024-05-27 14:31:57,397 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02846617504903128 +2024-05-27 14:31:57,397 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5959254275460476 +2024-05-27 14:31:57,397 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.018736415346305 +2024-05-27 14:31:57,397 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.21464322697975 +2024-05-27 14:31:57,397 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4591738711236664 +2024-05-27 14:31:57,397 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.13138357107695303 +2024-05-27 14:31:57,401 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028466 NaN NaN +0.283333 NaN 14.170547 0.152991 +1.195000 0.058023 NaN NaN +1.613611 0.074463 NaN NaN +1.916667 NaN 13.703139 0.382020 +2.361389 0.116272 NaN NaN +2.700000 NaN 13.256229 0.601005 +3.286389 0.201776 NaN NaN +3.616667 NaN 12.385425 1.027698 +3.819444 0.277223 NaN NaN +4.050000 NaN 11.775824 1.326402 +4.410833 0.394352 NaN NaN +4.750000 NaN 10.389333 2.005780 + +2024-05-27 14:31:57,405 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.9938636968473546 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0020436563855865497 + +2024-05-27 14:31:57,405 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0020436563855865497 +2024-05-27 14:31:57,407 - physiofit - INFO - Results for ydgJ: + optimal +ydgJ X_0 0.028466 +ydgJ growth_rate 0.595925 +ydgJ Glc_q -5.018736 +ydgJ Glc_M0 14.214643 +ydgJ Ace_q 2.459174 +ydgJ Ace_M0 0.131384 +2024-05-27 14:31:57,412 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:58,385 - physiofit - INFO - Running optimization for ydhR +2024-05-27 14:31:58,388 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:58,388 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:58,392 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +957 0.000000 0.030240 NaN NaN +958 0.066667 NaN 15.379307 0.014885 +959 1.188889 0.048384 NaN NaN +960 1.716667 NaN 14.676852 0.300482 +961 2.276944 0.078624 NaN NaN +962 2.800000 NaN 14.046365 0.711010 +963 3.128333 0.125496 NaN NaN +964 3.633333 NaN 12.887440 1.135885 +965 3.771389 0.169344 NaN NaN +966 4.266667 NaN 11.814086 1.574312 +967 4.415556 0.247968 NaN NaN +968 4.822778 0.331128 NaN NaN +969 4.883333 NaN 10.857663 2.099463 +Experimental matrix: +[[3.02400000e-02 nan nan] + [ nan 1.53793073e+01 1.48850213e-02] + [4.83840000e-02 nan nan] + [ nan 1.46768520e+01 3.00482385e-01] + [7.86240000e-02 nan nan] + [ nan 1.40463653e+01 7.11009763e-01] + [1.25496000e-01 nan nan] + [ nan 1.28874403e+01 1.13588469e+00] + [1.69344000e-01 nan nan] + [ nan 1.18140859e+01 1.57431219e+00] + [2.47968000e-01 nan nan] + [3.31128000e-01 nan nan] + [ nan 1.08576627e+01 2.09946285e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:58,392 - physiofit - INFO - mc : False +2024-05-27 14:31:58,392 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:58,392 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:58,393 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:31:58,797 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:31:58,798 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.3115846220212988 + x: [ 2.386e-02 5.370e-01 -8.119e+00 1.525e+01 + 3.691e+00 7.769e-02] + nit: 84 + nfev: 7951 + population: [[ 2.400e-02 5.356e-01 ... 3.692e+00 7.592e-02] + [ 2.359e-02 5.387e-01 ... 3.662e+00 8.320e-02] + ... + [ 2.412e-02 5.343e-01 ... 3.683e+00 7.610e-02] + [ 2.378e-02 5.383e-01 ... 3.686e+00 7.656e-02]] + population_energies: [ 2.312e+00 2.376e+00 ... 2.351e+00 2.326e+00] + jac: [-2.652e-01 -2.163e-02 4.167e-02 -2.176e-02 + -6.961e-03 -1.611e-02] +2024-05-27 14:31:58,799 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02386013135135421 +2024-05-27 14:31:58,799 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5370202098075176 +2024-05-27 14:31:58,799 - physiofit.physiofit.base.fitter - INFO - Glc_q = -8.118805198800478 +2024-05-27 14:31:58,799 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.245070347210703 +2024-05-27 14:31:58,799 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.6909973032820886 +2024-05-27 14:31:58,799 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.07769252079844413 +2024-05-27 14:31:58,802 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.023860 NaN NaN +0.066667 NaN 15.231922 0.083670 +1.188889 0.045181 NaN NaN +1.716667 NaN 14.698926 0.325982 +2.276944 0.081043 NaN NaN +2.800000 NaN 13.983221 0.651358 +3.128333 0.128020 NaN NaN +3.633333 NaN 13.067405 1.067710 +3.771389 0.180823 NaN NaN +4.266667 NaN 12.039088 1.535207 +4.415556 0.255559 NaN NaN +4.822778 0.318028 NaN NaN +4.883333 NaN 10.638849 2.171788 + +2024-05-27 14:31:58,804 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.3115846220212988 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0005078646080262099 + +2024-05-27 14:31:58,805 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0005078646080262099 +2024-05-27 14:31:58,808 - physiofit - INFO - Results for ydhR: + optimal +ydhR X_0 0.023860 +ydhR growth_rate 0.537020 +ydhR Glc_q -8.118805 +ydhR Glc_M0 15.245070 +ydhR Ace_q 3.690997 +ydhR Ace_M0 0.077693 +2024-05-27 14:31:58,813 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:31:59,773 - physiofit - INFO - Running optimization for ydhS +2024-05-27 14:31:59,775 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:31:59,775 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:31:59,779 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +970 0.000000 0.042336 NaN NaN +971 0.066667 NaN 14.860138 0.006147 +972 1.188889 0.084672 NaN NaN +973 1.716667 NaN 14.699567 0.362373 +974 2.276944 0.128520 NaN NaN +975 2.800000 NaN 13.336938 0.866735 +976 3.128333 0.198072 NaN NaN +977 3.633333 NaN 12.351462 1.507195 +978 3.771389 0.267624 NaN NaN +979 4.266667 NaN 11.123400 2.218548 +980 4.415556 0.385560 NaN NaN +981 4.822778 0.583632 NaN NaN +982 4.883333 NaN 9.274395 3.076994 +Experimental matrix: +[[4.23360000e-02 nan nan] + [ nan 1.48601384e+01 6.14724118e-03] + [8.46720000e-02 nan nan] + [ nan 1.46995674e+01 3.62372602e-01] + [1.28520000e-01 nan nan] + [ nan 1.33369378e+01 8.66735049e-01] + [1.98072000e-01 nan nan] + [ nan 1.23514625e+01 1.50719503e+00] + [2.67624000e-01 nan nan] + [ nan 1.11233997e+01 2.21854754e+00] + [3.85560000e-01 nan nan] + [5.83632000e-01 nan nan] + [ nan 9.27439533e+00 3.07699448e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:31:59,779 - physiofit - INFO - mc : False +2024-05-27 14:31:59,779 - physiofit - INFO - iterations : 100 +2024-05-27 14:31:59,780 - physiofit - INFO - debug_mode : False +2024-05-27 14:31:59,780 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:00,218 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:00,219 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 12.550744975947994 + x: [ 2.958e-02 6.046e-01 -6.449e+00 1.496e+01 + 3.479e+00 7.325e-02] + nit: 90 + nfev: 8722 + population: [[ 2.965e-02 6.038e-01 ... 3.460e+00 7.405e-02] + [ 2.947e-02 6.049e-01 ... 3.507e+00 4.504e-02] + ... + [ 2.968e-02 6.043e-01 ... 3.487e+00 5.150e-02] + [ 2.939e-02 6.056e-01 ... 3.504e+00 8.194e-02]] + population_energies: [ 1.255e+01 1.268e+01 ... 1.263e+01 1.262e+01] + jac: [ 1.206e-02 2.431e-03 -4.725e-05 -6.644e-05 + -1.922e-04 -4.801e-04] +2024-05-27 14:32:00,221 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02957697034279259 +2024-05-27 14:32:00,221 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6046481422807204 +2024-05-27 14:32:00,221 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.448767307330838 +2024-05-27 14:32:00,221 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.955105090072621 +2024-05-27 14:32:00,221 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.4789988095405135 +2024-05-27 14:32:00,221 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.07325161989833832 +2024-05-27 14:32:00,225 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.029577 NaN NaN +0.066667 NaN 14.942130 0.080252 +1.188889 0.060695 NaN NaN +1.716667 NaN 14.379884 0.383573 +2.276944 0.117184 NaN NaN +2.800000 NaN 13.555827 0.828138 +3.128333 0.196083 NaN NaN +3.633333 NaN 12.432476 1.434166 +3.771389 0.289270 NaN NaN +4.266667 NaN 11.108242 2.148568 +4.415556 0.427030 NaN NaN +4.822778 0.546252 NaN NaN +4.883333 NaN 9.227334 3.163285 + +2024-05-27 14:32:00,229 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 12.550744975947994 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.5169195152014432 + +2024-05-27 14:32:00,229 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.5169195152014432 +2024-05-27 14:32:00,231 - physiofit - INFO - Results for ydhS: + optimal +ydhS X_0 0.029577 +ydhS growth_rate 0.604648 +ydhS Glc_q -6.448767 +ydhS Glc_M0 14.955105 +ydhS Ace_q 3.478999 +ydhS Ace_M0 0.073252 +2024-05-27 14:32:00,236 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:01,342 - physiofit - INFO - Running optimization for ydhZ +2024-05-27 14:32:01,344 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:01,344 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:01,348 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +983 0.000000 0.034776 NaN NaN +984 0.283333 NaN 14.294054 0.041944 +985 1.195000 0.065016 NaN NaN +986 1.613611 0.080136 NaN NaN +987 1.916667 NaN 14.079384 0.398443 +988 2.361389 0.123984 NaN NaN +989 2.700000 NaN 13.572950 0.704032 +990 3.286389 0.193536 NaN NaN +991 3.616667 NaN 12.364356 1.174866 +992 3.819444 0.291816 NaN NaN +993 4.050000 NaN 11.907925 1.419899 +994 4.410833 0.418824 NaN NaN +995 4.750000 NaN 10.086716 2.024342 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.29405371 0.0419441 ] + [ 0.065016 nan nan] + [ 0.080136 nan nan] + [ nan 14.07938446 0.39844251] + [ 0.123984 nan nan] + [ nan 13.5729497 0.70403159] + [ 0.193536 nan nan] + [ nan 12.36435624 1.17486626] + [ 0.291816 nan nan] + [ nan 11.90792464 1.41989945] + [ 0.418824 nan nan] + [ nan 10.08671612 2.0243425 ]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:01,349 - physiofit - INFO - mc : False +2024-05-27 14:32:01,349 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:01,349 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:01,349 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:01,787 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:01,788 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.4153833351744742 + x: [ 2.943e-02 5.992e-01 -5.479e+00 1.454e+01 + 2.471e+00 1.383e-01] + nit: 88 + nfev: 8598 + population: [[ 2.950e-02 5.988e-01 ... 2.467e+00 1.440e-01] + [ 2.934e-02 5.998e-01 ... 2.504e+00 1.296e-01] + ... + [ 2.969e-02 5.962e-01 ... 2.490e+00 1.268e-01] + [ 2.887e-02 6.044e-01 ... 2.442e+00 1.531e-01]] + population_energies: [ 2.415e+00 2.448e+00 ... 2.430e+00 2.440e+00] + jac: [-1.005e-02 -1.240e-03 4.441e-07 3.593e-05 + 2.887e-06 1.630e-05] +2024-05-27 14:32:01,789 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.029425718949536918 +2024-05-27 14:32:01,789 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5992047343893457 +2024-05-27 14:32:01,789 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.478588457114929 +2024-05-27 14:32:01,789 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.540718895450972 +2024-05-27 14:32:01,789 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4710410428616547 +2024-05-27 14:32:01,789 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1382795045472518 +2024-05-27 14:32:01,793 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.029426 NaN NaN +0.283333 NaN 14.490936 0.160733 +1.195000 0.060215 NaN NaN +1.613611 0.077382 NaN NaN +1.916667 NaN 13.961368 0.399588 +2.361389 0.121125 NaN NaN +2.700000 NaN 13.453182 0.628798 +3.286389 0.210838 NaN NaN +3.616667 NaN 12.460180 1.076678 +3.819444 0.290179 NaN NaN +4.050000 NaN 11.763569 1.390874 +4.410833 0.413584 NaN NaN +4.750000 NaN 10.176154 2.106856 + +2024-05-27 14:32:01,797 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.4153833351744742 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0006465567235570876 + +2024-05-27 14:32:01,797 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0006465567235570876 +2024-05-27 14:32:01,799 - physiofit - INFO - Results for ydhZ: + optimal +ydhZ X_0 0.029426 +ydhZ growth_rate 0.599205 +ydhZ Glc_q -5.478588 +ydhZ Glc_M0 14.540719 +ydhZ Ace_q 2.471041 +ydhZ Ace_M0 0.138280 +2024-05-27 14:32:01,804 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:02,760 - physiofit - INFO - Running optimization for ydiH +2024-05-27 14:32:02,762 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:02,762 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:02,767 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +996 0.000000 0.031752 NaN NaN +997 0.066667 NaN 15.862285 0.016010 +998 1.188889 0.060480 NaN NaN +999 1.716667 NaN 15.222186 0.368064 +1000 2.276944 0.095256 NaN NaN +1001 2.800000 NaN 13.673946 0.820029 +1002 3.128333 0.151200 NaN NaN +1003 3.633333 NaN 12.702572 1.399265 +1004 3.771389 0.213192 NaN NaN +1005 4.266667 NaN 11.613402 1.982735 +1006 4.415556 0.320544 NaN NaN +1007 4.822778 0.412776 NaN NaN +1008 4.883333 NaN 10.236057 2.707230 +Experimental matrix: +[[ 0.031752 nan nan] + [ nan 15.86228504 0.01601024] + [ 0.06048 nan nan] + [ nan 15.22218587 0.36806443] + [ 0.095256 nan nan] + [ nan 13.67394643 0.8200286 ] + [ 0.1512 nan nan] + [ nan 12.70257178 1.39926528] + [ 0.213192 nan nan] + [ nan 11.61340171 1.98273513] + [ 0.320544 nan nan] + [ 0.412776 nan nan] + [ nan 10.23605707 2.70723008]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:02,767 - physiofit - INFO - mc : False +2024-05-27 14:32:02,767 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:02,767 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:02,768 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:03,196 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:03,197 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.5870672926564575 + x: [ 2.847e-02 5.490e-01 -8.028e+00 1.562e+01 + 3.839e+00 6.716e-02] + nit: 88 + nfev: 8402 + population: [[ 2.855e-02 5.483e-01 ... 3.836e+00 6.800e-02] + [ 2.823e-02 5.506e-01 ... 3.816e+00 6.819e-02] + ... + [ 2.883e-02 5.468e-01 ... 3.810e+00 6.704e-02] + [ 2.882e-02 5.466e-01 ... 3.804e+00 6.272e-02]] + population_energies: [ 3.587e+00 3.627e+00 ... 3.610e+00 3.645e+00] + jac: [-9.872e-03 -7.758e-03 -1.746e-02 2.691e-03 + 1.121e-02 -5.046e-04] +2024-05-27 14:32:03,198 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.028466894775204435 +2024-05-27 14:32:03,198 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.549006588956749 +2024-05-27 14:32:03,199 - physiofit.physiofit.base.fitter - INFO - Glc_q = -8.028340619486459 +2024-05-27 14:32:03,199 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.619801096277213 +2024-05-27 14:32:03,199 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.839377185316386 +2024-05-27 14:32:03,199 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.0671632336473951 +2024-05-27 14:32:03,202 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028467 NaN NaN +0.066667 NaN 15.604283 0.074585 +1.188889 0.054677 NaN NaN +1.716667 NaN 14.967782 0.378977 +2.276944 0.099365 NaN NaN +2.800000 NaN 14.099689 0.794123 +3.128333 0.158573 NaN NaN +3.633333 NaN 12.976334 1.331343 +3.771389 0.225712 NaN NaN +4.266667 NaN 11.704049 1.939785 +4.415556 0.321472 NaN NaN +4.822778 0.402011 NaN NaN +4.883333 NaN 9.958596 2.774510 + +2024-05-27 14:32:03,205 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.5870672926564575 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0051564407787545495 + +2024-05-27 14:32:03,205 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0051564407787545495 +2024-05-27 14:32:03,207 - physiofit - INFO - Results for ydiH: + optimal +ydiH X_0 0.028467 +ydiH growth_rate 0.549007 +ydiH Glc_q -8.028341 +ydiH Glc_M0 15.619801 +ydiH Ace_q 3.839377 +ydiH Ace_M0 0.067163 +2024-05-27 14:32:03,213 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:04,192 - physiofit - INFO - Running optimization for ydiJ +2024-05-27 14:32:04,195 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:04,195 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:04,199 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1009 1.950000 NaN 13.620370 0.400549 +1010 2.501389 0.114912 NaN NaN +1011 3.250000 NaN 12.996162 0.951222 +1012 3.341944 0.166320 NaN NaN +1013 3.997500 0.240408 NaN NaN +1014 4.083333 NaN 12.110798 1.480842 +1015 4.523333 0.349272 NaN NaN +1016 4.766667 NaN 10.817174 2.046703 +Experimental matrix: +[[ nan 13.62036994 0.40054869] + [ 0.114912 nan nan] + [ nan 12.99616183 0.95122232] + [ 0.16632 nan nan] + [ 0.240408 nan nan] + [ nan 12.110798 1.48084182] + [ 0.349272 nan nan] + [ nan 10.81717421 2.04670329]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:04,200 - physiofit - INFO - mc : False +2024-05-27 14:32:04,200 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:04,200 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:04,201 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:04,693 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:04,694 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.1248608631742953 + x: [ 2.421e-02 5.854e-01 -5.178e+00 1.415e+01 + 3.003e+00 1.940e-01] + nit: 100 + nfev: 9482 + population: [[ 2.432e-02 5.845e-01 ... 2.999e+00 1.943e-01] + [ 2.437e-02 5.840e-01 ... 2.990e+00 1.969e-01] + ... + [ 2.465e-02 5.811e-01 ... 2.985e+00 1.898e-01] + [ 2.427e-02 5.842e-01 ... 2.987e+00 2.035e-01]] + population_energies: [ 1.125e+00 1.130e+00 ... 1.134e+00 1.135e+00] + jac: [ 3.697e-02 3.269e-03 -3.295e-05 -8.347e-05 + 6.859e-05 1.384e-04] +2024-05-27 14:32:04,694 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02420925198562736 +2024-05-27 14:32:04,694 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5853717464304172 +2024-05-27 14:32:04,695 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.178436742274981 +2024-05-27 14:32:04,695 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.154890288857494 +2024-05-27 14:32:04,695 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.0034338160979175 +2024-05-27 14:32:04,695 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.193965465471882 +2024-05-27 14:32:04,698 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.698423 0.458711 +2.501389 0.104687 NaN NaN +3.250000 NaN 12.933647 0.902272 +3.341944 0.171231 NaN NaN +3.997500 0.251328 NaN NaN +4.083333 NaN 12.031141 1.425715 +4.523333 0.341916 NaN NaN +4.766667 NaN 10.881284 2.092620 + +2024-05-27 14:32:04,701 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.1248608631742953 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.019566642475858643 + +2024-05-27 14:32:04,702 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.019566642475858643 +2024-05-27 14:32:04,703 - physiofit - INFO - Results for ydiJ: + optimal +ydiJ X_0 0.024209 +ydiJ growth_rate 0.585372 +ydiJ Glc_q -5.178437 +ydiJ Glc_M0 14.154890 +ydiJ Ace_q 3.003434 +ydiJ Ace_M0 0.193965 +2024-05-27 14:32:04,709 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:05,688 - physiofit - INFO - Running optimization for ydiZ +2024-05-27 14:32:05,691 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:05,691 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:05,694 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1017 1.950000 NaN 13.608670 0.375124 +1018 2.501389 0.116424 NaN NaN +1019 3.250000 NaN 12.793622 0.872535 +1020 3.341944 0.182952 NaN NaN +1021 3.997500 0.261576 NaN NaN +1022 4.083333 NaN 12.166892 1.412452 +1023 4.523333 0.409752 NaN NaN +1024 4.766667 NaN 10.526321 1.920829 +Experimental matrix: +[[ nan 13.60866995 0.37512444] + [ 0.116424 nan nan] + [ nan 12.79362206 0.87253495] + [ 0.182952 nan nan] + [ 0.261576 nan nan] + [ nan 12.16689238 1.4124519 ] + [ 0.409752 nan nan] + [ nan 10.52632137 1.92082852]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:05,694 - physiofit - INFO - mc : False +2024-05-27 14:32:05,694 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:05,694 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:05,695 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:06,170 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:06,171 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.4947472294950517 + x: [ 1.993e-02 6.625e-01 -5.024e+00 1.404e+01 + 2.570e+00 2.420e-01] + nit: 105 + nfev: 9694 + population: [[ 2.029e-02 6.585e-01 ... 2.570e+00 2.389e-01] + [ 1.941e-02 6.686e-01 ... 2.537e+00 2.462e-01] + ... + [ 1.978e-02 6.656e-01 ... 2.520e+00 2.651e-01] + [ 1.962e-02 6.666e-01 ... 2.572e+00 2.572e-01]] + population_energies: [ 2.495e+00 2.548e+00 ... 2.539e+00 2.527e+00] + jac: [ 9.790e-02 4.610e-03 -7.501e-03 2.101e-03 + -1.536e-03 1.499e-03] +2024-05-27 14:32:06,171 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.019932225253371832 +2024-05-27 14:32:06,171 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6624601111009357 +2024-05-27 14:32:06,171 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.023935007134119 +2024-05-27 14:32:06,172 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.039569297087006 +2024-05-27 14:32:06,172 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5702118199000195 +2024-05-27 14:32:06,172 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.24195411801703268 +2024-05-27 14:32:06,175 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.640607 0.446061 +2.501389 0.104523 NaN NaN +3.250000 NaN 12.889141 0.830506 +3.341944 0.182407 NaN NaN +3.997500 0.281610 NaN NaN +4.083333 NaN 11.930117 1.321136 +4.523333 0.398962 NaN NaN +4.766667 NaN 10.635864 1.983267 + +2024-05-27 14:32:06,178 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.4947472294950517 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.1309449296011432 + +2024-05-27 14:32:06,178 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.1309449296011432 +2024-05-27 14:32:06,182 - physiofit - INFO - Results for ydiZ: + optimal +ydiZ X_0 0.019932 +ydiZ growth_rate 0.662460 +ydiZ Glc_q -5.023935 +ydiZ Glc_M0 14.039569 +ydiZ Ace_q 2.570212 +ydiZ Ace_M0 0.241954 +2024-05-27 14:32:06,187 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:07,159 - physiofit - INFO - Running optimization for ydjA +2024-05-27 14:32:07,161 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:07,162 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:07,166 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1025 1.950000 NaN 13.818524 0.444434 +1026 2.501389 0.108864 NaN NaN +1027 3.250000 NaN 12.869754 1.230542 +1028 3.341944 0.163296 NaN NaN +1029 3.997500 0.229824 NaN NaN +1030 4.083333 NaN 11.795047 1.835333 +1031 4.523333 0.314496 NaN NaN +1032 4.766667 NaN 10.701184 2.747713 +Experimental matrix: +[[ nan 13.81852384 0.44443382] + [ 0.108864 nan nan] + [ nan 12.86975381 1.23054161] + [ 0.163296 nan nan] + [ 0.229824 nan nan] + [ nan 11.79504728 1.83533349] + [ 0.314496 nan nan] + [ nan 10.70118423 2.74771312]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:07,166 - physiofit - INFO - mc : False +2024-05-27 14:32:07,166 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:07,166 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:07,166 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:07,690 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:07,692 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.46985102142979396 + x: [ 2.816e-02 5.305e-01 -6.065e+00 1.436e+01 + 4.377e+00 7.271e-02] + nit: 106 + nfev: 10001 + population: [[ 2.820e-02 5.303e-01 ... 4.376e+00 7.178e-02] + [ 2.867e-02 5.269e-01 ... 4.347e+00 7.117e-02] + ... + [ 2.770e-02 5.349e-01 ... 4.402e+00 7.492e-02] + [ 2.828e-02 5.298e-01 ... 4.366e+00 6.923e-02]] + population_energies: [ 4.699e-01 4.780e-01 ... 4.814e-01 4.729e-01] + jac: [-2.036e-04 -2.647e-05 -1.271e-06 -1.810e-06 + 4.441e-08 1.804e-06] +2024-05-27 14:32:07,693 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.028160211441072665 +2024-05-27 14:32:07,693 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5305177881226733 +2024-05-27 14:32:07,693 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.064643936606016 +2024-05-27 14:32:07,693 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.363296957521671 +2024-05-27 14:32:07,694 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.3766026434382495 +2024-05-27 14:32:07,694 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.07271464220385548 +2024-05-27 14:32:07,697 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.779431 0.494066 +2.501389 0.106159 NaN NaN +3.250000 NaN 12.879933 1.143197 +3.341944 0.165815 NaN NaN +3.997500 0.234781 NaN NaN +4.083333 NaN 11.876255 1.867510 +4.523333 0.310325 NaN NaN +4.766667 NaN 10.648890 2.753248 + +2024-05-27 14:32:07,701 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.46985102142979396 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.0018137375038733705 + +2024-05-27 14:32:07,701 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0018137375038733705 +2024-05-27 14:32:07,704 - physiofit - INFO - Results for ydjA: + optimal +ydjA X_0 0.028160 +ydjA growth_rate 0.530518 +ydjA Glc_q -6.064644 +ydjA Glc_M0 14.363297 +ydjA Ace_q 4.376603 +ydjA Ace_M0 0.072715 +2024-05-27 14:32:07,709 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:08,683 - physiofit - INFO - Running optimization for ydjF +2024-05-27 14:32:08,686 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:08,686 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:08,690 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1033 1.950000 NaN 13.673694 0.387139 +1034 2.501389 0.110376 NaN NaN +1035 3.250000 NaN 12.981520 0.943087 +1036 3.341944 0.167832 NaN NaN +1037 3.997500 0.219240 NaN NaN +1038 4.083333 NaN 11.864424 1.482314 +1039 4.523333 0.346248 NaN NaN +1040 4.766667 NaN 10.219013 1.929293 +Experimental matrix: +[[ nan 13.67369364 0.38713881] + [ 0.110376 nan nan] + [ nan 12.98151976 0.94308664] + [ 0.167832 nan nan] + [ 0.21924 nan nan] + [ nan 11.86442396 1.48231388] + [ 0.346248 nan nan] + [ nan 10.21901265 1.92929319]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:08,691 - physiofit - INFO - mc : False +2024-05-27 14:32:08,691 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:08,691 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:08,691 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:09,191 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:09,192 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.1532029710020524 + x: [ 2.235e-02 5.974e-01 -6.634e+00 1.435e+01 + 2.920e+00 2.327e-01] + nit: 88 + nfev: 8416 + population: [[ 2.220e-02 5.989e-01 ... 2.904e+00 2.341e-01] + [ 2.237e-02 5.976e-01 ... 2.934e+00 2.143e-01] + ... + [ 2.287e-02 5.927e-01 ... 2.902e+00 2.302e-01] + [ 2.159e-02 6.054e-01 ... 2.908e+00 2.437e-01]] + population_energies: [ 3.153e+00 3.201e+00 ... 3.181e+00 3.170e+00] + jac: [-7.709e-03 -3.505e-04 5.183e-03 -1.690e-03 + 4.265e-04 -9.637e-05] +2024-05-27 14:32:09,193 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.022349568906281383 +2024-05-27 14:32:09,193 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5974460903740829 +2024-05-27 14:32:09,194 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.633734814121742 +2024-05-27 14:32:09,194 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.349484146797634 +2024-05-27 14:32:09,194 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.9196472786377674 +2024-05-27 14:32:09,194 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.23265408339638835 +2024-05-27 14:32:09,198 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.802051 0.473591 +2.501389 0.099609 NaN NaN +3.250000 NaN 12.867834 0.884760 +3.341944 0.164587 NaN NaN +3.997500 0.243495 NaN NaN +4.083333 NaN 11.751733 1.375979 +4.523333 0.333371 NaN NaN +4.766667 NaN 10.316853 2.007500 + +2024-05-27 14:32:09,203 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.1532029710020524 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.21061277327579628 + +2024-05-27 14:32:09,203 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.21061277327579628 +2024-05-27 14:32:09,205 - physiofit - INFO - Results for ydjF: + optimal +ydjF X_0 0.022350 +ydjF growth_rate 0.597446 +ydjF Glc_q -6.633735 +ydjF Glc_M0 14.349484 +ydjF Ace_q 2.919647 +ydjF Ace_M0 0.232654 +2024-05-27 14:32:09,211 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:10,180 - physiofit - INFO - Running optimization for yeaC +2024-05-27 14:32:10,182 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:10,182 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:10,186 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1041 0.000000 0.034776 NaN NaN +1042 0.066667 NaN 15.123799 0.019899 +1043 1.188889 0.074088 NaN NaN +1044 1.716667 NaN 14.817109 0.341188 +1045 2.276944 0.111888 NaN NaN +1046 2.800000 NaN 13.656428 0.727324 +1047 3.128333 0.173880 NaN NaN +1048 3.633333 NaN 12.893331 1.174184 +1049 3.771389 0.252504 NaN NaN +1050 4.266667 NaN 11.592983 1.731583 +1051 4.415556 0.359856 NaN NaN +1052 4.822778 0.421848 NaN NaN +1053 4.883333 NaN 10.111573 2.211406 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 15.12379921 0.01989918] + [ 0.074088 nan nan] + [ nan 14.81710867 0.3411879 ] + [ 0.111888 nan nan] + [ nan 13.65642802 0.72732377] + [ 0.17388 nan nan] + [ nan 12.89333118 1.17418354] + [ 0.252504 nan nan] + [ nan 11.59298344 1.73158278] + [ 0.359856 nan nan] + [ 0.421848 nan nan] + [ nan 10.11157343 2.21140577]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:10,186 - physiofit - INFO - mc : False +2024-05-27 14:32:10,186 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:10,186 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:10,187 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:10,673 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:10,674 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.6920674329067702 + x: [ 3.702e-02 5.076e-01 -6.452e+00 1.527e+01 + 2.799e+00 6.333e-02] + nit: 104 + nfev: 9625 + population: [[ 3.676e-02 5.093e-01 ... 2.795e+00 6.681e-02] + [ 3.674e-02 5.093e-01 ... 2.812e+00 6.480e-02] + ... + [ 3.687e-02 5.087e-01 ... 2.775e+00 7.499e-02] + [ 3.689e-02 5.083e-01 ... 2.792e+00 7.678e-02]] + population_energies: [ 1.692e+00 1.714e+00 ... 1.704e+00 1.710e+00] + jac: [-1.084e-05 -2.016e-05 -1.110e-06 -2.931e-06 + 6.661e-08 -8.216e-07] +2024-05-27 14:32:10,675 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.037024453241958785 +2024-05-27 14:32:10,675 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5076095367640956 +2024-05-27 14:32:10,675 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.452118175463109 +2024-05-27 14:32:10,675 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.271056940078704 +2024-05-27 14:32:10,675 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.798544683012991 +2024-05-27 14:32:10,675 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.06332727058201311 +2024-05-27 14:32:10,679 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.037024 NaN NaN +0.066667 NaN 15.254859 0.070353 +1.188889 0.067699 NaN NaN +1.716667 NaN 14.616793 0.347108 +2.276944 0.117610 NaN NaN +2.800000 NaN 13.792151 0.704789 +3.128333 0.181191 NaN NaN +3.633333 NaN 12.765640 1.150028 +3.771389 0.251130 NaN NaN +4.266667 NaN 11.637203 1.639477 +4.415556 0.348263 NaN NaN +4.822778 0.428233 NaN NaN +4.883333 NaN 10.128578 2.293828 + +2024-05-27 14:32:10,683 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.6920674329067702 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 8.702775609683112e-05 + +2024-05-27 14:32:10,683 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 8.702775609683112e-05 +2024-05-27 14:32:10,685 - physiofit - INFO - Results for yeaC: + optimal +yeaC X_0 0.037024 +yeaC growth_rate 0.507610 +yeaC Glc_q -6.452118 +yeaC Glc_M0 15.271057 +yeaC Ace_q 2.798545 +yeaC Ace_M0 0.063327 +2024-05-27 14:32:10,692 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:11,681 - physiofit - INFO - Running optimization for yeaD +2024-05-27 14:32:11,684 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:11,684 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:11,687 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1054 0.000000 0.033264 NaN NaN +1055 0.283333 NaN 14.326051 0.038734 +1056 1.195000 0.060480 NaN NaN +1057 1.613611 0.075600 NaN NaN +1058 1.916667 NaN 14.078243 0.377214 +1059 2.361389 0.116424 NaN NaN +1060 2.700000 NaN 13.462826 0.685933 +1061 3.286389 0.204120 NaN NaN +1062 3.616667 NaN 12.382761 1.197443 +1063 3.819444 0.285768 NaN NaN +1064 4.050000 NaN 11.901279 1.440135 +1065 4.410833 0.430920 NaN NaN +1066 4.750000 NaN 10.288582 2.047387 +Experimental matrix: +[[ 0.033264 nan nan] + [ nan 14.32605078 0.03873373] + [ 0.06048 nan nan] + [ 0.0756 nan nan] + [ nan 14.07824341 0.37721354] + [ 0.116424 nan nan] + [ nan 13.4628255 0.68593343] + [ 0.20412 nan nan] + [ nan 12.38276145 1.19744302] + [ 0.285768 nan nan] + [ nan 11.90127927 1.4401349 ] + [ 0.43092 nan nan] + [ nan 10.28858168 2.04738668]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:11,688 - physiofit - INFO - mc : False +2024-05-27 14:32:11,688 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:11,688 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:11,688 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:12,142 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:12,143 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.8813957713496472 + x: [ 2.734e-02 6.210e-01 -5.234e+00 1.446e+01 + 2.517e+00 1.379e-01] + nit: 92 + nfev: 8951 + population: [[ 2.748e-02 6.198e-01 ... 2.510e+00 1.366e-01] + [ 2.762e-02 6.181e-01 ... 2.512e+00 1.304e-01] + ... + [ 2.751e-02 6.202e-01 ... 2.504e+00 1.299e-01] + [ 2.744e-02 6.209e-01 ... 2.500e+00 1.414e-01]] + population_energies: [ 1.881e+00 1.916e+00 ... 1.902e+00 1.890e+00] + jac: [-1.728e-03 -7.567e-04 4.468e-05 -1.643e-06 + 9.272e-04 1.560e-03] +2024-05-27 14:32:12,143 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.027340042997822032 +2024-05-27 14:32:12,144 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.621041728164042 +2024-05-27 14:32:12,144 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.234388412610486 +2024-05-27 14:32:12,144 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.458760696578231 +2024-05-27 14:32:12,144 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.517272651097428 +2024-05-27 14:32:12,144 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.13788855711359885 +2024-05-27 14:32:12,149 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.027340 NaN NaN +0.283333 NaN 14.414427 0.159209 +1.195000 0.057426 NaN NaN +1.613611 0.074476 NaN NaN +1.916667 NaN 13.931492 0.391458 +2.361389 0.118495 NaN NaN +2.700000 NaN 13.456728 0.619777 +3.286389 0.210469 NaN NaN +3.616667 NaN 12.511416 1.074387 +3.819444 0.293063 NaN NaN +4.050000 NaN 11.838897 1.397809 +4.410833 0.423123 NaN NaN +4.750000 NaN 10.286783 2.144237 + +2024-05-27 14:32:12,153 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.8813957713496472 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.00015994436491955925 + +2024-05-27 14:32:12,153 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00015994436491955925 +2024-05-27 14:32:12,154 - physiofit - INFO - Results for yeaD: + optimal +yeaD X_0 0.027340 +yeaD growth_rate 0.621042 +yeaD Glc_q -5.234388 +yeaD Glc_M0 14.458761 +yeaD Ace_q 2.517273 +yeaD Ace_M0 0.137889 +2024-05-27 14:32:12,160 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:13,135 - physiofit - INFO - Running optimization for yeaG +2024-05-27 14:32:13,137 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:13,138 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:13,141 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1067 1.950000 NaN 13.737149 0.423096 +1068 2.501389 0.108864 NaN NaN +1069 3.250000 NaN 12.375047 0.966109 +1070 3.341944 0.166320 NaN NaN +1071 3.997500 0.226800 NaN NaN +1072 4.083333 NaN 10.782679 1.534724 +1073 4.523333 0.353808 NaN NaN +1074 4.766667 NaN 9.268057 2.169263 +Experimental matrix: +[[ nan 13.73714897 0.42309566] + [ 0.108864 nan nan] + [ nan 12.37504694 0.96610868] + [ 0.16632 nan nan] + [ 0.2268 nan nan] + [ nan 10.78267917 1.5347244 ] + [ 0.353808 nan nan] + [ nan 9.26805713 2.16926329]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:13,142 - physiofit - INFO - mc : False +2024-05-27 14:32:13,142 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:13,142 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:13,142 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:13,580 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:13,581 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.2656105078188684 + x: [ 2.201e-02 6.058e-01 -8.397e+00 1.430e+01 + 3.256e+00 2.018e-01] + nit: 91 + nfev: 8973 + population: [[ 2.207e-02 6.049e-01 ... 3.241e+00 2.046e-01] + [ 2.141e-02 6.119e-01 ... 3.256e+00 1.942e-01] + ... + [ 2.227e-02 6.026e-01 ... 3.252e+00 2.014e-01] + [ 2.212e-02 6.042e-01 ... 3.241e+00 2.079e-01]] + population_energies: [ 2.266e+00 2.369e+00 ... 2.276e+00 2.280e+00] + jac: [ 1.348e-03 -1.023e-04 -3.144e-05 -7.110e-05 + -7.918e-05 -1.317e-04] +2024-05-27 14:32:13,581 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02200682134349738 +2024-05-27 14:32:13,581 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6057844521460668 +2024-05-27 14:32:13,581 - physiofit.physiofit.base.fitter - INFO - Glc_q = -8.397102292091693 +2024-05-27 14:32:13,581 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.304134858147691 +2024-05-27 14:32:13,581 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.256054182133859 +2024-05-27 14:32:13,581 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.20176196964821042 +2024-05-27 14:32:13,585 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.615171 0.468914 +2.501389 0.100149 NaN NaN +3.250000 NaN 12.424405 0.930645 +3.341944 0.166642 NaN NaN +3.997500 0.247888 NaN NaN +4.083333 NaN 10.989687 1.486970 +4.523333 0.340876 NaN NaN +4.766667 NaN 9.133662 2.206661 + +2024-05-27 14:32:13,588 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.2656105078188684 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.1062777625025187 + +2024-05-27 14:32:13,589 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.1062777625025187 +2024-05-27 14:32:13,590 - physiofit - INFO - Results for yeaG: + optimal +yeaG X_0 0.022007 +yeaG growth_rate 0.605784 +yeaG Glc_q -8.397102 +yeaG Glc_M0 14.304135 +yeaG Ace_q 3.256054 +yeaG Ace_M0 0.201762 +2024-05-27 14:32:13,596 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:14,556 - physiofit - INFO - Running optimization for yeaO +2024-05-27 14:32:14,559 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:14,560 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:14,564 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1075 1.828889 0.055944 NaN NaN +1076 2.261389 0.074088 NaN NaN +1077 2.774167 0.096768 NaN NaN +1078 2.800000 NaN 12.225484 0.623281 +1079 3.208889 0.125496 NaN NaN +1080 3.706389 0.170856 NaN NaN +1081 3.733333 NaN 11.464245 1.048362 +1082 4.225833 0.220752 NaN NaN +1083 4.283333 NaN 10.757425 1.381117 +1084 4.635556 0.332640 NaN NaN +1085 4.750000 NaN 10.207385 1.781757 +1086 4.967500 0.421848 NaN NaN +1087 5.116667 NaN 9.190777 2.070829 +1088 5.433333 NaN 8.258053 2.479300 +Experimental matrix: +[[ 0.055944 nan nan] + [ 0.074088 nan nan] + [ 0.096768 nan nan] + [ nan 12.22548366 0.62328103] + [ 0.125496 nan nan] + [ 0.170856 nan nan] + [ nan 11.46424456 1.04836185] + [ 0.220752 nan nan] + [ nan 10.75742494 1.38111713] + [ 0.33264 nan nan] + [ nan 10.20738546 1.78175691] + [ 0.421848 nan nan] + [ nan 9.19077711 2.07082867] + [ nan 8.25805317 2.47929965]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:14,564 - physiofit - INFO - mc : False +2024-05-27 14:32:14,564 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:14,564 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:14,565 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:15,082 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:15,083 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.22163270370321 + x: [ 1.361e-02 6.866e-01 -5.646e+00 1.285e+01 + 2.632e+00 3.980e-01] + nit: 106 + nfev: 10204 + population: [[ 1.383e-02 6.827e-01 ... 2.626e+00 3.954e-01] + [ 1.381e-02 6.829e-01 ... 2.621e+00 4.077e-01] + ... + [ 1.346e-02 6.897e-01 ... 2.587e+00 4.169e-01] + [ 1.385e-02 6.829e-01 ... 2.616e+00 4.063e-01]] + population_energies: [ 3.222e+00 3.271e+00 ... 3.251e+00 3.244e+00] + jac: [-9.927e-03 -2.021e-03 -8.065e-05 7.585e-05 + -2.850e-04 -1.750e-05] +2024-05-27 14:32:15,084 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.013612801622688922 +2024-05-27 14:32:15,084 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6866155915545925 +2024-05-27 14:32:15,084 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.645631156485332 +2024-05-27 14:32:15,084 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 12.852171594943073 +2024-05-27 14:32:15,084 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.6316911301776846 +2024-05-27 14:32:15,084 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.3979913299288361 +2024-05-27 14:32:15,088 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.047787 NaN NaN +2.261389 0.064310 NaN NaN +2.774167 0.091450 NaN NaN +2.800000 NaN 12.198703 0.702604 +3.208889 0.123259 NaN NaN +3.706389 0.173448 NaN NaN +3.733333 NaN 11.511316 1.023027 +4.225833 0.247778 NaN NaN +4.283333 NaN 10.844726 1.333755 +4.635556 0.328276 NaN NaN +4.750000 NaN 10.044223 1.706907 +4.967500 0.412309 NaN NaN +5.116667 NaN 9.208302 2.096568 +5.433333 NaN 8.296108 2.521785 + +2024-05-27 14:32:15,092 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.22163270370321 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.0013874091005433 + +2024-05-27 14:32:15,093 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0013874091005433 +2024-05-27 14:32:15,095 - physiofit - INFO - Results for yeaO: + optimal +yeaO X_0 0.013613 +yeaO growth_rate 0.686616 +yeaO Glc_q -5.645631 +yeaO Glc_M0 12.852172 +yeaO Ace_q 2.631691 +yeaO Ace_M0 0.397991 +2024-05-27 14:32:15,100 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:16,180 - physiofit - INFO - Running optimization for yeaY +2024-05-27 14:32:16,183 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:16,183 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:16,187 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1089 0.000000 0.031752 NaN NaN +1090 0.066667 NaN 14.865148 0.008764 +1091 1.188889 0.061992 NaN NaN +1092 1.716667 NaN 15.235785 0.354264 +1093 2.276944 0.092232 NaN NaN +1094 2.800000 NaN 13.609637 0.762892 +1095 3.128333 0.161784 NaN NaN +1096 3.633333 NaN 12.462686 1.188220 +1097 3.771389 0.204120 NaN NaN +1098 4.266667 NaN 11.725110 1.738006 +1099 4.415556 0.311472 NaN NaN +1100 4.822778 0.370440 NaN NaN +1101 4.883333 NaN 10.520221 2.309255 +Experimental matrix: +[[3.17520000e-02 nan nan] + [ nan 1.48651479e+01 8.76439553e-03] + [6.19920000e-02 nan nan] + [ nan 1.52357847e+01 3.54264417e-01] + [9.22320000e-02 nan nan] + [ nan 1.36096372e+01 7.62892327e-01] + [1.61784000e-01 nan nan] + [ nan 1.24626855e+01 1.18822001e+00] + [2.04120000e-01 nan nan] + [ nan 1.17251103e+01 1.73800625e+00] + [3.11472000e-01 nan nan] + [3.70440000e-01 nan nan] + [ nan 1.05202212e+01 2.30925497e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:16,187 - physiofit - INFO - mc : False +2024-05-27 14:32:16,187 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:16,187 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:16,188 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:16,616 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:16,618 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.738287472912887 + x: [ 3.160e-02 5.110e-01 -6.987e+00 1.516e+01 + 3.352e+00 5.853e-02] + nit: 82 + nfev: 7904 + population: [[ 3.222e-02 5.064e-01 ... 3.334e+00 5.987e-02] + [ 3.151e-02 5.132e-01 ... 3.372e+00 4.490e-02] + ... + [ 3.196e-02 5.095e-01 ... 3.313e+00 5.606e-02] + [ 3.178e-02 5.094e-01 ... 3.380e+00 4.588e-02]] + population_energies: [ 4.738e+00 4.875e+00 ... 4.784e+00 4.758e+00] + jac: [-4.947e-05 -1.235e-05 -2.398e-06 -7.994e-07 + 5.329e-07 1.510e-06] +2024-05-27 14:32:16,619 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03159761705373175 +2024-05-27 14:32:16,619 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5109547776538022 +2024-05-27 14:32:16,619 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.986937369863735 +2024-05-27 14:32:16,619 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.15754400310036 +2024-05-27 14:32:16,619 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.3523008915775314 +2024-05-27 14:32:16,620 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.05852655796782447 +2024-05-27 14:32:16,625 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.031598 NaN NaN +0.066667 NaN 15.142572 0.065710 +1.188889 0.058006 NaN NaN +1.716667 NaN 14.550906 0.349589 +2.276944 0.101139 NaN NaN +2.800000 NaN 13.782893 0.718078 +3.128333 0.156260 NaN NaN +3.633333 NaN 12.823868 1.178214 +3.771389 0.217042 NaN NaN +4.266667 NaN 11.767073 1.685259 +4.415556 0.301639 NaN NaN +4.822778 0.371409 NaN NaN +4.883333 NaN 10.351275 2.364553 + +2024-05-27 14:32:16,630 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.738287472912887 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.019488456319143414 + +2024-05-27 14:32:16,630 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.019488456319143414 +2024-05-27 14:32:16,633 - physiofit - INFO - Results for yeaY: + optimal +yeaY X_0 0.031598 +yeaY growth_rate 0.510955 +yeaY Glc_q -6.986937 +yeaY Glc_M0 15.157544 +yeaY Ace_q 3.352301 +yeaY Ace_M0 0.058527 +2024-05-27 14:32:16,935 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:17,916 - physiofit - INFO - Running optimization for yebG +2024-05-27 14:32:17,919 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:17,919 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:17,923 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1102 0.000000 0.036288 NaN NaN +1103 0.066667 NaN 15.350220 0.015261 +1104 1.188889 0.065016 NaN NaN +1105 1.716667 NaN 14.926735 0.417948 +1106 2.276944 0.114912 NaN NaN +1107 2.800000 NaN 13.289589 0.962264 +1108 3.128333 0.181440 NaN NaN +1109 3.633333 NaN 12.287517 1.694284 +1110 3.771389 0.276696 NaN NaN +1111 4.266667 NaN 11.014542 2.535319 +1112 4.415556 0.379512 NaN NaN +1113 4.822778 0.607824 NaN NaN +1114 4.883333 NaN 9.326901 3.429277 +Experimental matrix: +[[3.62880000e-02 nan nan] + [ nan 1.53502196e+01 1.52609846e-02] + [6.50160000e-02 nan nan] + [ nan 1.49267352e+01 4.17947794e-01] + [1.14912000e-01 nan nan] + [ nan 1.32895894e+01 9.62263750e-01] + [1.81440000e-01 nan nan] + [ nan 1.22875172e+01 1.69428435e+00] + [2.76696000e-01 nan nan] + [ nan 1.10145421e+01 2.53531930e+00] + [3.79512000e-01 nan nan] + [6.07824000e-01 nan nan] + [ nan 9.32690078e+00 3.42927664e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:17,923 - physiofit - INFO - mc : False +2024-05-27 14:32:17,923 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:17,923 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:17,924 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:18,296 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:18,298 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 17.542417168146848 + x: [ 2.413e-02 6.537e-01 -7.034e+00 1.511e+01 + 3.992e+00 1.404e-01] + nit: 78 + nfev: 7432 + population: [[ 2.392e-02 6.561e-01 ... 4.006e+00 1.425e-01] + [ 2.403e-02 6.553e-01 ... 4.016e+00 1.147e-01] + ... + [ 2.470e-02 6.497e-01 ... 3.959e+00 1.520e-01] + [ 2.405e-02 6.567e-01 ... 3.871e+00 1.847e-01]] + population_energies: [ 1.754e+01 1.766e+01 ... 1.766e+01 1.790e+01] + jac: [ 2.957e-03 1.435e-04 7.354e-05 1.833e-04 + 1.076e-04 -2.842e-06] +2024-05-27 14:32:18,299 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.024134993243930227 +2024-05-27 14:32:18,299 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6537332251835191 +2024-05-27 14:32:18,299 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.0342231604644585 +2024-05-27 14:32:18,299 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.111046016413539 +2024-05-27 14:32:18,299 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.9918419677742683 +2024-05-27 14:32:18,300 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1403940954127225 +2024-05-27 14:32:18,303 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.024135 NaN NaN +0.066667 NaN 15.099478 0.146959 +1.188889 0.052503 NaN NaN +1.716667 NaN 14.573028 0.445713 +2.276944 0.106930 NaN NaN +2.800000 NaN 13.751101 0.912148 +3.128333 0.186561 NaN NaN +3.633333 NaN 12.578117 1.577803 +3.771389 0.284049 NaN NaN +4.266667 NaN 11.145769 2.390644 +4.415556 0.432792 NaN NaN +4.822778 0.564801 NaN NaN +4.883333 NaN 9.048030 3.581087 + +2024-05-27 14:32:18,307 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 17.542417168146848 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.8243211508919197 + +2024-05-27 14:32:18,307 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.8243211508919197 +2024-05-27 14:32:18,310 - physiofit - INFO - Results for yebG: + optimal +yebG X_0 0.024135 +yebG growth_rate 0.653733 +yebG Glc_q -7.034223 +yebG Glc_M0 15.111046 +yebG Ace_q 3.991842 +yebG Ace_M0 0.140394 +2024-05-27 14:32:18,315 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:19,294 - physiofit - INFO - Running optimization for yebO +2024-05-27 14:32:19,296 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:19,297 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:19,300 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1115 0.000000 0.036288 NaN NaN +1116 0.066667 NaN 15.479921 0.012086 +1117 1.188889 0.066528 NaN NaN +1118 1.716667 NaN 15.531011 0.329566 +1119 2.276944 0.114912 NaN NaN +1120 2.800000 NaN 13.747404 0.673982 +1121 3.128333 0.166320 NaN NaN +1122 3.633333 NaN 12.518863 1.059419 +1123 3.771389 0.229824 NaN NaN +1124 4.266667 NaN 12.155398 1.523758 +1125 4.415556 0.337176 NaN NaN +1126 4.822778 0.424872 NaN NaN +1127 4.883333 NaN 10.582704 1.983750 +Experimental matrix: +[[3.62880000e-02 nan nan] + [ nan 1.54799211e+01 1.20859706e-02] + [6.65280000e-02 nan nan] + [ nan 1.55310114e+01 3.29565595e-01] + [1.14912000e-01 nan nan] + [ nan 1.37474043e+01 6.73982164e-01] + [1.66320000e-01 nan nan] + [ nan 1.25188633e+01 1.05941881e+00] + [2.29824000e-01 nan nan] + [ nan 1.21553978e+01 1.52375806e+00] + [3.37176000e-01 nan nan] + [4.24872000e-01 nan nan] + [ nan 1.05827044e+01 1.98375050e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:19,300 - physiofit - INFO - mc : False +2024-05-27 14:32:19,301 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:19,301 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:19,301 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:19,703 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:19,705 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.303861578329012 + x: [ 3.421e-02 5.183e-01 -6.705e+00 1.555e+01 + 2.589e+00 7.589e-02] + nit: 86 + nfev: 8222 + population: [[ 3.411e-02 5.188e-01 ... 2.599e+00 7.446e-02] + [ 3.351e-02 5.218e-01 ... 2.604e+00 1.020e-01] + ... + [ 3.362e-02 5.224e-01 ... 2.667e+00 6.541e-02] + [ 3.424e-02 5.175e-01 ... 2.593e+00 7.772e-02]] + population_energies: [ 5.304e+00 5.503e+00 ... 5.396e+00 5.344e+00] + jac: [-1.478e-02 4.415e-03 1.155e-05 1.468e-03 + -6.396e-04 -1.846e-03] +2024-05-27 14:32:19,705 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03420871467016434 +2024-05-27 14:32:19,705 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5183297832325737 +2024-05-27 14:32:19,705 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.705158703831577 +2024-05-27 14:32:19,705 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.549396431719558 +2024-05-27 14:32:19,705 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.588580987541504 +2024-05-27 14:32:19,706 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.07588612130561759 +2024-05-27 14:32:19,709 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.034209 NaN NaN +0.066667 NaN 15.533838 0.081893 +1.188889 0.063353 NaN NaN +1.716667 NaN 14.914529 0.320982 +2.276944 0.111351 NaN NaN +2.800000 NaN 14.102882 0.634325 +3.128333 0.173121 NaN NaN +3.633333 NaN 13.082337 1.028314 +3.771389 0.241605 NaN NaN +4.266667 NaN 11.951755 1.464785 +4.415556 0.337375 NaN NaN +4.822778 0.416660 NaN NaN +4.883333 NaN 10.430116 2.052226 + +2024-05-27 14:32:19,712 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.303861578329012 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.03211928119744161 + +2024-05-27 14:32:19,712 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.03211928119744161 +2024-05-27 14:32:19,714 - physiofit - INFO - Results for yebO: + optimal +yebO X_0 0.034209 +yebO growth_rate 0.518330 +yebO Glc_q -6.705159 +yebO Glc_M0 15.549396 +yebO Ace_q 2.588581 +yebO Ace_M0 0.075886 +2024-05-27 14:32:19,718 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:20,708 - physiofit - INFO - Running optimization for yebT +2024-05-27 14:32:20,711 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:20,711 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:20,714 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1128 1.950000 NaN 13.848096 0.413319 +1129 2.501389 0.117936 NaN NaN +1130 3.250000 NaN 12.978895 0.985904 +1131 3.341944 0.184464 NaN NaN +1132 3.997500 0.264600 NaN NaN +1133 4.083333 NaN 11.500263 1.486455 +1134 4.523333 0.379512 NaN NaN +1135 4.766667 NaN 9.809098 2.023390 +Experimental matrix: +[[ nan 13.84809577 0.41331926] + [ 0.117936 nan nan] + [ nan 12.97889491 0.98590406] + [ 0.184464 nan nan] + [ 0.2646 nan nan] + [ nan 11.50026279 1.48645478] + [ 0.379512 nan nan] + [ nan 9.80909773 2.02339041]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:20,716 - physiofit - INFO - mc : False +2024-05-27 14:32:20,716 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:20,716 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:20,716 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:21,243 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:21,245 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.9300682637092608 + x: [ 2.553e-02 5.934e-01 -6.948e+00 1.459e+01 + 2.688e+00 2.367e-01] + nit: 106 + nfev: 10008 + population: [[ 2.534e-02 5.952e-01 ... 2.703e+00 2.295e-01] + [ 2.579e-02 5.917e-01 ... 2.695e+00 2.274e-01] + ... + [ 2.566e-02 5.913e-01 ... 2.675e+00 2.456e-01] + [ 2.585e-02 5.906e-01 ... 2.661e+00 2.350e-01]] + population_energies: [ 9.301e-01 9.391e-01 ... 9.453e-01 9.537e-01] + jac: [ 8.216e-03 4.694e-04 1.095e-03 -3.330e-04 + -2.454e-06 2.235e-04] +2024-05-27 14:32:21,245 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025532334272011428 +2024-05-27 14:32:21,245 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5933963797740068 +2024-05-27 14:32:21,246 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.948466295535062 +2024-05-27 14:32:21,246 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.59485099008357 +2024-05-27 14:32:21,246 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.687821216482662 +2024-05-27 14:32:21,246 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.23670471042463748 +2024-05-27 14:32:21,251 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.942856 0.488911 +2.501389 0.112647 NaN NaN +3.250000 NaN 12.837045 0.916663 +3.341944 0.185498 NaN NaN +3.997500 0.273704 NaN NaN +4.083333 NaN 11.521377 1.425593 +4.523333 0.373932 NaN NaN +4.766667 NaN 9.835039 2.077906 + +2024-05-27 14:32:21,258 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.9300682637092608 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.011875132336814108 + +2024-05-27 14:32:21,258 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.011875132336814108 +2024-05-27 14:32:21,262 - physiofit - INFO - Results for yebT: + optimal +yebT X_0 0.025532 +yebT growth_rate 0.593396 +yebT Glc_q -6.948466 +yebT Glc_M0 14.594851 +yebT Ace_q 2.687821 +yebT Ace_M0 0.236705 +2024-05-27 14:32:21,269 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:22,238 - physiofit - INFO - Running optimization for yebV +2024-05-27 14:32:22,240 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:22,240 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:22,245 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1136 0.000000 0.034776 NaN NaN +1137 0.283333 NaN 14.132997 0.033758 +1138 1.195000 0.063504 NaN NaN +1139 1.613611 0.080136 NaN NaN +1140 1.916667 NaN 14.185292 0.369990 +1141 2.361389 0.127008 NaN NaN +1142 2.700000 NaN 13.296535 0.660532 +1143 3.286389 0.220752 NaN NaN +1144 3.616667 NaN 12.958790 1.187804 +1145 3.819444 0.312984 NaN NaN +1146 4.050000 NaN 12.048988 1.445271 +1147 4.410833 0.430920 NaN NaN +1148 4.750000 NaN 10.224490 1.788287 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.13299716 0.03375796] + [ 0.063504 nan nan] + [ 0.080136 nan nan] + [ nan 14.18529193 0.36998992] + [ 0.127008 nan nan] + [ nan 13.29653461 0.66053167] + [ 0.220752 nan nan] + [ nan 12.95878965 1.18780403] + [ 0.312984 nan nan] + [ nan 12.04898835 1.44527089] + [ 0.43092 nan nan] + [ nan 10.22449025 1.78828682]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:22,246 - physiofit - INFO - mc : False +2024-05-27 14:32:22,246 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:22,246 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:22,247 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:22,608 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:22,610 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.685821026392044 + x: [ 3.223e-02 5.891e-01 -4.778e+00 1.450e+01 + 2.137e+00 1.567e-01] + nit: 76 + nfev: 7238 + population: [[ 3.219e-02 5.887e-01 ... 2.132e+00 1.540e-01] + [ 3.255e-02 5.847e-01 ... 2.178e+00 1.533e-01] + ... + [ 3.221e-02 5.884e-01 ... 2.094e+00 1.591e-01] + [ 3.208e-02 5.885e-01 ... 2.195e+00 1.411e-01]] + population_energies: [ 4.686e+00 4.776e+00 ... 4.772e+00 4.775e+00] + jac: [ 9.239e-03 4.401e-04 -2.961e-02 1.924e-02 + -3.207e-02 1.057e-02] +2024-05-27 14:32:22,610 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.032229845007689745 +2024-05-27 14:32:22,611 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5890713430788245 +2024-05-27 14:32:22,611 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.777848635981626 +2024-05-27 14:32:22,611 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.502115099718122 +2024-05-27 14:32:22,611 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.136818201603816 +2024-05-27 14:32:22,611 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1567262755063316 +2024-05-27 14:32:22,615 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.032230 NaN NaN +0.283333 NaN 14.454632 0.177962 +1.195000 0.065159 NaN NaN +1.613611 0.083381 NaN NaN +1.916667 NaN 13.955055 0.401391 +2.361389 0.129531 NaN NaN +2.700000 NaN 13.481003 0.613403 +3.286389 0.223366 NaN NaN +3.616667 NaN 12.562748 1.024078 +3.819444 0.305765 NaN NaN +4.050000 NaN 11.922756 1.310304 +4.410833 0.433195 NaN NaN +4.750000 NaN 10.472933 1.958715 + +2024-05-27 14:32:22,620 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.685821026392044 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.018525904697575514 + +2024-05-27 14:32:22,621 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.018525904697575514 +2024-05-27 14:32:22,623 - physiofit - INFO - Results for yebV: + optimal +yebV X_0 0.032230 +yebV growth_rate 0.589071 +yebV Glc_q -4.777849 +yebV Glc_M0 14.502115 +yebV Ace_q 2.136818 +yebV Ace_M0 0.156726 +2024-05-27 14:32:22,629 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:23,607 - physiofit - INFO - Running optimization for yebY +2024-05-27 14:32:23,609 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:23,609 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:23,613 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1149 0.000000 0.034776 NaN NaN +1150 0.066667 NaN 14.904602 0.010225 +1151 1.188889 0.068040 NaN NaN +1152 1.716667 NaN 15.140530 0.364571 +1153 2.276944 0.107352 NaN NaN +1154 2.800000 NaN 13.289232 0.762785 +1155 3.128333 0.173880 NaN NaN +1156 3.633333 NaN 12.375228 1.259377 +1157 3.771389 0.235872 NaN NaN +1158 4.266667 NaN 11.097262 1.666192 +1159 4.415556 0.337176 NaN NaN +1160 4.822778 0.424872 NaN NaN +1161 4.883333 NaN 9.854012 2.373103 +Experimental matrix: +[[3.47760000e-02 nan nan] + [ nan 1.49046021e+01 1.02253172e-02] + [6.80400000e-02 nan nan] + [ nan 1.51405296e+01 3.64570663e-01] + [1.07352000e-01 nan nan] + [ nan 1.32892324e+01 7.62785165e-01] + [1.73880000e-01 nan nan] + [ nan 1.23752281e+01 1.25937689e+00] + [2.35872000e-01 nan nan] + [ nan 1.10972618e+01 1.66619151e+00] + [3.37176000e-01 nan nan] + [4.24872000e-01 nan nan] + [ nan 9.85401201e+00 2.37310299e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:23,614 - physiofit - INFO - mc : False +2024-05-27 14:32:23,614 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:23,614 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:23,615 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:24,081 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:24,082 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.8959699415713227 + x: [ 3.412e-02 5.201e-01 -7.187e+00 1.515e+01 + 3.039e+00 6.736e-02] + nit: 91 + nfev: 8798 + population: [[ 3.447e-02 5.177e-01 ... 3.048e+00 6.154e-02] + [ 3.384e-02 5.208e-01 ... 3.083e+00 6.293e-02] + ... + [ 3.431e-02 5.193e-01 ... 3.028e+00 7.444e-02] + [ 3.420e-02 5.186e-01 ... 3.049e+00 6.192e-02]] + population_energies: [ 3.896e+00 4.032e+00 ... 3.923e+00 3.930e+00] + jac: [-2.250e-03 -3.525e-04 -6.306e-06 6.350e-06 + -2.003e-05 -1.652e-05] +2024-05-27 14:32:24,083 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03411726727295433 +2024-05-27 14:32:24,083 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5201219941343395 +2024-05-27 14:32:24,083 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.186559310189773 +2024-05-27 14:32:24,083 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.154568790297036 +2024-05-27 14:32:24,083 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.038588330903048 +2024-05-27 14:32:24,084 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.06735599784811826 +2024-05-27 14:32:24,087 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.034117 NaN NaN +0.066667 NaN 15.137936 0.074388 +1.188889 0.063318 NaN NaN +1.716667 NaN 14.474742 0.354797 +2.276944 0.111508 NaN NaN +2.800000 NaN 13.603550 0.723151 +3.128333 0.173629 NaN NaN +3.633333 NaN 12.506293 1.187088 +3.771389 0.242593 NaN NaN +4.266667 NaN 11.289155 1.701712 +4.415556 0.339146 NaN NaN +4.822778 0.419153 NaN NaN +4.883333 NaN 9.649190 2.395115 + +2024-05-27 14:32:24,090 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.8959699415713227 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.007751546201880148 + +2024-05-27 14:32:24,090 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.007751546201880148 +2024-05-27 14:32:24,093 - physiofit - INFO - Results for yebY: + optimal +yebY X_0 0.034117 +yebY growth_rate 0.520122 +yebY Glc_q -7.186559 +yebY Glc_M0 15.154569 +yebY Ace_q 3.038588 +yebY Ace_M0 0.067356 +2024-05-27 14:32:24,098 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:25,093 - physiofit - INFO - Running optimization for yecA +2024-05-27 14:32:25,096 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:25,097 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:25,104 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1162 1.950000 NaN 13.983429 0.364265 +1163 2.501389 0.110376 NaN NaN +1164 3.250000 NaN 13.112090 0.969716 +1165 3.341944 0.158760 NaN NaN +1166 3.997500 0.237384 NaN NaN +1167 4.083333 NaN 12.086190 1.602574 +1168 4.523333 0.356832 NaN NaN +1169 4.766667 NaN 11.195670 2.361752 +Experimental matrix: +[[ nan 13.98342874 0.36426529] + [ 0.110376 nan nan] + [ nan 13.11208996 0.96971597] + [ 0.15876 nan nan] + [ 0.237384 nan nan] + [ nan 12.08618996 1.60257388] + [ 0.356832 nan nan] + [ nan 11.19566961 2.36175177]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:25,104 - physiofit - INFO - mc : False +2024-05-27 14:32:25,104 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:25,105 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:25,106 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:25,628 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:25,630 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.5534876988245174 + x: [ 2.067e-02 6.238e-01 -5.199e+00 1.429e+01 + 3.702e+00 1.194e-01] + nit: 104 + nfev: 9800 + population: [[ 2.087e-02 6.215e-01 ... 3.702e+00 1.121e-01] + [ 2.111e-02 6.189e-01 ... 3.677e+00 1.068e-01] + ... + [ 2.098e-02 6.215e-01 ... 3.663e+00 1.250e-01] + [ 1.997e-02 6.323e-01 ... 3.697e+00 1.208e-01]] + population_energies: [ 1.553e+00 1.581e+00 ... 1.578e+00 1.584e+00] + jac: [-2.861e-03 7.741e-04 1.742e-02 -1.198e-02 + 1.617e-02 -3.527e-03] +2024-05-27 14:32:25,630 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.020670906307843993 +2024-05-27 14:32:25,631 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.623816132789155 +2024-05-27 14:32:25,631 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.199334453475143 +2024-05-27 14:32:25,631 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.286832169263267 +2024-05-27 14:32:25,631 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.7015694804291623 +2024-05-27 14:32:25,631 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.11939837923249076 +2024-05-27 14:32:25,637 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.877625 0.410725 +2.501389 0.098409 NaN NaN +3.250000 NaN 13.150719 0.928233 +3.341944 0.166249 NaN NaN +3.997500 0.250243 NaN NaN +4.083333 NaN 12.258692 1.563295 +4.523333 0.347393 NaN NaN +4.766667 NaN 11.089075 2.395982 + +2024-05-27 14:32:25,643 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.5534876988245174 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.04413728738075581 + +2024-05-27 14:32:25,644 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.04413728738075581 +2024-05-27 14:32:25,648 - physiofit - INFO - Results for yecA: + optimal +yecA X_0 0.020671 +yecA growth_rate 0.623816 +yecA Glc_q -5.199334 +yecA Glc_M0 14.286832 +yecA Ace_q 3.701569 +yecA Ace_M0 0.119398 +2024-05-27 14:32:25,655 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:26,615 - physiofit - INFO - Running optimization for yecF +2024-05-27 14:32:26,617 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:26,618 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:26,621 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1170 0.000000 0.036288 NaN NaN +1171 0.066667 NaN 15.749048 0.017467 +1172 1.188889 0.063504 NaN NaN +1173 1.716667 NaN 15.531029 0.371047 +1174 2.276944 0.114912 NaN NaN +1175 2.800000 NaN 12.909276 0.738237 +1176 3.128333 0.179928 NaN NaN +1177 3.633333 NaN 12.402615 1.178068 +1178 3.771389 0.257040 NaN NaN +1179 4.266667 NaN 11.677403 1.755707 +1180 4.415556 0.356832 NaN NaN +1181 4.822778 0.491400 NaN NaN +1182 4.883333 NaN 9.652474 2.233657 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 15.74904809 0.01746713] + [ 0.063504 nan nan] + [ nan 15.53102924 0.37104738] + [ 0.114912 nan nan] + [ nan 12.90927568 0.73823667] + [ 0.179928 nan nan] + [ nan 12.40261534 1.17806785] + [ 0.25704 nan nan] + [ nan 11.67740338 1.75570706] + [ 0.356832 nan nan] + [ 0.4914 nan nan] + [ nan 9.65247366 2.23365676]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:26,622 - physiofit - INFO - mc : False +2024-05-27 14:32:26,622 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:26,622 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:26,623 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:27,048 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:27,049 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 11.407535432050587 + x: [ 3.259e-02 5.539e-01 -7.347e+00 1.554e+01 + 2.718e+00 1.054e-01] + nit: 83 + nfev: 7924 + population: [[ 3.244e-02 5.543e-01 ... 2.725e+00 1.117e-01] + [ 3.263e-02 5.543e-01 ... 2.727e+00 1.074e-01] + ... + [ 3.296e-02 5.499e-01 ... 2.742e+00 1.079e-01] + [ 3.363e-02 5.491e-01 ... 2.673e+00 1.083e-01]] + population_energies: [ 1.141e+01 1.154e+01 ... 1.150e+01 1.170e+01] + jac: [ 9.255e-02 6.190e-03 -2.778e-02 2.333e-02 + -4.913e-02 1.806e-02] +2024-05-27 14:32:27,049 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.032585384127146615 +2024-05-27 14:32:27,050 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.553912627121434 +2024-05-27 14:32:27,050 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.346923224715675 +2024-05-27 14:32:27,050 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.537665509349496 +2024-05-27 14:32:27,050 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.7184854694325984 +2024-05-27 14:32:27,051 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.10544407445678343 +2024-05-27 14:32:27,054 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.032585 NaN NaN +0.066667 NaN 15.521407 0.111460 +1.188889 0.062954 NaN NaN +1.716667 NaN 14.851331 0.359400 +2.276944 0.115018 NaN NaN +2.800000 NaN 13.931613 0.699711 +3.128333 0.184323 NaN NaN +3.633333 NaN 12.735971 1.142118 +3.771389 0.263192 NaN NaN +4.266667 NaN 11.377026 1.644951 +4.415556 0.376040 NaN NaN +4.822778 0.471190 NaN NaN +4.883333 NaN 9.506965 2.336905 + +2024-05-27 14:32:27,058 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 11.407535432050587 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.4232824122308697 + +2024-05-27 14:32:27,059 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.4232824122308697 +2024-05-27 14:32:27,062 - physiofit - INFO - Results for yecF: + optimal +yecF X_0 0.032585 +yecF growth_rate 0.553913 +yecF Glc_q -7.346923 +yecF Glc_M0 15.537666 +yecF Ace_q 2.718485 +yecF Ace_M0 0.105444 +2024-05-27 14:32:27,068 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:28,064 - physiofit - INFO - Running optimization for yecJ +2024-05-27 14:32:28,067 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:28,067 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:28,071 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1183 0.000000 0.037800 NaN NaN +1184 0.066667 NaN 15.333053 0.013638 +1185 1.188889 0.072576 NaN NaN +1186 1.716667 NaN 14.694491 0.352269 +1187 2.276944 0.119448 NaN NaN +1188 2.800000 NaN 13.483980 0.767678 +1189 3.128333 0.189000 NaN NaN +1190 3.633333 NaN 12.291394 1.196535 +1191 3.771389 0.276696 NaN NaN +1192 4.266667 NaN 11.049202 1.649740 +1193 4.415556 0.412776 NaN NaN +1194 4.822778 0.644112 NaN NaN +1195 4.883333 NaN 9.691920 2.189253 +Experimental matrix: +[[3.78000000e-02 nan nan] + [ nan 1.53330531e+01 1.36380037e-02] + [7.25760000e-02 nan nan] + [ nan 1.46944915e+01 3.52269036e-01] + [1.19448000e-01 nan nan] + [ nan 1.34839797e+01 7.67678478e-01] + [1.89000000e-01 nan nan] + [ nan 1.22913939e+01 1.19653508e+00] + [2.76696000e-01 nan nan] + [ nan 1.10492017e+01 1.64973989e+00] + [4.12776000e-01 nan nan] + [6.44112000e-01 nan nan] + [ nan 9.69191969e+00 2.18925332e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:28,071 - physiofit - INFO - mc : False +2024-05-27 14:32:28,071 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:28,071 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:28,072 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:28,504 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:28,505 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 17.33594468507354 + x: [ 2.291e-02 6.785e-01 -6.332e+00 1.498e+01 + 2.381e+00 1.941e-01] + nit: 86 + nfev: 8138 + population: [[ 2.297e-02 6.779e-01 ... 2.359e+00 2.106e-01] + [ 2.322e-02 6.767e-01 ... 2.364e+00 1.955e-01] + ... + [ 2.246e-02 6.826e-01 ... 2.357e+00 2.122e-01] + [ 2.277e-02 6.798e-01 ... 2.354e+00 2.346e-01]] + population_energies: [ 1.734e+01 1.741e+01 ... 1.745e+01 1.749e+01] + jac: [-5.240e-01 -1.354e-01 1.818e-03 1.070e-02 + 3.186e-02 -7.995e-03] +2024-05-27 14:32:28,505 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02290516992902295 +2024-05-27 14:32:28,505 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6784883958628671 +2024-05-27 14:32:28,505 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.332125163352192 +2024-05-27 14:32:28,505 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.975641046607752 +2024-05-27 14:32:28,505 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.380931549183441 +2024-05-27 14:32:28,505 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1941303140048578 +2024-05-27 14:32:28,509 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.022905 NaN NaN +0.066667 NaN 14.965750 0.197850 +1.188889 0.051316 NaN NaN +1.716667 NaN 14.504267 0.371371 +2.276944 0.107366 NaN NaN +2.800000 NaN 13.760517 0.651027 +3.128333 0.191311 NaN NaN +3.633333 NaN 12.674325 1.059444 +3.771389 0.295955 NaN NaN +4.266667 NaN 11.324202 1.567102 +4.415556 0.458182 NaN NaN +4.822778 0.603992 NaN NaN +4.883333 NaN 9.316111 2.322161 + +2024-05-27 14:32:28,512 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 17.33594468507354 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.815601812563618 + +2024-05-27 14:32:28,513 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.815601812563618 +2024-05-27 14:32:28,515 - physiofit - INFO - Results for yecJ: + optimal +yecJ X_0 0.022905 +yecJ growth_rate 0.678488 +yecJ Glc_q -6.332125 +yecJ Glc_M0 14.975641 +yecJ Ace_q 2.380932 +yecJ Ace_M0 0.194130 +2024-05-27 14:32:28,521 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:29,512 - physiofit - INFO - Running optimization for yecR +2024-05-27 14:32:29,514 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:29,515 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:29,518 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1196 0.000000 0.034776 NaN NaN +1197 0.066667 NaN 14.916747 0.011431 +1198 1.188889 0.065016 NaN NaN +1199 1.716667 NaN 14.984827 0.328391 +1200 2.276944 0.086184 NaN NaN +1201 2.800000 NaN 13.574357 0.688534 +1202 3.128333 0.130032 NaN NaN +1203 3.633333 NaN 13.187407 1.091427 +1204 3.771389 0.166320 NaN NaN +1205 4.266667 NaN 12.555452 1.529696 +1206 4.415556 0.241920 NaN NaN +1207 4.822778 0.276696 NaN NaN +1208 4.883333 NaN 11.117352 2.001045 +Experimental matrix: +[[3.47760000e-02 nan nan] + [ nan 1.49167468e+01 1.14305108e-02] + [6.50160000e-02 nan nan] + [ nan 1.49848267e+01 3.28390966e-01] + [8.61840000e-02 nan nan] + [ nan 1.35743575e+01 6.88534092e-01] + [1.30032000e-01 nan nan] + [ nan 1.31874066e+01 1.09142663e+00] + [1.66320000e-01 nan nan] + [ nan 1.25554516e+01 1.52969596e+00] + [2.41920000e-01 nan nan] + [2.76696000e-01 nan nan] + [ nan 1.11173518e+01 2.00104529e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:29,519 - physiofit - INFO - mc : False +2024-05-27 14:32:29,519 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:29,519 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:29,519 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:29,966 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:29,967 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.7192009455882933 + x: [ 3.303e-02 4.423e-01 -6.765e+00 1.515e+01 + 3.506e+00 3.116e-02] + nit: 88 + nfev: 8605 + population: [[ 3.280e-02 4.436e-01 ... 3.519e+00 3.213e-02] + [ 3.317e-02 4.412e-01 ... 3.496e+00 3.877e-02] + ... + [ 3.263e-02 4.448e-01 ... 3.548e+00 3.311e-02] + [ 3.361e-02 4.380e-01 ... 3.471e+00 4.329e-02]] + population_energies: [ 2.719e+00 2.739e+00 ... 2.741e+00 2.788e+00] + jac: [ 1.557e-02 -1.255e-03 1.390e-05 -2.875e-04 + 7.132e-05 1.301e-04] +2024-05-27 14:32:29,967 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03302500004967569 +2024-05-27 14:32:29,967 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.4422550875064526 +2024-05-27 14:32:29,967 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.76518410455015 +2024-05-27 14:32:29,967 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.146635868922806 +2024-05-27 14:32:29,967 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.505586007392038 +2024-05-27 14:32:29,967 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.031164085239709382 +2024-05-27 14:32:29,971 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.033025 NaN NaN +0.066667 NaN 15.131519 0.038997 +1.188889 0.055872 NaN NaN +1.716667 NaN 14.572456 0.328693 +2.276944 0.090401 NaN NaN +2.800000 NaN 13.909040 0.672462 +3.128333 0.131734 NaN NaN +3.633333 NaN 13.132403 1.074900 +3.771389 0.175069 NaN NaN +4.266667 NaN 12.317987 1.496914 +4.415556 0.232774 NaN NaN +4.822778 0.278708 NaN NaN +4.883333 NaN 11.272706 2.038559 + +2024-05-27 14:32:29,975 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.7192009455882933 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0012278982802804166 + +2024-05-27 14:32:29,975 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0012278982802804166 +2024-05-27 14:32:29,977 - physiofit - INFO - Results for yecR: + optimal +yecR X_0 0.033025 +yecR growth_rate 0.442255 +yecR Glc_q -6.765184 +yecR Glc_M0 15.146636 +yecR Ace_q 3.505586 +yecR Ace_M0 0.031164 +2024-05-27 14:32:29,983 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:31,115 - physiofit - INFO - Running optimization for yedD +2024-05-27 14:32:31,118 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:31,118 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:31,126 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1209 1.828889 0.087696 NaN NaN +1210 2.261389 0.074088 NaN NaN +1211 2.774167 0.104328 NaN NaN +1212 2.800000 NaN 12.467967 0.638087 +1213 3.208889 0.128520 NaN NaN +1214 3.706389 0.172368 NaN NaN +1215 3.733333 NaN 11.704798 1.177698 +1216 4.225833 0.220752 NaN NaN +1217 4.283333 NaN 11.062336 1.624487 +1218 4.635556 0.314496 NaN NaN +1219 4.750000 NaN 10.265469 2.149025 +1220 4.967500 0.412776 NaN NaN +1221 5.116667 NaN 9.558802 2.603224 +1222 5.433333 NaN 8.605503 3.067494 +Experimental matrix: +[[ 0.087696 nan nan] + [ 0.074088 nan nan] + [ 0.104328 nan nan] + [ nan 12.46796652 0.63808697] + [ 0.12852 nan nan] + [ 0.172368 nan nan] + [ nan 11.70479797 1.17769832] + [ 0.220752 nan nan] + [ nan 11.06233632 1.62448655] + [ 0.314496 nan nan] + [ nan 10.26546947 2.1490249 ] + [ 0.412776 nan nan] + [ nan 9.55880185 2.60322399] + [ nan 8.60550303 3.06749353]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:31,127 - physiofit - INFO - mc : False +2024-05-27 14:32:31,127 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:31,127 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:31,128 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:31,656 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:31,658 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.97090610709646 + x: [ 1.771e-02 6.243e-01 -5.602e+00 1.321e+01 + 3.568e+00 2.231e-01] + nit: 97 + nfev: 9541 + population: [[ 1.764e-02 6.249e-01 ... 3.558e+00 2.334e-01] + [ 1.791e-02 6.221e-01 ... 3.483e+00 2.307e-01] + ... + [ 1.724e-02 6.297e-01 ... 3.640e+00 2.121e-01] + [ 1.744e-02 6.259e-01 ... 3.570e+00 2.298e-01]] + population_energies: [ 5.971e+00 6.188e+00 ... 6.063e+00 6.059e+00] + jac: [ 4.352e-02 5.907e-03 -7.736e-05 -2.540e-04 + 2.427e-04 6.566e-04] +2024-05-27 14:32:31,658 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.017705802710855263 +2024-05-27 14:32:31,659 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6242767206602633 +2024-05-27 14:32:31,659 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.602246361976733 +2024-05-27 14:32:31,659 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.207078348251212 +2024-05-27 14:32:31,659 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.5679816137145615 +2024-05-27 14:32:31,659 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.22314796008340718 +2024-05-27 14:32:31,664 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.055458 NaN NaN +2.261389 0.072648 NaN NaN +2.774167 0.100057 NaN NaN +2.800000 NaN 12.453462 0.703114 +3.208889 0.131253 NaN NaN +3.706389 0.179057 NaN NaN +3.733333 NaN 11.731858 1.162692 +4.225833 0.247641 NaN NaN +4.283333 NaN 11.062419 1.589047 +4.635556 0.319821 NaN NaN +4.750000 NaN 10.283347 2.085226 +4.967500 0.393463 NaN NaN +5.116667 NaN 9.490441 2.590215 +5.433333 NaN 8.643321 3.129732 + +2024-05-27 14:32:31,667 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.97090610709646 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.0327805573547852 + +2024-05-27 14:32:31,668 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0327805573547852 +2024-05-27 14:32:31,671 - physiofit - INFO - Results for yedD: + optimal +yedD X_0 0.017706 +yedD growth_rate 0.624277 +yedD Glc_q -5.602246 +yedD Glc_M0 13.207078 +yedD Ace_q 3.567982 +yedD Ace_M0 0.223148 +2024-05-27 14:32:31,678 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:32,663 - physiofit - INFO - Running optimization for yedV +2024-05-27 14:32:32,665 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:32,666 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:32,670 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1223 0.000000 0.031752 NaN NaN +1224 0.066667 NaN 14.004277 0.013059 +1225 1.188889 0.052920 NaN NaN +1226 1.716667 NaN 15.303256 0.325073 +1227 2.276944 0.084672 NaN NaN +1228 2.800000 NaN 13.675106 0.722570 +1229 3.128333 0.134568 NaN NaN +1230 3.633333 NaN 12.811064 1.169403 +1231 3.771389 0.175392 NaN NaN +1232 4.266667 NaN 12.152076 1.627777 +1233 4.415556 0.244944 NaN NaN +1234 4.822778 0.337176 NaN NaN +1235 4.883333 NaN 10.929794 2.136393 +Experimental matrix: +[[3.17520000e-02 nan nan] + [ nan 1.40042772e+01 1.30592124e-02] + [5.29200000e-02 nan nan] + [ nan 1.53032563e+01 3.25073444e-01] + [8.46720000e-02 nan nan] + [ nan 1.36751055e+01 7.22570138e-01] + [1.34568000e-01 nan nan] + [ nan 1.28110643e+01 1.16940283e+00] + [1.75392000e-01 nan nan] + [ nan 1.21520762e+01 1.62777664e+00] + [2.44944000e-01 nan nan] + [3.37176000e-01 nan nan] + [ nan 1.09297936e+01 2.13639255e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:32,670 - physiofit - INFO - mc : False +2024-05-27 14:32:32,670 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:32,670 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:32,671 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:33,137 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:33,138 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 9.5689929491735 + x: [ 2.461e-02 5.340e-01 -6.555e+00 1.477e+01 + 3.687e+00 8.467e-02] + nit: 96 + nfev: 9143 + population: [[ 2.473e-02 5.326e-01 ... 3.741e+00 7.165e-02] + [ 2.492e-02 5.310e-01 ... 3.736e+00 6.919e-02] + ... + [ 2.455e-02 5.361e-01 ... 3.661e+00 9.319e-02] + [ 2.336e-02 5.429e-01 ... 3.747e+00 1.090e-01]] + population_energies: [ 9.569e+00 9.668e+00 ... 9.643e+00 9.753e+00] + jac: [ 1.169e-04 -6.697e-05 2.897e-03 -5.615e-04 + -3.087e-04 4.814e-05] +2024-05-27 14:32:33,138 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.024614594799702922 +2024-05-27 14:32:33,138 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5339586389280689 +2024-05-27 14:32:33,138 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.554619064414243 +2024-05-27 14:32:33,138 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.77153771793638 +2024-05-27 14:32:33,138 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.686826382336303 +2024-05-27 14:32:33,138 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.08467181974911439 +2024-05-27 14:32:33,141 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.024615 NaN NaN +0.066667 NaN 14.760588 0.090831 +1.188889 0.046440 NaN NaN +1.716667 NaN 14.318047 0.339750 +2.276944 0.083024 NaN NaN +2.800000 NaN 13.726162 0.672672 +3.128333 0.130809 NaN NaN +3.633333 NaN 12.970955 1.097459 +3.771389 0.184400 NaN NaN +4.266667 NaN 12.124846 1.573376 +4.415556 0.260099 NaN NaN +4.822778 0.323275 NaN NaN +4.883333 NaN 10.974915 2.220187 + +2024-05-27 14:32:33,145 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 9.5689929491735 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.27125795399687314 + +2024-05-27 14:32:33,145 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.27125795399687314 +2024-05-27 14:32:33,147 - physiofit - INFO - Results for yedV: + optimal +yedV X_0 0.024615 +yedV growth_rate 0.533959 +yedV Glc_q -6.554619 +yedV Glc_M0 14.771538 +yedV Ace_q 3.686826 +yedV Ace_M0 0.084672 +2024-05-27 14:32:33,154 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:34,167 - physiofit - INFO - Running optimization for yegD +2024-05-27 14:32:34,170 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:34,170 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:34,174 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1236 0.000000 0.039312 NaN NaN +1237 0.283333 NaN 13.881149 0.031223 +1238 1.195000 0.074088 NaN NaN +1239 1.613611 0.092232 NaN NaN +1240 1.916667 NaN 14.065701 0.392390 +1241 2.361389 0.130032 NaN NaN +1242 2.700000 NaN 13.221312 0.585353 +1243 3.286389 0.229824 NaN NaN +1244 3.616667 NaN 12.199514 1.212148 +1245 3.819444 0.322056 NaN NaN +1246 4.050000 NaN 11.591194 1.210249 +1247 4.410833 0.464184 NaN NaN +1248 4.750000 NaN 9.690332 2.180141 +Experimental matrix: +[[ 0.039312 nan nan] + [ nan 13.88114931 0.03122281] + [ 0.074088 nan nan] + [ 0.092232 nan nan] + [ nan 14.06570122 0.39238976] + [ 0.130032 nan nan] + [ nan 13.22131237 0.58535315] + [ 0.229824 nan nan] + [ nan 12.19951394 1.21214801] + [ 0.322056 nan nan] + [ nan 11.59119393 1.21024868] + [ 0.464184 nan nan] + [ nan 9.6903319 2.18014072]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:34,175 - physiofit - INFO - mc : False +2024-05-27 14:32:34,175 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:34,175 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:34,176 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:34,635 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:34,636 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.4884030568919457 + x: [ 3.263e-02 6.007e-01 -5.048e+00 1.431e+01 + 2.340e+00 6.789e-02] + nit: 94 + nfev: 9110 + population: [[ 3.238e-02 6.027e-01 ... 2.335e+00 7.094e-02] + [ 3.280e-02 5.989e-01 ... 2.337e+00 7.641e-02] + ... + [ 3.188e-02 6.065e-01 ... 2.329e+00 7.449e-02] + [ 3.267e-02 6.005e-01 ... 2.324e+00 6.468e-02]] + population_energies: [ 3.488e+00 3.505e+00 ... 3.526e+00 3.539e+00] + jac: [-2.725e-02 -9.111e-03 -1.525e-03 -3.523e-03 + -3.808e-03 -1.169e-02] +2024-05-27 14:32:34,636 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.032633791343627205 +2024-05-27 14:32:34,636 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6007016405893061 +2024-05-27 14:32:34,636 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.04837221418323 +2024-05-27 14:32:34,636 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.312275353358974 +2024-05-27 14:32:34,636 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3404827066397424 +2024-05-27 14:32:34,636 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.06788570551274506 +2024-05-27 14:32:34,640 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.032634 NaN NaN +0.283333 NaN 14.261389 0.091477 +1.195000 0.066899 NaN NaN +1.613611 0.086026 NaN NaN +1.916667 NaN 13.719207 0.342839 +2.361389 0.134806 NaN NaN +2.700000 NaN 13.198053 0.584452 +3.286389 0.234977 NaN NaN +3.616667 NaN 12.178397 1.057176 +3.819444 0.323660 NaN NaN +4.050000 NaN 11.462399 1.389121 +4.410833 0.461713 NaN NaN +4.750000 NaN 9.829385 2.146205 + +2024-05-27 14:32:34,643 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.4884030568919457 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.004483241470784785 + +2024-05-27 14:32:34,643 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.004483241470784785 +2024-05-27 14:32:34,645 - physiofit - INFO - Results for yegD: + optimal +yegD X_0 0.032634 +yegD growth_rate 0.600702 +yegD Glc_q -5.048372 +yegD Glc_M0 14.312275 +yegD Ace_q 2.340483 +yegD Ace_M0 0.067886 +2024-05-27 14:32:34,650 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:35,709 - physiofit - INFO - Running optimization for yegQ +2024-05-27 14:32:35,712 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:35,712 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:35,716 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1249 0.000000 0.031752 NaN NaN +1250 0.066667 NaN 15.486099 0.010598 +1251 1.188889 0.055944 NaN NaN +1252 1.716667 NaN 15.000999 0.315410 +1253 2.276944 0.099792 NaN NaN +1254 2.800000 NaN 13.404166 0.688527 +1255 3.128333 0.157248 NaN NaN +1256 3.633333 NaN 12.804085 1.108201 +1257 3.771389 0.211680 NaN NaN +1258 4.266667 NaN 11.890149 1.513354 +1259 4.415556 0.320544 NaN NaN +1260 4.822778 0.370440 NaN NaN +1261 4.883333 NaN 10.265574 1.825895 +Experimental matrix: +[[3.17520000e-02 nan nan] + [ nan 1.54860994e+01 1.05977294e-02] + [5.59440000e-02 nan nan] + [ nan 1.50009987e+01 3.15410253e-01] + [9.97920000e-02 nan nan] + [ nan 1.34041658e+01 6.88527188e-01] + [1.57248000e-01 nan nan] + [ nan 1.28040853e+01 1.10820136e+00] + [2.11680000e-01 nan nan] + [ nan 1.18901486e+01 1.51335373e+00] + [3.20544000e-01 nan nan] + [3.70440000e-01 nan nan] + [ nan 1.02655736e+01 1.82589513e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:35,716 - physiofit - INFO - mc : False +2024-05-27 14:32:35,716 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:35,717 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:35,717 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:36,117 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:36,118 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.859157645958297 + x: [ 3.310e-02 5.031e-01 -7.357e+00 1.540e+01 + 2.644e+00 1.002e-01] + nit: 83 + nfev: 8050 + population: [[ 3.353e-02 5.003e-01 ... 2.658e+00 9.359e-02] + [ 3.330e-02 5.016e-01 ... 2.667e+00 1.019e-01] + ... + [ 3.352e-02 4.999e-01 ... 2.665e+00 9.246e-02] + [ 3.421e-02 4.964e-01 ... 2.615e+00 9.731e-02]] + population_energies: [ 3.859e+00 3.906e+00 ... 3.876e+00 3.974e+00] + jac: [ 2.618e-02 3.842e-03 3.553e-06 -4.219e-05 + 3.033e-05 6.062e-05] +2024-05-27 14:32:36,118 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03309738911473731 +2024-05-27 14:32:36,119 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5031063105209923 +2024-05-27 14:32:36,119 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.357387926356274 +2024-05-27 14:32:36,119 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.395827831896895 +2024-05-27 14:32:36,119 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.6443185248607675 +2024-05-27 14:32:36,120 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.10022702107853343 +2024-05-27 14:32:36,123 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.033097 NaN NaN +0.066667 NaN 15.379318 0.106161 +1.188889 0.060195 NaN NaN +1.716667 NaN 14.731839 0.338871 +2.276944 0.104063 NaN NaN +2.800000 NaN 13.899923 0.637870 +3.128333 0.159707 NaN NaN +3.633333 NaN 12.868725 1.008493 +3.771389 0.220713 NaN NaN +4.266667 NaN 11.738810 1.414595 +4.415556 0.305194 NaN NaN +4.822778 0.374587 NaN NaN +4.883333 NaN 10.232450 1.955996 + +2024-05-27 14:32:36,126 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.859157645958297 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0074006633526321145 + +2024-05-27 14:32:36,127 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0074006633526321145 +2024-05-27 14:32:36,128 - physiofit - INFO - Results for yegQ: + optimal +yegQ X_0 0.033097 +yegQ growth_rate 0.503106 +yegQ Glc_q -7.357388 +yegQ Glc_M0 15.395828 +yegQ Ace_q 2.644319 +yegQ Ace_M0 0.100227 +2024-05-27 14:32:36,135 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:37,091 - physiofit - INFO - Running optimization for yehS +2024-05-27 14:32:37,093 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:37,093 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:37,097 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1262 0.000000 0.037800 NaN NaN +1263 0.066667 NaN 14.195819 0.014545 +1264 1.188889 0.071064 NaN NaN +1265 1.716667 NaN 15.236019 0.340996 +1266 2.276944 0.117936 NaN NaN +1267 2.800000 NaN 13.698114 0.755017 +1268 3.128333 0.184464 NaN NaN +1269 3.633333 NaN 12.201922 1.165718 +1270 3.771389 0.264600 NaN NaN +1271 4.266667 NaN 11.396876 1.659406 +1272 4.415556 0.379512 NaN NaN +1273 4.822778 0.571536 NaN NaN +1274 4.883333 NaN 9.726532 2.228836 +Experimental matrix: +[[3.78000000e-02 nan nan] + [ nan 1.41958194e+01 1.45452209e-02] + [7.10640000e-02 nan nan] + [ nan 1.52360191e+01 3.40996262e-01] + [1.17936000e-01 nan nan] + [ nan 1.36981143e+01 7.55016872e-01] + [1.84464000e-01 nan nan] + [ nan 1.22019225e+01 1.16571823e+00] + [2.64600000e-01 nan nan] + [ nan 1.13968755e+01 1.65940650e+00] + [3.79512000e-01 nan nan] + [5.71536000e-01 nan nan] + [ nan 9.72653169e+00 2.22883589e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:37,097 - physiofit - INFO - mc : False +2024-05-27 14:32:37,097 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:37,097 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:37,098 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:37,511 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:37,512 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 15.553196560717081 + x: [ 2.508e-02 6.368e-01 -6.148e+00 1.483e+01 + 2.588e+00 1.503e-01] + nit: 86 + nfev: 8453 + population: [[ 2.558e-02 6.327e-01 ... 2.554e+00 1.602e-01] + [ 2.404e-02 6.441e-01 ... 2.624e+00 1.457e-01] + ... + [ 2.492e-02 6.394e-01 ... 2.700e+00 1.352e-01] + [ 2.587e-02 6.304e-01 ... 2.635e+00 1.475e-01]] + population_energies: [ 1.555e+01 1.599e+01 ... 1.593e+01 1.582e+01] + jac: [-7.359e-03 -8.768e-04 -1.865e-05 1.226e-05 + -3.890e-05 -9.575e-05] +2024-05-27 14:32:37,513 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025076694289178667 +2024-05-27 14:32:37,513 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6368029428643616 +2024-05-27 14:32:37,513 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.148444415700809 +2024-05-27 14:32:37,513 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.826273315343228 +2024-05-27 14:32:37,513 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5880554970294085 +2024-05-27 14:32:37,513 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15031982955407505 +2024-05-27 14:32:37,517 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.025077 NaN NaN +0.066667 NaN 14.815773 0.154740 +1.188889 0.053465 NaN NaN +1.716667 NaN 14.345970 0.352493 +2.276944 0.106901 NaN NaN +2.800000 NaN 13.628274 0.654592 +3.128333 0.183841 NaN NaN +3.633333 NaN 12.620090 1.078965 +3.771389 0.276876 NaN NaN +4.266667 NaN 11.403850 1.590915 +4.415556 0.417288 NaN NaN +4.822778 0.540826 NaN NaN +4.883333 NaN 9.641326 2.332812 + +2024-05-27 14:32:37,520 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 15.553196560717081 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.7258992749038824 + +2024-05-27 14:32:37,521 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.7258992749038824 +2024-05-27 14:32:37,523 - physiofit - INFO - Results for yehS: + optimal +yehS X_0 0.025077 +yehS growth_rate 0.636803 +yehS Glc_q -6.148444 +yehS Glc_M0 14.826273 +yehS Ace_q 2.588055 +yehS Ace_M0 0.150320 +2024-05-27 14:32:37,529 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:38,487 - physiofit - INFO - Running optimization for yeiR +2024-05-27 14:32:38,489 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:38,489 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:38,493 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1275 1.950000 NaN 13.759949 0.390911 +1276 2.501389 0.114912 NaN NaN +1277 3.250000 NaN 12.994782 0.930675 +1278 3.341944 0.175392 NaN NaN +1279 3.997500 0.243432 NaN NaN +1280 4.083333 NaN 12.009923 1.453928 +1281 4.523333 0.356832 NaN NaN +1282 4.766667 NaN 10.668117 1.923777 +Experimental matrix: +[[ nan 13.75994924 0.39091106] + [ 0.114912 nan nan] + [ nan 12.99478194 0.93067483] + [ 0.175392 nan nan] + [ 0.243432 nan nan] + [ nan 12.00992313 1.4539278 ] + [ 0.356832 nan nan] + [ nan 10.66811729 1.92377679]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:38,493 - physiofit - INFO - mc : False +2024-05-27 14:32:38,493 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:38,493 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:38,494 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:38,943 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:38,944 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.2654721931572204 + x: [ 2.540e-02 5.790e-01 -5.561e+00 1.432e+01 + 2.737e+00 2.114e-01] + nit: 98 + nfev: 9442 + population: [[ 2.548e-02 5.780e-01 ... 2.753e+00 2.075e-01] + [ 2.546e-02 5.793e-01 ... 2.752e+00 2.074e-01] + ... + [ 2.549e-02 5.779e-01 ... 2.775e+00 2.047e-01] + [ 2.531e-02 5.797e-01 ... 2.778e+00 1.966e-01]] + population_energies: [ 1.265e+00 1.277e+00 ... 1.283e+00 1.273e+00] + jac: [ 1.791e-02 -2.739e-04 -1.129e-04 -2.323e-04 + 4.065e-04 8.501e-04] +2024-05-27 14:32:38,944 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025399589791227625 +2024-05-27 14:32:38,944 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5790451996361089 +2024-05-27 14:32:38,944 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.561032084385985 +2024-05-27 14:32:38,944 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.315661192681072 +2024-05-27 14:32:38,944 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.7369402661673448 +2024-05-27 14:32:38,945 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.21142824888183992 +2024-05-27 14:32:38,948 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.805113 0.462702 +2.501389 0.108110 NaN NaN +3.250000 NaN 12.957946 0.879647 +3.341944 0.175892 NaN NaN +3.997500 0.257100 NaN NaN +4.083333 NaN 11.964635 1.368519 +4.523333 0.348608 NaN NaN +4.766667 NaN 10.705054 1.988440 + +2024-05-27 14:32:38,951 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.2654721931572204 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.026472567478161162 + +2024-05-27 14:32:38,951 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.026472567478161162 +2024-05-27 14:32:38,953 - physiofit - INFO - Results for yeiR: + optimal +yeiR X_0 0.025400 +yeiR growth_rate 0.579045 +yeiR Glc_q -5.561032 +yeiR Glc_M0 14.315661 +yeiR Ace_q 2.736940 +yeiR Ace_M0 0.211428 +2024-05-27 14:32:38,959 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:39,895 - physiofit - INFO - Running optimization for yejF +2024-05-27 14:32:39,898 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:39,898 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:39,902 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1283 1.828889 0.061992 NaN NaN +1284 2.261389 0.080136 NaN NaN +1285 2.774167 0.110376 NaN NaN +1286 2.800000 NaN 12.382593 0.651209 +1287 3.208889 0.136080 NaN NaN +1288 3.706389 0.196560 NaN NaN +1289 3.733333 NaN 11.622903 1.123195 +1290 4.225833 0.243432 NaN NaN +1291 4.283333 NaN 10.871863 1.490365 +1292 4.635556 0.326592 NaN NaN +1293 4.750000 NaN 9.910935 1.856852 +1294 4.967500 0.435456 NaN NaN +1295 5.116667 NaN 9.238721 2.248520 +1296 5.433333 NaN 9.031997 2.527948 +Experimental matrix: +[[ 0.061992 nan nan] + [ 0.080136 nan nan] + [ 0.110376 nan nan] + [ nan 12.3825926 0.65120868] + [ 0.13608 nan nan] + [ 0.19656 nan nan] + [ nan 11.62290298 1.12319507] + [ 0.243432 nan nan] + [ nan 10.87186267 1.49036452] + [ 0.326592 nan nan] + [ nan 9.9109351 1.85685203] + [ 0.435456 nan nan] + [ nan 9.23872147 2.24851975] + [ nan 9.03199736 2.52794838]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:39,903 - physiofit - INFO - mc : False +2024-05-27 14:32:39,903 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:39,903 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:39,904 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:40,345 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:40,346 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.410342998359171 + x: [ 1.860e-02 6.264e-01 -4.927e+00 1.293e+01 + 2.599e+00 3.753e-01] + nit: 94 + nfev: 8823 + population: [[ 1.854e-02 6.270e-01 ... 2.598e+00 3.781e-01] + [ 1.886e-02 6.229e-01 ... 2.627e+00 3.561e-01] + ... + [ 1.857e-02 6.270e-01 ... 2.600e+00 3.777e-01] + [ 1.880e-02 6.239e-01 ... 2.579e+00 3.915e-01]] + population_energies: [ 4.410e+00 4.427e+00 ... 4.417e+00 4.489e+00] + jac: [-2.136e-02 2.519e-03 -4.282e-02 -8.668e-03 + -3.158e-02 2.334e-02] +2024-05-27 14:32:40,346 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.01859762846415186 +2024-05-27 14:32:40,346 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6264142312094847 +2024-05-27 14:32:40,347 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.9271003625201875 +2024-05-27 14:32:40,347 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 12.925826891649857 +2024-05-27 14:32:40,347 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5989273427851463 +2024-05-27 14:32:40,347 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.3753009475610265 +2024-05-27 14:32:40,350 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.058479 NaN NaN +2.261389 0.076677 NaN NaN +2.774167 0.105722 NaN NaN +2.800000 NaN 12.226980 0.743926 +3.208889 0.138813 NaN NaN +3.706389 0.189572 NaN NaN +3.733333 NaN 11.555637 1.098043 +4.225833 0.262475 NaN NaN +4.283333 NaN 10.931877 1.427062 +4.635556 0.339275 NaN NaN +4.750000 NaN 10.205181 1.810376 +4.967500 0.417693 NaN NaN +5.116667 NaN 9.464930 2.200841 +5.433333 NaN 8.673491 2.618306 + +2024-05-27 14:32:40,354 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.410342998359171 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.0075519836277965395 + +2024-05-27 14:32:40,354 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0075519836277965395 +2024-05-27 14:32:40,356 - physiofit - INFO - Results for yejF: + optimal +yejF X_0 0.018598 +yejF growth_rate 0.626414 +yejF Glc_q -4.927100 +yejF Glc_M0 12.925827 +yejF Ace_q 2.598927 +yejF Ace_M0 0.375301 +2024-05-27 14:32:40,362 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:41,326 - physiofit - INFO - Running optimization for yfaT +2024-05-27 14:32:41,329 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:41,329 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:41,333 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1297 0.000000 0.034776 NaN NaN +1298 0.066667 NaN 15.980768 0.015510 +1299 1.188889 0.066528 NaN NaN +1300 1.716667 NaN 15.235090 0.351452 +1301 2.276944 0.114912 NaN NaN +1302 2.800000 NaN 13.466809 0.689176 +1303 3.128333 0.175392 NaN NaN +1304 3.633333 NaN 12.862810 1.104614 +1305 3.771389 0.243432 NaN NaN +1306 4.266667 NaN 11.758807 1.576219 +1307 4.415556 0.356832 NaN NaN +1308 4.822778 0.430920 NaN NaN +1309 4.883333 NaN 10.064414 2.039463 +Experimental matrix: +[[3.47760000e-02 nan nan] + [ nan 1.59807682e+01 1.55104630e-02] + [6.65280000e-02 nan nan] + [ nan 1.52350899e+01 3.51452145e-01] + [1.14912000e-01 nan nan] + [ nan 1.34668089e+01 6.89175502e-01] + [1.75392000e-01 nan nan] + [ nan 1.28628100e+01 1.10461358e+00] + [2.43432000e-01 nan nan] + [ nan 1.17588072e+01 1.57621860e+00] + [3.56832000e-01 nan nan] + [4.30920000e-01 nan nan] + [ nan 1.00644136e+01 2.03946323e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:41,333 - physiofit - INFO - mc : False +2024-05-27 14:32:41,333 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:41,333 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:41,334 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:41,699 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:41,701 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.3045555097508927 + x: [ 3.652e-02 5.112e-01 -7.277e+00 1.574e+01 + 2.553e+00 8.039e-02] + nit: 80 + nfev: 7647 + population: [[ 3.662e-02 5.108e-01 ... 2.550e+00 8.306e-02] + [ 3.691e-02 5.090e-01 ... 2.548e+00 7.459e-02] + ... + [ 3.723e-02 5.069e-01 ... 2.527e+00 8.794e-02] + [ 3.674e-02 5.103e-01 ... 2.560e+00 7.803e-02]] + population_energies: [ 3.305e+00 3.313e+00 ... 3.327e+00 3.387e+00] + jac: [ 7.043e-03 5.993e-04 1.488e-03 5.257e-03 + 3.287e-04 6.891e-04] +2024-05-27 14:32:41,703 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03652311808078611 +2024-05-27 14:32:41,703 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5111783885181634 +2024-05-27 14:32:41,703 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.276889588840574 +2024-05-27 14:32:41,704 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.743122074061887 +2024-05-27 14:32:41,704 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5530721487930235 +2024-05-27 14:32:41,704 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.08039245181489119 +2024-05-27 14:32:41,708 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.036523 NaN NaN +0.066667 NaN 15.725098 0.086716 +1.188889 0.067066 NaN NaN +1.716667 NaN 15.012660 0.336672 +2.276944 0.116964 NaN NaN +2.800000 NaN 14.087610 0.661223 +3.128333 0.180744 NaN NaN +3.633333 NaN 12.932250 1.066577 +3.771389 0.251087 NaN NaN +4.266667 NaN 11.658897 1.513329 +4.415556 0.349004 NaN NaN +4.822778 0.429768 NaN NaN +4.883333 NaN 9.952738 2.111929 + +2024-05-27 14:32:41,714 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.3045555097508927 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.00340642671652474 + +2024-05-27 14:32:41,714 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00340642671652474 +2024-05-27 14:32:41,717 - physiofit - INFO - Results for yfaT: + optimal +yfaT X_0 0.036523 +yfaT growth_rate 0.511178 +yfaT Glc_q -7.276890 +yfaT Glc_M0 15.743122 +yfaT Ace_q 2.553072 +yfaT Ace_M0 0.080392 +2024-05-27 14:32:41,723 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:43,070 - physiofit - INFO - Running optimization for yfcD +2024-05-27 14:32:43,073 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:43,073 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:43,077 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1310 0.000000 0.037800 NaN NaN +1311 0.066667 NaN 14.819432 0.016389 +1312 1.188889 0.063504 NaN NaN +1313 1.716667 NaN 15.074272 0.345403 +1314 2.276944 0.113400 NaN NaN +1315 2.800000 NaN 13.427484 0.720777 +1316 3.128333 0.178416 NaN NaN +1317 3.633333 NaN 12.536661 1.141348 +1318 3.771389 0.240408 NaN NaN +1319 4.266667 NaN 11.706140 1.610331 +1320 4.415556 0.403704 NaN NaN +1321 4.822778 0.563976 NaN NaN +1322 4.883333 NaN 10.047507 2.077567 +Experimental matrix: +[[ 0.0378 nan nan] + [ nan 14.8194318 0.01638905] + [ 0.063504 nan nan] + [ nan 15.07427188 0.34540267] + [ 0.1134 nan nan] + [ nan 13.42748366 0.72077716] + [ 0.178416 nan nan] + [ nan 12.53666128 1.14134785] + [ 0.240408 nan nan] + [ nan 11.7061402 1.61033106] + [ 0.403704 nan nan] + [ 0.563976 nan nan] + [ nan 10.04750745 2.07756676]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:43,078 - physiofit - INFO - mc : False +2024-05-27 14:32:43,078 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:43,078 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:43,079 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:43,465 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:43,466 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 10.170817907881512 + x: [ 2.273e-02 6.582e-01 -6.060e+00 1.492e+01 + 2.469e+00 1.777e-01] + nit: 78 + nfev: 7796 + population: [[ 2.291e-02 6.561e-01 ... 2.489e+00 1.698e-01] + [ 2.211e-02 6.646e-01 ... 2.486e+00 1.646e-01] + ... + [ 2.298e-02 6.554e-01 ... 2.431e+00 1.656e-01] + [ 2.268e-02 6.583e-01 ... 2.442e+00 1.858e-01]] + population_energies: [ 1.017e+01 1.027e+01 ... 1.027e+01 1.019e+01] + jac: [ 7.283e-06 8.527e-06 7.105e-07 -8.882e-07 + 1.421e-06 1.421e-06] +2024-05-27 14:32:43,467 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02272579045293171 +2024-05-27 14:32:43,467 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6581570369644054 +2024-05-27 14:32:43,467 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.060162518966726 +2024-05-27 14:32:43,468 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.917567625153513 +2024-05-27 14:32:43,468 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4688231704757935 +2024-05-27 14:32:43,468 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1777344301776245 +2024-05-27 14:32:43,471 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.022726 NaN NaN +0.066667 NaN 14.908182 0.181558 +1.188889 0.049699 NaN NaN +1.716667 NaN 14.479149 0.356340 +2.276944 0.101706 NaN NaN +2.800000 NaN 13.805499 0.630775 +3.128333 0.178116 NaN NaN +3.633333 NaN 12.840150 1.024045 +3.771389 0.271963 NaN NaN +4.266667 NaN 11.657600 1.505798 +4.415556 0.415561 NaN NaN +4.822778 0.543291 NaN NaN +4.883333 NaN 9.920916 2.213299 + +2024-05-27 14:32:43,475 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 10.170817907881512 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.32009012276062454 + +2024-05-27 14:32:43,475 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.32009012276062454 +2024-05-27 14:32:43,477 - physiofit - INFO - Results for yfcD: + optimal +yfcD X_0 0.022726 +yfcD growth_rate 0.658157 +yfcD Glc_q -6.060163 +yfcD Glc_M0 14.917568 +yfcD Ace_q 2.468823 +yfcD Ace_M0 0.177734 +2024-05-27 14:32:43,483 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:44,455 - physiofit - INFO - Running optimization for yfcL +2024-05-27 14:32:44,457 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:44,458 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:44,461 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1323 0.000000 0.034776 NaN NaN +1324 0.066667 NaN 15.541054 0.016953 +1325 1.188889 0.072576 NaN NaN +1326 1.716667 NaN 15.570225 0.337752 +1327 2.276944 0.113400 NaN NaN +1328 2.800000 NaN 13.717049 0.725391 +1329 3.128333 0.158760 NaN NaN +1330 3.633333 NaN 12.415390 1.134079 +1331 3.771389 0.219240 NaN NaN +1332 4.266667 NaN 11.739381 1.640573 +1333 4.415556 0.343224 NaN NaN +1334 4.822778 0.406728 NaN NaN +1335 4.883333 NaN 10.250830 2.157443 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 15.54105436 0.01695301] + [ 0.072576 nan nan] + [ nan 15.5702251 0.33775187] + [ 0.1134 nan nan] + [ nan 13.71704898 0.72539132] + [ 0.15876 nan nan] + [ nan 12.41538965 1.13407896] + [ 0.21924 nan nan] + [ nan 11.73938133 1.64057309] + [ 0.343224 nan nan] + [ 0.406728 nan nan] + [ nan 10.25083039 2.1574426 ]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:44,462 - physiofit - INFO - mc : False +2024-05-27 14:32:44,462 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:44,462 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:44,462 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:44,902 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:44,903 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 6.03458139037968 + x: [ 3.463e-02 5.099e-01 -7.467e+00 1.564e+01 + 2.864e+00 6.670e-02] + nit: 93 + nfev: 8859 + population: [[ 3.439e-02 5.121e-01 ... 2.873e+00 6.714e-02] + [ 3.554e-02 5.038e-01 ... 2.909e+00 3.109e-02] + ... + [ 3.383e-02 5.151e-01 ... 2.824e+00 9.125e-02] + [ 3.469e-02 5.111e-01 ... 2.830e+00 8.075e-02]] + population_energies: [ 6.035e+00 6.153e+00 ... 6.189e+00 6.102e+00] + jac: [-1.350e-01 -1.242e-02 2.461e-04 7.004e-04 + -1.108e-03 -3.425e-03] +2024-05-27 14:32:44,903 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.034626647239201704 +2024-05-27 14:32:44,903 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5099447470177645 +2024-05-27 14:32:44,903 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.4673930762583245 +2024-05-27 14:32:44,903 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.64416510852894 +2024-05-27 14:32:44,904 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.8642223451550612 +2024-05-27 14:32:44,904 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.06670068736069852 +2024-05-27 14:32:44,907 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.034627 NaN NaN +0.066667 NaN 15.626631 0.073426 +1.188889 0.063491 NaN NaN +1.716667 NaN 14.934363 0.338955 +2.276944 0.110580 NaN NaN +2.800000 NaN 14.036946 0.683172 +3.128333 0.170699 NaN NaN +3.633333 NaN 12.917394 1.112592 +3.771389 0.236944 NaN NaN +4.266667 NaN 11.684604 1.585445 +4.415556 0.329084 NaN NaN +4.822778 0.405035 NaN NaN +4.883333 NaN 10.034066 2.218532 + +2024-05-27 14:32:44,910 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 6.03458139037968 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.05511468040270874 + +2024-05-27 14:32:44,911 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.05511468040270874 +2024-05-27 14:32:44,912 - physiofit - INFO - Results for yfcL: + optimal +yfcL X_0 0.034627 +yfcL growth_rate 0.509945 +yfcL Glc_q -7.467393 +yfcL Glc_M0 15.644165 +yfcL Ace_q 2.864222 +yfcL Ace_M0 0.066701 +2024-05-27 14:32:44,918 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:45,928 - physiofit - INFO - Running optimization for yfdI +2024-05-27 14:32:45,931 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:45,931 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:45,935 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1336 0.000000 0.037800 NaN NaN +1337 0.283333 NaN 14.317281 0.046314 +1338 1.195000 0.066528 NaN NaN +1339 1.613611 0.077112 NaN NaN +1340 1.916667 NaN 13.807872 0.411548 +1341 2.361389 0.116424 NaN NaN +1342 2.700000 NaN 13.693160 0.696410 +1343 3.286389 0.195048 NaN NaN +1344 3.616667 NaN 12.345526 1.122538 +1345 3.819444 0.291816 NaN NaN +1346 4.050000 NaN 11.946463 1.431109 +1347 4.410833 0.361368 NaN NaN +1348 4.750000 NaN 10.667054 1.905729 +Experimental matrix: +[[ 0.0378 nan nan] + [ nan 14.31728141 0.0463145 ] + [ 0.066528 nan nan] + [ 0.077112 nan nan] + [ nan 13.80787152 0.41154805] + [ 0.116424 nan nan] + [ nan 13.69316009 0.69641036] + [ 0.195048 nan nan] + [ nan 12.34552632 1.12253766] + [ 0.291816 nan nan] + [ nan 11.94646269 1.43110894] + [ 0.361368 nan nan] + [ nan 10.66705378 1.90572861]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:45,936 - physiofit - INFO - mc : False +2024-05-27 14:32:45,936 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:45,936 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:45,936 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:46,360 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:46,362 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.1380217003166178 + x: [ 3.520e-02 5.331e-01 -4.971e+00 1.445e+01 + 2.457e+00 1.171e-01] + nit: 89 + nfev: 8485 + population: [[ 3.518e-02 5.328e-01 ... 2.453e+00 1.201e-01] + [ 3.566e-02 5.302e-01 ... 2.457e+00 1.177e-01] + ... + [ 3.529e-02 5.313e-01 ... 2.460e+00 1.130e-01] + [ 3.561e-02 5.293e-01 ... 2.445e+00 1.194e-01]] + population_energies: [ 3.138e+00 3.154e+00 ... 3.163e+00 3.160e+00] + jac: [ 2.065e-02 5.999e-04 -1.684e-02 1.909e-03 + 1.651e-02 -4.339e-03] +2024-05-27 14:32:46,362 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03519939491736402 +2024-05-27 14:32:46,362 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5330509979642242 +2024-05-27 14:32:46,362 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.970588350438119 +2024-05-27 14:32:46,362 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.452327487203215 +2024-05-27 14:32:46,362 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4565579544257865 +2024-05-27 14:32:46,362 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.11713376680212921 +2024-05-27 14:32:46,365 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.035199 NaN NaN +0.283333 NaN 14.398816 0.143580 +1.195000 0.066555 NaN NaN +1.613611 0.083193 NaN NaN +1.916667 NaN 13.868786 0.405531 +2.361389 0.123937 NaN NaN +2.700000 NaN 13.396264 0.639060 +3.286389 0.202926 NaN NaN +3.616667 NaN 12.524048 1.070126 +3.819444 0.269613 NaN NaN +4.050000 NaN 11.937706 1.359907 +4.410833 0.369529 NaN NaN +4.750000 NaN 10.651938 1.995357 + +2024-05-27 14:32:46,369 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.1380217003166178 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.002610776216743493 + +2024-05-27 14:32:46,369 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.002610776216743493 +2024-05-27 14:32:46,371 - physiofit - INFO - Results for yfdI: + optimal +yfdI X_0 0.035199 +yfdI growth_rate 0.533051 +yfdI Glc_q -4.970588 +yfdI Glc_M0 14.452327 +yfdI Ace_q 2.456558 +yfdI Ace_M0 0.117134 +2024-05-27 14:32:46,377 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:47,335 - physiofit - INFO - Running optimization for yfeC +2024-05-27 14:32:47,337 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:47,338 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:47,341 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1349 1.828889 0.063504 NaN NaN +1350 2.261389 0.078624 NaN NaN +1351 2.774167 0.110376 NaN NaN +1352 2.800000 NaN 12.540557 0.590945 +1353 3.208889 0.119448 NaN NaN +1354 3.706389 0.164808 NaN NaN +1355 3.733333 NaN 11.741487 1.052326 +1356 4.225833 0.205632 NaN NaN +1357 4.283333 NaN 10.936153 1.389942 +1358 4.635556 0.266112 NaN NaN +1359 4.750000 NaN 10.272874 1.799163 +1360 4.967500 0.320544 NaN NaN +1361 5.116667 NaN 9.798535 2.174153 +1362 5.433333 NaN 8.989453 2.514518 +Experimental matrix: +[[ 0.063504 nan nan] + [ 0.078624 nan nan] + [ 0.110376 nan nan] + [ nan 12.54055707 0.5909451 ] + [ 0.119448 nan nan] + [ 0.164808 nan nan] + [ nan 11.74148686 1.05232568] + [ 0.205632 nan nan] + [ nan 10.93615262 1.38994237] + [ 0.266112 nan nan] + [ nan 10.27287406 1.79916261] + [ 0.320544 nan nan] + [ nan 9.79853474 2.17415276] + [ nan 8.98945279 2.51451811]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:47,342 - physiofit - INFO - mc : False +2024-05-27 14:32:47,342 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:47,342 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:47,342 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:47,839 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:47,840 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.9464773040733772 + x: [ 2.416e-02 5.171e-01 -6.044e+00 1.338e+01 + 3.339e+00 1.133e-01] + nit: 111 + nfev: 10409 + population: [[ 2.421e-02 5.165e-01 ... 3.333e+00 1.182e-01] + [ 2.394e-02 5.182e-01 ... 3.340e+00 1.154e-01] + ... + [ 2.419e-02 5.171e-01 ... 3.340e+00 1.147e-01] + [ 2.441e-02 5.146e-01 ... 3.333e+00 1.156e-01]] + population_energies: [ 9.465e-01 9.666e-01 ... 9.594e-01 9.509e-01] + jac: [ 3.476e-03 4.322e-04 -1.013e-03 5.062e-04 + 2.753e-05 -6.060e-05] +2024-05-27 14:32:47,840 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02416384652944555 +2024-05-27 14:32:47,840 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5170912549777581 +2024-05-27 14:32:47,840 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.044002149584911 +2024-05-27 14:32:47,841 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.380523703024366 +2024-05-27 14:32:47,841 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.338965402711689 +2024-05-27 14:32:47,841 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1132890211297008 +2024-05-27 14:32:47,845 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.062213 NaN NaN +2.261389 0.077805 NaN NaN +2.774167 0.101429 NaN NaN +2.800000 NaN 12.461475 0.621011 +3.208889 0.126995 NaN NaN +3.706389 0.164252 NaN NaN +3.733333 NaN 11.716178 1.032745 +4.225833 0.214863 NaN NaN +4.283333 NaN 11.075755 1.386542 +4.635556 0.265566 NaN NaN +4.750000 NaN 10.369669 1.776614 +4.967500 0.315295 NaN NaN +5.116667 NaN 9.682140 2.156434 +5.433333 NaN 8.973894 2.547700 + +2024-05-27 14:32:47,849 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.9464773040733772 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 6.980746409869015e-07 + +2024-05-27 14:32:47,849 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 6.980746409869015e-07 +2024-05-27 14:32:47,852 - physiofit - INFO - Results for yfeC: + optimal +yfeC X_0 0.024164 +yfeC growth_rate 0.517091 +yfeC Glc_q -6.044002 +yfeC Glc_M0 13.380524 +yfeC Ace_q 3.338965 +yfeC Ace_M0 0.113289 +2024-05-27 14:32:47,857 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:48,811 - physiofit - INFO - Running optimization for yfeY +2024-05-27 14:32:48,815 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:48,815 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:48,818 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1363 0.000000 0.034776 NaN NaN +1364 0.066667 NaN 15.678075 0.012534 +1365 1.188889 0.061992 NaN NaN +1366 1.716667 NaN 14.531854 0.323737 +1367 2.276944 0.107352 NaN NaN +1368 2.800000 NaN 13.493815 0.729390 +1369 3.128333 0.157248 NaN NaN +1370 3.633333 NaN 12.693457 1.189348 +1371 3.771389 0.246456 NaN NaN +1372 4.266667 NaN 11.497934 1.623049 +1373 4.415556 0.374976 NaN NaN +1374 4.822778 0.563976 NaN NaN +1375 4.883333 NaN 9.613952 2.092291 +Experimental matrix: +[[3.47760000e-02 nan nan] + [ nan 1.56780752e+01 1.25339836e-02] + [6.19920000e-02 nan nan] + [ nan 1.45318538e+01 3.23736754e-01] + [1.07352000e-01 nan nan] + [ nan 1.34938150e+01 7.29389677e-01] + [1.57248000e-01 nan nan] + [ nan 1.26934572e+01 1.18934838e+00] + [2.46456000e-01 nan nan] + [ nan 1.14979342e+01 1.62304914e+00] + [3.74976000e-01 nan nan] + [5.63976000e-01 nan nan] + [ nan 9.61395153e+00 2.09229135e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:48,819 - physiofit - INFO - mc : False +2024-05-27 14:32:48,819 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:48,819 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:48,819 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:49,226 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:49,229 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 12.253437251227274 + x: [ 2.026e-02 6.783e-01 -7.199e+00 1.515e+01 + 2.609e+00 1.870e-01] + nit: 86 + nfev: 8362 + population: [[ 2.047e-02 6.760e-01 ... 2.603e+00 1.920e-01] + [ 2.039e-02 6.770e-01 ... 2.558e+00 2.005e-01] + ... + [ 2.042e-02 6.774e-01 ... 2.589e+00 1.839e-01] + [ 2.062e-02 6.737e-01 ... 2.550e+00 2.143e-01]] + population_energies: [ 1.225e+01 1.234e+01 ... 1.228e+01 1.234e+01] + jac: [ 4.250e-02 1.119e-02 -5.077e-02 -7.887e-04 + 1.078e-01 -3.362e-02] +2024-05-27 14:32:49,229 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.020262311544010852 +2024-05-27 14:32:49,229 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6783275550715984 +2024-05-27 14:32:49,229 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.198798162710247 +2024-05-27 14:32:49,229 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.147835191004466 +2024-05-27 14:32:49,229 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.6086408575395486 +2024-05-27 14:32:49,230 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.18697753547732684 +2024-05-27 14:32:49,234 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.020262 NaN NaN +0.066667 NaN 15.137888 0.190582 +1.188889 0.045387 NaN NaN +1.716667 NaN 14.673855 0.358735 +2.276944 0.094943 NaN NaN +2.800000 NaN 13.926149 0.629682 +3.128333 0.169152 NaN NaN +3.633333 NaN 12.834344 1.025321 +3.771389 0.261648 NaN NaN +4.266667 NaN 11.477400 1.517039 +4.415556 0.405028 NaN NaN +4.822778 0.533888 NaN NaN +4.883333 NaN 9.459367 2.248317 + +2024-05-27 14:32:49,239 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 12.253437251227274 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.4930203980304295 + +2024-05-27 14:32:49,239 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.4930203980304295 +2024-05-27 14:32:49,241 - physiofit - INFO - Results for yfeY: + optimal +yfeY X_0 0.020262 +yfeY growth_rate 0.678328 +yfeY Glc_q -7.198798 +yfeY Glc_M0 15.147835 +yfeY Ace_q 2.608641 +yfeY Ace_M0 0.186978 +2024-05-27 14:32:49,248 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:50,196 - physiofit - INFO - Running optimization for yfgD +2024-05-27 14:32:50,198 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:50,198 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:50,201 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1376 0.050000 NaN 14.048779 0.011768 +1377 1.950000 NaN 14.038282 0.419953 +1378 2.833333 NaN 13.528037 0.724421 +1379 2.876944 0.149688 NaN NaN +1380 3.678056 0.228312 NaN NaN +1381 3.983333 NaN 12.067119 1.303646 +1382 4.092222 0.279720 NaN NaN +1383 4.565000 0.373464 NaN NaN +1384 4.883333 NaN 9.965426 2.098731 +1385 5.166667 NaN 9.381706 2.605544 +Experimental matrix: +[[ nan 1.40487795e+01 1.17684297e-02] + [ nan 1.40382822e+01 4.19953376e-01] + [ nan 1.35280374e+01 7.24420671e-01] + [1.49688000e-01 nan nan] + [2.28312000e-01 nan nan] + [ nan 1.20671195e+01 1.30364619e+00] + [2.79720000e-01 nan nan] + [3.73464000e-01 nan nan] + [ nan 9.96542601e+00 2.09873141e+00] + [ nan 9.38170641e+00 2.60554405e+00]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:50,201 - physiofit - INFO - mc : False +2024-05-27 14:32:50,202 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:50,202 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:50,202 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:50,604 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:50,605 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.067229298033587 + x: [ 2.874e-02 5.611e-01 -5.785e+00 1.444e+01 + 2.813e+00 9.151e-02] + nit: 90 + nfev: 8372 + population: [[ 2.870e-02 5.615e-01 ... 2.813e+00 9.183e-02] + [ 2.838e-02 5.649e-01 ... 2.802e+00 9.232e-02] + ... + [ 2.809e-02 5.672e-01 ... 2.800e+00 1.002e-01] + [ 2.899e-02 5.592e-01 ... 2.788e+00 1.011e-01]] + population_energies: [ 2.067e+00 2.085e+00 ... 2.091e+00 2.117e+00] + jac: [ 2.737e-02 1.585e-03 -3.374e-03 1.571e-03 + 1.478e-02 -4.961e-03] +2024-05-27 14:32:50,606 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.028740416215061713 +2024-05-27 14:32:50,606 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5610666574818527 +2024-05-27 14:32:50,606 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.7854281477413645 +2024-05-27 14:32:50,606 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.438761572955949 +2024-05-27 14:32:50,606 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.813335060691203 +2024-05-27 14:32:50,607 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.09151326198430629 +2024-05-27 14:32:50,610 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.430330 0.095613 +1.950000 NaN 13.850069 0.377782 +2.833333 NaN 13.282313 0.653870 +2.876944 0.144382 NaN NaN +3.678056 0.226317 NaN NaN +3.983333 NaN 11.965463 1.294227 +4.092222 0.285520 NaN NaN +4.565000 0.372253 NaN NaN +4.883333 NaN 10.146024 2.178983 +5.166667 NaN 9.355317 2.563488 + +2024-05-27 14:32:50,614 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.067229298033587 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.0042015670803674365 + +2024-05-27 14:32:50,614 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0042015670803674365 +2024-05-27 14:32:50,616 - physiofit - INFO - Results for yfgD: + optimal +yfgD X_0 0.028740 +yfgD growth_rate 0.561067 +yfgD Glc_q -5.785428 +yfgD Glc_M0 14.438762 +yfgD Ace_q 2.813335 +yfgD Ace_M0 0.091513 +2024-05-27 14:32:50,624 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:51,587 - physiofit - INFO - Running optimization for yfhG +2024-05-27 14:32:51,590 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:51,590 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:51,593 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1386 0.000000 0.052920 NaN NaN +1387 0.066667 NaN 15.996448 0.009703 +1388 1.188889 0.080136 NaN NaN +1389 1.716667 NaN 14.864219 0.356201 +1390 2.276944 0.114912 NaN NaN +1391 2.800000 NaN 13.689849 0.803414 +1392 3.128333 0.170856 NaN NaN +1393 3.633333 NaN 12.733257 1.348206 +1394 3.771389 0.240408 NaN NaN +1395 4.266667 NaN 11.175430 1.857590 +1396 4.415556 0.349272 NaN NaN +1397 4.822778 0.452088 NaN NaN +1398 4.883333 NaN 10.241911 2.634260 +Experimental matrix: +[[5.29200000e-02 nan nan] + [ nan 1.59964483e+01 9.70317565e-03] + [8.01360000e-02 nan nan] + [ nan 1.48642186e+01 3.56200812e-01] + [1.14912000e-01 nan nan] + [ nan 1.36898487e+01 8.03413612e-01] + [1.70856000e-01 nan nan] + [ nan 1.27332571e+01 1.34820616e+00] + [2.40408000e-01 nan nan] + [ nan 1.11754297e+01 1.85759009e+00] + [3.49272000e-01 nan nan] + [4.52088000e-01 nan nan] + [ nan 1.02419110e+01 2.63426021e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:51,594 - physiofit - INFO - mc : False +2024-05-27 14:32:51,594 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:51,594 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:51,594 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:52,022 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:52,023 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.277720483739606 + x: [ 3.722e-02 5.103e-01 -7.145e+00 1.563e+01 + 3.237e+00 3.092e-02] + nit: 91 + nfev: 8728 + population: [[ 3.700e-02 5.120e-01 ... 3.230e+00 3.770e-02] + [ 3.741e-02 5.090e-01 ... 3.222e+00 4.455e-02] + ... + [ 3.693e-02 5.110e-01 ... 3.258e+00 4.789e-02] + [ 3.667e-02 5.149e-01 ... 3.240e+00 4.445e-02]] + population_energies: [ 5.278e+00 5.304e+00 ... 5.356e+00 5.427e+00] + jac: [-2.304e-04 -7.212e-05 4.530e-06 1.519e-05 + -8.704e-06 1.323e-05] +2024-05-27 14:32:52,023 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03721546009238486 +2024-05-27 14:32:52,024 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5103369155671126 +2024-05-27 14:32:52,024 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.1446547779891985 +2024-05-27 14:32:52,024 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.627083028666833 +2024-05-27 14:32:52,024 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.2370376114989265 +2024-05-27 14:32:52,024 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.030915779570544394 +2024-05-27 14:32:52,028 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.037215 NaN NaN +0.066667 NaN 15.609052 0.039085 +1.188889 0.068269 NaN NaN +1.716667 NaN 14.896904 0.361739 +2.276944 0.118954 NaN NaN +2.800000 NaN 13.973242 0.780224 +3.128333 0.183686 NaN NaN +3.633333 NaN 12.820527 1.302486 +3.771389 0.255036 NaN NaN +4.266667 NaN 11.550859 1.877735 +4.415556 0.354300 NaN NaN +4.822778 0.436141 NaN NaN +4.883333 NaN 9.850531 2.648105 + +2024-05-27 14:32:52,032 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.277720483739606 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.03144024459705456 + +2024-05-27 14:32:52,032 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.03144024459705456 +2024-05-27 14:32:52,034 - physiofit - INFO - Results for yfhG: + optimal +yfhG X_0 0.037215 +yfhG growth_rate 0.510337 +yfhG Glc_q -7.144655 +yfhG Glc_M0 15.627083 +yfhG Ace_q 3.237038 +yfhG Ace_M0 0.030916 +2024-05-27 14:32:52,040 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:52,986 - physiofit - INFO - Running optimization for yfhm +2024-05-27 14:32:52,988 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:52,988 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:52,992 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1399 1.828889 0.058968 NaN NaN +1400 2.261389 0.078624 NaN NaN +1401 2.774167 0.113400 NaN NaN +1402 2.800000 NaN 12.439119 0.592995 +1403 3.208889 0.140616 NaN NaN +1404 3.706389 0.176904 NaN NaN +1405 3.733333 NaN 11.877361 1.029523 +1406 4.225833 0.241920 NaN NaN +1407 4.283333 NaN 11.307967 1.372366 +1408 4.635556 0.326592 NaN NaN +1409 4.750000 NaN 10.651405 1.765192 +1410 4.967500 0.400680 NaN NaN +1411 5.116667 NaN 9.807483 2.060684 +1412 5.433333 NaN 9.022080 2.381211 +Experimental matrix: +[[ 0.058968 nan nan] + [ 0.078624 nan nan] + [ 0.1134 nan nan] + [ nan 12.43911858 0.59299533] + [ 0.140616 nan nan] + [ 0.176904 nan nan] + [ nan 11.87736124 1.02952275] + [ 0.24192 nan nan] + [ nan 11.30796747 1.37236566] + [ 0.326592 nan nan] + [ nan 10.65140535 1.76519196] + [ 0.40068 nan nan] + [ nan 9.80748291 2.06068435] + [ nan 9.02207954 2.3812109 ]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:52,992 - physiofit - INFO - mc : False +2024-05-27 14:32:52,993 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:52,993 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:52,993 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:53,500 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:53,502 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.311086073504977 + x: [ 1.960e-02 6.052e-01 -4.989e+00 1.325e+01 + 2.572e+00 2.979e-01] + nit: 115 + nfev: 10566 + population: [[ 1.950e-02 6.065e-01 ... 2.573e+00 2.989e-01] + [ 1.947e-02 6.067e-01 ... 2.582e+00 2.972e-01] + ... + [ 1.990e-02 6.021e-01 ... 2.553e+00 2.995e-01] + [ 1.981e-02 6.025e-01 ... 2.570e+00 2.993e-01]] + population_energies: [ 1.311e+00 1.314e+00 ... 1.330e+00 1.317e+00] + jac: [-1.414e-02 -1.786e-03 -1.655e-02 1.908e-02 + -1.476e-02 1.292e-04] +2024-05-27 14:32:53,503 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.019596265615763244 +2024-05-27 14:32:53,503 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6051855967308594 +2024-05-27 14:32:53,503 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.989136908487301 +2024-05-27 14:32:53,503 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.247964229004094 +2024-05-27 14:32:53,504 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5723823917563022 +2024-05-27 14:32:53,504 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.2979187004018037 +2024-05-27 14:32:53,508 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.059273 NaN NaN +2.261389 0.077007 NaN NaN +2.774167 0.105028 NaN NaN +2.800000 NaN 12.530026 0.668085 +3.208889 0.136635 NaN NaN +3.706389 0.184637 NaN NaN +3.733333 NaN 11.862347 1.012338 +4.225833 0.252839 NaN NaN +4.283333 NaN 11.251307 1.327388 +4.635556 0.323989 NaN NaN +4.750000 NaN 10.547007 1.690523 +4.967500 0.396073 NaN NaN +5.116667 NaN 9.835822 2.057208 +5.433333 NaN 9.080925 2.446430 + +2024-05-27 14:32:53,514 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.311086073504977 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 5.83228517349714e-06 + +2024-05-27 14:32:53,514 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 5.83228517349714e-06 +2024-05-27 14:32:53,517 - physiofit - INFO - Results for yfhm: + optimal +yfhm X_0 0.019596 +yfhm growth_rate 0.605186 +yfhm Glc_q -4.989137 +yfhm Glc_M0 13.247964 +yfhm Ace_q 2.572382 +yfhm Ace_M0 0.297919 +2024-05-27 14:32:53,522 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:54,460 - physiofit - INFO - Running optimization for yfiF +2024-05-27 14:32:54,463 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:54,463 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:54,466 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1413 1.950000 NaN 13.351395 0.366080 +1414 2.501389 0.114912 NaN NaN +1415 3.250000 NaN 12.784865 0.906584 +1416 3.341944 0.170856 NaN NaN +1417 3.997500 0.240408 NaN NaN +1418 4.083333 NaN 11.725041 1.385255 +1419 4.523333 0.349272 NaN NaN +1420 4.766667 NaN 10.613158 1.931670 +Experimental matrix: +[[ nan 13.35139502 0.3660802 ] + [ 0.114912 nan nan] + [ nan 12.78486514 0.90658373] + [ 0.170856 nan nan] + [ 0.240408 nan nan] + [ nan 11.7250414 1.38525512] + [ 0.349272 nan nan] + [ nan 10.61315762 1.93166975]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:54,468 - physiofit - INFO - mc : False +2024-05-27 14:32:54,468 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:54,468 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:54,468 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:54,939 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:54,941 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.0467110446675645 + x: [ 2.529e-02 5.756e-01 -5.120e+00 1.390e+01 + 2.823e+00 1.675e-01] + nit: 106 + nfev: 9903 + population: [[ 2.532e-02 5.756e-01 ... 2.833e+00 1.637e-01] + [ 2.513e-02 5.763e-01 ... 2.824e+00 1.798e-01] + ... + [ 2.531e-02 5.752e-01 ... 2.841e+00 1.604e-01] + [ 2.543e-02 5.742e-01 ... 2.828e+00 1.663e-01]] + population_energies: [ 1.047e+00 1.080e+00 ... 1.050e+00 1.051e+00] + jac: [ 4.620e-03 5.000e-04 -9.316e-03 4.171e-03 + -2.271e-03 9.045e-04] +2024-05-27 14:32:54,941 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025291404784631297 +2024-05-27 14:32:54,942 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.575583495683092 +2024-05-27 14:32:54,942 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.119864475619018 +2024-05-27 14:32:54,942 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.895782103432518 +2024-05-27 14:32:54,943 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.8231846030222725 +2024-05-27 14:32:54,943 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.16750080299991688 +2024-05-27 14:32:54,946 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.429605 0.424559 +2.501389 0.106722 NaN NaN +3.250000 NaN 12.660141 0.848856 +3.341944 0.173128 NaN NaN +3.997500 0.252487 NaN NaN +4.083333 NaN 11.761115 1.344594 +4.523333 0.341730 NaN NaN +4.766667 NaN 10.624040 1.971598 + +2024-05-27 14:32:54,950 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.0467110446675645 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.016220591408266757 + +2024-05-27 14:32:54,951 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.016220591408266757 +2024-05-27 14:32:54,953 - physiofit - INFO - Results for yfiF: + optimal +yfiF X_0 0.025291 +yfiF growth_rate 0.575583 +yfiF Glc_q -5.119864 +yfiF Glc_M0 13.895782 +yfiF Ace_q 2.823185 +yfiF Ace_M0 0.167501 +2024-05-27 14:32:54,960 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:55,889 - physiofit - INFO - Running optimization for ygaM +2024-05-27 14:32:55,892 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:55,892 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:55,896 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1421 1.828889 0.063504 NaN NaN +1422 2.261389 0.081648 NaN NaN +1423 2.774167 0.104328 NaN NaN +1424 2.800000 NaN 12.376857 0.587559 +1425 3.208889 0.137592 NaN NaN +1426 3.706389 0.167832 NaN NaN +1427 3.733333 NaN 11.714923 1.112318 +1428 4.225833 0.232848 NaN NaN +1429 4.283333 NaN 11.336306 1.602245 +1430 4.635556 0.305424 NaN NaN +1431 4.750000 NaN 10.492996 2.122674 +1432 4.967500 0.388584 NaN NaN +1433 5.116667 NaN 10.112037 2.675722 +1434 5.433333 NaN 9.360098 3.255515 +Experimental matrix: +[[ 0.063504 nan nan] + [ 0.081648 nan nan] + [ 0.104328 nan nan] + [ nan 12.37685707 0.5875595 ] + [ 0.137592 nan nan] + [ 0.167832 nan nan] + [ nan 11.71492256 1.11231833] + [ 0.232848 nan nan] + [ nan 11.33630644 1.60224475] + [ 0.305424 nan nan] + [ nan 10.49299569 2.12267371] + [ 0.388584 nan nan] + [ nan 10.11203741 2.67572168] + [ nan 9.36009794 3.25551503]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:55,896 - physiofit - INFO - mc : False +2024-05-27 14:32:55,896 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:55,896 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:55,897 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:56,421 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:56,422 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.3021221946333568 + x: [ 1.926e-02 5.996e-01 -4.496e+00 1.298e+01 + 4.017e+00 3.176e-02] + nit: 114 + nfev: 10819 + population: [[ 1.940e-02 5.980e-01 ... 4.022e+00 2.279e-02] + [ 1.958e-02 5.963e-01 ... 4.027e+00 1.652e-02] + ... + [ 1.952e-02 5.971e-01 ... 4.022e+00 1.671e-02] + [ 1.947e-02 5.974e-01 ... 4.032e+00 1.498e-02]] + population_energies: [ 1.302e+00 1.312e+00 ... 1.321e+00 1.312e+00] + jac: [-6.529e-02 -7.688e-03 -6.946e-03 3.799e-03 + -1.365e-03 3.803e-04] +2024-05-27 14:32:56,423 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.019259399813305586 +2024-05-27 14:32:56,423 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5995931341600532 +2024-05-27 14:32:56,423 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.4958310042867815 +2024-05-27 14:32:56,423 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 12.98144613342998 +2024-05-27 14:32:56,424 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.017446160563417 +2024-05-27 14:32:56,424 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.03175599361115874 +2024-05-27 14:32:56,427 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.057661 NaN NaN +2.261389 0.074732 NaN NaN +2.774167 0.101633 NaN NaN +2.800000 NaN 12.351900 0.594314 +3.208889 0.131898 NaN NaN +3.706389 0.177740 NaN NaN +3.733333 NaN 11.771427 1.113021 +4.225833 0.242689 NaN NaN +4.283333 NaN 11.242311 1.585837 +4.635556 0.310271 NaN NaN +4.750000 NaN 10.634154 2.129281 +4.967500 0.378599 NaN NaN +5.116667 NaN 10.021468 2.676774 +5.433333 NaN 9.372359 3.256813 + +2024-05-27 14:32:56,431 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.3021221946333568 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 5.580452871759907e-06 + +2024-05-27 14:32:56,432 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 5.580452871759907e-06 +2024-05-27 14:32:56,434 - physiofit - INFO - Results for ygaM: + optimal +ygaM X_0 0.019259 +ygaM growth_rate 0.599593 +ygaM Glc_q -4.495831 +ygaM Glc_M0 12.981446 +ygaM Ace_q 4.017446 +ygaM Ace_M0 0.031756 +2024-05-27 14:32:56,441 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:57,390 - physiofit - INFO - Running optimization for ygaU +2024-05-27 14:32:57,392 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:57,392 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:57,395 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1435 1.950000 NaN 13.790386 0.415898 +1436 2.501389 0.101304 NaN NaN +1437 3.250000 NaN 13.164467 1.150924 +1438 3.341944 0.158760 NaN NaN +1439 3.997500 0.216216 NaN NaN +1440 4.083333 NaN 11.498459 1.888492 +1441 4.523333 0.340200 NaN NaN +1442 4.766667 NaN 10.110764 2.677154 +Experimental matrix: +[[ nan 13.79038625 0.41589829] + [ 0.101304 nan nan] + [ nan 13.16446742 1.15092414] + [ 0.15876 nan nan] + [ 0.216216 nan nan] + [ nan 11.4984593 1.88849248] + [ 0.3402 nan nan] + [ nan 10.11076418 2.67715373]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:57,396 - physiofit - INFO - mc : False +2024-05-27 14:32:57,396 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:57,396 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:57,396 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:57,826 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:57,827 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.6812902400549268 + x: [ 1.972e-02 6.217e-01 -7.550e+00 1.447e+01 + 4.420e+00 1.684e-01] + nit: 93 + nfev: 9125 + population: [[ 1.986e-02 6.204e-01 ... 4.411e+00 1.678e-01] + [ 1.917e-02 6.275e-01 ... 4.450e+00 1.449e-01] + ... + [ 1.977e-02 6.219e-01 ... 4.438e+00 1.638e-01] + [ 2.011e-02 6.176e-01 ... 4.429e+00 1.533e-01]] + population_energies: [ 2.681e+00 2.795e+00 ... 2.698e+00 2.690e+00] + jac: [-2.836e-03 -4.817e-04 -3.997e-06 8.349e-06 + 5.196e-05 1.566e-04] +2024-05-27 14:32:57,828 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.019722310084158687 +2024-05-27 14:32:57,828 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6216809923575196 +2024-05-27 14:32:57,828 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.5502596583353725 +2024-05-27 14:32:57,828 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.472002989234458 +2024-05-27 14:32:57,828 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.420365981629611 +2024-05-27 14:32:57,828 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.16842313798872577 +2024-05-27 14:32:57,832 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.906451 0.499530 +2.501389 0.093393 NaN NaN +3.250000 NaN 12.905070 1.085798 +3.341944 0.157492 NaN NaN +3.997500 0.236730 NaN NaN +4.083333 NaN 11.678881 1.803681 +4.523333 0.328265 NaN NaN +4.766667 NaN 10.073676 2.743462 + +2024-05-27 14:32:57,835 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.6812902400549268 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.1523477764240725 + +2024-05-27 14:32:57,835 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.1523477764240725 +2024-05-27 14:32:57,838 - physiofit - INFO - Results for ygaU: + optimal +ygaU X_0 0.019722 +ygaU growth_rate 0.621681 +ygaU Glc_q -7.550260 +ygaU Glc_M0 14.472003 +ygaU Ace_q 4.420366 +ygaU Ace_M0 0.168423 +2024-05-27 14:32:57,845 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:32:58,770 - physiofit - INFO - Running optimization for ygdI +2024-05-27 14:32:58,772 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:32:58,773 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:32:58,776 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1443 0.000000 0.034776 NaN NaN +1444 0.283333 NaN 14.233871 0.037765 +1445 1.195000 0.061992 NaN NaN +1446 1.613611 0.077112 NaN NaN +1447 1.916667 NaN 13.718664 0.378113 +1448 2.361389 0.113400 NaN NaN +1449 2.700000 NaN 13.428513 0.565351 +1450 3.286389 0.198072 NaN NaN +1451 3.616667 NaN 12.624077 1.225063 +1452 3.819444 0.288792 NaN NaN +1453 4.050000 NaN 11.754528 1.331761 +1454 4.410833 0.400680 NaN NaN +1455 4.750000 NaN 10.478688 2.156622 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.23387093 0.03776502] + [ 0.061992 nan nan] + [ 0.077112 nan nan] + [ nan 13.71866405 0.3781133 ] + [ 0.1134 nan nan] + [ nan 13.42851252 0.5653513 ] + [ 0.198072 nan nan] + [ nan 12.62407664 1.22506341] + [ 0.288792 nan nan] + [ nan 11.75452757 1.33176072] + [ 0.40068 nan nan] + [ nan 10.4786883 2.15662192]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:32:58,777 - physiofit - INFO - mc : False +2024-05-27 14:32:58,777 - physiofit - INFO - iterations : 100 +2024-05-27 14:32:58,777 - physiofit - INFO - debug_mode : False +2024-05-27 14:32:58,778 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:32:59,196 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:32:59,196 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.4817330918367242 + x: [ 2.916e-02 5.942e-01 -4.921e+00 1.431e+01 + 2.714e+00 6.609e-02] + nit: 89 + nfev: 8436 + population: [[ 2.925e-02 5.934e-01 ... 2.717e+00 6.470e-02] + [ 2.940e-02 5.916e-01 ... 2.720e+00 7.034e-02] + ... + [ 2.890e-02 5.962e-01 ... 2.706e+00 7.554e-02] + [ 2.937e-02 5.925e-01 ... 2.707e+00 6.852e-02]] + population_energies: [ 1.482e+00 1.512e+00 ... 1.490e+00 1.488e+00] + jac: [ 6.547e-02 4.561e-03 8.477e-03 -2.095e-03 + -5.669e-03 1.673e-03] +2024-05-27 14:32:59,197 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.029164955066255587 +2024-05-27 14:32:59,198 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5942047264395073 +2024-05-27 14:32:59,198 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.92061665608734 +2024-05-27 14:32:59,198 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.307265588752703 +2024-05-27 14:32:59,198 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.7141153523857575 +2024-05-27 14:32:59,198 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.06608631682997522 +2024-05-27 14:32:59,202 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.029165 NaN NaN +0.283333 NaN 14.262981 0.090513 +1.195000 0.059326 NaN NaN +1.613611 0.076080 NaN NaN +1.916667 NaN 13.794454 0.348943 +2.361389 0.118643 NaN NaN +2.700000 NaN 13.347329 0.595568 +3.286389 0.205564 NaN NaN +3.616667 NaN 12.477394 1.075407 +3.819444 0.282167 NaN NaN +4.050000 NaN 11.869075 1.410944 +4.410833 0.400978 NaN NaN +4.750000 NaN 10.486884 2.173334 + +2024-05-27 14:32:59,206 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.4817330918367242 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 4.017976195532894e-05 + +2024-05-27 14:32:59,207 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 4.017976195532894e-05 +2024-05-27 14:32:59,211 - physiofit - INFO - Results for ygdI: + optimal +ygdI X_0 0.029165 +ygdI growth_rate 0.594205 +ygdI Glc_q -4.920617 +ygdI Glc_M0 14.307266 +ygdI Ace_q 2.714115 +ygdI Ace_M0 0.066086 +2024-05-27 14:32:59,217 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:00,149 - physiofit - INFO - Running optimization for ygeA +2024-05-27 14:33:00,151 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:00,152 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:00,155 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1456 1.950000 NaN 13.653565 0.365865 +1457 2.501389 0.092232 NaN NaN +1458 3.250000 NaN 12.923013 0.873755 +1459 3.341944 0.161784 NaN NaN +1460 3.997500 0.204120 NaN NaN +1461 4.083333 NaN 12.117560 1.318741 +1462 4.523333 0.311472 NaN NaN +1463 4.766667 NaN 10.720047 1.742119 +Experimental matrix: +[[ nan 13.65356462 0.36586512] + [ 0.092232 nan nan] + [ nan 12.92301288 0.87375548] + [ 0.161784 nan nan] + [ 0.20412 nan nan] + [ nan 12.11755961 1.31874129] + [ 0.311472 nan nan] + [ nan 10.72004715 1.74211946]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:00,156 - physiofit - INFO - mc : False +2024-05-27 14:33:00,156 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:00,156 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:00,157 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:00,608 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:00,609 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.8828254061115932 + x: [ 2.124e-02 5.877e-01 -6.046e+00 1.418e+01 + 2.826e+00 2.227e-01] + nit: 97 + nfev: 9254 + population: [[ 2.125e-02 5.872e-01 ... 2.820e+00 2.199e-01] + [ 2.121e-02 5.888e-01 ... 2.802e+00 2.276e-01] + ... + [ 2.125e-02 5.878e-01 ... 2.856e+00 2.160e-01] + [ 2.090e-02 5.909e-01 ... 2.827e+00 2.263e-01]] + population_energies: [ 1.883e+00 1.893e+00 ... 1.893e+00 1.889e+00] + jac: [-3.704e-03 4.923e-05 1.353e-03 -4.168e-04 + 6.470e-05 -2.300e-04] +2024-05-27 14:33:00,609 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.021240500636061217 +2024-05-27 14:33:00,609 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.587659092462654 +2024-05-27 14:33:00,610 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.046063229371446 +2024-05-27 14:33:00,610 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.177203271263332 +2024-05-27 14:33:00,610 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.8260199618876953 +2024-05-27 14:33:00,610 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.222709499858052 +2024-05-27 14:33:00,613 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.708372 0.441848 +2.501389 0.092377 NaN NaN +3.250000 NaN 12.920137 0.810281 +3.341944 0.151386 NaN NaN +3.997500 0.222533 NaN NaN +4.083333 NaN 11.987778 1.246079 +4.523333 0.303108 NaN NaN +4.766667 NaN 10.797853 1.802268 + +2024-05-27 14:33:00,617 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.8828254061115932 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.06984661927207655 + +2024-05-27 14:33:00,617 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.06984661927207655 +2024-05-27 14:33:00,619 - physiofit - INFO - Results for ygeA: + optimal +ygeA X_0 0.021241 +ygeA growth_rate 0.587659 +ygeA Glc_q -6.046063 +ygeA Glc_M0 14.177203 +ygeA Ace_q 2.826020 +ygeA Ace_M0 0.222709 +2024-05-27 14:33:00,624 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:01,590 - physiofit - INFO - Running optimization for ygeV +2024-05-27 14:33:01,592 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:01,594 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:01,597 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1464 0.050000 NaN 14.045480 0.014499 +1465 1.950000 NaN 13.942066 0.440967 +1466 2.833333 NaN 13.093327 0.764262 +1467 2.876944 0.154224 NaN NaN +1468 3.678056 0.264600 NaN NaN +1469 3.983333 NaN 11.679387 1.445645 +1470 4.092222 0.338688 NaN NaN +1471 4.565000 0.449064 NaN NaN +1472 4.883333 NaN 9.282608 2.073088 +1473 5.166667 NaN 8.453635 2.262026 +Experimental matrix: +[[ nan 14.04548016 0.01449869] + [ nan 13.94206649 0.44096656] + [ nan 13.09332656 0.7642623 ] + [ 0.154224 nan nan] + [ 0.2646 nan nan] + [ nan 11.67938725 1.44564455] + [ 0.338688 nan nan] + [ 0.449064 nan nan] + [ nan 9.28260821 2.07308756] + [ nan 8.45363504 2.26202567]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:01,597 - physiofit - INFO - mc : False +2024-05-27 14:33:01,597 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:01,597 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:01,598 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:02,095 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:02,096 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.7350096187896353 + x: [ 2.934e-02 5.968e-01 -5.746e+00 1.433e+01 + 2.147e+00 2.043e-01] + nit: 109 + nfev: 10299 + population: [[ 2.942e-02 5.963e-01 ... 2.155e+00 1.971e-01] + [ 2.898e-02 6.002e-01 ... 2.145e+00 2.153e-01] + ... + [ 2.865e-02 6.023e-01 ... 2.165e+00 2.047e-01] + [ 2.955e-02 5.953e-01 ... 2.153e+00 1.852e-01]] + population_energies: [ 3.735e+00 3.779e+00 ... 3.751e+00 3.906e+00] + jac: [-3.487e-02 -3.886e-03 -2.806e-04 2.892e-04 + -3.810e-05 9.645e-04] +2024-05-27 14:33:02,096 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.0293350959386446 +2024-05-27 14:33:02,097 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.596846216640764 +2024-05-27 14:33:02,097 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.746405657780017 +2024-05-27 14:33:02,097 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.325040462751227 +2024-05-27 14:33:02,097 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.147264564569841 +2024-05-27 14:33:02,097 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.20431724357874642 +2024-05-27 14:33:02,101 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.316485 0.207514 +1.950000 NaN 13.703047 0.436738 +2.833333 NaN 13.075186 0.671351 +2.876944 0.163347 NaN NaN +3.678056 0.263491 NaN NaN +3.983333 NaN 11.563585 1.236193 +4.092222 0.337381 NaN NaN +4.565000 0.447371 NaN NaN +4.883333 NaN 9.398942 2.045057 +5.166667 NaN 8.439289 2.403651 + +2024-05-27 14:33:02,105 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.7350096187896353 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.041489597618105764 + +2024-05-27 14:33:02,105 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.041489597618105764 +2024-05-27 14:33:02,107 - physiofit - INFO - Results for ygeV: + optimal +ygeV X_0 0.029335 +ygeV growth_rate 0.596846 +ygeV Glc_q -5.746406 +ygeV Glc_M0 14.325040 +ygeV Ace_q 2.147265 +ygeV Ace_M0 0.204317 +2024-05-27 14:33:02,114 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:03,054 - physiofit - INFO - Running optimization for yggE +2024-05-27 14:33:03,057 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:03,057 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:03,060 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1474 1.950000 NaN 13.670128 0.358161 +1475 2.501389 0.105840 NaN NaN +1476 3.250000 NaN 12.803864 0.861437 +1477 3.341944 0.160272 NaN NaN +1478 3.997500 0.208656 NaN NaN +1479 4.083333 NaN 12.059444 1.345623 +1480 4.523333 0.303912 NaN NaN +1481 4.766667 NaN 10.974942 1.905070 +Experimental matrix: +[[ nan 13.67012751 0.35816132] + [ 0.10584 nan nan] + [ nan 12.80386407 0.86143744] + [ 0.160272 nan nan] + [ 0.208656 nan nan] + [ nan 12.0594443 1.34562291] + [ 0.303912 nan nan] + [ nan 10.97494238 1.90507044]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:03,060 - physiofit - INFO - mc : False +2024-05-27 14:33:03,060 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:03,061 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:03,061 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:03,478 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:03,479 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.9088260669654198 + x: [ 2.670e-02 5.316e-01 -5.408e+00 1.413e+01 + 3.131e+00 1.027e-01] + nit: 93 + nfev: 8789 + population: [[ 2.641e-02 5.343e-01 ... 3.149e+00 1.003e-01] + [ 2.718e-02 5.265e-01 ... 3.124e+00 1.017e-01] + ... + [ 2.674e-02 5.313e-01 ... 3.124e+00 1.088e-01] + [ 2.704e-02 5.280e-01 ... 3.134e+00 9.831e-02]] + population_energies: [ 9.088e-01 9.164e-01 ... 9.162e-01 9.147e-01] + jac: [-3.230e-02 -3.700e-03 8.017e-04 -1.984e-04 + -6.550e-05 2.248e-04] +2024-05-27 14:33:03,480 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02670288818586314 +2024-05-27 14:33:03,480 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5315575211751379 +2024-05-27 14:33:03,480 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.407585119171033 +2024-05-27 14:33:03,480 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.129918652070952 +2024-05-27 14:33:03,480 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.130900524192101 +2024-05-27 14:33:03,480 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.10271554132003463 +2024-05-27 14:33:03,484 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.635667 0.388879 +2.501389 0.100928 NaN NaN +3.250000 NaN 12.873012 0.830444 +3.341944 0.157781 NaN NaN +3.997500 0.223558 NaN NaN +4.083333 NaN 12.021120 1.323674 +4.523333 0.295652 NaN NaN +4.766667 NaN 10.978559 1.927300 + +2024-05-27 14:33:03,488 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.9088260669654198 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.011166401738684788 + +2024-05-27 14:33:03,488 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.011166401738684788 +2024-05-27 14:33:03,490 - physiofit - INFO - Results for yggE: + optimal +yggE X_0 0.026703 +yggE growth_rate 0.531558 +yggE Glc_q -5.407585 +yggE Glc_M0 14.129919 +yggE Ace_q 3.130901 +yggE Ace_M0 0.102716 +2024-05-27 14:33:03,496 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:04,461 - physiofit - INFO - Running optimization for yggL +2024-05-27 14:33:04,464 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:04,464 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:04,468 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1482 0.050000 NaN 14.787840 0.016258 +1483 1.950000 NaN 13.505500 0.470571 +1484 2.833333 NaN 13.652500 0.842017 +1485 2.876944 0.166320 NaN NaN +1486 3.678056 0.269136 NaN NaN +1487 3.983333 NaN 11.815677 1.607918 +1488 4.092222 0.355320 NaN NaN +1489 4.565000 0.464184 NaN NaN +1490 4.883333 NaN 8.816160 2.091026 +1491 5.166667 NaN 8.078349 2.517938 +Experimental matrix: +[[ nan 14.78784018 0.01625768] + [ nan 13.50550017 0.47057132] + [ nan 13.65250032 0.84201654] + [ 0.16632 nan nan] + [ 0.269136 nan nan] + [ nan 11.81567689 1.60791761] + [ 0.35532 nan nan] + [ 0.464184 nan nan] + [ nan 8.81615953 2.0910258 ] + [ nan 8.0783486 2.51793787]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:04,468 - physiofit - INFO - mc : False +2024-05-27 14:33:04,468 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:04,468 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:04,468 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:04,864 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:04,866 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 6.393074821744672 + x: [ 3.205e-02 5.845e-01 -6.302e+00 1.474e+01 + 2.208e+00 2.182e-01] + nit: 86 + nfev: 8229 + population: [[ 3.231e-02 5.827e-01 ... 2.196e+00 2.179e-01] + [ 3.236e-02 5.823e-01 ... 2.202e+00 2.010e-01] + ... + [ 3.077e-02 5.942e-01 ... 2.225e+00 2.092e-01] + [ 3.192e-02 5.868e-01 ... 2.184e+00 2.145e-01]] + population_energies: [ 6.393e+00 6.479e+00 ... 6.472e+00 6.454e+00] + jac: [-3.132e-01 8.715e-03 -3.411e-04 -1.537e-03 + -1.991e-02 -5.237e-02] +2024-05-27 14:33:04,868 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03205075413665382 +2024-05-27 14:33:04,868 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5845327615215212 +2024-05-27 14:33:04,868 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.302292348711154 +2024-05-27 14:33:04,868 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.742917440805192 +2024-05-27 14:33:04,868 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.207576831265489 +2024-05-27 14:33:04,868 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.21818208459141325 +2024-05-27 14:33:04,871 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.732669 0.221772 +1.950000 NaN 14.008158 0.475555 +2.833333 NaN 13.277991 0.731319 +2.876944 0.172257 NaN NaN +3.678056 0.275136 NaN NaN +3.983333 NaN 11.542517 1.339223 +4.092222 0.350499 NaN NaN +4.565000 0.462068 NaN NaN +4.883333 NaN 9.087700 2.199101 +5.166667 NaN 8.006829 2.577710 + +2024-05-27 14:33:04,875 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 6.393074821744672 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.21877109409613663 + +2024-05-27 14:33:04,875 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.21877109409613663 +2024-05-27 14:33:04,877 - physiofit - INFO - Results for yggL: + optimal +yggL X_0 0.032051 +yggL growth_rate 0.584533 +yggL Glc_q -6.302292 +yggL Glc_M0 14.742917 +yggL Ace_q 2.207577 +yggL Ace_M0 0.218182 +2024-05-27 14:33:04,883 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:05,849 - physiofit - INFO - Running optimization for yggN +2024-05-27 14:33:05,851 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:05,851 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:05,855 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1492 0.050000 NaN 14.289995 0.013706 +1493 1.950000 NaN 13.976892 0.424205 +1494 2.833333 NaN 13.747603 0.762328 +1495 2.876944 0.167832 NaN NaN +1496 3.678056 0.263088 NaN NaN +1497 3.983333 NaN 11.808273 1.306150 +1498 4.092222 0.344736 NaN NaN +1499 4.565000 0.479304 NaN NaN +1500 4.883333 NaN 9.177371 1.971160 +1501 5.166667 NaN 8.544461 2.510712 +Experimental matrix: +[[ nan 1.42899951e+01 1.37057049e-02] + [ nan 1.39768922e+01 4.24205365e-01] + [ nan 1.37476034e+01 7.62328239e-01] + [1.67832000e-01 nan nan] + [2.63088000e-01 nan nan] + [ nan 1.18082734e+01 1.30615036e+00] + [3.44736000e-01 nan nan] + [4.79304000e-01 nan nan] + [ nan 9.17737095e+00 1.97115987e+00] + [ nan 8.54446077e+00 2.51071184e+00]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:05,855 - physiofit - INFO - mc : False +2024-05-27 14:33:05,855 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:05,855 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:05,856 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:06,286 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:06,287 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.6046388338007915 + x: [ 2.577e-02 6.378e-01 -5.878e+00 1.457e+01 + 2.199e+00 1.758e-01] + nit: 90 + nfev: 8729 + population: [[ 2.557e-02 6.398e-01 ... 2.192e+00 1.767e-01] + [ 2.549e-02 6.391e-01 ... 2.209e+00 1.755e-01] + ... + [ 2.572e-02 6.379e-01 ... 2.189e+00 1.626e-01] + [ 2.559e-02 6.393e-01 ... 2.186e+00 1.965e-01]] + population_energies: [ 3.605e+00 3.652e+00 ... 3.676e+00 3.645e+00] + jac: [-7.653e-04 -9.774e-05 -1.377e-06 -1.998e-06 + 4.530e-06 5.151e-06] +2024-05-27 14:33:06,287 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025766738040349083 +2024-05-27 14:33:06,288 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6378421797211792 +2024-05-27 14:33:06,288 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.877659632787148 +2024-05-27 14:33:06,288 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.567731953364842 +2024-05-27 14:33:06,288 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.1985666904513765 +2024-05-27 14:33:06,288 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1758467924675176 +2024-05-27 14:33:06,292 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.560038 0.178725 +1.950000 NaN 13.981558 0.395108 +2.833333 NaN 13.358345 0.628224 +2.876944 0.161438 NaN NaN +3.678056 0.269105 NaN NaN +3.983333 NaN 11.792309 1.214007 +4.092222 0.350470 NaN NaN +4.565000 0.473823 NaN NaN +4.883333 NaN 9.455964 2.087928 +5.166667 NaN 8.396382 2.484270 + +2024-05-27 14:33:06,296 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.6046388338007915 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.03657459660158687 + +2024-05-27 14:33:06,297 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.03657459660158687 +2024-05-27 14:33:06,299 - physiofit - INFO - Results for yggN: + optimal +yggN X_0 0.025767 +yggN growth_rate 0.637842 +yggN Glc_q -5.877660 +yggN Glc_M0 14.567732 +yggN Ace_q 2.198567 +yggN Ace_M0 0.175847 +2024-05-27 14:33:06,306 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:07,241 - physiofit - INFO - Running optimization for yghJ +2024-05-27 14:33:07,244 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:07,244 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:07,248 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1502 1.828889 0.069552 NaN NaN +1503 2.261389 0.078624 NaN NaN +1504 2.774167 0.102816 NaN NaN +1505 2.800000 NaN 12.004052 0.642121 +1506 3.208889 0.137592 NaN NaN +1507 3.706389 0.178416 NaN NaN +1508 3.733333 NaN 10.688917 1.113319 +1509 4.225833 0.232848 NaN NaN +1510 4.283333 NaN 10.799182 1.521739 +1511 4.635556 0.311472 NaN NaN +1512 4.750000 NaN 10.209621 1.953893 +1513 4.967500 0.394632 NaN NaN +1514 5.116667 NaN 9.115922 2.251369 +1515 5.433333 NaN 8.235201 2.611748 +Experimental matrix: +[[ 0.069552 nan nan] + [ 0.078624 nan nan] + [ 0.102816 nan nan] + [ nan 12.00405194 0.64212134] + [ 0.137592 nan nan] + [ 0.178416 nan nan] + [ nan 10.68891695 1.11331927] + [ 0.232848 nan nan] + [ nan 10.79918168 1.52173946] + [ 0.311472 nan nan] + [ nan 10.20962081 1.95389278] + [ 0.394632 nan nan] + [ nan 9.11592179 2.25136933] + [ nan 8.23520106 2.61174756]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:07,248 - physiofit - INFO - mc : False +2024-05-27 14:33:07,249 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:07,249 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:07,249 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:07,736 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:07,737 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.9831615095730615 + x: [ 1.980e-02 5.970e-01 -5.171e+00 1.262e+01 + 2.911e+00 3.083e-01] + nit: 103 + nfev: 10060 + population: [[ 1.992e-02 5.957e-01 ... 2.918e+00 3.042e-01] + [ 2.017e-02 5.925e-01 ... 2.952e+00 2.855e-01] + ... + [ 2.028e-02 5.903e-01 ... 2.935e+00 3.025e-01] + [ 1.959e-02 5.987e-01 ... 2.957e+00 2.895e-01]] + population_energies: [ 3.983e+00 4.027e+00 ... 4.052e+00 4.023e+00] + jac: [-2.008e-03 -1.273e-04 2.367e-05 2.891e-05 + 1.785e-05 2.398e-05] +2024-05-27 14:33:07,738 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.019804972203146705 +2024-05-27 14:33:07,738 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5969674284938808 +2024-05-27 14:33:07,738 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.170869593024542 +2024-05-27 14:33:07,738 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 12.616607420548032 +2024-05-27 14:33:07,738 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.910525986020974 +2024-05-27 14:33:07,738 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.30832991053674963 +2024-05-27 14:33:07,742 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.059011 NaN NaN +2.261389 0.076394 NaN NaN +2.774167 0.103754 NaN NaN +2.800000 NaN 11.875485 0.725485 +3.208889 0.134496 NaN NaN +3.706389 0.181005 NaN NaN +3.733333 NaN 11.194884 1.108575 +4.225833 0.246810 NaN NaN +4.283333 NaN 10.575659 1.457118 +4.635556 0.315200 NaN NaN +4.750000 NaN 9.864875 1.857197 +4.967500 0.384279 NaN NaN +5.116667 NaN 9.149572 2.259819 +5.433333 NaN 8.392423 2.685996 + +2024-05-27 14:33:07,745 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.9831615095730615 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.004433373392056694 + +2024-05-27 14:33:07,746 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.004433373392056694 +2024-05-27 14:33:07,748 - physiofit - INFO - Results for yghJ: + optimal +yghJ X_0 0.019805 +yghJ growth_rate 0.596967 +yghJ Glc_q -5.170870 +yghJ Glc_M0 12.616607 +yghJ Ace_q 2.910526 +yghJ Ace_M0 0.308330 +2024-05-27 14:33:07,754 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:08,706 - physiofit - INFO - Running optimization for ygiC +2024-05-27 14:33:08,709 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:08,709 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:08,712 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1516 1.950000 NaN 13.886400 0.390771 +1517 2.501389 0.120960 NaN NaN +1518 3.250000 NaN 12.877958 0.924860 +1519 3.341944 0.187488 NaN NaN +1520 3.997500 0.273672 NaN NaN +1521 4.083333 NaN 11.806983 1.456281 +1522 4.523333 0.394632 NaN NaN +1523 4.766667 NaN 10.499725 2.006122 +Experimental matrix: +[[ nan 13.88639955 0.3907712 ] + [ 0.12096 nan nan] + [ nan 12.87795765 0.92486006] + [ 0.187488 nan nan] + [ 0.273672 nan nan] + [ nan 11.80698344 1.45628129] + [ 0.394632 nan nan] + [ nan 10.49972533 2.00612222]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:08,713 - physiofit - INFO - mc : False +2024-05-27 14:33:08,713 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:08,713 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:08,713 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:09,197 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:09,199 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.7806806264033566 + x: [ 2.552e-02 6.018e-01 -5.518e+00 1.435e+01 + 2.633e+00 2.011e-01] + nit: 109 + nfev: 10089 + population: [[ 2.537e-02 6.031e-01 ... 2.635e+00 2.039e-01] + [ 2.496e-02 6.072e-01 ... 2.633e+00 2.102e-01] + ... + [ 2.584e-02 5.984e-01 ... 2.630e+00 2.035e-01] + [ 2.533e-02 6.031e-01 ... 2.632e+00 2.050e-01]] + population_energies: [ 7.807e-01 7.876e-01 ... 7.876e-01 7.844e-01] + jac: [ 6.775e-03 -4.579e-04 1.698e-02 -2.330e-03 + 5.795e-03 -3.428e-03] +2024-05-27 14:33:09,199 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02551976342811743 +2024-05-27 14:33:09,199 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6017683748101914 +2024-05-27 14:33:09,199 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.518396388802931 +2024-05-27 14:33:09,199 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.349580456881483 +2024-05-27 14:33:09,199 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.633233142089465 +2024-05-27 14:33:09,200 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.20107544493367713 +2024-05-27 14:33:09,203 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.826977 0.450448 +2.501389 0.114974 NaN NaN +3.250000 NaN 12.929243 0.878823 +3.341944 0.190667 NaN NaN +3.997500 0.282880 NaN NaN +4.083333 NaN 11.852001 1.392854 +4.523333 0.388173 NaN NaN +4.766667 NaN 10.462599 2.055840 + +2024-05-27 14:33:09,210 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.7806806264033566 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.007418304238424585 + +2024-05-27 14:33:09,210 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.007418304238424585 +2024-05-27 14:33:09,212 - physiofit - INFO - Results for ygiC: + optimal +ygiC X_0 0.025520 +ygiC growth_rate 0.601768 +ygiC Glc_q -5.518396 +ygiC Glc_M0 14.349580 +ygiC Ace_q 2.633233 +ygiC Ace_M0 0.201075 +2024-05-27 14:33:09,220 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:10,156 - physiofit - INFO - Running optimization for ygjR +2024-05-27 14:33:10,158 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:10,159 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:10,162 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1524 0.050000 NaN 14.735425 0.016349 +1525 1.950000 NaN 13.980204 0.436566 +1526 2.833333 NaN 14.177504 0.827426 +1527 2.876944 0.149688 NaN NaN +1528 3.678056 0.240408 NaN NaN +1529 3.983333 NaN 11.920626 1.504139 +1530 4.092222 0.328104 NaN NaN +1531 4.565000 0.403704 NaN NaN +1532 4.883333 NaN 9.345015 2.233396 +1533 5.166667 NaN 8.918659 2.623674 +Experimental matrix: +[[ nan 14.73542516 0.01634936] + [ nan 13.98020416 0.43656599] + [ nan 14.17750443 0.82742588] + [ 0.149688 nan nan] + [ 0.240408 nan nan] + [ nan 11.92062604 1.50413871] + [ 0.328104 nan nan] + [ 0.403704 nan nan] + [ nan 9.34501469 2.23339644] + [ nan 8.91865948 2.6236737 ]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:10,163 - physiofit - INFO - mc : False +2024-05-27 14:33:10,163 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:10,163 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:10,164 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:10,678 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:10,679 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.398412431700766 + x: [ 3.076e-02 5.666e-01 -6.481e+00 1.495e+01 + 2.626e+00 1.529e-01] + nit: 86 + nfev: 8306 + population: [[ 3.097e-02 5.649e-01 ... 2.629e+00 1.448e-01] + [ 3.143e-02 5.620e-01 ... 2.634e+00 1.360e-01] + ... + [ 3.078e-02 5.663e-01 ... 2.618e+00 1.478e-01] + [ 3.090e-02 5.651e-01 ... 2.652e+00 1.492e-01]] + population_energies: [ 5.398e+00 5.454e+00 ... 5.425e+00 5.431e+00] + jac: [-6.569e-02 -1.089e-02 -2.949e-05 -2.575e-04 + 6.093e-05 -3.452e-04] +2024-05-27 14:33:10,679 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03076305840095105 +2024-05-27 14:33:10,679 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5665905231875037 +2024-05-27 14:33:10,679 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.481123901229987 +2024-05-27 14:33:10,679 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.945905350848529 +2024-05-27 14:33:10,680 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.6255757595875435 +2024-05-27 14:33:10,680 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1529162449720034 +2024-05-27 14:33:10,684 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.935794 0.157013 +1.950000 NaN 14.235512 0.440704 +2.833333 NaN 13.545529 0.720224 +2.876944 0.157019 NaN NaN +3.678056 0.247217 NaN NaN +3.983333 NaN 11.935951 1.372282 +4.092222 0.312601 NaN NaN +4.565000 0.408626 NaN NaN +4.883333 NaN 9.699728 2.278202 +5.166667 NaN 8.724893 2.673118 + +2024-05-27 14:33:10,687 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.398412431700766 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.13697403236147673 + +2024-05-27 14:33:10,688 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.13697403236147673 +2024-05-27 14:33:10,690 - physiofit - INFO - Results for ygjR: + optimal +ygjR X_0 0.030763 +ygjR growth_rate 0.566591 +ygjR Glc_q -6.481124 +ygjR Glc_M0 14.945905 +ygjR Ace_q 2.625576 +ygjR Ace_M0 0.152916 +2024-05-27 14:33:10,696 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:12,109 - physiofit - INFO - Running optimization for yhBT +2024-05-27 14:33:12,112 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:12,112 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:12,116 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1534 0.000000 0.034776 NaN NaN +1535 0.283333 NaN 14.625416 0.038550 +1536 1.195000 0.060480 NaN NaN +1537 1.613611 0.074088 NaN NaN +1538 1.916667 NaN 14.002803 0.394429 +1539 2.361389 0.113400 NaN NaN +1540 2.700000 NaN 13.337287 0.668521 +1541 3.286389 0.184464 NaN NaN +1542 3.616667 NaN 12.816694 1.134287 +1543 3.819444 0.255528 NaN NaN +1544 4.050000 NaN 11.856629 1.363793 +1545 4.410833 0.367416 NaN NaN +1546 4.750000 NaN 10.714844 1.854134 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.62541617 0.03854962] + [ 0.06048 nan nan] + [ 0.074088 nan nan] + [ nan 14.00280295 0.39442932] + [ 0.1134 nan nan] + [ nan 13.33728729 0.66852123] + [ 0.184464 nan nan] + [ nan 12.81669387 1.13428741] + [ 0.255528 nan nan] + [ nan 11.85662917 1.36379254] + [ 0.367416 nan nan] + [ nan 10.71484383 1.85413374]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:12,116 - physiofit - INFO - mc : False +2024-05-27 14:33:12,116 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:12,116 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:12,116 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:12,570 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:12,571 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.8374120430939942 + x: [ 3.054e-02 5.598e-01 -5.410e+00 1.457e+01 + 2.515e+00 1.283e-01] + nit: 93 + nfev: 8992 + population: [[ 3.062e-02 5.589e-01 ... 2.511e+00 1.308e-01] + [ 3.076e-02 5.586e-01 ... 2.481e+00 1.315e-01] + ... + [ 3.055e-02 5.591e-01 ... 2.514e+00 1.256e-01] + [ 3.092e-02 5.566e-01 ... 2.507e+00 1.297e-01]] + population_energies: [ 1.837e+00 1.852e+00 ... 1.848e+00 1.850e+00] + jac: [ 1.560e-03 -9.770e-06 4.130e-06 -3.681e-05 + 5.318e-05 6.042e-05] +2024-05-27 14:33:12,571 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.030537085984507297 +2024-05-27 14:33:12,571 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.559760590857689 +2024-05-27 14:33:12,571 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.4100245420195066 +2024-05-27 14:33:12,571 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.57118404633587 +2024-05-27 14:33:12,571 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5154615407513514 +2024-05-27 14:33:12,572 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.12832332830657006 +2024-05-27 14:33:12,576 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.030537 NaN NaN +0.283333 NaN 14.520459 0.151908 +1.195000 0.059612 NaN NaN +1.613611 0.075353 NaN NaN +1.916667 NaN 14.003407 0.392319 +2.361389 0.114521 NaN NaN +2.700000 NaN 13.528504 0.613131 +3.286389 0.192199 NaN NaN +3.616667 NaN 12.631517 1.030197 +3.819444 0.259023 NaN NaN +4.050000 NaN 12.018038 1.315442 +4.410833 0.360666 NaN NaN +4.750000 NaN 10.651745 1.950718 + +2024-05-27 14:33:12,580 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.8374120430939942 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.00013974561341415255 + +2024-05-27 14:33:12,580 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00013974561341415255 +2024-05-27 14:33:12,582 - physiofit - INFO - Results for yhBT: + optimal +yhBT X_0 0.030537 +yhBT growth_rate 0.559761 +yhBT Glc_q -5.410025 +yhBT Glc_M0 14.571184 +yhBT Ace_q 2.515462 +yhBT Ace_M0 0.128323 +2024-05-27 14:33:12,588 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:13,534 - physiofit - INFO - Running optimization for yhaJ +2024-05-27 14:33:13,537 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:13,537 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:13,540 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1547 0.050000 NaN 14.723793 0.025130 +1548 1.950000 NaN 13.975358 0.431269 +1549 2.833333 NaN 12.836910 0.760593 +1550 2.876944 0.173880 NaN NaN +1551 3.678056 0.269136 NaN NaN +1552 3.983333 NaN 11.740334 1.441752 +1553 4.092222 0.358344 NaN NaN +1554 4.565000 0.458136 NaN NaN +1555 4.883333 NaN 9.301553 2.084217 +1556 5.166667 NaN 8.586185 2.497934 +Experimental matrix: +[[ nan 14.72379311 0.02513012] + [ nan 13.975358 0.43126935] + [ nan 12.83691022 0.76059296] + [ 0.17388 nan nan] + [ 0.269136 nan nan] + [ nan 11.74033433 1.44175206] + [ 0.358344 nan nan] + [ 0.458136 nan nan] + [ nan 9.30155347 2.08421689] + [ nan 8.58618464 2.49793364]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:13,541 - physiofit - INFO - mc : False +2024-05-27 14:33:13,541 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:13,541 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:13,541 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:13,905 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:13,907 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.460250034482087 + x: [ 3.664e-02 5.521e-01 -5.647e+00 1.460e+01 + 2.196e+00 1.400e-01] + nit: 80 + nfev: 7563 + population: [[ 3.665e-02 5.520e-01 ... 2.211e+00 1.345e-01] + [ 3.702e-02 5.492e-01 ... 2.173e+00 1.516e-01] + ... + [ 3.723e-02 5.478e-01 ... 2.201e+00 1.409e-01] + [ 3.709e-02 5.491e-01 ... 2.215e+00 1.244e-01]] + population_energies: [ 2.460e+00 2.559e+00 ... 2.479e+00 2.490e+00] + jac: [-7.192e-04 6.107e-04 3.189e-05 5.227e-05 + -6.524e-05 1.714e-04] +2024-05-27 14:33:13,907 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.036636018619087704 +2024-05-27 14:33:13,908 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5521348884366338 +2024-05-27 14:33:13,908 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.646990386949527 +2024-05-27 14:33:13,908 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.603487076312978 +2024-05-27 14:33:13,908 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.19646488247861 +2024-05-27 14:33:13,908 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.13997241694523319 +2024-05-27 14:33:13,911 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.592999 0.144052 +1.950000 NaN 13.878497 0.421966 +2.833333 NaN 13.187237 0.690840 +2.876944 0.179378 NaN NaN +3.678056 0.279168 NaN NaN +3.983333 NaN 11.598779 1.308690 +4.092222 0.350896 NaN NaN +4.565000 0.455560 NaN NaN +4.883333 NaN 9.423614 2.154746 +5.166667 NaN 8.483012 2.520605 + +2024-05-27 14:33:13,916 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.460250034482087 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.00855760384711891 + +2024-05-27 14:33:13,917 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00855760384711891 +2024-05-27 14:33:13,919 - physiofit - INFO - Results for yhaJ: + optimal +yhaJ X_0 0.036636 +yhaJ growth_rate 0.552135 +yhaJ Glc_q -5.646990 +yhaJ Glc_M0 14.603487 +yhaJ Ace_q 2.196465 +yhaJ Ace_M0 0.139972 +2024-05-27 14:33:13,926 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:14,909 - physiofit - INFO - Running optimization for yhbS +2024-05-27 14:33:14,912 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:14,912 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:14,916 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1557 1.950000 NaN 13.781415 0.376392 +1558 2.501389 0.101304 NaN NaN +1559 3.250000 NaN 12.777902 0.873337 +1560 3.341944 0.152712 NaN NaN +1561 3.997500 0.201096 NaN NaN +1562 4.083333 NaN 11.669439 1.306748 +1563 4.523333 0.294840 NaN NaN +1564 4.766667 NaN 10.394655 1.857204 +Experimental matrix: +[[ nan 13.78141466 0.37639192] + [ 0.101304 nan nan] + [ nan 12.77790185 0.87333654] + [ 0.152712 nan nan] + [ 0.201096 nan nan] + [ nan 11.66943902 1.30674769] + [ 0.29484 nan nan] + [ nan 10.39465518 1.85720384]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:14,917 - physiofit - INFO - mc : False +2024-05-27 14:33:14,917 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:14,917 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:14,918 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:15,498 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:15,499 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.8822782022225526 + x: [ 2.478e-02 5.411e-01 -7.171e+00 1.437e+01 + 3.097e+00 1.467e-01] + nit: 123 + nfev: 11755 + population: [[ 2.464e-02 5.424e-01 ... 3.114e+00 1.418e-01] + [ 2.418e-02 5.475e-01 ... 3.080e+00 1.551e-01] + ... + [ 2.485e-02 5.405e-01 ... 3.093e+00 1.535e-01] + [ 2.455e-02 5.438e-01 ... 3.112e+00 1.475e-01]] + population_energies: [ 8.823e-01 8.922e-01 ... 8.869e-01 8.887e-01] + jac: [-3.960e-03 -3.847e-04 3.109e-07 7.683e-06 + 2.576e-06 9.936e-06] +2024-05-27 14:33:15,500 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.024782797544884008 +2024-05-27 14:33:15,500 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5411325606205177 +2024-05-27 14:33:15,500 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.170834574938964 +2024-05-27 14:33:15,500 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.370883629000154 +2024-05-27 14:33:15,500 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.0970924603210883 +2024-05-27 14:33:15,500 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.14674547660244494 +2024-05-27 14:33:15,504 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.755912 0.412353 +2.501389 0.095941 NaN NaN +3.250000 NaN 12.792948 0.828258 +3.341944 0.151197 NaN NaN +3.997500 0.215579 NaN NaN +4.083333 NaN 11.706725 1.297399 +4.523333 0.286538 NaN NaN +4.766667 NaN 10.367828 1.875670 + +2024-05-27 14:33:15,508 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.8822782022225526 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.010315986182737574 + +2024-05-27 14:33:15,508 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.010315986182737574 +2024-05-27 14:33:15,510 - physiofit - INFO - Results for yhbS: + optimal +yhbS X_0 0.024783 +yhbS growth_rate 0.541133 +yhbS Glc_q -7.170835 +yhbS Glc_M0 14.370884 +yhbS Ace_q 3.097092 +yhbS Ace_M0 0.146745 +2024-05-27 14:33:15,515 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:16,511 - physiofit - INFO - Running optimization for yhbw +2024-05-27 14:33:16,514 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:16,514 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:16,517 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1565 1.828889 0.063504 NaN NaN +1566 2.261389 0.080136 NaN NaN +1567 2.774167 0.114912 NaN NaN +1568 2.800000 NaN 12.600204 0.625524 +1569 3.208889 0.136080 NaN NaN +1570 3.706389 0.178416 NaN NaN +1571 3.733333 NaN 11.672038 1.042462 +1572 4.225833 0.219240 NaN NaN +1573 4.283333 NaN 11.238807 1.399258 +1574 4.635556 0.296352 NaN NaN +1575 4.750000 NaN 10.387580 1.733602 +1576 4.967500 0.359856 NaN NaN +1577 5.116667 NaN 9.704234 2.056151 +1578 5.433333 NaN 8.670152 2.323165 +Experimental matrix: +[[ 0.063504 nan nan] + [ 0.080136 nan nan] + [ 0.114912 nan nan] + [ nan 12.60020442 0.62552378] + [ 0.13608 nan nan] + [ 0.178416 nan nan] + [ nan 11.67203814 1.04246184] + [ 0.21924 nan nan] + [ nan 11.23880652 1.39925794] + [ 0.296352 nan nan] + [ nan 10.38757994 1.73360238] + [ 0.359856 nan nan] + [ nan 9.7042337 2.05615132] + [ nan 8.67015222 2.32316529]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:16,518 - physiofit - INFO - mc : False +2024-05-27 14:33:16,518 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:16,518 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:16,518 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:17,044 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:17,046 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.5831703135184363 + x: [ 2.334e-02 5.472e-01 -5.971e+00 1.352e+01 + 2.677e+00 2.705e-01] + nit: 107 + nfev: 10315 + population: [[ 2.339e-02 5.469e-01 ... 2.682e+00 2.683e-01] + [ 2.343e-02 5.466e-01 ... 2.682e+00 2.726e-01] + ... + [ 2.350e-02 5.461e-01 ... 2.682e+00 2.634e-01] + [ 2.350e-02 5.456e-01 ... 2.682e+00 2.707e-01]] + population_energies: [ 1.583e+00 1.595e+00 ... 1.590e+00 1.594e+00] + jac: [-1.227e-02 -1.472e-03 1.890e-05 3.708e-06 + 5.429e-05 1.811e-04] +2024-05-27 14:33:17,046 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.023336294937813216 +2024-05-27 14:33:17,046 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.547176389016742 +2024-05-27 14:33:17,047 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.971146163868579 +2024-05-27 14:33:17,047 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.522008543282723 +2024-05-27 14:33:17,047 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.676567698633269 +2024-05-27 14:33:17,047 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.27051653786090485 +2024-05-27 14:33:17,051 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.063481 NaN NaN +2.261389 0.080430 NaN NaN +2.774167 0.106481 NaN NaN +2.800000 NaN 12.598135 0.684643 +3.208889 0.135076 NaN NaN +3.706389 0.177338 NaN NaN +3.733333 NaN 11.812697 1.036716 +4.225833 0.235635 NaN NaN +4.283333 NaN 11.123072 1.345841 +4.635556 0.294853 NaN NaN +4.750000 NaN 10.351108 1.691873 +4.967500 0.353580 NaN NaN +5.116667 NaN 9.590037 2.033024 +5.433333 NaN 8.797967 2.388069 + +2024-05-27 14:33:17,058 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.5831703135184363 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 1.9407324172596673e-05 + +2024-05-27 14:33:17,059 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 1.9407324172596673e-05 +2024-05-27 14:33:17,063 - physiofit - INFO - Results for yhbw: + optimal +yhbw X_0 0.023336 +yhbw growth_rate 0.547176 +yhbw Glc_q -5.971146 +yhbw Glc_M0 13.522009 +yhbw Ace_q 2.676568 +yhbw Ace_M0 0.270517 +2024-05-27 14:33:17,069 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:18,034 - physiofit - INFO - Running optimization for yhcB +2024-05-27 14:33:18,037 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:18,037 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:18,040 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1579 0.050000 NaN 14.321053 0.018185 +1580 1.950000 NaN 14.322058 0.425385 +1581 2.833333 NaN 13.755293 0.728438 +1582 2.876944 0.154224 NaN NaN +1583 3.678056 0.223776 NaN NaN +1584 3.983333 NaN 12.237018 1.318424 +1585 4.092222 0.328104 NaN NaN +1586 4.565000 0.424872 NaN NaN +1587 4.883333 NaN 9.925932 1.843005 +1588 5.166667 NaN 9.480219 2.488998 +Experimental matrix: +[[ nan 14.32105266 0.01818473] + [ nan 14.32205825 0.42538496] + [ nan 13.75529294 0.7284379 ] + [ 0.154224 nan nan] + [ 0.223776 nan nan] + [ nan 12.23701811 1.31842398] + [ 0.328104 nan nan] + [ 0.424872 nan nan] + [ nan 9.92593205 1.84300479] + [ nan 9.48021868 2.48899841]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:18,041 - physiofit - INFO - mc : False +2024-05-27 14:33:18,041 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:18,041 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:18,041 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:18,481 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:18,482 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.2030929802169155 + x: [ 2.430e-02 6.268e-01 -5.604e+00 1.463e+01 + 2.362e+00 1.709e-01] + nit: 97 + nfev: 9289 + population: [[ 2.471e-02 6.231e-01 ... 2.366e+00 1.628e-01] + [ 2.471e-02 6.225e-01 ... 2.344e+00 1.955e-01] + ... + [ 2.483e-02 6.223e-01 ... 2.338e+00 1.737e-01] + [ 2.498e-02 6.192e-01 ... 2.350e+00 1.733e-01]] + population_energies: [ 5.203e+00 5.296e+00 ... 5.239e+00 5.267e+00] + jac: [-1.024e-02 1.193e-02 2.772e-03 8.039e-04 + -1.739e-03 -1.680e-03] +2024-05-27 14:33:18,483 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02430365221527784 +2024-05-27 14:33:18,483 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6267573775511178 +2024-05-27 14:33:18,483 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.603726401575717 +2024-05-27 14:33:18,483 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.632849166027711 +2024-05-27 14:33:18,483 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.361506530021439 +2024-05-27 14:33:18,483 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.17093727761971056 +2024-05-27 14:33:18,487 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.625932 0.173852 +1.950000 NaN 14.112522 0.390212 +2.833333 NaN 13.567002 0.620104 +2.876944 0.147492 NaN NaN +3.678056 0.243685 NaN NaN +3.983333 NaN 12.211982 1.191132 +4.092222 0.315910 NaN NaN +4.565000 0.424866 NaN NaN +4.883333 NaN 10.212696 2.033666 +5.166667 NaN 9.311524 2.413435 + +2024-05-27 14:33:18,491 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.2030929802169155 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.12279530964173817 + +2024-05-27 14:33:18,491 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.12279530964173817 +2024-05-27 14:33:18,494 - physiofit - INFO - Results for yhcB: + optimal +yhcB X_0 0.024304 +yhcB growth_rate 0.626757 +yhcB Glc_q -5.603726 +yhcB Glc_M0 14.632849 +yhcB Ace_q 2.361507 +yhcB Ace_M0 0.170937 +2024-05-27 14:33:18,502 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:19,513 - physiofit - INFO - Running optimization for yhcH +2024-05-27 14:33:19,516 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:19,516 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:19,520 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1589 0.050000 NaN 14.274925 0.019476 +1590 1.950000 NaN 13.895991 0.427762 +1591 2.833333 NaN 13.318348 0.748494 +1592 2.876944 0.167832 NaN NaN +1593 3.678056 0.254016 NaN NaN +1594 3.983333 NaN 11.844891 1.384492 +1595 4.092222 0.328104 NaN NaN +1596 4.565000 0.403704 NaN NaN +1597 4.883333 NaN 9.673787 1.561034 +1598 5.166667 NaN 8.716447 2.345026 +Experimental matrix: +[[ nan 14.27492523 0.01947612] + [ nan 13.89599119 0.42776187] + [ nan 13.3183478 0.74849353] + [ 0.167832 nan nan] + [ 0.254016 nan nan] + [ nan 11.8448913 1.38449225] + [ 0.328104 nan nan] + [ 0.403704 nan nan] + [ nan 9.67378667 1.56103372] + [ nan 8.71644749 2.34502589]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:19,520 - physiofit - INFO - mc : False +2024-05-27 14:33:19,521 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:19,521 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:19,521 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:19,948 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:19,949 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 6.027378755895124 + x: [ 3.766e-02 5.222e-01 -5.719e+00 1.456e+01 + 2.041e+00 1.526e-01] + nit: 93 + nfev: 8873 + population: [[ 3.775e-02 5.220e-01 ... 2.032e+00 1.532e-01] + [ 3.656e-02 5.291e-01 ... 1.960e+00 1.943e-01] + ... + [ 3.860e-02 5.174e-01 ... 1.988e+00 1.548e-01] + [ 3.858e-02 5.167e-01 ... 2.019e+00 1.515e-01]] + population_energies: [ 6.027e+00 6.200e+00 ... 6.141e+00 6.098e+00] + jac: [-5.107e-05 3.197e-06 3.286e-06 9.948e-06 + 5.240e-06 8.438e-06] +2024-05-27 14:33:19,949 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03765552851577726 +2024-05-27 14:33:19,949 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5221684723330726 +2024-05-27 14:33:19,949 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.719239313789888 +2024-05-27 14:33:19,950 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.555422797977519 +2024-05-27 14:33:19,950 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.0412660622924244 +2024-05-27 14:33:19,950 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15259105997883057 +2024-05-27 14:33:19,953 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.544513 0.156485 +1.950000 NaN 13.826118 0.412889 +2.833333 NaN 13.156997 0.651706 +2.876944 0.169140 NaN NaN +3.678056 0.256992 NaN NaN +3.983333 NaN 11.666624 1.183638 +4.092222 0.319038 NaN NaN +4.565000 0.408372 NaN NaN +4.883333 NaN 9.686159 1.890491 +5.166667 NaN 8.843979 2.191075 + +2024-05-27 14:33:19,957 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 6.027378755895124 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.18704222439024515 + +2024-05-27 14:33:19,958 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.18704222439024515 +2024-05-27 14:33:19,960 - physiofit - INFO - Results for yhcH: + optimal +yhcH X_0 0.037656 +yhcH growth_rate 0.522168 +yhcH Glc_q -5.719239 +yhcH Glc_M0 14.555423 +yhcH Ace_q 2.041266 +yhcH Ace_M0 0.152591 +2024-05-27 14:33:19,967 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:20,941 - physiofit - INFO - Running optimization for yhdP +2024-05-27 14:33:20,943 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:20,944 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:20,947 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1599 0.000000 0.033264 NaN NaN +1600 0.283333 NaN 13.982246 0.044146 +1601 1.195000 0.060480 NaN NaN +1602 1.613611 0.077112 NaN NaN +1603 1.916667 NaN 13.864630 0.393354 +1604 2.361389 0.119448 NaN NaN +1605 2.700000 NaN 13.003160 0.692293 +1606 3.286389 0.201096 NaN NaN +1607 3.616667 NaN 12.401061 1.171851 +1608 3.819444 0.273672 NaN NaN +1609 4.050000 NaN 12.155672 1.478044 +1610 4.410833 0.382536 NaN NaN +1611 4.750000 NaN 10.385343 1.937668 +Experimental matrix: +[[ 0.033264 nan nan] + [ nan 13.98224633 0.04414646] + [ 0.06048 nan nan] + [ 0.077112 nan nan] + [ nan 13.86463015 0.39335449] + [ 0.119448 nan nan] + [ nan 13.00315997 0.69229259] + [ 0.201096 nan nan] + [ nan 12.40106108 1.17185143] + [ 0.273672 nan nan] + [ nan 12.15567229 1.47804425] + [ 0.382536 nan nan] + [ nan 10.38534317 1.93766795]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:20,948 - physiofit - INFO - mc : False +2024-05-27 14:33:20,948 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:20,948 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:20,949 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:21,365 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:21,366 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.390830683021236 + x: [ 3.192e-02 5.622e-01 -4.718e+00 1.417e+01 + 2.526e+00 1.283e-01] + nit: 88 + nfev: 8276 + population: [[ 3.198e-02 5.613e-01 ... 2.525e+00 1.265e-01] + [ 3.203e-02 5.622e-01 ... 2.494e+00 1.356e-01] + ... + [ 3.238e-02 5.590e-01 ... 2.513e+00 1.298e-01] + [ 3.137e-02 5.673e-01 ... 2.521e+00 1.222e-01]] + population_energies: [ 2.391e+00 2.418e+00 ... 2.420e+00 2.430e+00] + jac: [ 5.894e-03 4.323e-04 -1.262e-02 7.033e-03 + 1.585e-02 -5.425e-03] +2024-05-27 14:33:21,366 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.0319160913531224 +2024-05-27 14:33:21,366 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5622314552698467 +2024-05-27 14:33:21,367 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.718277367216056 +2024-05-27 14:33:21,367 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.172677377921879 +2024-05-27 14:33:21,367 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.525559183716357 +2024-05-27 14:33:21,367 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.12827061369476564 +2024-05-27 14:33:21,370 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.031916 NaN NaN +0.283333 NaN 14.126424 0.153029 +1.195000 0.062488 NaN NaN +1.613611 0.079070 NaN NaN +1.916667 NaN 13.653694 0.406068 +2.361389 0.120393 NaN NaN +2.700000 NaN 13.218303 0.639120 +3.286389 0.202517 NaN NaN +3.616667 NaN 12.394197 1.080241 +3.819444 0.273287 NaN NaN +4.050000 NaN 11.829664 1.382419 +4.410833 0.381084 NaN NaN +4.750000 NaN 10.570576 2.056373 + +2024-05-27 14:33:21,374 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.390830683021236 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0006113494379048908 + +2024-05-27 14:33:21,374 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0006113494379048908 +2024-05-27 14:33:21,376 - physiofit - INFO - Results for yhdP: + optimal +yhdP X_0 0.031916 +yhdP growth_rate 0.562231 +yhdP Glc_q -4.718277 +yhdP Glc_M0 14.172677 +yhdP Ace_q 2.525559 +yhdP Ace_M0 0.128271 +2024-05-27 14:33:21,381 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:22,305 - physiofit - INFO - Running optimization for yheO +2024-05-27 14:33:22,308 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:22,308 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:22,311 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1612 1.828889 0.060480 NaN NaN +1613 2.261389 0.089208 NaN NaN +1614 2.774167 0.119448 NaN NaN +1615 2.800000 NaN 12.109053 0.711102 +1616 3.208889 0.143640 NaN NaN +1617 3.706389 0.187488 NaN NaN +1618 3.733333 NaN 11.301020 1.273323 +1619 4.225833 0.282744 NaN NaN +1620 4.283333 NaN 10.599638 1.729090 +1621 4.635556 0.335664 NaN NaN +1622 4.750000 NaN 9.662310 2.285578 +1623 4.967500 0.418824 NaN NaN +1624 5.116667 NaN 8.836120 2.618729 +1625 5.433333 NaN 7.893388 3.032042 +Experimental matrix: +[[ 0.06048 nan nan] + [ 0.089208 nan nan] + [ 0.119448 nan nan] + [ nan 12.10905317 0.71110187] + [ 0.14364 nan nan] + [ 0.187488 nan nan] + [ nan 11.30101951 1.27332343] + [ 0.282744 nan nan] + [ nan 10.59963755 1.72909039] + [ 0.335664 nan nan] + [ nan 9.66230993 2.28557783] + [ 0.418824 nan nan] + [ nan 8.83612015 2.61872932] + [ nan 7.89338819 3.03204178]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:22,312 - physiofit - INFO - mc : False +2024-05-27 14:33:22,312 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:22,312 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:22,312 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:22,885 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:22,886 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.097645264594759 + x: [ 2.257e-02 5.867e-01 -5.748e+00 1.305e+01 + 3.163e+00 2.981e-01] + nit: 125 + nfev: 11767 + population: [[ 2.258e-02 5.867e-01 ... 3.181e+00 2.884e-01] + [ 2.260e-02 5.864e-01 ... 3.167e+00 2.901e-01] + ... + [ 2.258e-02 5.871e-01 ... 3.160e+00 3.041e-01] + [ 2.253e-02 5.868e-01 ... 3.159e+00 3.082e-01]] + population_energies: [ 2.098e+00 2.105e+00 ... 2.120e+00 2.127e+00] + jac: [ 2.423e-02 5.167e-03 3.089e-02 -1.961e-02 + -8.186e-03 5.784e-03] +2024-05-27 14:33:22,886 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02257205291050396 +2024-05-27 14:33:22,886 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5866979912916549 +2024-05-27 14:33:22,886 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.7482098800247865 +2024-05-27 14:33:22,886 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.0534725469548 +2024-05-27 14:33:22,886 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.1630464918753627 +2024-05-27 14:33:22,887 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.29807445692294715 +2024-05-27 14:33:22,891 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.066004 NaN NaN +2.261389 0.085069 NaN NaN +2.774167 0.114929 NaN NaN +2.800000 NaN 12.131408 0.805456 +3.208889 0.148318 NaN NaN +3.706389 0.198590 NaN NaN +3.733333 NaN 11.297921 1.264095 +4.225833 0.269347 NaN NaN +4.283333 NaN 10.545136 1.678328 +4.635556 0.342538 NaN NaN +4.750000 NaN 9.685506 2.151353 +4.967500 0.416187 NaN NaN +5.116667 NaN 8.824068 2.625373 +5.433333 NaN 7.915414 3.125375 + +2024-05-27 14:33:22,896 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.097645264594759 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.00011142556307103383 + +2024-05-27 14:33:22,896 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00011142556307103383 +2024-05-27 14:33:22,898 - physiofit - INFO - Results for yheO: + optimal +yheO X_0 0.022572 +yheO growth_rate 0.586698 +yheO Glc_q -5.748210 +yheO Glc_M0 13.053473 +yheO Ace_q 3.163046 +yheO Ace_M0 0.298074 +2024-05-27 14:33:22,905 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:23,945 - physiofit - INFO - Running optimization for yheS +2024-05-27 14:33:23,948 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:23,948 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:23,952 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1626 0.050000 NaN 14.382066 0.023136 +1627 1.950000 NaN 13.784220 0.462071 +1628 2.833333 NaN 13.718084 0.804900 +1629 2.876944 0.184464 NaN NaN +1630 3.678056 0.291816 NaN NaN +1631 3.983333 NaN 11.591506 1.476197 +1632 4.092222 0.387072 NaN NaN +1633 4.565000 0.603288 NaN NaN +1634 4.883333 NaN 9.030295 2.252820 +1635 5.166667 NaN 8.015510 2.715341 +Experimental matrix: +[[ nan 14.38206556 0.02313645] + [ nan 13.78421958 0.46207146] + [ nan 13.71808401 0.80489953] + [ 0.184464 nan nan] + [ 0.291816 nan nan] + [ nan 11.5915057 1.47619675] + [ 0.387072 nan nan] + [ 0.603288 nan nan] + [ nan 9.03029479 2.25282044] + [ nan 8.01551033 2.71534067]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:23,952 - physiofit - INFO - mc : False +2024-05-27 14:33:23,952 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:23,952 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:23,953 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:24,397 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:24,398 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 7.545176343588894 + x: [ 2.005e-02 7.387e-01 -5.408e+00 1.441e+01 + 2.089e+00 2.624e-01] + nit: 95 + nfev: 9165 + population: [[ 2.020e-02 7.371e-01 ... 2.098e+00 2.541e-01] + [ 2.071e-02 7.310e-01 ... 2.110e+00 2.379e-01] + ... + [ 1.953e-02 7.444e-01 ... 2.083e+00 2.487e-01] + [ 2.018e-02 7.378e-01 ... 2.082e+00 2.506e-01]] + population_energies: [ 7.545e+00 7.629e+00 ... 7.661e+00 7.583e+00] + jac: [ 1.725e+00 1.470e-01 -9.443e-02 -9.262e-02 + 1.861e-02 3.089e-02] +2024-05-27 14:33:24,398 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.020047580246004223 +2024-05-27 14:33:24,399 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.738711408237219 +2024-05-27 14:33:24,399 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.407654032724419 +2024-05-27 14:33:24,399 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.409622686237942 +2024-05-27 14:33:24,399 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.0893159825205783 +2024-05-27 14:33:24,399 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.262366501562713 +2024-05-27 14:33:24,403 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.404101 0.264500 +1.950000 NaN 13.936664 0.445100 +2.833333 NaN 13.366285 0.665473 +2.876944 0.167895 NaN NaN +3.678056 0.303424 NaN NaN +3.983333 NaN 11.773321 1.280935 +4.092222 0.412023 NaN NaN +4.565000 0.584248 NaN NaN +4.883333 NaN 9.145613 2.296183 +5.166667 NaN 7.885897 2.782891 + +2024-05-27 14:33:24,406 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 7.545176343588894 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.3268326972759035 + +2024-05-27 14:33:24,407 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.3268326972759035 +2024-05-27 14:33:24,408 - physiofit - INFO - Results for yheS: + optimal +yheS X_0 0.020048 +yheS growth_rate 0.738711 +yheS Glc_q -5.407654 +yheS Glc_M0 14.409623 +yheS Ace_q 2.089316 +yheS Ace_M0 0.262367 +2024-05-27 14:33:24,415 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:25,362 - physiofit - INFO - Running optimization for yhhM +2024-05-27 14:33:25,365 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:25,365 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:25,368 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1636 1.950000 NaN 13.608013 0.381508 +1637 2.501389 0.110376 NaN NaN +1638 3.250000 NaN 12.842543 0.884743 +1639 3.341944 0.161784 NaN NaN +1640 3.997500 0.217728 NaN NaN +1641 4.083333 NaN 11.618844 1.324321 +1642 4.523333 0.337176 NaN NaN +1643 4.766667 NaN 10.359158 1.798292 +Experimental matrix: +[[ nan 13.60801254 0.38150794] + [ 0.110376 nan nan] + [ nan 12.84254293 0.88474339] + [ 0.161784 nan nan] + [ 0.217728 nan nan] + [ nan 11.61884378 1.32432078] + [ 0.337176 nan nan] + [ nan 10.35915789 1.79829178]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:25,369 - physiofit - INFO - mc : False +2024-05-27 14:33:25,369 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:25,369 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:25,370 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:25,873 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:25,875 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.169135385262698 + x: [ 2.271e-02 5.883e-01 -6.403e+00 1.418e+01 + 2.710e+00 2.214e-01] + nit: 110 + nfev: 10347 + population: [[ 2.294e-02 5.860e-01 ... 2.737e+00 2.079e-01] + [ 2.274e-02 5.886e-01 ... 2.726e+00 2.116e-01] + ... + [ 2.210e-02 5.941e-01 ... 2.750e+00 2.061e-01] + [ 2.294e-02 5.863e-01 ... 2.699e+00 2.242e-01]] + population_energies: [ 2.169e+00 2.177e+00 ... 2.211e+00 2.187e+00] + jac: [-1.971e-02 1.093e-03 2.491e-04 2.947e-04 + 7.372e-06 9.224e-05] +2024-05-27 14:33:25,875 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.022712793534749098 +2024-05-27 14:33:25,875 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5883329194968521 +2024-05-27 14:33:25,876 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.402956441285707 +2024-05-27 14:33:25,876 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.176288996535474 +2024-05-27 14:33:25,876 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.710280208790876 +2024-05-27 14:33:25,876 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.22137814165735456 +2024-05-27 14:33:25,879 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.644953 0.446285 +2.501389 0.098946 NaN NaN +3.250000 NaN 12.750714 0.824804 +3.341944 0.162244 NaN NaN +3.997500 0.238600 NaN NaN +4.083333 NaN 11.692240 1.272841 +4.523333 0.325107 NaN NaN +4.766667 NaN 10.340681 1.844936 + +2024-05-27 14:33:25,882 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.169135385262698 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.0964955941333414 + +2024-05-27 14:33:25,882 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0964955941333414 +2024-05-27 14:33:25,884 - physiofit - INFO - Results for yhhM: + optimal +yhhM X_0 0.022713 +yhhM growth_rate 0.588333 +yhhM Glc_q -6.402956 +yhhM Glc_M0 14.176289 +yhhM Ace_q 2.710280 +yhhM Ace_M0 0.221378 +2024-05-27 14:33:25,890 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:26,804 - physiofit - INFO - Running optimization for yhhX +2024-05-27 14:33:26,807 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:26,807 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:26,811 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1644 1.828889 0.057456 NaN NaN +1645 2.261389 0.078624 NaN NaN +1646 2.774167 0.114912 NaN NaN +1647 2.800000 NaN 12.109666 0.631445 +1648 3.208889 0.139104 NaN NaN +1649 3.706389 0.184464 NaN NaN +1650 3.733333 NaN 11.516562 1.116044 +1651 4.225833 0.270648 NaN NaN +1652 4.283333 NaN 10.975237 1.501140 +1653 4.635556 0.323568 NaN NaN +1654 4.750000 NaN 9.992222 1.892130 +1655 4.967500 0.382536 NaN NaN +1656 5.116667 NaN 9.200772 2.218644 +1657 5.433333 NaN 8.033590 2.489428 +Experimental matrix: +[[ 0.057456 nan nan] + [ 0.078624 nan nan] + [ 0.114912 nan nan] + [ nan 12.10966615 0.63144522] + [ 0.139104 nan nan] + [ 0.184464 nan nan] + [ nan 11.51656177 1.11604402] + [ 0.270648 nan nan] + [ nan 10.97523698 1.50113969] + [ 0.323568 nan nan] + [ nan 9.9922221 1.89213041] + [ 0.382536 nan nan] + [ nan 9.20077219 2.21864388] + [ nan 8.03358964 2.48942786]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:26,811 - physiofit - INFO - mc : False +2024-05-27 14:33:26,811 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:26,811 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:26,812 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:27,217 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:27,218 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.4747218711551033 + x: [ 2.265e-02 5.727e-01 -5.914e+00 1.325e+01 + 2.695e+00 3.008e-01] + nit: 89 + nfev: 8338 + population: [[ 2.271e-02 5.718e-01 ... 2.699e+00 3.007e-01] + [ 2.249e-02 5.746e-01 ... 2.711e+00 3.022e-01] + ... + [ 2.248e-02 5.744e-01 ... 2.673e+00 3.001e-01] + [ 2.291e-02 5.699e-01 ... 2.696e+00 2.962e-01]] + population_energies: [ 2.475e+00 2.500e+00 ... 2.516e+00 2.484e+00] + jac: [ 3.518e-02 -3.990e-03 -3.634e-02 5.998e-02 + 4.376e-02 -4.143e-02] +2024-05-27 14:33:27,218 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02265240452772343 +2024-05-27 14:33:27,218 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5726770922036772 +2024-05-27 14:33:27,218 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.913963842110521 +2024-05-27 14:33:27,218 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.247236404430307 +2024-05-27 14:33:27,218 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.695214739813855 +2024-05-27 14:33:27,218 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.3007802106852573 +2024-05-27 14:33:27,221 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.064562 NaN NaN +2.261389 0.082708 NaN NaN +2.774167 0.110938 NaN NaN +2.800000 NaN 12.318452 0.724062 +3.208889 0.142298 NaN NaN +3.706389 0.189205 NaN NaN +3.733333 NaN 11.496888 1.098480 +4.225833 0.254755 NaN NaN +4.283333 NaN 10.762265 1.433274 +4.635556 0.322126 NaN NaN +4.750000 NaN 9.929287 1.812894 +4.967500 0.389568 NaN NaN +5.116667 NaN 9.099372 2.191118 +5.433333 NaN 8.228131 2.588175 + +2024-05-27 14:33:27,225 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.4747218711551033 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.00030139819842427184 + +2024-05-27 14:33:27,225 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00030139819842427184 +2024-05-27 14:33:27,227 - physiofit - INFO - Results for yhhX: + optimal +yhhX X_0 0.022652 +yhhX growth_rate 0.572677 +yhhX Glc_q -5.913964 +yhhX Glc_M0 13.247236 +yhhX Ace_q 2.695215 +yhhX Ace_M0 0.300780 +2024-05-27 14:33:27,235 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:28,196 - physiofit - INFO - Running optimization for yhiI +2024-05-27 14:33:28,200 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:28,200 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:28,205 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1658 0.000000 0.031752 NaN NaN +1659 0.066667 NaN 15.547429 0.004223 +1660 1.188889 0.065016 NaN NaN +1661 1.716667 NaN 14.235395 0.347969 +1662 2.276944 0.105840 NaN NaN +1663 2.800000 NaN 13.211125 0.714152 +1664 3.128333 0.157248 NaN NaN +1665 3.633333 NaN 12.808542 1.163428 +1666 3.771389 0.214704 NaN NaN +1667 4.266667 NaN 12.010890 1.612397 +1668 4.415556 0.297864 NaN NaN +1669 4.822778 0.358344 NaN NaN +1670 4.883333 NaN 10.449242 2.060116 +Experimental matrix: +[[3.17520000e-02 nan nan] + [ nan 1.55474288e+01 4.22290244e-03] + [6.50160000e-02 nan nan] + [ nan 1.42353952e+01 3.47969308e-01] + [1.05840000e-01 nan nan] + [ nan 1.32111249e+01 7.14151651e-01] + [1.57248000e-01 nan nan] + [ nan 1.28085424e+01 1.16342786e+00] + [2.14704000e-01 nan nan] + [ nan 1.20108905e+01 1.61239658e+00] + [2.97864000e-01 nan nan] + [3.58344000e-01 nan nan] + [ nan 1.04492425e+01 2.06011635e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:28,206 - physiofit - INFO - mc : False +2024-05-27 14:33:28,206 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:28,206 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:28,207 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:28,615 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:28,616 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.1741529525534298 + x: [ 3.721e-02 4.684e-01 -6.612e+00 1.512e+01 + 2.958e+00 5.587e-02] + nit: 90 + nfev: 8449 + population: [[ 3.746e-02 4.670e-01 ... 2.951e+00 5.512e-02] + [ 3.796e-02 4.644e-01 ... 2.905e+00 6.950e-02] + ... + [ 3.808e-02 4.629e-01 ... 2.941e+00 5.089e-02] + [ 3.729e-02 4.672e-01 ... 2.987e+00 5.430e-02]] + population_energies: [ 3.174e+00 3.223e+00 ... 3.200e+00 3.194e+00] + jac: [-4.363e-04 1.416e-04 -1.303e-03 4.942e-04 + 2.124e-04 9.663e-05] +2024-05-27 14:33:28,616 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03721382672736421 +2024-05-27 14:33:28,616 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.46843101528066083 +2024-05-27 14:33:28,617 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.611584893242076 +2024-05-27 14:33:28,617 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.11786784633744 +2024-05-27 14:33:28,617 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.9576973321579825 +2024-05-27 14:33:28,617 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.05586945210993456 +2024-05-27 14:33:28,621 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.037214 NaN NaN +0.066667 NaN 15.101206 0.063323 +1.188889 0.064948 NaN NaN +1.716667 NaN 14.469306 0.346004 +2.276944 0.108123 NaN NaN +2.800000 NaN 13.693325 0.693140 +3.128333 0.161110 NaN NaN +3.633333 NaN 12.762278 1.109644 +3.771389 0.217743 NaN NaN +4.266667 NaN 11.767309 1.554745 +4.415556 0.294437 NaN NaN +4.822778 0.356316 NaN NaN +4.883333 NaN 10.469252 2.135431 + +2024-05-27 14:33:28,625 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.1741529525534298 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0027699882642176826 + +2024-05-27 14:33:28,625 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0027699882642176826 +2024-05-27 14:33:28,628 - physiofit - INFO - Results for yhiI: + optimal +yhiI X_0 0.037214 +yhiI growth_rate 0.468431 +yhiI Glc_q -6.611585 +yhiI Glc_M0 15.117868 +yhiI Ace_q 2.957697 +yhiI Ace_M0 0.055869 +2024-05-27 14:33:28,635 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:29,584 - physiofit - INFO - Running optimization for yhiN +2024-05-27 14:33:29,587 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:29,587 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:29,590 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1671 0.050000 NaN 14.139166 0.019761 +1672 1.950000 NaN 13.992580 0.382517 +1673 2.833333 NaN 13.574003 0.715849 +1674 2.876944 0.133056 NaN NaN +1675 3.678056 0.196560 NaN NaN +1676 3.983333 NaN 12.209599 1.293279 +1677 4.092222 0.261576 NaN NaN +1678 4.565000 0.337176 NaN NaN +1679 4.883333 NaN 10.772134 2.137254 +1680 5.166667 NaN 10.064630 2.298878 +Experimental matrix: +[[ nan 14.13916644 0.01976119] + [ nan 13.99258001 0.38251693] + [ nan 13.57400348 0.71584913] + [ 0.133056 nan nan] + [ 0.19656 nan nan] + [ nan 12.20959903 1.29327863] + [ 0.261576 nan nan] + [ 0.337176 nan nan] + [ nan 10.77213378 2.13725406] + [ nan 10.06462977 2.29887833]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:29,590 - physiofit - INFO - mc : False +2024-05-27 14:33:29,590 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:29,590 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:29,591 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:30,161 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:30,163 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.6536206618908673 + x: [ 2.706e-02 5.511e-01 -5.355e+00 1.437e+01 + 2.883e+00 1.102e-01] + nit: 119 + nfev: 11388 + population: [[ 2.711e-02 5.501e-01 ... 2.894e+00 1.077e-01] + [ 2.701e-02 5.507e-01 ... 2.891e+00 1.084e-01] + ... + [ 2.684e-02 5.524e-01 ... 2.914e+00 1.082e-01] + [ 2.679e-02 5.534e-01 ... 2.892e+00 1.172e-01]] + population_energies: [ 1.654e+00 1.673e+00 ... 1.685e+00 1.668e+00] + jac: [-5.545e-02 -5.505e-03 -4.134e-04 -5.915e-04 + -6.238e-04 2.162e-04] +2024-05-27 14:33:30,163 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.027062095753310592 +2024-05-27 14:33:30,163 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5510523862371995 +2024-05-27 14:33:30,163 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.355358753432197 +2024-05-27 14:33:30,163 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.373572011349145 +2024-05-27 14:33:30,163 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.8834618974865647 +2024-05-27 14:33:30,163 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.11022764025090993 +2024-05-27 14:33:30,166 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.366225 0.114184 +1.950000 NaN 13.866327 0.383341 +2.833333 NaN 13.383352 0.643387 +2.876944 0.132090 NaN NaN +3.678056 0.205395 NaN NaN +3.983333 NaN 12.274765 1.240279 +4.092222 0.258052 NaN NaN +4.565000 0.334852 NaN NaN +4.883333 NaN 10.758360 2.056750 +5.166667 NaN 10.103020 2.409602 + +2024-05-27 14:33:30,169 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.6536206618908673 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.0016281715330182778 + +2024-05-27 14:33:30,170 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0016281715330182778 +2024-05-27 14:33:30,171 - physiofit - INFO - Results for yhiN: + optimal +yhiN X_0 0.027062 +yhiN growth_rate 0.551052 +yhiN Glc_q -5.355359 +yhiN Glc_M0 14.373572 +yhiN Ace_q 2.883462 +yhiN Ace_M0 0.110228 +2024-05-27 14:33:30,177 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:31,161 - physiofit - INFO - Running optimization for yiaF +2024-05-27 14:33:31,163 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:31,163 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:31,167 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1681 0.050000 NaN 14.202142 0.021710 +1682 1.950000 NaN 13.722384 0.425561 +1683 2.833333 NaN 13.170718 0.765500 +1684 2.876944 0.167832 NaN NaN +1685 3.678056 0.273672 NaN NaN +1686 3.983333 NaN 11.868191 1.459339 +1687 4.092222 0.361368 NaN NaN +1688 4.565000 0.485352 NaN NaN +1689 4.883333 NaN 9.555433 2.123212 +1690 5.166667 NaN 8.612890 2.472481 +Experimental matrix: +[[ nan 14.20214156 0.0217097 ] + [ nan 13.7223841 0.42556072] + [ nan 13.17071785 0.76549997] + [ 0.167832 nan nan] + [ 0.273672 nan nan] + [ nan 11.86819088 1.45933861] + [ 0.361368 nan nan] + [ 0.485352 nan nan] + [ nan 9.55543305 2.12321236] + [ nan 8.61288983 2.47248101]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:31,167 - physiofit - INFO - mc : False +2024-05-27 14:33:31,167 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:31,167 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:31,168 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:31,645 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:31,646 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.279063142611328 + x: [ 2.903e-02 6.155e-01 -5.193e+00 1.430e+01 + 2.173e+00 1.879e-01] + nit: 97 + nfev: 9093 + population: [[ 2.929e-02 6.134e-01 ... 2.169e+00 1.875e-01] + [ 2.891e-02 6.174e-01 ... 2.164e+00 1.851e-01] + ... + [ 2.827e-02 6.217e-01 ... 2.165e+00 2.022e-01] + [ 2.904e-02 6.150e-01 ... 2.173e+00 1.916e-01]] + population_energies: [ 2.279e+00 2.311e+00 ... 2.302e+00 2.285e+00] + jac: [-1.453e-03 -1.045e-04 7.831e-03 -7.705e-03 + -1.068e-02 5.609e-03] +2024-05-27 14:33:31,646 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.0290289799086073 +2024-05-27 14:33:31,647 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6154735884782447 +2024-05-27 14:33:31,647 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.192546665827875 +2024-05-27 14:33:31,647 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.301035657073381 +2024-05-27 14:33:31,647 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.17274264237305 +2024-05-27 14:33:31,648 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1878781511872244 +2024-05-27 14:33:31,651 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.293382 0.191081 +1.950000 NaN 13.732680 0.425698 +2.833333 NaN 13.145248 0.671500 +2.876944 0.170541 NaN NaN +3.678056 0.279231 NaN NaN +3.983333 NaN 11.703218 1.274896 +4.092222 0.360304 NaN NaN +4.565000 0.481994 NaN NaN +4.883333 NaN 9.599398 2.155208 +5.166667 NaN 8.657017 2.549532 + +2024-05-27 14:33:31,655 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.279063142611328 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.006280631427326775 + +2024-05-27 14:33:31,655 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.006280631427326775 +2024-05-27 14:33:31,658 - physiofit - INFO - Results for yiaF: + optimal +yiaF X_0 0.029029 +yiaF growth_rate 0.615474 +yiaF Glc_q -5.192547 +yiaF Glc_M0 14.301036 +yiaF Ace_q 2.172743 +yiaF Ace_M0 0.187878 +2024-05-27 14:33:31,664 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:32,640 - physiofit - INFO - Running optimization for yibL +2024-05-27 14:33:32,643 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:32,643 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:32,648 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1691 0.050000 NaN 14.716657 0.021062 +1692 1.950000 NaN 14.228133 0.418534 +1693 2.833333 NaN 13.689613 0.797638 +1694 2.876944 0.134568 NaN NaN +1695 3.678056 0.219240 NaN NaN +1696 3.983333 NaN 11.856762 1.464002 +1697 4.092222 0.290304 NaN NaN +1698 4.565000 0.400680 NaN NaN +1699 4.883333 NaN 9.436133 1.967243 +1700 5.166667 NaN 8.623352 2.441496 +Experimental matrix: +[[ nan 14.71665702 0.02106232] + [ nan 14.22813314 0.41853358] + [ nan 13.68961314 0.79763753] + [ 0.134568 nan nan] + [ 0.21924 nan nan] + [ nan 11.85676174 1.46400232] + [ 0.290304 nan nan] + [ 0.40068 nan nan] + [ nan 9.43613275 1.96724346] + [ nan 8.62335214 2.44149587]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:32,648 - physiofit - INFO - mc : False +2024-05-27 14:33:32,648 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:32,648 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:32,649 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:33,113 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:33,119 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.601388139094857 + x: [ 2.323e-02 6.195e-01 -7.140e+00 1.482e+01 + 2.559e+00 2.077e-01] + nit: 102 + nfev: 9571 + population: [[ 2.333e-02 6.185e-01 ... 2.571e+00 2.026e-01] + [ 2.427e-02 6.107e-01 ... 2.510e+00 2.211e-01] + ... + [ 2.347e-02 6.159e-01 ... 2.557e+00 1.982e-01] + [ 2.300e-02 6.224e-01 ... 2.597e+00 1.935e-01]] + population_energies: [ 3.601e+00 3.714e+00 ... 3.727e+00 3.648e+00] + jac: [ 1.281e-01 1.057e-02 -1.445e-02 -3.968e-02 + 3.872e-02 -1.230e-02] +2024-05-27 14:33:33,125 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.023227246620336425 +2024-05-27 14:33:33,126 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6195379710492022 +2024-05-27 14:33:33,126 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.140410089044937 +2024-05-27 14:33:33,126 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.818033710927212 +2024-05-27 14:33:33,126 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.55897929732318 +2024-05-27 14:33:33,127 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.2076677906767956 +2024-05-27 14:33:33,131 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.809611 0.210686 +1.950000 NaN 14.189704 0.432848 +2.833333 NaN 13.536938 0.666787 +2.876944 0.138062 NaN NaN +3.678056 0.226789 NaN NaN +3.983333 NaN 11.927706 1.243503 +4.092222 0.293129 NaN NaN +4.565000 0.392885 NaN NaN +4.883333 NaN 9.570400 2.088314 +5.166667 NaN 8.512092 2.467590 + +2024-05-27 14:33:33,137 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.601388139094857 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.036456864718779805 + +2024-05-27 14:33:33,137 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.036456864718779805 +2024-05-27 14:33:33,139 - physiofit - INFO - Results for yibL: + optimal +yibL X_0 0.023227 +yibL growth_rate 0.619538 +yibL Glc_q -7.140410 +yibL Glc_M0 14.818034 +yibL Ace_q 2.558979 +yibL Ace_M0 0.207668 +2024-05-27 14:33:33,145 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:34,086 - physiofit - INFO - Running optimization for yibN +2024-05-27 14:33:34,089 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:34,089 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:34,092 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1701 0.050000 NaN 14.452971 0.019774 +1702 1.950000 NaN 14.027723 0.395204 +1703 2.833333 NaN 13.120677 0.663788 +1704 2.876944 0.151200 NaN NaN +1705 3.678056 0.226800 NaN NaN +1706 3.983333 NaN 12.588156 1.316726 +1707 4.092222 0.312984 NaN NaN +1708 4.565000 0.394632 NaN NaN +1709 4.883333 NaN 9.911486 1.460674 +1710 5.166667 NaN 9.689589 2.182363 +Experimental matrix: +[[ nan 14.45297121 0.01977424] + [ nan 14.02772347 0.39520374] + [ nan 13.12067728 0.66378818] + [ 0.1512 nan nan] + [ 0.2268 nan nan] + [ nan 12.58815585 1.31672575] + [ 0.312984 nan nan] + [ 0.394632 nan nan] + [ nan 9.91148616 1.46067362] + [ nan 9.68958936 2.18236263]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:34,092 - physiofit - INFO - mc : False +2024-05-27 14:33:34,093 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:34,093 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:34,093 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:34,487 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:34,488 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 7.7694623111331556 + x: [ 2.957e-02 5.680e-01 -5.367e+00 1.451e+01 + 2.045e+00 1.636e-01] + nit: 87 + nfev: 8256 + population: [[ 2.979e-02 5.665e-01 ... 2.047e+00 1.623e-01] + [ 3.033e-02 5.625e-01 ... 2.031e+00 1.721e-01] + ... + [ 2.886e-02 5.733e-01 ... 2.058e+00 1.602e-01] + [ 3.072e-02 5.601e-01 ... 2.051e+00 1.625e-01]] + population_energies: [ 7.769e+00 7.798e+00 ... 7.797e+00 7.852e+00] + jac: [ 2.123e-01 1.630e-02 4.933e-03 1.038e-02 + 1.374e-02 1.939e-02] +2024-05-27 14:33:34,489 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.029570152346406402 +2024-05-27 14:33:34,489 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5680368210815601 +2024-05-27 14:33:34,489 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.366924421295795 +2024-05-27 14:33:34,489 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.510641657120814 +2024-05-27 14:33:34,489 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.045089424164264 +2024-05-27 14:33:34,490 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.16358449211539122 +2024-05-27 14:33:34,493 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.502593 0.166652 +1.950000 NaN 13.944245 0.379413 +2.833333 NaN 13.393103 0.589427 +2.876944 0.151559 NaN NaN +3.678056 0.238898 NaN NaN +3.983333 NaN 12.105473 1.080084 +4.092222 0.302263 NaN NaN +4.565000 0.395382 NaN NaN +4.883333 NaN 10.313948 1.762753 +5.166667 NaN 9.532339 2.060588 + +2024-05-27 14:33:34,498 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 7.7694623111331556 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.34865600161180366 + +2024-05-27 14:33:34,499 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.34865600161180366 +2024-05-27 14:33:34,501 - physiofit - INFO - Results for yibN: + optimal +yibN X_0 0.029570 +yibN growth_rate 0.568037 +yibN Glc_q -5.366924 +yibN Glc_M0 14.510642 +yibN Ace_q 2.045089 +yibN Ace_M0 0.163584 +2024-05-27 14:33:34,507 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:35,442 - physiofit - INFO - Running optimization for yibT +2024-05-27 14:33:35,445 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:35,445 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:35,448 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1711 0.050000 NaN 14.223975 0.025371 +1712 1.950000 NaN 14.058709 0.449573 +1713 2.833333 NaN 13.445400 0.883916 +1714 2.876944 0.158760 NaN NaN +1715 3.678056 0.264600 NaN NaN +1716 3.983333 NaN 12.096783 1.759117 +1717 4.092222 0.350784 NaN NaN +1718 4.565000 0.439992 NaN NaN +1719 4.883333 NaN 9.536691 2.325282 +1720 5.166667 NaN 8.459339 3.085291 +Experimental matrix: +[[ nan 14.2239749 0.02537118] + [ nan 14.05870949 0.44957272] + [ nan 13.4454002 0.88391608] + [ 0.15876 nan nan] + [ 0.2646 nan nan] + [ nan 12.09678345 1.75911716] + [ 0.350784 nan nan] + [ 0.439992 nan nan] + [ nan 9.53669101 2.32528202] + [ nan 8.45933924 3.08529104]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:35,449 - physiofit - INFO - mc : False +2024-05-27 14:33:35,449 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:35,449 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:35,449 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:35,842 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:35,846 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.78113459217461 + x: [ 3.073e-02 5.862e-01 -5.804e+00 1.460e+01 + 2.769e+00 1.650e-01] + nit: 84 + nfev: 8287 + population: [[ 3.073e-02 5.857e-01 ... 2.783e+00 1.601e-01] + [ 3.167e-02 5.776e-01 ... 2.748e+00 1.652e-01] + ... + [ 3.025e-02 5.897e-01 ... 2.828e+00 1.551e-01] + [ 3.013e-02 5.910e-01 ... 2.802e+00 1.698e-01]] + population_energies: [ 5.781e+00 5.886e+00 ... 5.872e+00 5.852e+00] + jac: [-1.615e-02 -4.915e-03 1.118e-04 6.596e-04 + 4.303e-04 -1.572e-03] +2024-05-27 14:33:35,848 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.030728747578707347 +2024-05-27 14:33:35,848 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5861673272104828 +2024-05-27 14:33:35,848 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.803831563578623 +2024-05-27 14:33:35,848 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.603449510299539 +2024-05-27 14:33:35,849 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.7691878797185634 +2024-05-27 14:33:35,849 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1649964066969611 +2024-05-27 14:33:35,854 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.594400 0.169314 +1.950000 NaN 13.953486 0.475114 +2.833333 NaN 13.306239 0.783936 +2.876944 0.165931 NaN NaN +3.678056 0.265378 NaN NaN +3.983333 NaN 11.765227 1.519200 +4.092222 0.338297 NaN NaN +4.565000 0.446327 NaN NaN +4.883333 NaN 9.581909 2.560929 +5.166667 NaN 8.619706 3.020026 + +2024-05-27 14:33:35,859 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.78113459217461 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.1666961200461119 + +2024-05-27 14:33:35,859 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.1666961200461119 +2024-05-27 14:33:35,861 - physiofit - INFO - Results for yibT: + optimal +yibT X_0 0.030729 +yibT growth_rate 0.586167 +yibT Glc_q -5.803832 +yibT Glc_M0 14.603450 +yibT Ace_q 2.769188 +yibT Ace_M0 0.164996 +2024-05-27 14:33:35,867 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:36,836 - physiofit - INFO - Running optimization for yicH +2024-05-27 14:33:36,839 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:36,839 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:36,842 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1721 0.050000 NaN 14.376491 0.020473 +1722 1.950000 NaN 13.584192 0.419875 +1723 2.833333 NaN 13.321782 0.745015 +1724 2.876944 0.154224 NaN NaN +1725 3.678056 0.219240 NaN NaN +1726 3.983333 NaN 11.999386 1.506164 +1727 4.092222 0.309960 NaN NaN +1728 4.565000 0.391608 NaN NaN +1729 4.883333 NaN 9.615630 1.897751 +1730 5.166667 NaN 9.245179 2.613220 +Experimental matrix: +[[ nan 14.37649106 0.02047267] + [ nan 13.58419167 0.4198752 ] + [ nan 13.321782 0.74501529] + [ 0.154224 nan nan] + [ 0.21924 nan nan] + [ nan 11.999386 1.50616359] + [ 0.30996 nan nan] + [ 0.391608 nan nan] + [ nan 9.61562982 1.89775139] + [ nan 9.24517902 2.61322026]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:36,843 - physiofit - INFO - mc : False +2024-05-27 14:33:36,843 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:36,843 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:36,843 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:37,273 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:37,274 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.456832454738542 + x: [ 3.012e-02 5.611e-01 -5.743e+00 1.438e+01 + 2.584e+00 1.394e-01] + nit: 91 + nfev: 8917 + population: [[ 3.014e-02 5.611e-01 ... 2.560e+00 1.479e-01] + [ 3.223e-02 5.446e-01 ... 2.542e+00 1.445e-01] + ... + [ 3.025e-02 5.598e-01 ... 2.560e+00 1.419e-01] + [ 2.904e-02 5.687e-01 ... 2.635e+00 1.329e-01]] + population_energies: [ 5.457e+00 5.544e+00 ... 5.479e+00 5.549e+00] + jac: [ 4.836e-02 3.433e-03 -2.156e-04 -2.539e-04 + 2.363e-04 2.809e-04] +2024-05-27 14:33:37,274 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03011504317565567 +2024-05-27 14:33:37,274 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5610889334675475 +2024-05-27 14:33:37,275 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.742852470537169 +2024-05-27 14:33:37,275 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.382067393257332 +2024-05-27 14:33:37,275 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5837713089127474 +2024-05-27 14:33:37,275 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1393948301646615 +2024-05-27 14:33:37,278 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.373298 0.143340 +1.950000 NaN 13.769743 0.414886 +2.833333 NaN 13.179177 0.680588 +2.876944 0.151297 NaN NaN +3.678056 0.237161 NaN NaN +3.983333 NaN 11.809392 1.296869 +4.092222 0.299204 NaN NaN +4.565000 0.390097 NaN NaN +4.883333 NaN 9.916772 2.148379 +5.166667 NaN 9.094251 2.518440 + +2024-05-27 14:33:37,281 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.456832454738542 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.14134966513231226 + +2024-05-27 14:33:37,282 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.14134966513231226 +2024-05-27 14:33:37,285 - physiofit - INFO - Results for yicH: + optimal +yicH X_0 0.030115 +yicH growth_rate 0.561089 +yicH Glc_q -5.742852 +yicH Glc_M0 14.382067 +yicH Ace_q 2.583771 +yicH Ace_M0 0.139395 +2024-05-27 14:33:37,290 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:38,229 - physiofit - INFO - Running optimization for yidB +2024-05-27 14:33:38,232 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:38,232 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:38,236 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1731 0.050000 NaN 14.761930 0.019591 +1732 1.950000 NaN 14.169616 0.455989 +1733 2.833333 NaN 13.565380 0.944400 +1734 2.876944 0.143640 NaN NaN +1735 3.678056 0.220752 NaN NaN +1736 3.983333 NaN 11.860688 1.422447 +1737 4.092222 0.299376 NaN NaN +1738 4.565000 0.388584 NaN NaN +1739 4.883333 NaN 9.779090 2.195725 +1740 5.166667 NaN 9.193665 2.537382 +Experimental matrix: +[[ nan 14.76193048 0.01959146] + [ nan 14.16961608 0.45598913] + [ nan 13.56537962 0.94440005] + [ 0.14364 nan nan] + [ 0.220752 nan nan] + [ nan 11.86068804 1.42244715] + [ 0.299376 nan nan] + [ 0.388584 nan nan] + [ nan 9.77909047 2.19572515] + [ nan 9.19366469 2.53738194]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:38,236 - physiofit - INFO - mc : False +2024-05-27 14:33:38,236 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:38,236 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:38,237 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:38,647 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:38,648 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.967623086142789 + x: [ 2.967e-02 5.604e-01 -6.364e+00 1.479e+01 + 2.654e+00 1.912e-01] + nit: 87 + nfev: 8312 + population: [[ 2.929e-02 5.633e-01 ... 2.664e+00 1.926e-01] + [ 2.958e-02 5.616e-01 ... 2.656e+00 1.920e-01] + ... + [ 2.958e-02 5.612e-01 ... 2.646e+00 1.876e-01] + [ 3.010e-02 5.566e-01 ... 2.652e+00 1.889e-01]] + population_energies: [ 2.968e+00 2.981e+00 ... 2.978e+00 2.976e+00] + jac: [ 6.298e-04 1.647e-04 -2.407e-05 -1.528e-05 + -5.769e-05 -6.737e-05] +2024-05-27 14:33:38,649 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02967127074427498 +2024-05-27 14:33:38,649 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5604310196847591 +2024-05-27 14:33:38,649 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.363651784042062 +2024-05-27 14:33:38,649 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.791115876807442 +2024-05-27 14:33:38,650 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.653577955325119 +2024-05-27 14:33:38,650 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.19118033336640583 +2024-05-27 14:33:38,653 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.781541 0.195173 +1.950000 NaN 14.123103 0.469735 +2.833333 NaN 13.479370 0.738165 +2.876944 0.148786 NaN NaN +3.678056 0.233102 NaN NaN +3.983333 NaN 11.987289 1.360348 +4.092222 0.294002 NaN NaN +4.565000 0.383196 NaN NaN +4.883333 NaN 9.927051 2.219446 +5.166667 NaN 9.032013 2.592668 + +2024-05-27 14:33:38,658 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.967623086142789 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.017824247170714014 + +2024-05-27 14:33:38,658 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.017824247170714014 +2024-05-27 14:33:38,660 - physiofit - INFO - Results for yidB: + optimal +yidB X_0 0.029671 +yidB growth_rate 0.560431 +yidB Glc_q -6.363652 +yidB Glc_M0 14.791116 +yidB Ace_q 2.653578 +yidB Ace_M0 0.191180 +2024-05-27 14:33:38,669 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:39,621 - physiofit - INFO - Running optimization for yidR +2024-05-27 14:33:39,624 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:39,624 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:39,628 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1741 0.000000 0.036288 NaN NaN +1742 0.283333 NaN 14.019119 0.047932 +1743 1.195000 0.069552 NaN NaN +1744 1.613611 0.089208 NaN NaN +1745 1.916667 NaN 13.655713 0.407257 +1746 2.361389 0.142128 NaN NaN +1747 2.700000 NaN 13.663775 0.756647 +1748 3.286389 0.250992 NaN NaN +1749 3.616667 NaN 12.484192 1.180472 +1750 3.819444 0.322056 NaN NaN +1751 4.050000 NaN 11.369791 1.501498 +1752 4.410833 0.470232 NaN NaN +1753 4.750000 NaN 10.059238 1.871850 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 14.01911877 0.04793205] + [ 0.069552 nan nan] + [ 0.089208 nan nan] + [ nan 13.6557132 0.40725706] + [ 0.142128 nan nan] + [ nan 13.66377531 0.75664728] + [ 0.250992 nan nan] + [ nan 12.48419219 1.18047172] + [ 0.322056 nan nan] + [ nan 11.36979118 1.50149795] + [ 0.470232 nan nan] + [ nan 10.05923768 1.87184987]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:39,628 - physiofit - INFO - mc : False +2024-05-27 14:33:39,628 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:39,628 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:39,629 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:40,043 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:40,045 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.2961604223344905 + x: [ 3.622e-02 5.795e-01 -4.611e+00 1.433e+01 + 2.015e+00 1.789e-01] + nit: 91 + nfev: 8742 + population: [[ 3.636e-02 5.784e-01 ... 2.008e+00 1.838e-01] + [ 3.652e-02 5.767e-01 ... 1.995e+00 1.826e-01] + ... + [ 3.625e-02 5.789e-01 ... 2.012e+00 1.800e-01] + [ 3.625e-02 5.791e-01 ... 2.020e+00 1.801e-01]] + population_energies: [ 4.296e+00 4.335e+00 ... 4.304e+00 4.324e+00] + jac: [-4.759e-03 -4.133e-04 3.695e-05 2.141e-05 + -2.916e-04 -4.432e-04] +2024-05-27 14:33:40,047 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03622231008339644 +2024-05-27 14:33:40,047 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5794607119046284 +2024-05-27 14:33:40,047 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.611299652587715 +2024-05-27 14:33:40,047 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.332006684815072 +2024-05-27 14:33:40,047 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.0145496506465093 +2024-05-27 14:33:40,047 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.17892427956089435 +2024-05-27 14:33:40,051 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.036222 NaN NaN +0.283333 NaN 14.280574 0.201394 +1.195000 0.072395 NaN NaN +1.613611 0.092268 NaN NaN +1.916667 NaN 13.745041 0.435354 +2.361389 0.142310 NaN NaN +2.700000 NaN 13.242264 0.655003 +3.286389 0.243230 NaN NaN +3.616667 NaN 12.276391 1.076966 +3.819444 0.331257 NaN NaN +4.050000 NaN 11.607361 1.369247 +4.410833 0.466650 NaN NaN +4.750000 NaN 10.100200 2.027684 + +2024-05-27 14:33:40,054 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.2961604223344905 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.012386301332297735 + +2024-05-27 14:33:40,054 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.012386301332297735 +2024-05-27 14:33:40,056 - physiofit - INFO - Results for yidR: + optimal +yidR X_0 0.036222 +yidR growth_rate 0.579461 +yidR Glc_q -4.611300 +yidR Glc_M0 14.332007 +yidR Ace_q 2.014550 +yidR Ace_M0 0.178924 +2024-05-27 14:33:40,063 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:40,986 - physiofit - INFO - Running optimization for yieP +2024-05-27 14:33:40,988 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:40,988 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:40,992 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1754 0.000000 0.031752 NaN NaN +1755 0.283333 NaN 13.903187 0.049541 +1756 1.195000 0.055944 NaN NaN +1757 1.613611 0.072576 NaN NaN +1758 1.916667 NaN 14.028202 0.423096 +1759 2.361389 0.101304 NaN NaN +1760 2.700000 NaN 13.518335 0.653951 +1761 3.286389 0.175392 NaN NaN +1762 3.616667 NaN 12.910480 1.330962 +1763 3.819444 0.208656 NaN NaN +1764 4.050000 NaN 12.541209 1.682464 +1765 4.410833 0.343224 NaN NaN +1766 4.750000 NaN 11.136059 2.447819 +Experimental matrix: +[[ 0.031752 nan nan] + [ nan 13.90318683 0.04954128] + [ 0.055944 nan nan] + [ 0.072576 nan nan] + [ nan 14.02820244 0.42309582] + [ 0.101304 nan nan] + [ nan 13.51833535 0.65395137] + [ 0.175392 nan nan] + [ nan 12.91048014 1.33096153] + [ 0.208656 nan nan] + [ nan 12.54120877 1.68246366] + [ 0.343224 nan nan] + [ nan 11.13605889 2.44781943]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:40,992 - physiofit - INFO - mc : False +2024-05-27 14:33:40,992 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:40,992 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:40,993 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:41,420 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:41,422 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.7489200214842198 + x: [ 2.575e-02 5.779e-01 -4.490e+00 1.424e+01 + 3.763e+00 6.363e-02] + nit: 94 + nfev: 8984 + population: [[ 2.602e-02 5.757e-01 ... 3.751e+00 6.116e-02] + [ 2.621e-02 5.733e-01 ... 3.776e+00 5.487e-02] + ... + [ 2.553e-02 5.803e-01 ... 3.749e+00 7.110e-02] + [ 2.544e-02 5.812e-01 ... 3.767e+00 6.926e-02]] + population_energies: [ 3.749e+00 3.763e+00 ... 3.769e+00 3.757e+00] + jac: [-3.816e-03 2.387e-02 -4.574e-04 -4.661e-03 + -6.146e-03 -2.257e-03] +2024-05-27 14:33:41,422 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.025754526190486682 +2024-05-27 14:33:41,423 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5779447700135713 +2024-05-27 14:33:41,423 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.489835808433296 +2024-05-27 14:33:41,423 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.240297509516076 +2024-05-27 14:33:41,423 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.7629388955860015 +2024-05-27 14:33:41,423 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.06363462707022086 +2024-05-27 14:33:41,427 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.025755 NaN NaN +0.283333 NaN 14.204700 0.093469 +1.195000 0.051380 NaN NaN +1.613611 0.065444 NaN NaN +1.916667 NaN 13.834647 0.403611 +2.361389 0.100823 NaN NaN +2.700000 NaN 13.487814 0.694293 +3.286389 0.172080 NaN NaN +3.616667 NaN 12.822389 1.251986 +3.819444 0.234168 NaN NaN +4.050000 NaN 12.361920 1.637906 +4.410833 0.329583 NaN NaN +4.750000 NaN 11.325510 2.506523 + +2024-05-27 14:33:41,431 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.7489200214842198 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.006419278876254777 + +2024-05-27 14:33:41,433 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.006419278876254777 +2024-05-27 14:33:41,434 - physiofit - INFO - Results for yieP: + optimal +yieP X_0 0.025755 +yieP growth_rate 0.577945 +yieP Glc_q -4.489836 +yieP Glc_M0 14.240298 +yieP Ace_q 3.762939 +yieP Ace_M0 0.063635 +2024-05-27 14:33:41,441 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:42,373 - physiofit - INFO - Running optimization for yifL +2024-05-27 14:33:42,376 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:42,376 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:42,379 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1767 0.050000 NaN 14.444935 0.022410 +1768 1.950000 NaN 13.577399 0.397699 +1769 2.833333 NaN 13.537218 0.734115 +1770 2.876944 0.146664 NaN NaN +1771 3.678056 0.229824 NaN NaN +1772 3.983333 NaN 12.252383 1.357081 +1773 4.092222 0.302400 NaN NaN +1774 4.565000 0.400680 NaN NaN +1775 4.883333 NaN 10.024698 1.978856 +1776 5.166667 NaN 9.378531 2.334529 +Experimental matrix: +[[ nan 14.44493498 0.02241015] + [ nan 13.57739945 0.39769947] + [ nan 13.53721836 0.73411495] + [ 0.146664 nan nan] + [ 0.229824 nan nan] + [ nan 12.25238257 1.35708132] + [ 0.3024 nan nan] + [ 0.40068 nan nan] + [ nan 10.0246978 1.97885635] + [ nan 9.37853081 2.33452926]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:42,379 - physiofit - INFO - mc : False +2024-05-27 14:33:42,379 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:42,379 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:42,380 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:42,755 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:42,756 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.4557238260885392 + x: [ 2.735e-02 5.862e-01 -5.521e+00 1.443e+01 + 2.424e+00 1.583e-01] + nit: 82 + nfev: 7967 + population: [[ 2.748e-02 5.852e-01 ... 2.431e+00 1.595e-01] + [ 2.755e-02 5.836e-01 ... 2.411e+00 1.629e-01] + ... + [ 2.704e-02 5.892e-01 ... 2.410e+00 1.605e-01] + [ 2.738e-02 5.857e-01 ... 2.412e+00 1.562e-01]] + population_energies: [ 2.456e+00 2.486e+00 ... 2.466e+00 2.493e+00] + jac: [ 1.656e-03 1.013e-04 -1.648e-05 -6.266e-05 + -1.141e-05 -4.730e-05] +2024-05-27 14:33:42,756 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.027352239404836283 +2024-05-27 14:33:42,756 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5862187433062305 +2024-05-27 14:33:42,757 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.520709549265524 +2024-05-27 14:33:42,757 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.432490207759354 +2024-05-27 14:33:42,757 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4239493128086558 +2024-05-27 14:33:42,757 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15834969559511713 +2024-05-27 14:33:42,760 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.424828 0.161714 +1.950000 NaN 13.882135 0.399991 +2.833333 NaN 13.334045 0.640638 +2.876944 0.147720 NaN NaN +3.678056 0.236263 NaN NaN +3.983333 NaN 12.029041 1.213620 +4.092222 0.301188 NaN NaN +4.565000 0.397378 NaN NaN +4.883333 NaN 10.180007 2.025466 +5.166667 NaN 9.365101 2.383262 + +2024-05-27 14:33:42,763 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.4557238260885392 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.008494660947140114 + +2024-05-27 14:33:42,764 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.008494660947140114 +2024-05-27 14:33:42,765 - physiofit - INFO - Results for yifL: + optimal +yifL X_0 0.027352 +yifL growth_rate 0.586219 +yifL Glc_q -5.520710 +yifL Glc_M0 14.432490 +yifL Ace_q 2.423949 +yifL Ace_M0 0.158350 +2024-05-27 14:33:42,771 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:43,706 - physiofit - INFO - Running optimization for yigA +2024-05-27 14:33:43,708 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:43,708 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:43,712 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1777 0.050000 NaN 14.717063 0.026094 +1778 1.950000 NaN 14.057307 0.433474 +1779 2.833333 NaN 13.835033 0.823857 +1780 2.876944 0.140616 NaN NaN +1781 3.678056 0.234360 NaN NaN +1782 3.983333 NaN 11.888084 1.473012 +1783 4.092222 0.328104 NaN NaN +1784 4.565000 0.412776 NaN NaN +1785 4.883333 NaN 9.759670 2.159439 +1786 5.166667 NaN 8.807590 2.507416 +Experimental matrix: +[[ nan 14.71706318 0.02609417] + [ nan 14.05730655 0.4334742 ] + [ nan 13.83503291 0.82385747] + [ 0.140616 nan nan] + [ 0.23436 nan nan] + [ nan 11.88808351 1.47301186] + [ 0.328104 nan nan] + [ 0.412776 nan nan] + [ nan 9.75966997 2.15943874] + [ nan 8.80758975 2.50741581]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:43,713 - physiofit - INFO - mc : False +2024-05-27 14:33:43,713 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:43,713 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:43,713 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:44,184 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:44,186 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.6229890172634507 + x: [ 2.690e-02 5.994e-01 -6.335e+00 1.480e+01 + 2.519e+00 1.935e-01] + nit: 104 + nfev: 9828 + population: [[ 2.651e-02 6.030e-01 ... 2.518e+00 1.964e-01] + [ 2.717e-02 5.961e-01 ... 2.542e+00 1.942e-01] + ... + [ 2.696e-02 5.991e-01 ... 2.557e+00 1.886e-01] + [ 2.616e-02 6.060e-01 ... 2.517e+00 1.956e-01]] + population_energies: [ 3.623e+00 3.674e+00 ... 3.704e+00 3.650e+00] + jac: [ 1.677e-02 4.705e-03 1.640e-04 5.268e-04 + -2.060e-04 -8.590e-04] +2024-05-27 14:33:44,188 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02689657749377935 +2024-05-27 14:33:44,188 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5994445135924283 +2024-05-27 14:33:44,188 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.335137365206327 +2024-05-27 14:33:44,188 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.802768319059588 +2024-05-27 14:33:44,188 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.5186669826291626 +2024-05-27 14:33:44,188 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.19346877215246455 +2024-05-27 14:33:44,191 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.794120 0.196907 +1.950000 NaN 14.172153 0.444183 +2.833333 NaN 13.533485 0.698099 +2.876944 0.150892 NaN NaN +3.678056 0.243908 NaN NaN +3.983333 NaN 11.991691 1.311072 +4.092222 0.312642 NaN NaN +4.565000 0.415077 NaN NaN +4.883333 NaN 9.778068 2.191144 +5.166667 NaN 8.795284 2.581870 + +2024-05-27 14:33:44,196 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.6229890172634507 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.03724357638476307 + +2024-05-27 14:33:44,196 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.03724357638476307 +2024-05-27 14:33:44,198 - physiofit - INFO - Results for yigA: + optimal +yigA X_0 0.026897 +yigA growth_rate 0.599445 +yigA Glc_q -6.335137 +yigA Glc_M0 14.802768 +yigA Ace_q 2.518667 +yigA Ace_M0 0.193469 +2024-05-27 14:33:44,205 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:45,649 - physiofit - INFO - Running optimization for yigB +2024-05-27 14:33:45,651 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:45,651 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:45,654 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1787 0.050000 NaN 14.349029 0.015564 +1788 1.950000 NaN 13.938789 0.442083 +1789 2.833333 NaN 13.164479 0.713540 +1790 2.876944 0.173880 NaN NaN +1791 3.678056 0.273672 NaN NaN +1792 3.983333 NaN 11.862453 1.403796 +1793 4.092222 0.338688 NaN NaN +1794 4.565000 0.446040 NaN NaN +1795 4.883333 NaN 8.971320 2.273002 +1796 5.166667 NaN 8.385753 2.512246 +Experimental matrix: +[[ nan 14.34902893 0.01556413] + [ nan 13.93878876 0.44208281] + [ nan 13.16447879 0.71353982] + [ 0.17388 nan nan] + [ 0.273672 nan nan] + [ nan 11.86245288 1.40379554] + [ 0.338688 nan nan] + [ 0.44604 nan nan] + [ nan 8.97132036 2.27300154] + [ nan 8.38575339 2.51224615]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:45,655 - physiofit - INFO - mc : False +2024-05-27 14:33:45,655 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:45,655 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:45,656 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:46,082 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:46,083 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.090488996675564 + x: [ 3.517e-02 5.558e-01 -5.949e+00 1.459e+01 + 2.363e+00 1.122e-01] + nit: 85 + nfev: 8139 + population: [[ 3.512e-02 5.562e-01 ... 2.366e+00 1.080e-01] + [ 3.555e-02 5.537e-01 ... 2.380e+00 9.447e-02] + ... + [ 3.398e-02 5.636e-01 ... 2.377e+00 1.169e-01] + [ 3.469e-02 5.597e-01 ... 2.363e+00 1.228e-01]] + population_energies: [ 2.090e+00 2.115e+00 ... 2.131e+00 2.135e+00] + jac: [-2.594e-02 -3.849e-03 9.242e-03 4.707e-03 + -5.268e-03 1.992e-03] +2024-05-27 14:33:46,084 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.0351739716494696 +2024-05-27 14:33:46,084 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5557840420400874 +2024-05-27 14:33:46,084 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.9493443641988595 +2024-05-27 14:33:46,084 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.585000083264145 +2024-05-27 14:33:46,084 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3626947218241083 +2024-05-27 14:33:46,084 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.11223879253828668 +2024-05-27 14:33:46,088 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.574390 0.116452 +1.950000 NaN 13.848598 0.404690 +2.833333 NaN 13.143168 0.684841 +2.876944 0.174037 NaN NaN +3.678056 0.271649 NaN NaN +3.983333 NaN 11.515977 1.331056 +4.092222 0.341962 NaN NaN +4.565000 0.444727 NaN NaN +4.883333 NaN 9.279613 2.219195 +5.166667 NaN 8.310575 2.604034 + +2024-05-27 14:33:46,092 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.090488996675564 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.004401615621523875 + +2024-05-27 14:33:46,093 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.004401615621523875 +2024-05-27 14:33:46,095 - physiofit - INFO - Results for yigB: + optimal +yigB X_0 0.035174 +yigB growth_rate 0.555784 +yigB Glc_q -5.949344 +yigB Glc_M0 14.585000 +yigB Ace_q 2.362695 +yigB Ace_M0 0.112239 +2024-05-27 14:33:46,102 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:47,064 - physiofit - INFO - Running optimization for yigI +2024-05-27 14:33:47,067 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:47,067 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:47,070 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1797 0.050000 NaN 14.726224 0.016990 +1798 1.950000 NaN 13.714452 0.417203 +1799 2.833333 NaN 13.184159 0.760968 +1800 2.876944 0.176904 NaN NaN +1801 3.678056 0.263088 NaN NaN +1802 3.983333 NaN 11.708932 1.387326 +1803 4.092222 0.361368 NaN NaN +1804 4.565000 0.443016 NaN NaN +1805 4.883333 NaN 9.352869 2.080864 +1806 5.166667 NaN 8.740238 1.942728 +Experimental matrix: +[[ nan 14.72622409 0.01698967] + [ nan 13.71445199 0.41720252] + [ nan 13.18415891 0.76096834] + [ 0.176904 nan nan] + [ 0.263088 nan nan] + [ nan 11.70893153 1.38732592] + [ 0.361368 nan nan] + [ 0.443016 nan nan] + [ nan 9.35286899 2.08086415] + [ nan 8.74023779 1.94272827]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:47,071 - physiofit - INFO - mc : False +2024-05-27 14:33:47,071 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:47,071 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:47,071 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:47,474 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:47,476 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.916988086814991 + x: [ 4.112e-02 5.204e-01 -5.542e+00 1.464e+01 + 1.870e+00 1.772e-01] + nit: 87 + nfev: 8403 + population: [[ 4.185e-02 5.159e-01 ... 1.884e+00 1.671e-01] + [ 4.097e-02 5.223e-01 ... 1.905e+00 1.711e-01] + ... + [ 4.043e-02 5.240e-01 ... 1.883e+00 1.628e-01] + [ 4.136e-02 5.187e-01 ... 1.920e+00 1.629e-01]] + population_energies: [ 5.917e+00 6.018e+00 ... 5.991e+00 6.048e+00] + jac: [-3.879e-02 -2.115e-03 5.148e-04 3.491e-04 + 1.004e-03 1.510e-04] +2024-05-27 14:33:47,476 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.041122537894883994 +2024-05-27 14:33:47,476 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.520386181512388 +2024-05-27 14:33:47,476 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.542192507046417 +2024-05-27 14:33:47,476 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.642349628362123 +2024-05-27 14:33:47,477 - physiofit.physiofit.base.fitter - INFO - Ace_q = 1.8700622819906971 +2024-05-27 14:33:47,477 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1771956253263771 +2024-05-27 14:33:47,480 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.630805 0.181091 +1.950000 NaN 13.872115 0.437090 +2.833333 NaN 13.167062 0.674991 +2.876944 0.183769 NaN NaN +3.678056 0.278820 NaN NaN +3.983333 NaN 11.599564 1.203901 +4.092222 0.345880 NaN NaN +4.565000 0.442358 NaN NaN +4.883333 NaN 9.520331 1.905482 +5.166667 NaN 8.637034 2.203526 + +2024-05-27 14:33:47,483 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.916988086814991 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.1778113642830835 + +2024-05-27 14:33:47,485 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.1778113642830835 +2024-05-27 14:33:47,487 - physiofit - INFO - Results for yigI: + optimal +yigI X_0 0.041123 +yigI growth_rate 0.520386 +yigI Glc_q -5.542193 +yigI Glc_M0 14.642350 +yigI Ace_q 1.870062 +yigI Ace_M0 0.177196 +2024-05-27 14:33:47,492 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:48,438 - physiofit - INFO - Running optimization for yiiD +2024-05-27 14:33:48,440 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:48,441 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:48,444 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1807 0.050000 NaN 14.678869 0.009697 +1808 1.950000 NaN 13.985187 0.389158 +1809 2.833333 NaN 13.287961 0.671835 +1810 2.876944 0.146664 NaN NaN +1811 3.678056 0.229824 NaN NaN +1812 3.983333 NaN 11.926688 1.480855 +1813 4.092222 0.293328 NaN NaN +1814 4.565000 0.370440 NaN NaN +1815 4.883333 NaN 9.884941 2.153241 +1816 5.166667 NaN 9.317370 2.401697 +Experimental matrix: +[[ nan 1.46788695e+01 9.69732549e-03] + [ nan 1.39851874e+01 3.89157634e-01] + [ nan 1.32879607e+01 6.71834804e-01] + [1.46664000e-01 nan nan] + [2.29824000e-01 nan nan] + [ nan 1.19266877e+01 1.48085534e+00] + [2.93328000e-01 nan nan] + [3.70440000e-01 nan nan] + [ nan 9.88494057e+00 2.15324078e+00] + [ nan 9.31736987e+00 2.40169668e+00]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:48,445 - physiofit - INFO - mc : False +2024-05-27 14:33:48,445 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:48,445 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:48,446 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:48,839 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:48,841 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.4740088223442867 + x: [ 3.517e-02 5.146e-01 -6.017e+00 1.468e+01 + 2.661e+00 7.993e-02] + nit: 84 + nfev: 8196 + population: [[ 3.520e-02 5.145e-01 ... 2.674e+00 7.248e-02] + [ 3.397e-02 5.237e-01 ... 2.665e+00 8.106e-02] + ... + [ 3.475e-02 5.179e-01 ... 2.646e+00 8.031e-02] + [ 3.448e-02 5.192e-01 ... 2.691e+00 7.345e-02]] + population_energies: [ 1.474e+00 1.513e+00 ... 1.494e+00 1.492e+00] + jac: [ 6.062e-06 6.239e-06 -2.220e-07 5.995e-07 + -1.310e-06 -3.153e-06] +2024-05-27 14:33:48,842 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.035167229488810146 +2024-05-27 14:33:48,842 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.514572922543641 +2024-05-27 14:33:48,842 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.017174024756494 +2024-05-27 14:33:48,842 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.677220468566825 +2024-05-27 14:33:48,842 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.6614797557998466 +2024-05-27 14:33:48,843 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.07993328888298612 +2024-05-27 14:33:48,847 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.666503 0.084674 +1.950000 NaN 13.966787 0.394168 +2.833333 NaN 13.321328 0.679663 +2.876944 0.154549 NaN NaN +3.678056 0.233397 NaN NaN +3.983333 NaN 11.894972 1.310561 +4.092222 0.288837 NaN NaN +4.565000 0.368389 NaN NaN +4.883333 NaN 10.013959 2.142559 +5.166667 NaN 9.217468 2.494858 + +2024-05-27 14:33:48,851 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.4740088223442867 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.0009860001241546984 + +2024-05-27 14:33:48,852 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0009860001241546984 +2024-05-27 14:33:48,854 - physiofit - INFO - Results for yiiD: + optimal +yiiD X_0 0.035167 +yiiD growth_rate 0.514573 +yiiD Glc_q -6.017174 +yiiD Glc_M0 14.677220 +yiiD Ace_q 2.661480 +yiiD Ace_M0 0.079933 +2024-05-27 14:33:48,860 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:49,807 - physiofit - INFO - Running optimization for yjaG +2024-05-27 14:33:49,810 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:49,810 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:49,814 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1817 0.050000 NaN 14.018615 0.016161 +1818 1.950000 NaN 13.817865 0.353153 +1819 2.833333 NaN 13.359737 0.652956 +1820 2.876944 0.128520 NaN NaN +1821 3.678056 0.199584 NaN NaN +1822 3.983333 NaN 12.462789 1.241605 +1823 4.092222 0.279720 NaN NaN +1824 4.565000 0.385560 NaN NaN +1825 4.883333 NaN 10.150298 1.796366 +1826 5.166667 NaN 9.806175 2.138608 +Experimental matrix: +[[ nan 14.01861468 0.01616065] + [ nan 13.8178654 0.35315332] + [ nan 13.35973741 0.65295573] + [ 0.12852 nan nan] + [ 0.199584 nan nan] + [ nan 12.4627893 1.24160525] + [ 0.27972 nan nan] + [ 0.38556 nan nan] + [ nan 10.15029849 1.7963658 ] + [ nan 9.80617465 2.13860836]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:49,814 - physiofit - INFO - mc : False +2024-05-27 14:33:49,814 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:49,814 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:49,814 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:50,187 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:50,189 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.3133876341301467 + x: [ 1.879e-02 6.590e-01 -5.432e+00 1.418e+01 + 2.433e+00 1.776e-01] + nit: 82 + nfev: 7820 + population: [[ 1.835e-02 6.653e-01 ... 2.435e+00 1.820e-01] + [ 1.942e-02 6.522e-01 ... 2.409e+00 1.770e-01] + ... + [ 1.792e-02 6.713e-01 ... 2.467e+00 1.516e-01] + [ 1.859e-02 6.606e-01 ... 2.456e+00 1.654e-01]] + population_energies: [ 3.313e+00 3.339e+00 ... 3.455e+00 3.363e+00] + jac: [-2.350e-02 1.179e-03 -5.693e-05 1.253e-02 + -9.078e-03 4.686e-03] +2024-05-27 14:33:50,189 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.018789221814994143 +2024-05-27 14:33:50,189 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6589746479763678 +2024-05-27 14:33:50,189 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.432092415891859 +2024-05-27 14:33:50,189 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.179818182850351 +2024-05-27 14:33:50,190 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.432698796918131 +2024-05-27 14:33:50,190 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.17762907759045127 +2024-05-27 14:33:50,195 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.174630 0.179953 +1.950000 NaN 13.774847 0.358991 +2.833333 NaN 13.332683 0.557009 +2.876944 0.125100 NaN NaN +3.678056 0.212094 NaN NaN +3.983333 NaN 12.196772 1.065713 +4.092222 0.278649 NaN NaN +4.565000 0.380506 NaN NaN +4.883333 NaN 10.466014 1.840813 +5.166667 NaN 9.671861 2.196465 + +2024-05-27 14:33:50,198 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.3133876341301467 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.02694188888108901 + +2024-05-27 14:33:50,198 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.02694188888108901 +2024-05-27 14:33:50,200 - physiofit - INFO - Results for yjaG: + optimal +yjaG X_0 0.018789 +yjaG growth_rate 0.658975 +yjaG Glc_q -5.432092 +yjaG Glc_M0 14.179818 +yjaG Ace_q 2.432699 +yjaG Ace_M0 0.177629 +2024-05-27 14:33:50,207 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:51,145 - physiofit - INFO - Running optimization for yjbD +2024-05-27 14:33:51,147 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:51,147 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:51,151 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1827 0.050000 NaN 14.497274 0.022422 +1828 1.950000 NaN 13.849380 0.402885 +1829 2.833333 NaN 13.544784 0.724071 +1830 2.876944 0.158760 NaN NaN +1831 3.678056 0.234360 NaN NaN +1832 3.983333 NaN 11.963861 1.350273 +1833 4.092222 0.341712 NaN NaN +1834 4.565000 0.427896 NaN NaN +1835 4.883333 NaN 9.705847 1.630175 +1836 5.166667 NaN 8.904954 2.266666 +Experimental matrix: +[[ nan 14.49727436 0.02242155] + [ nan 13.84937976 0.40288477] + [ nan 13.54478351 0.72407067] + [ 0.15876 nan nan] + [ 0.23436 nan nan] + [ nan 11.96386078 1.35027273] + [ 0.341712 nan nan] + [ 0.427896 nan nan] + [ nan 9.70584729 1.63017469] + [ nan 8.90495394 2.26666584]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:51,151 - physiofit - INFO - mc : False +2024-05-27 14:33:51,151 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:51,151 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:51,152 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:51,609 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:51,610 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.754210991057825 + x: [ 2.849e-02 5.945e-01 -5.769e+00 1.457e+01 + 2.036e+00 1.863e-01] + nit: 99 + nfev: 9602 + population: [[ 2.834e-02 5.957e-01 ... 2.040e+00 1.827e-01] + [ 2.796e-02 6.003e-01 ... 2.019e+00 1.897e-01] + ... + [ 2.725e-02 6.052e-01 ... 2.026e+00 1.980e-01] + [ 2.817e-02 5.971e-01 ... 2.033e+00 1.884e-01]] + population_energies: [ 5.754e+00 5.798e+00 ... 5.822e+00 5.771e+00] + jac: [ 8.012e-04 -5.231e-05 -1.137e-05 -1.119e-05 + 3.304e-05 -2.487e-05] +2024-05-27 14:33:51,611 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02848753291749257 +2024-05-27 14:33:51,611 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5945297055785866 +2024-05-27 14:33:51,612 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.76931427489132 +2024-05-27 14:33:51,612 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.570245729330317 +2024-05-27 14:33:51,612 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.0363579842152033 +2024-05-27 14:33:51,612 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.18629771257230818 +2024-05-27 14:33:51,617 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.561905 0.189242 +1.950000 NaN 13.965442 0.399771 +2.833333 NaN 13.356728 0.614625 +2.876944 0.157574 NaN NaN +3.678056 0.253707 NaN NaN +3.983333 NaN 11.894759 1.130647 +4.092222 0.324542 NaN NaN +4.565000 0.429875 NaN NaN +4.883333 NaN 9.806035 1.867891 +5.166667 NaN 8.881230 2.194313 + +2024-05-27 14:33:51,623 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.754210991057825 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.16452672289603776 + +2024-05-27 14:33:51,623 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.16452672289603776 +2024-05-27 14:33:51,626 - physiofit - INFO - Results for yjbD: + optimal +yjbD X_0 0.028488 +yjbD growth_rate 0.594530 +yjbD Glc_q -5.769314 +yjbD Glc_M0 14.570246 +yjbD Ace_q 2.036358 +yjbD Ace_M0 0.186298 +2024-05-27 14:33:51,632 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:52,606 - physiofit - INFO - Running optimization for yjbR +2024-05-27 14:33:52,608 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:52,608 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:52,612 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1837 0.050000 NaN 14.613832 0.012858 +1838 1.950000 NaN 14.032121 0.415371 +1839 2.833333 NaN 13.218119 0.696633 +1840 2.876944 0.170856 NaN NaN +1841 3.678056 0.278208 NaN NaN +1842 3.983333 NaN 11.879149 1.233757 +1843 4.092222 0.353808 NaN NaN +1844 4.565000 0.449064 NaN NaN +1845 4.883333 NaN 9.551951 2.053279 +1846 5.166667 NaN 8.594992 2.312223 +Experimental matrix: +[[ nan 1.46138323e+01 1.28583435e-02] + [ nan 1.40321213e+01 4.15370641e-01] + [ nan 1.32181193e+01 6.96633311e-01] + [1.70856000e-01 nan nan] + [2.78208000e-01 nan nan] + [ nan 1.18791494e+01 1.23375654e+00] + [3.53808000e-01 nan nan] + [4.49064000e-01 nan nan] + [ nan 9.55195135e+00 2.05327892e+00] + [ nan 8.59499182e+00 2.31222308e+00]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:52,612 - physiofit - INFO - mc : False +2024-05-27 14:33:52,612 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:52,612 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:52,613 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:53,060 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:53,062 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.9259545822314862 + x: [ 3.611e-02 5.536e-01 -5.633e+00 1.469e+01 + 2.104e+00 1.087e-01] + nit: 95 + nfev: 9053 + population: [[ 3.616e-02 5.531e-01 ... 2.104e+00 1.110e-01] + [ 3.605e-02 5.540e-01 ... 2.100e+00 1.052e-01] + ... + [ 3.613e-02 5.534e-01 ... 2.100e+00 1.094e-01] + [ 3.540e-02 5.584e-01 ... 2.109e+00 1.109e-01]] + population_energies: [ 9.260e-01 9.367e-01 ... 9.315e-01 9.360e-01] + jac: [-1.827e-02 -5.334e-03 -2.181e-03 6.269e-03 + 2.213e-02 -1.162e-02] +2024-05-27 14:33:53,063 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03610795241043751 +2024-05-27 14:33:53,063 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5535759879236837 +2024-05-27 14:33:53,063 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.632920214566032 +2024-05-27 14:33:53,063 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.69054368838389 +2024-05-27 14:33:53,063 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.104399165337489 +2024-05-27 14:33:53,063 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.10869199904859284 +2024-05-27 14:33:53,067 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.680232 0.112544 +1.950000 NaN 13.976605 0.375412 +2.833333 NaN 13.294625 0.630192 +2.876944 0.177527 NaN NaN +3.678056 0.276607 NaN NaN +3.983333 NaN 11.725137 1.216536 +4.092222 0.347884 NaN NaN +4.565000 0.451957 NaN NaN +4.883333 NaN 9.572845 2.020610 +5.166667 NaN 8.641384 2.368594 + +2024-05-27 14:33:53,071 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.9259545822314862 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.0001207835498660805 + +2024-05-27 14:33:53,072 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0001207835498660805 +2024-05-27 14:33:53,073 - physiofit - INFO - Results for yjbR: + optimal +yjbR X_0 0.036108 +yjbR growth_rate 0.553576 +yjbR Glc_q -5.632920 +yjbR Glc_M0 14.690544 +yjbR Ace_q 2.104399 +yjbR Ace_M0 0.108692 +2024-05-27 14:33:53,081 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:54,056 - physiofit - INFO - Running optimization for yjcO +2024-05-27 14:33:54,058 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:54,058 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:54,062 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1847 0.050000 NaN 14.351086 0.018347 +1848 1.950000 NaN 13.960023 0.434852 +1849 2.833333 NaN 13.115478 0.752319 +1850 2.876944 0.170856 NaN NaN +1851 3.678056 0.260064 NaN NaN +1852 3.983333 NaN 11.990931 1.421836 +1853 4.092222 0.344736 NaN NaN +1854 4.565000 0.470232 NaN NaN +1855 4.883333 NaN 9.176620 2.090991 +1856 5.166667 NaN 8.305847 2.427655 +Experimental matrix: +[[ nan 14.35108625 0.01834676] + [ nan 13.96002291 0.4348517 ] + [ nan 13.11547753 0.75231887] + [ 0.170856 nan nan] + [ 0.260064 nan nan] + [ nan 11.99093146 1.4218357 ] + [ 0.344736 nan nan] + [ 0.470232 nan nan] + [ nan 9.17662014 2.09099125] + [ nan 8.30584725 2.42765474]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:54,062 - physiofit - INFO - mc : False +2024-05-27 14:33:54,062 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:54,062 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:54,062 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:54,510 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:54,511 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.0904839335618157 + x: [ 2.852e-02 6.111e-01 -5.895e+00 1.451e+01 + 2.207e+00 1.842e-01] + nit: 97 + nfev: 9268 + population: [[ 2.848e-02 6.118e-01 ... 2.198e+00 1.885e-01] + [ 2.934e-02 6.054e-01 ... 2.195e+00 1.849e-01] + ... + [ 2.788e-02 6.163e-01 ... 2.224e+00 1.782e-01] + [ 2.764e-02 6.176e-01 ... 2.221e+00 1.874e-01]] + population_energies: [ 3.090e+00 3.134e+00 ... 3.109e+00 3.158e+00] + jac: [ 1.280e-01 1.433e-02 -1.570e-04 4.840e-04 + -2.901e-04 1.454e-03] +2024-05-27 14:33:54,512 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02852493384331655 +2024-05-27 14:33:54,512 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6110574859413832 +2024-05-27 14:33:54,512 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.894989977084799 +2024-05-27 14:33:54,513 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.506430947834717 +2024-05-27 14:33:54,513 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.2065789000423903 +2024-05-27 14:33:54,513 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1841898048385601 +2024-05-27 14:33:54,516 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.497893 0.187386 +1.950000 NaN 13.875645 0.420302 +2.833333 NaN 13.227325 0.662977 +2.876944 0.165465 NaN NaN +3.678056 0.269962 NaN NaN +3.983333 NaN 11.643145 1.255959 +4.092222 0.347707 NaN NaN +4.565000 0.464172 NaN NaN +4.883333 NaN 9.342113 2.117268 +5.166667 NaN 8.313916 2.502137 + +2024-05-27 14:33:54,520 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.0904839335618157 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.02078631005696834 + +2024-05-27 14:33:54,520 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.02078631005696834 +2024-05-27 14:33:54,522 - physiofit - INFO - Results for yjcO: + optimal +yjcO X_0 0.028525 +yjcO growth_rate 0.611057 +yjcO Glc_q -5.894990 +yjcO Glc_M0 14.506431 +yjcO Ace_q 2.206579 +yjcO Ace_M0 0.184190 +2024-05-27 14:33:54,528 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:55,477 - physiofit - INFO - Running optimization for yjcZ +2024-05-27 14:33:55,479 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:55,480 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:55,483 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1857 1.828889 0.066528 NaN NaN +1858 2.261389 0.089208 NaN NaN +1859 2.774167 0.139104 NaN NaN +1860 2.800000 NaN 12.260926 0.650129 +1861 3.208889 0.149688 NaN NaN +1862 3.706389 0.195048 NaN NaN +1863 3.733333 NaN 11.653528 1.135661 +1864 4.225833 0.285768 NaN NaN +1865 4.283333 NaN 10.960518 1.494730 +1866 4.635556 0.371952 NaN NaN +1867 4.750000 NaN 10.086571 1.901590 +1868 4.967500 0.515592 NaN NaN +1869 5.116667 NaN 9.220449 2.200309 +1870 5.433333 NaN 8.388270 2.641513 +Experimental matrix: +[[ 0.066528 nan nan] + [ 0.089208 nan nan] + [ 0.139104 nan nan] + [ nan 12.26092571 0.6501292 ] + [ 0.149688 nan nan] + [ 0.195048 nan nan] + [ nan 11.653528 1.13566071] + [ 0.285768 nan nan] + [ nan 10.96051841 1.49473013] + [ 0.371952 nan nan] + [ nan 10.08657069 1.90158963] + [ 0.515592 nan nan] + [ nan 9.22044899 2.20030922] + [ nan 8.38827039 2.64151265]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:55,483 - physiofit - INFO - mc : False +2024-05-27 14:33:55,484 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:55,484 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:55,484 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:55,948 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:55,949 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 6.3708517642342075 + x: [ 1.762e-02 6.699e-01 -4.764e+00 1.300e+01 + 2.331e+00 4.098e-01] + nit: 102 + nfev: 9676 + population: [[ 1.745e-02 6.725e-01 ... 2.322e+00 4.146e-01] + [ 1.750e-02 6.716e-01 ... 2.318e+00 3.954e-01] + ... + [ 1.836e-02 6.615e-01 ... 2.330e+00 3.807e-01] + [ 1.741e-02 6.733e-01 ... 2.356e+00 3.878e-01]] + population_energies: [ 6.371e+00 6.476e+00 ... 6.478e+00 6.439e+00] + jac: [-9.911e-02 -1.063e-02 -2.639e-02 1.363e-02 + 1.049e-02 -3.728e-03] +2024-05-27 14:33:55,949 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.017622865959592296 +2024-05-27 14:33:55,950 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6699270102159101 +2024-05-27 14:33:55,950 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.763636576662693 +2024-05-27 14:33:55,950 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.00472257186088 +2024-05-27 14:33:55,950 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3314502844539096 +2024-05-27 14:33:55,951 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.40982851262761166 +2024-05-27 14:33:55,954 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.060004 NaN NaN +2.261389 0.080171 NaN NaN +2.774167 0.113034 NaN NaN +2.800000 NaN 12.312255 0.748740 +3.208889 0.151248 NaN NaN +3.706389 0.211074 NaN NaN +3.733333 NaN 11.601818 1.096447 +4.225833 0.298926 NaN NaN +4.283333 NaN 10.920988 1.429664 +4.635556 0.393343 NaN NaN +4.750000 NaN 10.110225 1.826472 +4.967500 0.491302 NaN NaN +5.116667 NaN 9.269393 2.237998 +5.433333 NaN 8.357026 2.684535 + +2024-05-27 14:33:55,957 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 6.3708517642342075 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 0.04373879809352204 + +2024-05-27 14:33:55,957 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.04373879809352204 +2024-05-27 14:33:55,960 - physiofit - INFO - Results for yjcZ: + optimal +yjcZ X_0 0.017623 +yjcZ growth_rate 0.669927 +yjcZ Glc_q -4.763637 +yjcZ Glc_M0 13.004723 +yjcZ Ace_q 2.331450 +yjcZ Ace_M0 0.409829 +2024-05-27 14:33:55,966 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:56,918 - physiofit - INFO - Running optimization for yjeI +2024-05-27 14:33:56,920 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:56,920 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:56,924 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1871 0.050000 NaN 14.278424 0.016277 +1872 1.950000 NaN 14.053371 0.457798 +1873 2.833333 NaN 13.398372 0.807519 +1874 2.876944 0.173880 NaN NaN +1875 3.678056 0.260064 NaN NaN +1876 3.983333 NaN 11.605824 1.500091 +1877 4.092222 0.387072 NaN NaN +1878 4.565000 0.585144 NaN NaN +1879 4.883333 NaN 9.044854 2.323662 +1880 5.166667 NaN 8.186359 2.598658 +Experimental matrix: +[[ nan 14.278424 0.01627651] + [ nan 14.05337096 0.45779801] + [ nan 13.39837209 0.80751871] + [ 0.17388 nan nan] + [ 0.260064 nan nan] + [ nan 11.60582354 1.50009075] + [ 0.387072 nan nan] + [ 0.585144 nan nan] + [ nan 9.04485444 2.32366248] + [ nan 8.18635882 2.59865781]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:56,924 - physiofit - INFO - mc : False +2024-05-27 14:33:56,924 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:56,924 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:56,925 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:57,288 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:57,290 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 9.000445187522141 + x: [ 1.760e-02 7.611e-01 -5.478e+00 1.432e+01 + 2.133e+00 2.893e-01] + nit: 79 + nfev: 7543 + population: [[ 1.782e-02 7.582e-01 ... 2.149e+00 2.803e-01] + [ 1.777e-02 7.593e-01 ... 2.115e+00 3.085e-01] + ... + [ 1.810e-02 7.539e-01 ... 2.179e+00 2.691e-01] + [ 1.792e-02 7.569e-01 ... 2.155e+00 2.732e-01]] + population_energies: [ 9.000e+00 9.145e+00 ... 9.126e+00 9.067e+00] + jac: [ 1.321e-01 -6.404e-03 3.197e-02 -2.120e-02 + -4.036e-03 6.585e-03] +2024-05-27 14:33:57,291 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.017604988435666484 +2024-05-27 14:33:57,291 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.76110778524722 +2024-05-27 14:33:57,291 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.477922805005081 +2024-05-27 14:33:57,292 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.315755743418212 +2024-05-27 14:33:57,292 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.132840875723315 +2024-05-27 14:33:57,292 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.2892556370507619 +2024-05-27 14:33:57,295 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.310841 0.291169 +1.950000 NaN 13.883520 0.457547 +2.833333 NaN 13.347627 0.666198 +2.876944 0.157252 NaN NaN +3.678056 0.289333 NaN NaN +3.983333 NaN 11.815368 1.262787 +4.092222 0.396551 NaN NaN +4.565000 0.568294 NaN NaN +4.883333 NaN 9.230919 2.269047 +5.166667 NaN 7.976685 2.757386 + +2024-05-27 14:33:57,299 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 9.000445187522141 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.46793867309487897 + +2024-05-27 14:33:57,301 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.46793867309487897 +2024-05-27 14:33:57,302 - physiofit - INFO - Results for yjeI: + optimal +yjeI X_0 0.017605 +yjeI growth_rate 0.761108 +yjeI Glc_q -5.477923 +yjeI Glc_M0 14.315756 +yjeI Ace_q 2.132841 +yjeI Ace_M0 0.289256 +2024-05-27 14:33:57,309 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:58,257 - physiofit - INFO - Running optimization for yjgJ +2024-05-27 14:33:58,259 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:58,260 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:58,263 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1881 0.050000 NaN 14.425757 0.015579 +1882 1.950000 NaN 13.866658 0.459922 +1883 2.833333 NaN 13.546526 0.796622 +1884 2.876944 0.181440 NaN NaN +1885 3.678056 0.294840 NaN NaN +1886 3.983333 NaN 11.871899 1.378324 +1887 4.092222 0.367416 NaN NaN +1888 4.565000 0.535248 NaN NaN +1889 4.883333 NaN 9.430640 2.190706 +1890 5.166667 NaN 8.543178 2.523372 +Experimental matrix: +[[ nan 14.42575682 0.0155795 ] + [ nan 13.86665829 0.45992226] + [ nan 13.5465255 0.79662202] + [ 0.18144 nan nan] + [ 0.29484 nan nan] + [ nan 11.87189887 1.37832356] + [ 0.367416 nan nan] + [ 0.535248 nan nan] + [ nan 9.43063999 2.1907059 ] + [ nan 8.54317843 2.52337221]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:58,263 - physiofit - INFO - mc : False +2024-05-27 14:33:58,264 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:58,264 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:58,264 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:33:58,652 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:33:58,653 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.3734320734411485 + x: [ 2.762e-02 6.443e-01 -5.215e+00 1.452e+01 + 2.078e+00 2.040e-01] + nit: 85 + nfev: 8209 + population: [[ 2.767e-02 6.440e-01 ... 2.086e+00 1.984e-01] + [ 2.739e-02 6.471e-01 ... 2.090e+00 2.101e-01] + ... + [ 2.735e-02 6.465e-01 ... 2.096e+00 2.008e-01] + [ 2.718e-02 6.474e-01 ... 2.089e+00 2.119e-01]] + population_energies: [ 3.373e+00 3.425e+00 ... 3.401e+00 3.403e+00] + jac: [ 5.603e-04 4.876e-05 1.510e-06 3.997e-06 + 1.021e-05 1.057e-05] +2024-05-27 14:33:58,653 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02762314502775057 +2024-05-27 14:33:58,653 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6442865456051783 +2024-05-27 14:33:58,653 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.214762720217971 +2024-05-27 14:33:58,653 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.515770237516342 +2024-05-27 14:33:58,653 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.078015587883628 +2024-05-27 14:33:58,653 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.2039757268894959 +2024-05-27 14:33:58,657 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.508451 0.206893 +1.950000 NaN 13.954007 0.427831 +2.833333 NaN 13.351877 0.667772 +2.876944 0.176308 NaN NaN +3.678056 0.295413 NaN NaN +3.983333 NaN 11.828594 1.274781 +4.092222 0.385761 NaN NaN +4.565000 0.523126 NaN NaN +4.883333 NaN 9.541369 2.186211 +5.166667 NaN 8.500361 2.601039 + +2024-05-27 14:33:58,661 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.3734320734411485 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.028777861136614562 + +2024-05-27 14:33:58,662 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.028777861136614562 +2024-05-27 14:33:58,665 - physiofit - INFO - Results for yjgJ: + optimal +yjgJ X_0 0.027623 +yjgJ growth_rate 0.644287 +yjgJ Glc_q -5.214763 +yjgJ Glc_M0 14.515770 +yjgJ Ace_q 2.078016 +yjgJ Ace_M0 0.203976 +2024-05-27 14:33:58,673 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:33:59,682 - physiofit - INFO - Running optimization for yjgM +2024-05-27 14:33:59,684 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:33:59,684 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:33:59,688 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1891 0.000000 0.036288 NaN NaN +1892 0.283333 NaN 14.447603 0.040252 +1893 1.195000 0.065016 NaN NaN +1894 1.613611 0.075600 NaN NaN +1895 1.916667 NaN 13.706022 0.376075 +1896 2.361389 0.113400 NaN NaN +1897 2.700000 NaN 13.214023 0.631353 +1898 3.286389 0.193536 NaN NaN +1899 3.616667 NaN 12.555972 1.074628 +1900 3.819444 0.270648 NaN NaN +1901 4.050000 NaN 12.240150 1.308906 +1902 4.410833 0.379512 NaN NaN +1903 4.750000 NaN 10.574833 1.963805 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 14.44760334 0.04025213] + [ 0.065016 nan nan] + [ 0.0756 nan nan] + [ nan 13.70602231 0.37607495] + [ 0.1134 nan nan] + [ nan 13.2140232 0.63135284] + [ 0.193536 nan nan] + [ nan 12.55597235 1.07462832] + [ 0.270648 nan nan] + [ nan 12.24015037 1.30890602] + [ 0.379512 nan nan] + [ nan 10.57483334 1.96380526]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:33:59,688 - physiofit - INFO - mc : False +2024-05-27 14:33:59,688 - physiofit - INFO - iterations : 100 +2024-05-27 14:33:59,688 - physiofit - INFO - debug_mode : False +2024-05-27 14:33:59,688 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:00,163 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:00,164 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.2476815839761657 + x: [ 3.081e-02 5.678e-01 -4.883e+00 1.435e+01 + 2.540e+00 8.655e-02] + nit: 102 + nfev: 9662 + population: [[ 3.077e-02 5.683e-01 ... 2.543e+00 8.312e-02] + [ 3.046e-02 5.709e-01 ... 2.509e+00 9.203e-02] + ... + [ 3.033e-02 5.706e-01 ... 2.572e+00 7.252e-02] + [ 3.140e-02 5.634e-01 ... 2.523e+00 8.191e-02]] + population_energies: [ 1.248e+00 1.280e+00 ... 1.301e+00 1.274e+00] + jac: [-6.133e-03 -4.601e-04 -3.419e-06 1.017e-04 + 3.437e-05 -1.776e-04] +2024-05-27 14:34:00,164 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.030805817872042812 +2024-05-27 14:34:00,164 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5677867395673246 +2024-05-27 14:34:00,164 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.882564075862746 +2024-05-27 14:34:00,164 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.351642700363868 +2024-05-27 14:34:00,165 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.540331703174488 +2024-05-27 14:34:00,165 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.08654781536465696 +2024-05-27 14:34:00,168 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.030806 NaN NaN +0.283333 NaN 14.305407 0.110604 +1.195000 0.060716 NaN NaN +1.613611 0.077007 NaN NaN +1.916667 NaN 13.830013 0.357945 +2.361389 0.117739 NaN NaN +2.700000 NaN 13.389453 0.587162 +3.286389 0.199073 NaN NaN +3.616667 NaN 12.551565 1.023104 +3.819444 0.269437 NaN NaN +4.050000 NaN 11.975533 1.322805 +4.410833 0.376951 NaN NaN +4.750000 NaN 10.686646 1.993396 + +2024-05-27 14:34:00,172 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.2476815839761657 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 1.4528702821474383e-05 + +2024-05-27 14:34:00,173 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 1.4528702821474383e-05 +2024-05-27 14:34:00,175 - physiofit - INFO - Results for yjgM: + optimal +yjgM X_0 0.030806 +yjgM growth_rate 0.567787 +yjgM Glc_q -4.882564 +yjgM Glc_M0 14.351643 +yjgM Ace_q 2.540332 +yjgM Ace_M0 0.086548 +2024-05-27 14:34:00,181 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:01,131 - physiofit - INFO - Running optimization for yjgR +2024-05-27 14:34:01,134 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:01,134 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:01,137 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1904 0.050000 NaN 14.324031 0.019086 +1905 1.950000 NaN 14.190925 0.452302 +1906 2.833333 NaN 13.510844 0.790423 +1907 2.876944 0.160272 NaN NaN +1908 3.678056 0.261576 NaN NaN +1909 3.983333 NaN 11.866948 1.510584 +1910 4.092222 0.355320 NaN NaN +1911 4.565000 0.452088 NaN NaN +1912 4.883333 NaN 9.438335 2.031235 +1913 5.166667 NaN 8.535282 2.604942 +Experimental matrix: +[[ nan 14.32403059 0.01908586] + [ nan 14.19092483 0.45230198] + [ nan 13.51084387 0.79042336] + [ 0.160272 nan nan] + [ 0.261576 nan nan] + [ nan 11.8669483 1.51058374] + [ 0.35532 nan nan] + [ 0.452088 nan nan] + [ nan 9.43833542 2.03123542] + [ nan 8.53528179 2.60494153]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:01,137 - physiofit - INFO - mc : False +2024-05-27 14:34:01,137 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:01,138 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:01,138 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:01,592 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:01,593 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.032613187108416 + x: [ 2.958e-02 5.990e-01 -5.866e+00 1.465e+01 + 2.305e+00 1.859e-01] + nit: 101 + nfev: 9544 + population: [[ 2.937e-02 6.004e-01 ... 2.297e+00 1.931e-01] + [ 2.924e-02 6.006e-01 ... 2.329e+00 1.859e-01] + ... + [ 2.908e-02 6.034e-01 ... 2.317e+00 1.765e-01] + [ 2.906e-02 6.034e-01 ... 2.299e+00 1.958e-01]] + population_energies: [ 4.033e+00 4.078e+00 ... 4.053e+00 4.051e+00] + jac: [ 1.654e-02 1.961e-03 -1.865e-05 -2.363e-05 + 2.744e-05 4.814e-05] +2024-05-27 14:34:01,594 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.029575974398804813 +2024-05-27 14:34:01,594 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5990328872223847 +2024-05-27 14:34:01,594 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.865708589367614 +2024-05-27 14:34:01,594 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.647107602489887 +2024-05-27 14:34:01,594 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3048494949297216 +2024-05-27 14:34:01,595 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.18586577118665035 +2024-05-27 14:34:01,600 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.638302 0.189326 +1.950000 NaN 14.005361 0.438031 +2.833333 NaN 13.355760 0.693283 +2.876944 0.165728 NaN NaN +3.678056 0.267800 NaN NaN +3.983333 NaN 11.788244 1.309217 +4.092222 0.343208 NaN NaN +4.565000 0.455569 NaN NaN +4.883333 NaN 9.538618 2.193177 +5.166667 NaN 8.540077 2.585539 + +2024-05-27 14:34:01,604 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.032613187108416 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.054136250825728836 + +2024-05-27 14:34:01,604 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.054136250825728836 +2024-05-27 14:34:01,608 - physiofit - INFO - Results for yjgR: + optimal +yjgR X_0 0.029576 +yjgR growth_rate 0.599033 +yjgR Glc_q -5.865709 +yjgR Glc_M0 14.647108 +yjgR Ace_q 2.304849 +yjgR Ace_M0 0.185866 +2024-05-27 14:34:01,614 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:02,567 - physiofit - INFO - Running optimization for yjhC +2024-05-27 14:34:02,570 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:02,570 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:02,573 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1914 0.000000 0.037800 NaN NaN +1915 0.283333 NaN 14.323926 0.042446 +1916 1.195000 0.069552 NaN NaN +1917 1.613611 0.089208 NaN NaN +1918 1.916667 NaN 14.035452 0.397463 +1919 2.361389 0.142128 NaN NaN +1920 2.700000 NaN 13.299131 0.676759 +1921 3.286389 0.234360 NaN NaN +1922 3.616667 NaN 12.445148 1.130203 +1923 3.819444 0.328104 NaN NaN +1924 4.050000 NaN 11.717446 1.438924 +1925 4.410833 0.452088 NaN NaN +1926 4.750000 NaN 10.305891 2.017552 +Experimental matrix: +[[ 0.0378 nan nan] + [ nan 14.32392575 0.04244648] + [ 0.069552 nan nan] + [ 0.089208 nan nan] + [ nan 14.0354518 0.39746309] + [ 0.142128 nan nan] + [ nan 13.29913066 0.67675874] + [ 0.23436 nan nan] + [ nan 12.44514779 1.13020346] + [ 0.328104 nan nan] + [ nan 11.71744559 1.43892359] + [ 0.452088 nan nan] + [ nan 10.30589052 2.01755244]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:02,575 - physiofit - INFO - mc : False +2024-05-27 14:34:02,575 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:02,575 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:02,575 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:03,055 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:03,056 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.8727302370655556 + x: [ 3.675e-02 5.693e-01 -4.633e+00 1.446e+01 + 2.201e+00 1.074e-01] + nit: 103 + nfev: 9850 + population: [[ 3.664e-02 5.702e-01 ... 2.210e+00 1.055e-01] + [ 3.689e-02 5.684e-01 ... 2.196e+00 1.067e-01] + ... + [ 3.686e-02 5.688e-01 ... 2.186e+00 1.196e-01] + [ 3.718e-02 5.662e-01 ... 2.188e+00 1.072e-01]] + population_energies: [ 8.727e-01 8.767e-01 ... 8.898e-01 8.845e-01] + jac: [-2.705e-02 -2.011e-03 1.204e-04 2.348e-04 + 2.728e-04 5.404e-04] +2024-05-27 14:34:03,056 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.036752585850773664 +2024-05-27 14:34:03,056 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5692630879371577 +2024-05-27 14:34:03,057 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.633016060030692 +2024-05-27 14:34:03,057 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.46302329146121 +2024-05-27 14:34:03,057 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.2006101382245014 +2024-05-27 14:34:03,057 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.10737364646756979 +2024-05-27 14:34:03,060 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.036753 NaN NaN +0.283333 NaN 14.410670 0.132241 +1.195000 0.072565 NaN NaN +1.613611 0.092091 NaN NaN +1.916667 NaN 13.871520 0.388329 +2.361389 0.140958 NaN NaN +2.700000 NaN 13.371053 0.626042 +3.286389 0.238657 NaN NaN +3.616667 NaN 12.418022 1.078717 +3.819444 0.323267 NaN NaN +4.050000 NaN 11.762207 1.390219 +4.410833 0.452656 NaN NaN +4.750000 NaN 10.293545 2.087810 + +2024-05-27 14:34:03,065 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.8727302370655556 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 1.6719546386507365e-06 + +2024-05-27 14:34:03,065 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 1.6719546386507365e-06 +2024-05-27 14:34:03,067 - physiofit - INFO - Results for yjhC: + optimal +yjhC X_0 0.036753 +yjhC growth_rate 0.569263 +yjhC Glc_q -4.633016 +yjhC Glc_M0 14.463023 +yjhC Ace_q 2.200610 +yjhC Ace_M0 0.107374 +2024-05-27 14:34:03,073 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:04,005 - physiofit - INFO - Running optimization for yjhU +2024-05-27 14:34:04,007 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:04,007 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:04,010 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1927 0.000000 0.037800 NaN NaN +1928 0.283333 NaN 14.282709 0.044372 +1929 1.195000 0.068040 NaN NaN +1930 1.613611 0.086184 NaN NaN +1931 1.916667 NaN 13.771767 0.359574 +1932 2.361389 0.130032 NaN NaN +1933 2.700000 NaN 13.609074 0.662578 +1934 3.286389 0.207144 NaN NaN +1935 3.616667 NaN 12.489467 1.111902 +1936 3.819444 0.303912 NaN NaN +1937 4.050000 NaN 12.034624 1.353108 +1938 4.410833 0.400680 NaN NaN +1939 4.750000 NaN 10.678536 1.885494 +Experimental matrix: +[[ 0.0378 nan nan] + [ nan 14.28270946 0.04437244] + [ 0.06804 nan nan] + [ 0.086184 nan nan] + [ nan 13.77176709 0.35957383] + [ 0.130032 nan nan] + [ nan 13.60907393 0.66257841] + [ 0.207144 nan nan] + [ nan 12.4894674 1.11190151] + [ 0.303912 nan nan] + [ nan 12.03462448 1.35310756] + [ 0.40068 nan nan] + [ nan 10.678536 1.88549376]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:04,011 - physiofit - INFO - mc : False +2024-05-27 14:34:04,011 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:04,011 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:04,011 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:04,408 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:04,409 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.574822520551332 + x: [ 3.592e-02 5.483e-01 -4.486e+00 1.440e+01 + 2.267e+00 1.004e-01] + nit: 87 + nfev: 8291 + population: [[ 3.585e-02 5.489e-01 ... 2.262e+00 1.030e-01] + [ 3.592e-02 5.474e-01 ... 2.279e+00 9.434e-02] + ... + [ 3.573e-02 5.499e-01 ... 2.265e+00 1.043e-01] + [ 3.613e-02 5.466e-01 ... 2.270e+00 1.007e-01]] + population_energies: [ 1.575e+00 1.587e+00 ... 1.583e+00 1.589e+00] + jac: [ 2.131e-03 2.788e-04 -7.187e-03 2.493e-03 + 1.255e-03 -2.930e-04] +2024-05-27 14:34:04,409 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.035917200916423295 +2024-05-27 14:34:04,410 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5483029376051027 +2024-05-27 14:34:04,410 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.486313124467216 +2024-05-27 14:34:04,410 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.399234491454841 +2024-05-27 14:34:04,410 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.266886804420999 +2024-05-27 14:34:04,411 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.10035599367081743 +2024-05-27 14:34:04,414 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.035917 NaN NaN +0.283333 NaN 14.349842 0.125313 +1.195000 0.069161 NaN NaN +1.613611 0.087005 NaN NaN +1.916667 NaN 13.852538 0.376596 +2.361389 0.131102 NaN NaN +2.700000 NaN 13.401573 0.604464 +3.286389 0.217708 NaN NaN +3.616667 NaN 12.558154 1.030635 +3.819444 0.291613 NaN NaN +4.050000 NaN 11.985559 1.319961 +4.410833 0.403303 NaN NaN +4.750000 NaN 10.718776 1.960053 + +2024-05-27 14:34:04,418 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.574822520551332 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 5.7373585208155e-05 + +2024-05-27 14:34:04,419 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 5.7373585208155e-05 +2024-05-27 14:34:04,421 - physiofit - INFO - Results for yjhU: + optimal +yjhU X_0 0.035917 +yjhU growth_rate 0.548303 +yjhU Glc_q -4.486313 +yjhU Glc_M0 14.399234 +yjhU Ace_q 2.266887 +yjhU Ace_M0 0.100356 +2024-05-27 14:34:04,427 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:05,344 - physiofit - INFO - Running optimization for yjjA +2024-05-27 14:34:05,346 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:05,346 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:05,349 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1940 0.000000 0.037800 NaN NaN +1941 0.283333 NaN 14.726900 0.048786 +1942 1.195000 0.069552 NaN NaN +1943 1.613611 0.078624 NaN NaN +1944 1.916667 NaN 13.614397 0.371287 +1945 2.361389 0.119448 NaN NaN +1946 2.700000 NaN 13.151913 0.625149 +1947 3.286389 0.199584 NaN NaN +1948 3.616667 NaN 13.002399 1.112960 +1949 3.819444 0.258552 NaN NaN +1950 4.050000 NaN 12.095744 1.370959 +1951 4.410833 0.391608 NaN NaN +1952 4.750000 NaN 10.581455 1.420639 +Experimental matrix: +[[ 0.0378 nan nan] + [ nan 14.72689953 0.04878598] + [ 0.069552 nan nan] + [ 0.078624 nan nan] + [ nan 13.61439718 0.37128704] + [ 0.119448 nan nan] + [ nan 13.15191265 0.62514944] + [ 0.199584 nan nan] + [ nan 13.00239936 1.11295958] + [ 0.258552 nan nan] + [ nan 12.09574437 1.3709592 ] + [ 0.391608 nan nan] + [ nan 10.58145547 1.4206387 ]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:05,350 - physiofit - INFO - mc : False +2024-05-27 14:34:05,350 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:05,350 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:05,350 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:05,666 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:05,668 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 7.6038264510474995 + x: [ 3.308e-02 5.528e-01 -4.941e+00 1.449e+01 + 1.909e+00 1.950e-01] + nit: 67 + nfev: 6631 + population: [[ 3.308e-02 5.527e-01 ... 1.888e+00 1.965e-01] + [ 3.321e-02 5.514e-01 ... 1.880e+00 2.028e-01] + ... + [ 3.259e-02 5.552e-01 ... 1.903e+00 2.030e-01] + [ 3.288e-02 5.533e-01 ... 1.852e+00 2.050e-01]] + population_energies: [ 7.604e+00 7.649e+00 ... 7.649e+00 7.691e+00] + jac: [ 8.526e-02 9.871e-03 -2.435e-04 1.714e-05 + 5.740e-04 1.856e-03] +2024-05-27 14:34:05,669 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03308084602223033 +2024-05-27 14:34:05,669 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5528275856134278 +2024-05-27 14:34:05,669 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.940940287415571 +2024-05-27 14:34:05,669 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.49266745465876 +2024-05-27 14:34:05,669 - physiofit.physiofit.base.fitter - INFO - Ace_q = 1.909061541583698 +2024-05-27 14:34:05,669 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1949706545620141 +2024-05-27 14:34:05,672 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.033081 NaN NaN +0.283333 NaN 14.442533 0.214342 +1.195000 0.064045 NaN NaN +1.613611 0.080721 NaN NaN +1.916667 NaN 13.935291 0.410328 +2.361389 0.122046 NaN NaN +2.700000 NaN 13.472986 0.588951 +3.286389 0.203519 NaN NaN +3.616667 NaN 12.604987 0.924325 +3.819444 0.273267 NaN NaN +4.050000 NaN 12.013982 1.152675 +4.410833 0.378943 NaN NaN +4.750000 NaN 10.703031 1.659196 + +2024-05-27 14:34:05,676 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 7.6038264510474995 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.13158119874157356 + +2024-05-27 14:34:05,676 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.13158119874157356 +2024-05-27 14:34:05,678 - physiofit - INFO - Results for yjjA: + optimal +yjjA X_0 0.033081 +yjjA growth_rate 0.552828 +yjjA Glc_q -4.940940 +yjjA Glc_M0 14.492667 +yjjA Ace_q 1.909062 +yjjA Ace_M0 0.194971 +2024-05-27 14:34:05,685 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:06,762 - physiofit - INFO - Running optimization for yjjV +2024-05-27 14:34:06,765 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:06,765 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:06,768 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1953 0.050000 NaN 14.218460 0.019562 +1954 1.950000 NaN 13.793926 0.449797 +1955 2.833333 NaN 13.666218 0.747676 +1956 2.876944 0.173880 NaN NaN +1957 3.678056 0.250992 NaN NaN +1958 3.983333 NaN 11.276599 1.432046 +1959 4.092222 0.328104 NaN NaN +1960 4.565000 0.400680 NaN NaN +1961 4.883333 NaN 9.189296 2.228547 +1962 5.166667 NaN 8.563589 2.488287 +Experimental matrix: +[[ nan 14.21845983 0.01956192] + [ nan 13.7939261 0.44979713] + [ nan 13.666218 0.74767558] + [ 0.17388 nan nan] + [ 0.250992 nan nan] + [ nan 11.2765991 1.43204612] + [ 0.328104 nan nan] + [ 0.40068 nan nan] + [ nan 9.18929626 2.22854705] + [ nan 8.56358929 2.48828726]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:06,769 - physiofit - INFO - mc : False +2024-05-27 14:34:06,769 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:06,769 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:06,769 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:07,242 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:07,243 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.6070847397465937 + x: [ 4.007e-02 5.065e-01 -6.086e+00 1.459e+01 + 2.450e+00 9.761e-02] + nit: 98 + nfev: 9302 + population: [[ 3.959e-02 5.093e-01 ... 2.460e+00 9.298e-02] + [ 4.190e-02 4.970e-01 ... 2.413e+00 9.088e-02] + ... + [ 3.955e-02 5.100e-01 ... 2.437e+00 1.046e-01] + [ 3.963e-02 5.092e-01 ... 2.470e+00 8.163e-02]] + population_energies: [ 3.607e+00 3.757e+00 ... 3.624e+00 3.640e+00] + jac: [ 3.095e-03 -8.842e-04 -6.439e-05 -1.204e-04 + 2.314e-04 2.291e-04] +2024-05-27 14:34:07,243 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.04006562773497436 +2024-05-27 14:34:07,243 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5065142527756358 +2024-05-27 14:34:07,244 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.08585521792229 +2024-05-27 14:34:07,244 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.591962223914518 +2024-05-27 14:34:07,244 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4498064416313468 +2024-05-27 14:34:07,244 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.09760670400309425 +2024-05-27 14:34:07,247 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.579615 0.102577 +1.950000 NaN 13.780783 0.424140 +2.833333 NaN 13.051418 0.717739 +2.876944 0.172041 NaN NaN +3.678056 0.258141 NaN NaN +3.983333 NaN 11.453087 1.361133 +4.092222 0.318393 NaN NaN +4.565000 0.404542 NaN NaN +4.883333 NaN 9.362258 2.202777 +5.166667 NaN 8.480915 2.557554 + +2024-05-27 14:34:07,250 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.6070847397465937 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.03666333506534139 + +2024-05-27 14:34:07,252 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.03666333506534139 +2024-05-27 14:34:07,255 - physiofit - INFO - Results for yjjV: + optimal +yjjV X_0 0.040066 +yjjV growth_rate 0.506514 +yjjV Glc_q -6.085855 +yjjV Glc_M0 14.591962 +yjjV Ace_q 2.449806 +yjjV Ace_M0 0.097607 +2024-05-27 14:34:07,261 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:08,525 - physiofit - INFO - Running optimization for ykgE +2024-05-27 14:34:08,527 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:08,528 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:08,531 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1963 0.000000 0.036288 NaN NaN +1964 0.283333 NaN 14.159396 0.048169 +1965 1.195000 0.061992 NaN NaN +1966 1.613611 0.074088 NaN NaN +1967 1.916667 NaN 13.797900 0.402308 +1968 2.361389 0.101304 NaN NaN +1969 2.700000 NaN 13.875835 0.700593 +1970 3.286389 0.152712 NaN NaN +1971 3.616667 NaN 12.719700 1.191590 +1972 3.819444 0.196560 NaN NaN +1973 4.050000 NaN 12.251345 1.484691 +1974 4.410833 0.279720 NaN NaN +1975 4.750000 NaN 11.580969 2.090404 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 14.15939616 0.04816901] + [ 0.061992 nan nan] + [ 0.074088 nan nan] + [ nan 13.79790018 0.40230799] + [ 0.101304 nan nan] + [ nan 13.87583507 0.70059345] + [ 0.152712 nan nan] + [ nan 12.71969967 1.19159009] + [ 0.19656 nan nan] + [ nan 12.25134546 1.48469092] + [ 0.27972 nan nan] + [ nan 11.58096904 2.09040369]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:08,533 - physiofit - INFO - mc : False +2024-05-27 14:34:08,533 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:08,533 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:08,534 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:08,978 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:08,979 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.6410861269323802 + x: [ 3.288e-02 4.789e-01 -4.694e+00 1.433e+01 + 3.470e+00 4.809e-02] + nit: 88 + nfev: 8269 + population: [[ 3.260e-02 4.815e-01 ... 3.463e+00 5.040e-02] + [ 3.280e-02 4.798e-01 ... 3.465e+00 4.108e-02] + ... + [ 3.273e-02 4.804e-01 ... 3.494e+00 4.212e-02] + [ 3.295e-02 4.772e-01 ... 3.445e+00 6.240e-02]] + population_energies: [ 1.641e+00 1.664e+00 ... 1.656e+00 1.668e+00] + jac: [-1.244e-02 -1.947e-03 1.636e-02 -5.342e-03 + 8.900e-03 -1.303e-03] +2024-05-27 14:34:08,979 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03288365066806137 +2024-05-27 14:34:08,980 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.4788680420741769 +2024-05-27 14:34:08,980 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.694392435440999 +2024-05-27 14:34:08,980 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.333289815641436 +2024-05-27 14:34:08,980 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.470124835346399 +2024-05-27 14:34:08,980 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.048092556591296444 +2024-05-27 14:34:08,984 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.032884 NaN NaN +0.283333 NaN 14.286446 0.082720 +1.195000 0.058278 NaN NaN +1.613611 0.071213 NaN NaN +1.916667 NaN 13.848505 0.406448 +2.361389 0.101877 NaN NaN +2.700000 NaN 13.481128 0.678016 +3.286389 0.158653 NaN NaN +3.616667 NaN 12.833851 1.156487 +3.819444 0.204790 NaN NaN +4.050000 NaN 12.413727 1.467046 +4.410833 0.271832 NaN NaN +4.750000 NaN 11.520924 2.127012 + +2024-05-27 14:34:08,988 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.6410861269323802 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 7.290502022407173e-05 + +2024-05-27 14:34:08,988 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 7.290502022407173e-05 +2024-05-27 14:34:08,992 - physiofit - INFO - Results for ykgE: + optimal +ykgE X_0 0.032884 +ykgE growth_rate 0.478868 +ykgE Glc_q -4.694392 +ykgE Glc_M0 14.333290 +ykgE Ace_q 3.470125 +ykgE Ace_M0 0.048093 +2024-05-27 14:34:08,999 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:09,987 - physiofit - INFO - Running optimization for ykgG +2024-05-27 14:34:09,989 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:09,989 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:09,993 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1976 0.000000 0.036288 NaN NaN +1977 0.283333 NaN 14.304584 0.036547 +1978 1.195000 0.061992 NaN NaN +1979 1.613611 0.074088 NaN NaN +1980 1.916667 NaN 13.964904 0.376280 +1981 2.361389 0.105840 NaN NaN +1982 2.700000 NaN 13.413796 0.638529 +1983 3.286389 0.182952 NaN NaN +1984 3.616667 NaN 12.396638 0.964352 +1985 3.819444 0.279720 NaN NaN +1986 4.050000 NaN 12.041288 1.221303 +1987 4.410833 0.397656 NaN NaN +1988 4.750000 NaN 10.494041 1.854965 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 14.30458422 0.03654694] + [ 0.061992 nan nan] + [ 0.074088 nan nan] + [ nan 13.9649045 0.37627983] + [ 0.10584 nan nan] + [ nan 13.41379643 0.63852852] + [ 0.182952 nan nan] + [ nan 12.39663797 0.96435172] + [ 0.27972 nan nan] + [ nan 12.04128816 1.22130302] + [ 0.397656 nan nan] + [ nan 10.49404051 1.85496527]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:09,993 - physiofit - INFO - mc : False +2024-05-27 14:34:09,994 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:09,994 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:09,994 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:10,482 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:10,483 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.8835363020456757 + x: [ 2.637e-02 6.132e-01 -5.174e+00 1.437e+01 + 2.354e+00 1.189e-01] + nit: 100 + nfev: 9524 + population: [[ 2.627e-02 6.140e-01 ... 2.364e+00 1.174e-01] + [ 2.658e-02 6.114e-01 ... 2.359e+00 1.155e-01] + ... + [ 2.606e-02 6.161e-01 ... 2.348e+00 1.256e-01] + [ 2.645e-02 6.117e-01 ... 2.354e+00 1.198e-01]] + population_energies: [ 1.884e+00 1.888e+00 ... 1.890e+00 1.894e+00] + jac: [ 5.399e-03 -8.709e-05 -1.981e-05 -1.001e-04 + 9.535e-05 4.290e-04] +2024-05-27 14:34:10,483 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02637168679748064 +2024-05-27 14:34:10,484 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6132248413757002 +2024-05-27 14:34:10,484 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.173751044730108 +2024-05-27 14:34:10,484 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.372875834431232 +2024-05-27 14:34:10,484 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.3543488250184472 +2024-05-27 14:34:10,484 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.11890405233690547 +2024-05-27 14:34:10,488 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.026372 NaN NaN +0.283333 NaN 14.330656 0.138116 +1.195000 0.054877 NaN NaN +1.613611 0.070937 NaN NaN +1.916667 NaN 13.874646 0.345627 +2.361389 0.112208 NaN NaN +2.700000 NaN 13.430206 0.547872 +3.286389 0.197865 NaN NaN +3.616667 NaN 12.551212 0.947864 +3.819444 0.274368 NaN NaN +4.050000 NaN 11.929003 1.231004 +4.410833 0.394305 NaN NaN +4.750000 NaN 10.499518 1.881500 + +2024-05-27 14:34:10,492 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.8835363020456757 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.00016098388864471796 + +2024-05-27 14:34:10,492 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00016098388864471796 +2024-05-27 14:34:10,494 - physiofit - INFO - Results for ykgG: + optimal +ykgG X_0 0.026372 +ykgG growth_rate 0.613225 +ykgG Glc_q -5.173751 +ykgG Glc_M0 14.372876 +ykgG Ace_q 2.354349 +ykgG Ace_M0 0.118904 +2024-05-27 14:34:10,501 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:11,488 - physiofit - INFO - Running optimization for ymbA +2024-05-27 14:34:11,490 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:11,490 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:11,495 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +1989 0.000000 0.037800 NaN NaN +1990 0.283333 NaN 14.161765 0.041582 +1991 1.195000 0.065016 NaN NaN +1992 1.613611 0.084672 NaN NaN +1993 1.916667 NaN 13.353817 0.423791 +1994 2.361389 0.123984 NaN NaN +1995 2.700000 NaN 13.672593 0.783164 +1996 3.286389 0.202608 NaN NaN +1997 3.616667 NaN 12.466259 1.123534 +1998 3.819444 0.291816 NaN NaN +1999 4.050000 NaN 11.811427 1.343289 +2000 4.410833 0.400680 NaN NaN +2001 4.750000 NaN 10.325925 1.702164 +Experimental matrix: +[[ 0.0378 nan nan] + [ nan 14.16176503 0.04158214] + [ 0.065016 nan nan] + [ 0.084672 nan nan] + [ nan 13.35381737 0.42379095] + [ 0.123984 nan nan] + [ nan 13.67259307 0.78316382] + [ 0.202608 nan nan] + [ nan 12.466259 1.12353432] + [ 0.291816 nan nan] + [ nan 11.81142665 1.34328874] + [ 0.40068 nan nan] + [ nan 10.32592465 1.70216407]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:11,495 - physiofit - INFO - mc : False +2024-05-27 14:34:11,495 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:11,495 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:11,496 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:11,940 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:11,941 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.2514202507476755 + x: [ 3.368e-02 5.604e-01 -4.768e+00 1.427e+01 + 2.048e+00 2.008e-01] + nit: 82 + nfev: 7904 + population: [[ 3.377e-02 5.596e-01 ... 2.064e+00 2.018e-01] + [ 3.430e-02 5.555e-01 ... 2.070e+00 1.864e-01] + ... + [ 3.338e-02 5.641e-01 ... 2.090e+00 1.803e-01] + [ 3.393e-02 5.587e-01 ... 2.036e+00 2.143e-01]] + population_energies: [ 4.251e+00 4.289e+00 ... 4.335e+00 4.278e+00] + jac: [ 2.864e-02 3.638e-03 6.937e-05 -9.797e-05 + 1.841e-04 8.331e-05] +2024-05-27 14:34:11,942 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03368145328694123 +2024-05-27 14:34:11,942 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5604459977173624 +2024-05-27 14:34:11,942 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.7679981762024894 +2024-05-27 14:34:11,942 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.266988203853256 +2024-05-27 14:34:11,942 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.0475386921909324 +2024-05-27 14:34:11,942 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.20078597389861502 +2024-05-27 14:34:11,945 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.033681 NaN NaN +0.283333 NaN 14.217675 0.221963 +1.195000 0.065804 NaN NaN +1.613611 0.083203 NaN NaN +1.916667 NaN 13.714639 0.437983 +2.361389 0.126517 NaN NaN +2.700000 NaN 13.252258 0.636545 +3.286389 0.212468 NaN NaN +3.616667 NaN 12.378406 1.011807 +3.819444 0.286443 NaN NaN +4.050000 NaN 11.780485 1.268574 +4.410833 0.399008 NaN NaN +4.750000 NaN 10.448313 1.840654 + +2024-05-27 14:34:11,950 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.2514202507476755 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.011788955785944482 + +2024-05-27 14:34:11,951 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.011788955785944482 +2024-05-27 14:34:11,953 - physiofit - INFO - Results for ymbA: + optimal +ymbA X_0 0.033681 +ymbA growth_rate 0.560446 +ymbA Glc_q -4.767998 +ymbA Glc_M0 14.266988 +ymbA Ace_q 2.047539 +ymbA Ace_M0 0.200786 +2024-05-27 14:34:11,959 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:12,922 - physiofit - INFO - Running optimization for ymjA +2024-05-27 14:34:12,925 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:12,925 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:12,929 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2002 1.828889 0.063504 NaN NaN +2003 2.261389 0.086184 NaN NaN +2004 2.774167 0.127008 NaN NaN +2005 2.800000 NaN 12.432679 0.517039 +2006 3.208889 0.151200 NaN NaN +2007 3.706389 0.198072 NaN NaN +2008 3.733333 NaN 12.144458 0.933574 +2009 4.225833 0.279720 NaN NaN +2010 4.283333 NaN 11.785006 1.273121 +2011 4.635556 0.353808 NaN NaN +2012 4.750000 NaN 10.877352 1.606636 +2013 4.967500 0.421848 NaN NaN +2014 5.116667 NaN 10.065176 1.867219 +2015 5.433333 NaN 9.614486 2.224816 +Experimental matrix: +[[ 0.063504 nan nan] + [ 0.086184 nan nan] + [ 0.127008 nan nan] + [ nan 12.43267898 0.51703923] + [ 0.1512 nan nan] + [ 0.198072 nan nan] + [ nan 12.14445754 0.933574 ] + [ 0.27972 nan nan] + [ nan 11.78500599 1.27312149] + [ 0.353808 nan nan] + [ nan 10.87735179 1.60663619] + [ 0.421848 nan nan] + [ nan 10.06517639 1.86721943] + [ nan 9.6144857 2.22481579]] +Time vector: [1.82888889 2.26138889 2.77416667 2.8 3.20888889 3.70638889 + 3.73333333 4.22583333 4.28333333 4.63555556 4.75 4.9675 + 5.11666667 5.43333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:12,929 - physiofit - INFO - mc : False +2024-05-27 14:34:12,929 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:12,929 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:12,929 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:13,497 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:13,499 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.5721608324303522 + x: [ 2.361e-02 5.818e-01 -4.069e+00 1.333e+01 + 2.229e+00 2.118e-01] + nit: 120 + nfev: 11324 + population: [[ 2.365e-02 5.812e-01 ... 2.232e+00 2.107e-01] + [ 2.373e-02 5.804e-01 ... 2.220e+00 2.178e-01] + ... + [ 2.391e-02 5.785e-01 ... 2.184e+00 2.353e-01] + [ 2.373e-02 5.801e-01 ... 2.218e+00 2.196e-01]] + population_energies: [ 1.572e+00 1.588e+00 ... 1.624e+00 1.592e+00] + jac: [-1.189e-02 -2.663e-03 -2.465e-05 -1.420e-04 + -6.377e-04 -1.006e-03] +2024-05-27 14:34:13,499 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.023609666466771283 +2024-05-27 14:34:13,499 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5818359691810313 +2024-05-27 14:34:13,500 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.069347293682226 +2024-05-27 14:34:13,500 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.328855871584357 +2024-05-27 14:34:13,500 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.229367159601094 +2024-05-27 14:34:13,500 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.21180580918160097 +2024-05-27 14:34:13,504 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.828889 0.068427 NaN NaN +2.261389 0.088007 NaN NaN +2.774167 0.118601 NaN NaN +2.800000 NaN 12.651926 0.582658 +3.208889 0.152735 NaN NaN +3.706389 0.204010 NaN NaN +3.733333 NaN 12.044598 0.915378 +4.225833 0.275999 NaN NaN +4.283333 NaN 11.497976 1.214842 +4.635556 0.350300 NaN NaN +4.750000 NaN 10.875299 1.555972 +4.967500 0.424931 NaN NaN +5.116667 NaN 10.252563 1.897134 +5.433333 NaN 9.596779 2.256402 + +2024-05-27 14:34:13,507 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.5721608324303522 +Number of measurements: 20 +Number of parameters to fit: 6 +Degrees of freedom: 14 +p-value = 1.857028266965434e-05 + +2024-05-27 14:34:13,508 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 1.857028266965434e-05 +2024-05-27 14:34:13,511 - physiofit - INFO - Results for ymjA: + optimal +ymjA X_0 0.023610 +ymjA growth_rate 0.581836 +ymjA Glc_q -4.069347 +ymjA Glc_M0 13.328856 +ymjA Ace_q 2.229367 +ymjA Ace_M0 0.211806 +2024-05-27 14:34:13,517 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:14,479 - physiofit - INFO - Running optimization for ynbE +2024-05-27 14:34:14,481 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:14,482 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:14,485 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2016 0.000000 0.036288 NaN NaN +2017 0.066667 NaN 15.640677 0.015468 +2018 1.188889 0.071064 NaN NaN +2019 1.716667 NaN 15.053215 0.354304 +2020 2.276944 0.105840 NaN NaN +2021 2.800000 NaN 13.567215 0.776773 +2022 3.128333 0.167832 NaN NaN +2023 3.633333 NaN 12.586536 1.332518 +2024 3.771389 0.223776 NaN NaN +2025 4.266667 NaN 11.514665 1.865342 +2026 4.415556 0.317520 NaN NaN +2027 4.822778 0.406728 NaN NaN +2028 4.883333 NaN 10.349333 2.617843 +Experimental matrix: +[[3.62880000e-02 nan nan] + [ nan 1.56406768e+01 1.54677789e-02] + [7.10640000e-02 nan nan] + [ nan 1.50532152e+01 3.54303861e-01] + [1.05840000e-01 nan nan] + [ nan 1.35672155e+01 7.76772560e-01] + [1.67832000e-01 nan nan] + [ nan 1.25865359e+01 1.33251821e+00] + [2.23776000e-01 nan nan] + [ nan 1.15146648e+01 1.86534198e+00] + [3.17520000e-01 nan nan] + [4.06728000e-01 nan nan] + [ nan 1.03493329e+01 2.61784265e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:14,486 - physiofit - INFO - mc : False +2024-05-27 14:34:14,486 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:14,486 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:14,487 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:14,981 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:14,983 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.6014037158754304 + x: [ 3.515e-02 5.022e-01 -7.298e+00 1.549e+01 + 3.512e+00 2.072e-02] + nit: 97 + nfev: 9121 + population: [[ 3.493e-02 5.034e-01 ... 3.525e+00 2.282e-02] + [ 3.486e-02 5.038e-01 ... 3.499e+00 2.878e-02] + ... + [ 3.617e-02 4.944e-01 ... 3.440e+00 3.296e-02] + [ 3.489e-02 5.040e-01 ... 3.515e+00 1.372e-02]] + population_energies: [ 2.601e+00 2.617e+00 ... 2.705e+00 2.620e+00] + jac: [ 1.792e-02 -5.253e-03 -4.563e-02 8.587e-03 + -2.294e-02 7.807e-03] +2024-05-27 14:34:14,983 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03514753215931796 +2024-05-27 14:34:14,984 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5021821535350194 +2024-05-27 14:34:14,984 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.298018654288932 +2024-05-27 14:34:14,984 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.48707446132154 +2024-05-27 14:34:14,984 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.511941289394231 +2024-05-27 14:34:14,984 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.020723059040901517 +2024-05-27 14:34:14,988 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.035148 NaN NaN +0.066667 NaN 15.469684 0.029091 +1.188889 0.063854 NaN NaN +1.716667 NaN 14.788279 0.356996 +2.276944 0.110277 NaN NaN +2.800000 NaN 13.913828 0.777798 +3.128333 0.169110 NaN NaN +3.633333 NaN 12.830845 1.298950 +3.771389 0.233569 NaN NaN +4.266667 NaN 11.644978 1.869611 +4.415556 0.322779 NaN NaN +4.822778 0.396021 NaN NaN +4.883333 NaN 10.064936 2.629956 + +2024-05-27 14:34:14,991 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.6014037158754304 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0009678312189012577 + +2024-05-27 14:34:14,991 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0009678312189012577 +2024-05-27 14:34:14,993 - physiofit - INFO - Results for ynbE: + optimal +ynbE X_0 0.035148 +ynbE growth_rate 0.502182 +ynbE Glc_q -7.298019 +ynbE Glc_M0 15.487074 +ynbE Ace_q 3.511941 +ynbE Ace_M0 0.020723 +2024-05-27 14:34:15,000 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:16,042 - physiofit - INFO - Running optimization for yncE +2024-05-27 14:34:16,045 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:16,045 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:16,049 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2029 0.000000 0.033264 NaN NaN +2030 0.066667 NaN 15.538355 0.014974 +2031 1.188889 0.054432 NaN NaN +2032 1.716667 NaN 15.090388 0.354378 +2033 2.276944 0.108864 NaN NaN +2034 2.800000 NaN 13.742450 0.786507 +2035 3.128333 0.167832 NaN NaN +2036 3.633333 NaN 12.394381 1.210482 +2037 3.771389 0.247968 NaN NaN +2038 4.266667 NaN 11.264622 1.693009 +2039 4.415556 0.374976 NaN NaN +2040 4.822778 0.563976 NaN NaN +2041 4.883333 NaN 9.895535 2.250121 +Experimental matrix: +[[3.32640000e-02 nan nan] + [ nan 1.55383551e+01 1.49737195e-02] + [5.44320000e-02 nan nan] + [ nan 1.50903881e+01 3.54377611e-01] + [1.08864000e-01 nan nan] + [ nan 1.37424500e+01 7.86506958e-01] + [1.67832000e-01 nan nan] + [ nan 1.23943812e+01 1.21048179e+00] + [2.47968000e-01 nan nan] + [ nan 1.12646218e+01 1.69300876e+00] + [3.74976000e-01 nan nan] + [5.63976000e-01 nan nan] + [ nan 9.89553472e+00 2.25012066e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:16,050 - physiofit - INFO - mc : False +2024-05-27 14:34:16,050 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:16,050 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:16,051 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:16,563 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:16,564 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 11.849198142676148 + x: [ 2.160e-02 6.646e-01 -7.205e+00 1.527e+01 + 2.734e+00 1.850e-01] + nit: 88 + nfev: 8332 + population: [[ 2.145e-02 6.669e-01 ... 2.669e+00 2.063e-01] + [ 2.256e-02 6.557e-01 ... 2.776e+00 1.602e-01] + ... + [ 2.206e-02 6.605e-01 ... 2.619e+00 2.062e-01] + [ 2.092e-02 6.723e-01 ... 2.701e+00 2.212e-01]] + population_energies: [ 1.185e+01 1.213e+01 ... 1.204e+01 1.202e+01] + jac: [ 2.905e-02 4.900e-03 -6.744e-02 7.036e-04 + 1.253e-02 1.390e-03] +2024-05-27 14:34:16,565 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.021600775139095155 +2024-05-27 14:34:16,565 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6646424778409353 +2024-05-27 14:34:16,565 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.20462684410508 +2024-05-27 14:34:16,565 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.271238881767337 +2024-05-27 14:34:16,565 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.73389865017585 +2024-05-27 14:34:16,565 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.18503644337645384 +2024-05-27 14:34:16,569 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.021601 NaN NaN +0.066667 NaN 15.260631 0.189062 +1.188889 0.047604 NaN NaN +1.716667 NaN 14.772547 0.374272 +2.276944 0.098109 NaN NaN +2.800000 NaN 13.999772 0.667513 +3.128333 0.172768 NaN NaN +3.633333 NaN 12.885659 1.090279 +3.771389 0.264901 NaN NaN +4.266667 NaN 11.514510 1.610581 +4.415556 0.406464 NaN NaN +4.822778 0.532803 NaN NaN +4.883333 NaN 9.492687 2.377791 + +2024-05-27 14:34:16,573 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 11.849198142676148 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.45995322282543943 + +2024-05-27 14:34:16,573 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.45995322282543943 +2024-05-27 14:34:16,576 - physiofit - INFO - Results for yncE: + optimal +yncE X_0 0.021601 +yncE growth_rate 0.664642 +yncE Glc_q -7.204627 +yncE Glc_M0 15.271239 +yncE Ace_q 2.733899 +yncE Ace_M0 0.185036 +2024-05-27 14:34:16,583 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:17,572 - physiofit - INFO - Running optimization for ynfK +2024-05-27 14:34:17,575 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:17,576 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:17,582 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2042 0.050000 NaN 14.460108 0.015673 +2043 1.950000 NaN 13.847820 0.403604 +2044 2.833333 NaN 13.424117 0.671707 +2045 2.876944 0.142128 NaN NaN +2046 3.678056 0.214704 NaN NaN +2047 3.983333 NaN 12.445058 1.233847 +2048 4.092222 0.279720 NaN NaN +2049 4.565000 0.358344 NaN NaN +2050 4.883333 NaN 10.012417 1.907537 +2051 5.166667 NaN 9.606194 1.907025 +Experimental matrix: +[[ nan 14.46010764 0.01567338] + [ nan 13.84782032 0.40360447] + [ nan 13.42411666 0.67170655] + [ 0.142128 nan nan] + [ 0.214704 nan nan] + [ nan 12.44505793 1.23384657] + [ 0.27972 nan nan] + [ 0.358344 nan nan] + [ nan 10.01241692 1.90753749] + [ nan 9.60619377 1.90702547]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:17,583 - physiofit - INFO - mc : False +2024-05-27 14:34:17,583 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:17,583 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:17,584 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:18,036 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:18,037 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.4033438795628927 + x: [ 3.044e-02 5.390e-01 -5.847e+00 1.456e+01 + 2.250e+00 1.518e-01] + nit: 94 + nfev: 9103 + population: [[ 3.027e-02 5.405e-01 ... 2.252e+00 1.464e-01] + [ 3.115e-02 5.334e-01 ... 2.233e+00 1.405e-01] + ... + [ 3.176e-02 5.299e-01 ... 2.227e+00 1.506e-01] + [ 3.204e-02 5.276e-01 ... 2.258e+00 1.345e-01]] + population_energies: [ 3.403e+00 3.450e+00 ... 3.457e+00 3.521e+00] + jac: [-1.744e-03 -2.816e-05 3.761e-05 5.240e-05 + -6.457e-05 -8.780e-05] +2024-05-27 14:34:18,038 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.0304363536186558 +2024-05-27 14:34:18,038 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5390427262217743 +2024-05-27 14:34:18,038 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.846539864756843 +2024-05-27 14:34:18,038 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.563967526493224 +2024-05-27 14:34:18,038 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.249576610533589 +2024-05-27 14:34:18,038 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1518493463356663 +2024-05-27 14:34:18,043 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.554949 0.155319 +1.950000 NaN 13.949655 0.388219 +2.833333 NaN 13.373674 0.609839 +2.876944 0.143514 NaN NaN +3.678056 0.221023 NaN NaN +3.983333 NaN 12.068035 1.112211 +4.092222 0.276309 NaN NaN +4.565000 0.356512 NaN NaN +4.883333 NaN 10.303450 1.791171 +5.166667 NaN 9.545955 2.082633 + +2024-05-27 14:34:18,047 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.4033438795628927 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.029721219494747646 + +2024-05-27 14:34:18,047 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.029721219494747646 +2024-05-27 14:34:18,049 - physiofit - INFO - Results for ynfK: + optimal +ynfK X_0 0.030436 +ynfK growth_rate 0.539043 +ynfK Glc_q -5.846540 +ynfK Glc_M0 14.563968 +ynfK Ace_q 2.249577 +ynfK Ace_M0 0.151849 +2024-05-27 14:34:18,056 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:19,070 - physiofit - INFO - Running optimization for yniA +2024-05-27 14:34:19,073 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:19,073 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:19,080 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2052 0.000000 0.040824 NaN NaN +2053 0.066667 NaN 15.516693 0.017404 +2054 1.188889 0.075600 NaN NaN +2055 1.716667 NaN 14.579866 0.341600 +2056 2.276944 0.113400 NaN NaN +2057 2.800000 NaN 13.826038 0.794919 +2058 3.128333 0.170856 NaN NaN +2059 3.633333 NaN 12.407887 1.310765 +2060 3.771389 0.223776 NaN NaN +2061 4.266667 NaN 11.539455 1.972289 +2062 4.415556 0.337176 NaN NaN +2063 4.822778 0.421848 NaN NaN +2064 4.883333 NaN 10.179551 2.749133 +Experimental matrix: +[[ 0.040824 nan nan] + [ nan 15.51669261 0.01740354] + [ 0.0756 nan nan] + [ nan 14.57986597 0.34160002] + [ 0.1134 nan nan] + [ nan 13.82603817 0.7949189 ] + [ 0.170856 nan nan] + [ nan 12.40788711 1.31076523] + [ 0.223776 nan nan] + [ nan 11.53945486 1.97228867] + [ 0.337176 nan nan] + [ 0.421848 nan nan] + [ nan 10.179551 2.74913264]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:19,080 - physiofit - INFO - mc : False +2024-05-27 14:34:19,080 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:19,080 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:19,081 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:19,498 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:19,499 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.337312543811716 + x: [ 3.529e-02 5.102e-01 -6.935e+00 1.532e+01 + 3.595e+00 2.656e-04] + nit: 92 + nfev: 8580 + population: [[ 3.544e-02 5.095e-01 ... 3.593e+00 2.769e-03] + [ 3.516e-02 5.111e-01 ... 3.549e+00 4.794e-03] + ... + [ 3.550e-02 5.088e-01 ... 3.602e+00 5.074e-03] + [ 3.542e-02 5.100e-01 ... 3.603e+00 2.179e-03]] + population_energies: [ 2.337e+00 2.393e+00 ... 2.353e+00 2.360e+00] + jac: [ 3.651e-04 -3.740e-03 5.131e-03 -1.081e-02 + -4.716e-05 6.186e-04] +2024-05-27 14:34:19,500 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03529002013754943 +2024-05-27 14:34:19,500 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.510247995570719 +2024-05-27 14:34:19,500 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.93503915373781 +2024-05-27 14:34:19,500 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.318015871581544 +2024-05-27 14:34:19,500 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.594941184458689 +2024-05-27 14:34:19,500 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.0002655840565852232 +2024-05-27 14:34:19,503 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.035290 NaN NaN +0.066667 NaN 15.301419 0.008869 +1.188889 0.064730 NaN NaN +1.716667 NaN 14.645987 0.348627 +2.276944 0.112776 NaN NaN +2.800000 NaN 13.795985 0.789246 +3.128333 0.174134 NaN NaN +3.633333 NaN 12.735284 1.339085 +3.771389 0.241760 NaN NaN +4.266667 NaN 11.567042 1.944671 +4.415556 0.335838 NaN NaN +4.822778 0.413399 NaN NaN +4.883333 NaN 10.002628 2.755622 + +2024-05-27 14:34:19,507 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.337312543811716 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0005398190982821101 + +2024-05-27 14:34:19,507 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0005398190982821101 +2024-05-27 14:34:19,509 - physiofit - INFO - Results for yniA: + optimal +yniA X_0 0.035290 +yniA growth_rate 0.510248 +yniA Glc_q -6.935039 +yniA Glc_M0 15.318016 +yniA Ace_q 3.594941 +yniA Ace_M0 0.000266 +2024-05-27 14:34:19,515 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:20,521 - physiofit - INFO - Running optimization for yoaC +2024-05-27 14:34:20,524 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:20,524 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:20,531 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2065 0.000000 0.036288 NaN NaN +2066 0.283333 NaN 13.874961 0.033154 +2067 1.195000 0.065016 NaN NaN +2068 1.613611 0.081648 NaN NaN +2069 1.916667 NaN 14.136943 0.393264 +2070 2.361389 0.110376 NaN NaN +2071 2.700000 NaN 13.362317 0.668538 +2072 3.286389 0.207144 NaN NaN +2073 3.616667 NaN 12.399424 1.101841 +2074 3.819444 0.294840 NaN NaN +2075 4.050000 NaN 11.782524 1.397485 +2076 4.410833 0.415800 NaN NaN +2077 4.750000 NaN 10.396622 1.974717 +Experimental matrix: +[[ 0.036288 nan nan] + [ nan 13.87496052 0.03315367] + [ 0.065016 nan nan] + [ 0.081648 nan nan] + [ nan 14.13694311 0.39326417] + [ 0.110376 nan nan] + [ nan 13.36231725 0.66853828] + [ 0.207144 nan nan] + [ nan 12.39942397 1.10184097] + [ 0.29484 nan nan] + [ nan 11.78252383 1.39748464] + [ 0.4158 nan nan] + [ nan 10.3966221 1.97471716]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:20,532 - physiofit - INFO - mc : False +2024-05-27 14:34:20,532 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:20,532 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:20,533 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:20,907 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:20,909 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.6029481246877664 + x: [ 2.966e-02 5.980e-01 -4.811e+00 1.427e+01 + 2.411e+00 1.222e-01] + nit: 78 + nfev: 7691 + population: [[ 2.956e-02 5.986e-01 ... 2.417e+00 1.215e-01] + [ 2.960e-02 5.978e-01 ... 2.430e+00 1.184e-01] + ... + [ 2.946e-02 5.991e-01 ... 2.425e+00 1.168e-01] + [ 2.920e-02 6.019e-01 ... 2.433e+00 1.198e-01]] + population_energies: [ 2.603e+00 2.623e+00 ... 2.610e+00 2.613e+00] + jac: [ 8.879e-02 -3.306e-02 -5.028e-04 1.549e-03 + 2.020e-03 1.283e-02] +2024-05-27 14:34:20,909 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.029658985653709294 +2024-05-27 14:34:20,910 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.597977653678712 +2024-05-27 14:34:20,910 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.810799459213429 +2024-05-27 14:34:20,910 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.267031859803494 +2024-05-27 14:34:20,910 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4111928418840294 +2024-05-27 14:34:20,910 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.12216960685878196 +2024-05-27 14:34:20,918 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.029659 NaN NaN +0.283333 NaN 14.222978 0.144249 +1.195000 0.060603 NaN NaN +1.613611 0.077841 NaN NaN +1.916667 NaN 13.754981 0.378812 +2.361389 0.121732 NaN NaN +2.700000 NaN 13.306490 0.603597 +3.286389 0.211654 NaN NaN +3.616667 NaN 12.431057 1.042368 +3.819444 0.291112 NaN NaN +4.050000 NaN 11.817408 1.349932 +4.410833 0.414613 NaN NaN +4.750000 NaN 10.420041 2.050298 + +2024-05-27 14:34:20,924 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.6029481246877664 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0009709368094362917 + +2024-05-27 14:34:20,924 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0009709368094362917 +2024-05-27 14:34:20,929 - physiofit - INFO - Results for yoaC: + optimal +yoaC X_0 0.029659 +yoaC growth_rate 0.597978 +yoaC Glc_q -4.810799 +yoaC Glc_M0 14.267032 +yoaC Ace_q 2.411193 +yoaC Ace_M0 0.122170 +2024-05-27 14:34:20,939 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:21,939 - physiofit - INFO - Running optimization for yodD +2024-05-27 14:34:21,942 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:21,943 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:21,946 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2078 0.000000 0.037800 NaN NaN +2079 0.283333 NaN 14.193421 0.042032 +2080 1.195000 0.069552 NaN NaN +2081 1.613611 0.086184 NaN NaN +2082 1.916667 NaN 14.259336 0.413806 +2083 2.361389 0.128520 NaN NaN +2084 2.700000 NaN 13.750626 0.646448 +2085 3.286389 0.210168 NaN NaN +2086 3.616667 NaN 12.699731 1.097621 +2087 3.819444 0.297864 NaN NaN +2088 4.050000 NaN 11.861320 1.365395 +2089 4.410833 0.400680 NaN NaN +2090 4.750000 NaN 10.482672 1.248239 +Experimental matrix: +[[ 0.0378 nan nan] + [ nan 14.19342051 0.04203187] + [ 0.069552 nan nan] + [ 0.086184 nan nan] + [ nan 14.25933584 0.41380617] + [ 0.12852 nan nan] + [ nan 13.75062591 0.6464484 ] + [ 0.210168 nan nan] + [ nan 12.69973106 1.09762073] + [ 0.297864 nan nan] + [ nan 11.86132016 1.36539492] + [ 0.40068 nan nan] + [ nan 10.48267234 1.24823894]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:21,947 - physiofit - INFO - mc : False +2024-05-27 14:34:21,947 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:21,947 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:21,947 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:22,410 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:22,411 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 7.884377581624365 + x: [ 3.632e-02 5.445e-01 -4.972e+00 1.464e+01 + 1.583e+00 2.415e-01] + nit: 90 + nfev: 8638 + population: [[ 3.631e-02 5.447e-01 ... 1.600e+00 2.326e-01] + [ 3.566e-02 5.498e-01 ... 1.589e+00 2.358e-01] + ... + [ 3.736e-02 5.388e-01 ... 1.603e+00 2.176e-01] + [ 3.594e-02 5.472e-01 ... 1.595e+00 2.340e-01]] + population_energies: [ 7.884e+00 7.913e+00 ... 7.971e+00 7.917e+00] + jac: [-1.245e-03 -1.904e-04 -4.405e-05 -1.089e-04 + -1.954e-04 -1.830e-04] +2024-05-27 14:34:22,411 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03631516568209004 +2024-05-27 14:34:22,411 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5444891252444495 +2024-05-27 14:34:22,411 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.972226713250939 +2024-05-27 14:34:22,412 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.636225205798052 +2024-05-27 14:34:22,412 - physiofit.physiofit.base.fitter - INFO - Ace_q = 1.5825631575391272 +2024-05-27 14:34:22,412 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.24153831900253042 +2024-05-27 14:34:22,416 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.036315 NaN NaN +0.283333 NaN 14.580907 0.259145 +1.195000 0.069609 NaN NaN +1.613611 0.087429 NaN NaN +1.916667 NaN 14.026220 0.435691 +2.361389 0.131366 NaN NaN +2.700000 NaN 13.525355 0.595107 +3.286389 0.217378 NaN NaN +3.616667 NaN 12.591680 0.892277 +3.819444 0.290581 NaN NaN +4.050000 NaN 11.959368 1.093530 +4.410833 0.400970 NaN NaN +4.750000 NaN 10.563564 1.537787 + +2024-05-27 14:34:22,420 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 7.884377581624365 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.14894962230924533 + +2024-05-27 14:34:22,420 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.14894962230924533 +2024-05-27 14:34:22,423 - physiofit - INFO - Results for yodD: + optimal +yodD X_0 0.036315 +yodD growth_rate 0.544489 +yodD Glc_q -4.972227 +yodD Glc_M0 14.636225 +yodD Ace_q 1.582563 +yodD Ace_M0 0.241538 +2024-05-27 14:34:22,428 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:24,099 - physiofit - INFO - Running optimization for yohn +2024-05-27 14:34:24,102 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:24,102 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:24,106 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2091 0.000000 0.037800 NaN NaN +2092 0.283333 NaN 14.236589 0.042827 +2093 1.195000 0.066528 NaN NaN +2094 1.613611 0.084672 NaN NaN +2095 1.916667 NaN 13.966206 0.418748 +2096 2.361389 0.131544 NaN NaN +2097 2.700000 NaN 13.134949 0.706959 +2098 3.286389 0.222264 NaN NaN +2099 3.616667 NaN 12.355082 1.058084 +2100 3.819444 0.319032 NaN NaN +2101 4.050000 NaN 11.781847 1.568023 +2102 4.410833 0.473256 NaN NaN +2103 4.750000 NaN 9.943044 2.178943 +Experimental matrix: +[[ 0.0378 nan nan] + [ nan 14.23658884 0.04282678] + [ 0.066528 nan nan] + [ 0.084672 nan nan] + [ nan 13.96620647 0.41874783] + [ 0.131544 nan nan] + [ nan 13.1349493 0.70695857] + [ 0.222264 nan nan] + [ nan 12.35508221 1.05808405] + [ 0.319032 nan nan] + [ nan 11.78184726 1.56802288] + [ 0.473256 nan nan] + [ nan 9.94304422 2.17894317]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:24,106 - physiofit - INFO - mc : False +2024-05-27 14:34:24,106 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:24,106 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:24,107 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:24,603 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:24,604 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.9380191016233774 + x: [ 3.010e-02 6.216e-01 -4.926e+00 1.435e+01 + 2.419e+00 1.199e-01] + nit: 95 + nfev: 9312 + population: [[ 3.022e-02 6.206e-01 ... 2.412e+00 1.236e-01] + [ 2.984e-02 6.245e-01 ... 2.424e+00 1.129e-01] + ... + [ 3.042e-02 6.192e-01 ... 2.449e+00 1.087e-01] + [ 3.049e-02 6.184e-01 ... 2.442e+00 1.052e-01]] + population_energies: [ 1.938e+00 1.958e+00 ... 1.975e+00 1.965e+00] + jac: [-8.066e-03 -1.118e-03 2.021e-05 4.707e-06 + -2.618e-05 1.177e-05] +2024-05-27 14:34:24,604 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.030099686799184525 +2024-05-27 14:34:24,604 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.621611962995518 +2024-05-27 14:34:24,605 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.926098200369518 +2024-05-27 14:34:24,605 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.353282321418376 +2024-05-27 14:34:24,605 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.418543401328584 +2024-05-27 14:34:24,605 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.11988079760370345 +2024-05-27 14:34:24,610 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.030100 NaN NaN +0.283333 NaN 14.307345 0.142435 +1.195000 0.063266 NaN NaN +1.613611 0.082069 NaN NaN +1.916667 NaN 13.806625 0.388271 +2.361389 0.130632 NaN NaN +2.700000 NaN 13.314067 0.630100 +3.286389 0.232148 NaN NaN +3.616667 NaN 12.332843 1.111846 +3.819444 0.323347 NaN NaN +4.050000 NaN 11.634521 1.454699 +4.410833 0.467006 NaN NaN +4.750000 NaN 10.022318 2.246234 + +2024-05-27 14:34:24,615 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.9380191016233774 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.00018931761322745893 + +2024-05-27 14:34:24,615 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.00018931761322745893 +2024-05-27 14:34:24,619 - physiofit - INFO - Results for yohn: + optimal +yohn X_0 0.030100 +yohn growth_rate 0.621612 +yohn Glc_q -4.926098 +yohn Glc_M0 14.353282 +yohn Ace_q 2.418543 +yohn Ace_M0 0.119881 +2024-05-27 14:34:24,626 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:26,380 - physiofit - INFO - Running optimization for ypeB +2024-05-27 14:34:26,384 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:26,384 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:26,389 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2104 0.000000 0.033264 NaN NaN +2105 0.283333 NaN 14.558985 0.034691 +2106 1.195000 0.057456 NaN NaN +2107 1.613611 0.069552 NaN NaN +2108 1.916667 NaN 13.431224 0.294081 +2109 2.361389 0.102816 NaN NaN +2110 2.700000 NaN 13.763966 0.525257 +2111 3.286389 0.179928 NaN NaN +2112 3.616667 NaN 13.113616 0.888375 +2113 3.819444 0.214704 NaN NaN +2114 4.050000 NaN 11.959472 0.978533 +2115 4.410833 0.343224 NaN NaN +2116 4.750000 NaN 10.889205 1.394808 +Experimental matrix: +[[ 0.033264 nan nan] + [ nan 14.55898457 0.03469125] + [ 0.057456 nan nan] + [ 0.069552 nan nan] + [ nan 13.43122416 0.29408057] + [ 0.102816 nan nan] + [ nan 13.76396618 0.52525681] + [ 0.179928 nan nan] + [ nan 13.11361557 0.88837476] + [ 0.214704 nan nan] + [ nan 11.95947208 0.97853252] + [ 0.343224 nan nan] + [ nan 10.88920542 1.39480759]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:26,390 - physiofit - INFO - mc : False +2024-05-27 14:34:26,390 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:26,390 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:26,391 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:26,844 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:26,845 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.119285677689284 + x: [ 2.723e-02 5.664e-01 -5.328e+00 1.445e+01 + 2.043e+00 1.106e-01] + nit: 84 + nfev: 8140 + population: [[ 2.730e-02 5.654e-01 ... 2.056e+00 1.029e-01] + [ 2.666e-02 5.706e-01 ... 2.077e+00 1.050e-01] + ... + [ 2.727e-02 5.657e-01 ... 2.067e+00 1.017e-01] + [ 2.731e-02 5.669e-01 ... 2.027e+00 1.054e-01]] + population_energies: [ 5.119e+00 5.142e+00 ... 5.148e+00 5.168e+00] + jac: [ 1.278e-03 2.589e-04 6.126e-03 -1.380e-03 + -6.448e-04 -3.118e-05] +2024-05-27 14:34:26,845 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.027225195673767886 +2024-05-27 14:34:26,845 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5664020235392395 +2024-05-27 14:34:26,845 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.327982278544968 +2024-05-27 14:34:26,845 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.453372781487435 +2024-05-27 14:34:26,845 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.0428476465256096 +2024-05-27 14:34:26,845 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.11057904078857109 +2024-05-27 14:34:26,849 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.027225 NaN NaN +0.283333 NaN 14.408792 0.127672 +1.195000 0.053570 NaN NaN +1.613611 0.067904 NaN NaN +1.916667 NaN 13.951103 0.303159 +2.361389 0.103714 NaN NaN +2.700000 NaN 13.527604 0.465536 +3.286389 0.175136 NaN NaN +3.616667 NaN 12.723123 0.773989 +3.819444 0.236863 NaN NaN +4.050000 NaN 12.170551 0.985856 +4.410833 0.331109 NaN NaN +4.750000 NaN 10.935150 1.459531 + +2024-05-27 14:34:26,853 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.119285677689284 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.027527556525354817 + +2024-05-27 14:34:26,853 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.027527556525354817 +2024-05-27 14:34:26,855 - physiofit - INFO - Results for ypeB: + optimal +ypeB X_0 0.027225 +ypeB growth_rate 0.566402 +ypeB Glc_q -5.327982 +ypeB Glc_M0 14.453373 +ypeB Ace_q 2.042848 +ypeB Ace_M0 0.110579 +2024-05-27 14:34:26,862 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:27,896 - physiofit - INFO - Running optimization for ypfJ +2024-05-27 14:34:27,899 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:27,899 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:27,903 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2117 0.000000 0.033264 NaN NaN +2118 0.283333 NaN 14.346660 0.038666 +2119 1.195000 0.057456 NaN NaN +2120 1.613611 0.074088 NaN NaN +2121 1.916667 NaN 13.720606 0.419735 +2122 2.361389 0.114912 NaN NaN +2123 2.700000 NaN 13.415603 0.714171 +2124 3.286389 0.192024 NaN NaN +2125 3.616667 NaN 12.787917 1.262095 +2126 3.819444 0.264600 NaN NaN +2127 4.050000 NaN 11.839731 1.536625 +2128 4.410833 0.388584 NaN NaN +2129 4.750000 NaN 10.465023 2.131834 +Experimental matrix: +[[ 0.033264 nan nan] + [ nan 14.34665972 0.03866577] + [ 0.057456 nan nan] + [ 0.074088 nan nan] + [ nan 13.72060634 0.4197354 ] + [ 0.114912 nan nan] + [ nan 13.41560292 0.71417091] + [ 0.192024 nan nan] + [ nan 12.78791714 1.26209464] + [ 0.2646 nan nan] + [ nan 11.83973127 1.53662486] + [ 0.388584 nan nan] + [ nan 10.46502258 2.13183434]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:27,903 - physiofit - INFO - mc : False +2024-05-27 14:34:27,903 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:27,903 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:27,904 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:28,363 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:28,364 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.8561166945420906 + x: [ 2.868e-02 5.872e-01 -5.177e+00 1.439e+01 + 2.821e+00 1.320e-01] + nit: 91 + nfev: 8609 + population: [[ 2.877e-02 5.863e-01 ... 2.833e+00 1.282e-01] + [ 2.883e-02 5.858e-01 ... 2.814e+00 1.282e-01] + ... + [ 2.909e-02 5.838e-01 ... 2.828e+00 1.221e-01] + [ 2.889e-02 5.865e-01 ... 2.786e+00 1.409e-01]] + population_energies: [ 1.856e+00 1.886e+00 ... 1.870e+00 1.892e+00] + jac: [-9.395e-03 -2.395e-03 -6.173e-06 -1.449e-04 + 3.406e-04 5.692e-04] +2024-05-27 14:34:28,366 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.028677475952552378 +2024-05-27 14:34:28,366 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5871693239603039 +2024-05-27 14:34:28,366 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.177153255649895 +2024-05-27 14:34:28,366 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.387337873359284 +2024-05-27 14:34:28,366 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.8207348119511306 +2024-05-27 14:34:28,366 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1319559227345339 +2024-05-27 14:34:28,369 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028677 NaN NaN +0.283333 NaN 14.341571 0.156892 +1.195000 0.057846 NaN NaN +1.613611 0.073964 NaN NaN +1.916667 NaN 13.861030 0.418711 +2.361389 0.114738 NaN NaN +2.700000 NaN 13.406006 0.666628 +3.286389 0.197508 NaN NaN +3.616667 NaN 12.526048 1.146067 +3.819444 0.270095 NaN NaN +4.050000 NaN 11.913497 1.479810 +4.410833 0.382228 NaN NaN +4.750000 NaN 10.527373 2.235030 + +2024-05-27 14:34:28,373 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.8561166945420906 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0001480691377215093 + +2024-05-27 14:34:28,373 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0001480691377215093 +2024-05-27 14:34:28,375 - physiofit - INFO - Results for ypfJ: + optimal +ypfJ X_0 0.028677 +ypfJ growth_rate 0.587169 +ypfJ Glc_q -5.177153 +ypfJ Glc_M0 14.387338 +ypfJ Ace_q 2.820735 +ypfJ Ace_M0 0.131956 +2024-05-27 14:34:28,382 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:29,365 - physiofit - INFO - Running optimization for yqcA +2024-05-27 14:34:29,367 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:29,367 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:29,371 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2130 1.950000 NaN 13.520349 0.341064 +2131 2.501389 0.095256 NaN NaN +2132 3.250000 NaN 13.342925 0.900929 +2133 3.341944 0.151200 NaN NaN +2134 3.997500 0.213192 NaN NaN +2135 4.083333 NaN 11.691354 1.242352 +2136 4.523333 0.320544 NaN NaN +2137 4.766667 NaN 11.152460 1.592004 +Experimental matrix: +[[ nan 13.52034858 0.34106388] + [ 0.095256 nan nan] + [ nan 13.34292508 0.9009288 ] + [ 0.1512 nan nan] + [ 0.213192 nan nan] + [ nan 11.69135414 1.24235222] + [ 0.320544 nan nan] + [ nan 11.15245979 1.59200448]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:29,371 - physiofit - INFO - mc : False +2024-05-27 14:34:29,371 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:29,371 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:29,372 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:29,877 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:29,878 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.3896918124408635 + x: [ 1.955e-02 6.126e-01 -5.396e+00 1.404e+01 + 2.481e+00 2.795e-01] + nit: 97 + nfev: 9254 + population: [[ 1.956e-02 6.129e-01 ... 2.427e+00 2.978e-01] + [ 1.971e-02 6.122e-01 ... 2.383e+00 3.259e-01] + ... + [ 1.928e-02 6.161e-01 ... 2.516e+00 2.856e-01] + [ 1.956e-02 6.109e-01 ... 2.470e+00 2.970e-01]] + population_energies: [ 3.390e+00 3.551e+00 ... 3.431e+00 3.433e+00] + jac: [ 3.607e-01 2.629e-02 1.139e-03 3.088e-03 + 1.247e-03 4.475e-03] +2024-05-27 14:34:29,879 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.019548025611714013 +2024-05-27 14:34:29,879 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6126292732142394 +2024-05-27 14:34:29,879 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.3963279468966485 +2024-05-27 14:34:29,879 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.035613770990283 +2024-05-27 14:34:29,879 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.4808126123763663 +2024-05-27 14:34:29,879 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.27952668293052757 +2024-05-27 14:34:29,883 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.639180 0.461776 +2.501389 0.090495 NaN NaN +3.250000 NaN 12.946836 0.780062 +3.341944 0.151449 NaN NaN +3.997500 0.226300 NaN NaN +4.083333 NaN 12.106825 1.166234 +4.523333 0.312311 NaN NaN +4.766667 NaN 11.014573 1.668367 + +2024-05-27 14:34:29,887 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.3896918124408635 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.24141684975303204 + +2024-05-27 14:34:29,887 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.24141684975303204 +2024-05-27 14:34:29,890 - physiofit - INFO - Results for yqcA: + optimal +yqcA X_0 0.019548 +yqcA growth_rate 0.612629 +yqcA Glc_q -5.396328 +yqcA Glc_M0 14.035614 +yqcA Ace_q 2.480813 +yqcA Ace_M0 0.279527 +2024-05-27 14:34:29,896 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:30,935 - physiofit - INFO - Running optimization for yqcC +2024-05-27 14:34:30,938 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:30,938 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:30,943 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2138 1.950000 NaN 13.562034 0.386830 +2139 2.501389 0.084672 NaN NaN +2140 3.250000 NaN 12.868561 0.953123 +2141 3.341944 0.134568 NaN NaN +2142 3.997500 0.175392 NaN NaN +2143 4.083333 NaN 11.941612 1.528816 +2144 4.523333 0.244944 NaN NaN +2145 4.766667 NaN 10.510725 2.161997 +Experimental matrix: +[[ nan 13.56203353 0.38683038] + [ 0.084672 nan nan] + [ nan 12.86856117 0.9531231 ] + [ 0.134568 nan nan] + [ 0.175392 nan nan] + [ nan 11.94161189 1.52881635] + [ 0.244944 nan nan] + [ nan 10.51072467 2.16199722]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:30,943 - physiofit - INFO - mc : False +2024-05-27 14:34:30,944 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:30,944 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:30,945 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:31,608 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:31,609 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.5444220124546165 + x: [ 2.260e-02 5.238e-01 -7.552e+00 1.425e+01 + 4.382e+00 8.075e-02] + nit: 114 + nfev: 10609 + population: [[ 2.241e-02 5.257e-01 ... 4.381e+00 8.450e-02] + [ 2.266e-02 5.236e-01 ... 4.384e+00 7.909e-02] + ... + [ 2.238e-02 5.257e-01 ... 4.377e+00 8.355e-02] + [ 2.275e-02 5.221e-01 ... 4.389e+00 7.477e-02]] + population_energies: [ 5.444e-01 5.474e-01 ... 5.498e-01 5.480e-01] + jac: [ 3.236e-03 -1.199e-05 8.927e-03 1.615e-03 + -9.056e-03 2.634e-03] +2024-05-27 14:34:31,609 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02260039355552099 +2024-05-27 14:34:31,609 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5238144708096837 +2024-05-27 14:34:31,609 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.551729923935991 +2024-05-27 14:34:31,609 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.248925366355172 +2024-05-27 14:34:31,609 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.3823271605282486 +2024-05-27 14:34:31,609 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.08075392143803839 +2024-05-27 14:34:31,613 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.669873 0.416782 +2.501389 0.083783 NaN NaN +3.250000 NaN 12.786919 0.929167 +3.341944 0.130129 NaN NaN +3.997500 0.183445 NaN NaN +4.083333 NaN 11.808437 1.496988 +4.523333 0.241617 NaN NaN +4.766667 NaN 10.617872 2.187882 + +2024-05-27 14:34:31,617 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.5444220124546165 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.002744817739583134 + +2024-05-27 14:34:31,618 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.002744817739583134 +2024-05-27 14:34:31,621 - physiofit - INFO - Results for yqcC: + optimal +yqcC X_0 0.022600 +yqcC growth_rate 0.523814 +yqcC Glc_q -7.551730 +yqcC Glc_M0 14.248925 +yqcC Ace_q 4.382327 +yqcC Ace_M0 0.080754 +2024-05-27 14:34:31,626 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:32,620 - physiofit - INFO - Running optimization for yqfE +2024-05-27 14:34:32,623 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:32,623 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:32,627 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2146 0.000000 0.034776 NaN NaN +2147 0.283333 NaN 14.636130 0.047032 +2148 1.195000 0.058968 NaN NaN +2149 1.613611 0.074088 NaN NaN +2150 1.916667 NaN 13.569237 0.425007 +2151 2.361389 0.114912 NaN NaN +2152 2.700000 NaN 13.227721 0.809677 +2153 3.286389 0.199584 NaN NaN +2154 3.616667 NaN 12.699979 1.537102 +2155 3.819444 0.300888 NaN NaN +2156 4.050000 NaN 11.636449 1.756423 +2157 4.410833 0.421848 NaN NaN +2158 4.750000 NaN 9.976513 2.469183 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.63612977 0.04703187] + [ 0.058968 nan nan] + [ 0.074088 nan nan] + [ nan 13.56923653 0.42500663] + [ 0.114912 nan nan] + [ nan 13.22772065 0.80967688] + [ 0.199584 nan nan] + [ nan 12.69997937 1.5371016 ] + [ 0.300888 nan nan] + [ nan 11.63644925 1.75642329] + [ 0.421848 nan nan] + [ nan 9.97651302 2.46918316]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:32,627 - physiofit - INFO - mc : False +2024-05-27 14:34:32,627 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:32,627 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:32,628 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:33,127 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:33,128 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.449696275472533 + x: [ 2.887e-02 6.066e-01 -5.521e+00 1.446e+01 + 3.066e+00 1.525e-01] + nit: 95 + nfev: 9018 + population: [[ 2.876e-02 6.070e-01 ... 3.061e+00 1.582e-01] + [ 2.865e-02 6.093e-01 ... 3.048e+00 1.597e-01] + ... + [ 2.932e-02 6.029e-01 ... 3.079e+00 1.565e-01] + [ 2.855e-02 6.089e-01 ... 3.071e+00 1.483e-01]] + population_energies: [ 4.450e+00 4.473e+00 ... 4.519e+00 4.474e+00] + jac: [-1.695e-01 -1.702e-02 -1.912e-02 4.615e-03 + 1.025e-02 -4.217e-03] +2024-05-27 14:34:33,128 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02886977107951087 +2024-05-27 14:34:33,128 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.6065994241382029 +2024-05-27 14:34:33,128 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.521187838533048 +2024-05-27 14:34:33,129 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.464000888219337 +2024-05-27 14:34:33,129 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.0659845573152533 +2024-05-27 14:34:33,129 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1525139704327093 +2024-05-27 14:34:33,133 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028870 NaN NaN +0.283333 NaN 14.414726 0.179877 +1.195000 0.059602 NaN NaN +1.613611 0.076831 NaN NaN +1.916667 NaN 13.886331 0.473301 +2.361389 0.120930 NaN NaN +2.700000 NaN 13.375104 0.757192 +3.286389 0.211943 NaN NaN +3.616667 NaN 12.369775 1.315464 +3.819444 0.292852 NaN NaN +4.050000 NaN 11.661158 1.708968 +4.410833 0.419223 NaN NaN +4.750000 NaN 10.039423 2.609537 + +2024-05-27 14:34:33,138 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.449696275472533 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.014599886539599918 + +2024-05-27 14:34:33,139 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.014599886539599918 +2024-05-27 14:34:33,141 - physiofit - INFO - Results for yqfE: + optimal +yqfE X_0 0.028870 +yqfE growth_rate 0.606599 +yqfE Glc_q -5.521188 +yqfE Glc_M0 14.464001 +yqfE Ace_q 3.065985 +yqfE Ace_M0 0.152514 +2024-05-27 14:34:33,147 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:34,159 - physiofit - INFO - Running optimization for yqiC +2024-05-27 14:34:34,162 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:34,162 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:34,166 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2159 0.050000 NaN 14.672400 0.022885 +2160 1.950000 NaN 14.461743 0.526140 +2161 2.833333 NaN 13.516563 0.921823 +2162 2.876944 0.163296 NaN NaN +2163 3.678056 0.254016 NaN NaN +2164 3.983333 NaN 11.722135 1.821637 +2165 4.092222 0.332640 NaN NaN +2166 4.565000 0.436968 NaN NaN +2167 4.883333 NaN 9.443924 2.840432 +2168 5.166667 NaN 8.559710 3.334679 +Experimental matrix: +[[ nan 14.67240024 0.02288523] + [ nan 14.46174262 0.52613976] + [ nan 13.51656323 0.921823 ] + [ 0.163296 nan nan] + [ 0.254016 nan nan] + [ nan 11.72213463 1.82163698] + [ 0.33264 nan nan] + [ 0.436968 nan nan] + [ nan 9.44392442 2.84043237] + [ nan 8.55970968 3.33467868]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:34,166 - physiofit - INFO - mc : False +2024-05-27 14:34:34,166 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:34,166 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:34,167 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:34,597 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:34,598 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.778554069874294 + x: [ 3.230e-02 5.685e-01 -6.311e+00 1.491e+01 + 3.196e+00 1.369e-01] + nit: 88 + nfev: 8486 + population: [[ 3.203e-02 5.705e-01 ... 3.197e+00 1.421e-01] + [ 3.210e-02 5.695e-01 ... 3.164e+00 1.610e-01] + ... + [ 3.252e-02 5.664e-01 ... 3.209e+00 1.222e-01] + [ 3.260e-02 5.660e-01 ... 3.199e+00 1.396e-01]] + population_energies: [ 1.779e+00 1.840e+00 ... 1.808e+00 1.798e+00] + jac: [ 4.623e-03 5.340e-04 1.126e-05 4.479e-05 + 6.395e-05 1.837e-04] +2024-05-27 14:34:34,598 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03230350603090675 +2024-05-27 14:34:34,599 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5685203119715653 +2024-05-27 14:34:34,599 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.31112645272294 +2024-05-27 14:34:34,600 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.908725234530895 +2024-05-27 14:34:34,600 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.195532601839127 +2024-05-27 14:34:34,600 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.13691991418238564 +2024-05-27 14:34:34,609 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.898385 0.142155 +1.950000 NaN 14.180710 0.505538 +2.833333 NaN 13.471867 0.864449 +2.876944 0.165799 NaN NaN +3.678056 0.261445 NaN NaN +3.983333 NaN 11.814963 1.703394 +4.092222 0.330857 NaN NaN +4.565000 0.432885 NaN NaN +4.883333 NaN 9.508537 2.871214 +5.166667 NaN 8.502017 3.380849 + +2024-05-27 14:34:34,614 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.778554069874294 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.0022271262691832393 + +2024-05-27 14:34:34,614 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0022271262691832393 +2024-05-27 14:34:34,617 - physiofit - INFO - Results for yqiC: + optimal +yqiC X_0 0.032304 +yqiC growth_rate 0.568520 +yqiC Glc_q -6.311126 +yqiC Glc_M0 14.908725 +yqiC Ace_q 3.195533 +yqiC Ace_M0 0.136920 +2024-05-27 14:34:34,623 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:35,657 - physiofit - INFO - Running optimization for yrbA +2024-05-27 14:34:35,659 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:35,659 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:35,663 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2169 0.050000 NaN 14.684286 0.010807 +2170 1.950000 NaN 14.654341 0.406953 +2171 2.833333 NaN 13.284970 0.667513 +2172 2.876944 0.148176 NaN NaN +2173 3.678056 0.229824 NaN NaN +2174 3.983333 NaN 12.102200 1.347098 +2175 4.092222 0.305424 NaN NaN +2176 4.565000 0.394632 NaN NaN +2177 4.883333 NaN 9.484994 1.866623 +2178 5.166667 NaN 9.280080 1.502243 +Experimental matrix: +[[ nan 1.46842862e+01 1.08073230e-02] + [ nan 1.46543409e+01 4.06952688e-01] + [ nan 1.32849704e+01 6.67512726e-01] + [1.48176000e-01 nan nan] + [2.29824000e-01 nan nan] + [ nan 1.21021998e+01 1.34709849e+00] + [3.05424000e-01 nan nan] + [3.94632000e-01 nan nan] + [ nan 9.48499352e+00 1.86662275e+00] + [ nan 9.28007965e+00 1.50224268e+00]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:35,664 - physiofit - INFO - mc : False +2024-05-27 14:34:35,664 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:35,664 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:35,664 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:36,032 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:36,034 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 11.779581052204984 + x: [ 3.261e-02 5.428e-01 -6.358e+00 1.492e+01 + 1.766e+00 2.251e-01] + nit: 78 + nfev: 7397 + population: [[ 3.303e-02 5.396e-01 ... 1.790e+00 2.138e-01] + [ 3.300e-02 5.414e-01 ... 1.753e+00 2.113e-01] + ... + [ 3.344e-02 5.375e-01 ... 1.692e+00 2.529e-01] + [ 3.371e-02 5.334e-01 ... 1.808e+00 2.308e-01]] + population_energies: [ 1.178e+01 1.183e+01 ... 1.195e+01 1.196e+01] + jac: [ 4.536e-02 1.180e-02 -5.988e-02 -1.279e-02 + 2.603e-02 -3.076e-03] +2024-05-27 14:34:36,034 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03261455526548245 +2024-05-27 14:34:36,034 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.542849682362135 +2024-05-27 14:34:36,034 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.357732058674002 +2024-05-27 14:34:36,034 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.918660457085293 +2024-05-27 14:34:36,034 - physiofit.physiofit.base.fitter - INFO - Ace_q = 1.7660001630416453 +2024-05-27 14:34:36,034 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.22509797773725604 +2024-05-27 14:34:36,037 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.908151 0.228017 +1.950000 NaN 14.199705 0.424804 +2.833333 NaN 13.522309 0.612965 +2.876944 0.155478 NaN NaN +3.678056 0.240180 NaN NaN +3.983333 NaN 11.980687 1.041185 +4.092222 0.300732 NaN NaN +4.565000 0.388723 NaN NaN +4.883333 NaN 9.889202 1.622141 +5.166667 NaN 8.989463 1.872063 + +2024-05-27 14:34:36,041 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 11.779581052204984 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.699920801057198 + +2024-05-27 14:34:36,041 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.699920801057198 +2024-05-27 14:34:36,043 - physiofit - INFO - Results for yrbA: + optimal +yrbA X_0 0.032615 +yrbA growth_rate 0.542850 +yrbA Glc_q -6.357732 +yrbA Glc_M0 14.918660 +yrbA Ace_q 1.766000 +yrbA Ace_M0 0.225098 +2024-05-27 14:34:36,048 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:37,083 - physiofit - INFO - Running optimization for yrbL +2024-05-27 14:34:37,086 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:37,086 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:37,090 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2179 1.950000 NaN 13.265400 0.380557 +2180 2.501389 0.113400 NaN NaN +2181 3.250000 NaN 12.594536 0.906498 +2182 3.341944 0.170856 NaN NaN +2183 3.997500 0.223776 NaN NaN +2184 4.083333 NaN 11.276817 1.360326 +2185 4.523333 0.337176 NaN NaN +2186 4.766667 NaN 10.197052 1.942890 +Experimental matrix: +[[ nan 13.26540035 0.38055736] + [ 0.1134 nan nan] + [ nan 12.5945356 0.90649848] + [ 0.170856 nan nan] + [ 0.223776 nan nan] + [ nan 11.2768169 1.36032588] + [ 0.337176 nan nan] + [ nan 10.19705216 1.94288963]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:37,091 - physiofit - INFO - mc : False +2024-05-27 14:34:37,091 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:37,091 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:37,092 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:37,532 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:37,535 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.784579663990094 + x: [ 2.593e-02 5.600e-01 -5.979e+00 1.387e+01 + 2.909e+00 1.566e-01] + nit: 96 + nfev: 8940 + population: [[ 2.586e-02 5.604e-01 ... 2.917e+00 1.601e-01] + [ 2.481e-02 5.701e-01 ... 2.913e+00 1.702e-01] + ... + [ 2.535e-02 5.661e-01 ... 2.913e+00 1.668e-01] + [ 2.599e-02 5.592e-01 ... 2.893e+00 1.616e-01]] + population_energies: [ 1.785e+00 1.818e+00 ... 1.799e+00 1.816e+00] + jac: [-9.518e-03 3.682e-03 -3.981e-03 1.391e-02 + 9.198e-03 -1.351e-02] +2024-05-27 14:34:37,535 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02592678622104198 +2024-05-27 14:34:37,536 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.560027863124413 +2024-05-27 14:34:37,536 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.978968392005037 +2024-05-27 14:34:37,536 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 13.870251558770196 +2024-05-27 14:34:37,537 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.9091591471506835 +2024-05-27 14:34:37,537 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.15664277374646998 +2024-05-27 14:34:37,544 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.322080 0.423364 +2.501389 0.105227 NaN NaN +3.250000 NaN 12.438529 0.853269 +3.341944 0.168487 NaN NaN +3.997500 0.243225 NaN NaN +4.083333 NaN 11.422459 1.347654 +4.523333 0.326513 NaN NaN +4.766667 NaN 10.152208 1.965714 + +2024-05-27 14:34:37,550 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.784579663990094 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.06159336665072238 + +2024-05-27 14:34:37,550 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.06159336665072238 +2024-05-27 14:34:37,555 - physiofit - INFO - Results for yrbL: + optimal +yrbL X_0 0.025927 +yrbL growth_rate 0.560028 +yrbL Glc_q -5.978968 +yrbL Glc_M0 13.870252 +yrbL Ace_q 2.909159 +yrbL Ace_M0 0.156643 +2024-05-27 14:34:37,564 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:38,574 - physiofit - INFO - Running optimization for ysgA +2024-05-27 14:34:38,576 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:38,576 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:38,580 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2187 0.000000 0.033264 NaN NaN +2188 0.283333 NaN 14.123446 0.044321 +2189 1.195000 0.058968 NaN NaN +2190 1.613611 0.074088 NaN NaN +2191 1.916667 NaN 13.615670 0.383178 +2192 2.361389 0.116424 NaN NaN +2193 2.700000 NaN 13.486988 0.647959 +2194 3.286389 0.187488 NaN NaN +2195 3.616667 NaN 12.450879 1.075998 +2196 3.819444 0.273672 NaN NaN +2197 4.050000 NaN 11.925689 1.300139 +2198 4.410833 0.394632 NaN NaN +2199 4.750000 NaN 10.879294 1.887774 +Experimental matrix: +[[ 0.033264 nan nan] + [ nan 14.12344592 0.04432099] + [ 0.058968 nan nan] + [ 0.074088 nan nan] + [ nan 13.61566996 0.38317834] + [ 0.116424 nan nan] + [ nan 13.48698796 0.64795887] + [ 0.187488 nan nan] + [ nan 12.45087896 1.07599838] + [ 0.273672 nan nan] + [ nan 11.92568873 1.30013863] + [ 0.394632 nan nan] + [ nan 10.87929448 1.88777362]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:38,580 - physiofit - INFO - mc : False +2024-05-27 14:34:38,580 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:38,580 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:38,581 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:39,072 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:39,073 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.4122929803448494 + x: [ 2.820e-02 5.952e-01 -4.426e+00 1.414e+01 + 2.417e+00 1.276e-01] + nit: 99 + nfev: 9189 + population: [[ 2.817e-02 5.958e-01 ... 2.416e+00 1.275e-01] + [ 2.825e-02 5.955e-01 ... 2.392e+00 1.333e-01] + ... + [ 2.838e-02 5.940e-01 ... 2.404e+00 1.316e-01] + [ 2.815e-02 5.960e-01 ... 2.396e+00 1.384e-01]] + population_energies: [ 1.412e+00 1.437e+00 ... 1.418e+00 1.421e+00] + jac: [-1.510e-02 -1.006e-03 -2.629e-03 -3.666e-03 + -1.796e-02 1.060e-02] +2024-05-27 14:34:39,074 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.028199540501593283 +2024-05-27 14:34:39,074 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5952315884982694 +2024-05-27 14:34:39,074 - physiofit.physiofit.base.fitter - INFO - Glc_q = -4.425843086975331 +2024-05-27 14:34:39,074 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.143116663959855 +2024-05-27 14:34:39,074 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.416507330830935 +2024-05-27 14:34:39,074 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.12761300055300515 +2024-05-27 14:34:39,078 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028200 NaN NaN +0.283333 NaN 14.104598 0.148644 +1.195000 0.057432 NaN NaN +1.613611 0.073683 NaN NaN +1.916667 NaN 13.696617 0.371402 +2.361389 0.114994 NaN NaN +2.700000 NaN 13.306828 0.584226 +3.286389 0.199431 NaN NaN +3.616667 NaN 12.547777 0.998667 +3.819444 0.273899 NaN NaN +4.050000 NaN 12.016645 1.288665 +4.410833 0.389465 NaN NaN +4.750000 NaN 10.809113 1.947976 + +2024-05-27 14:34:39,082 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.4122929803448494 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 3.0298770332291516e-05 + +2024-05-27 14:34:39,083 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 3.0298770332291516e-05 +2024-05-27 14:34:39,085 - physiofit - INFO - Results for ysgA: + optimal +ysgA X_0 0.028200 +ysgA growth_rate 0.595232 +ysgA Glc_q -4.425843 +ysgA Glc_M0 14.143117 +ysgA Ace_q 2.416507 +ysgA Ace_M0 0.127613 +2024-05-27 14:34:39,092 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:40,072 - physiofit - INFO - Running optimization for ytfB +2024-05-27 14:34:40,075 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:40,075 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:40,079 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2200 0.000000 0.034776 NaN NaN +2201 0.283333 NaN 14.369617 0.044806 +2202 1.195000 0.065016 NaN NaN +2203 1.613611 0.075600 NaN NaN +2204 1.916667 NaN 13.951133 0.407115 +2205 2.361389 0.113400 NaN NaN +2206 2.700000 NaN 13.160486 0.677042 +2207 3.286389 0.181440 NaN NaN +2208 3.616667 NaN 12.475923 1.175944 +2209 3.819444 0.285768 NaN NaN +2210 4.050000 NaN 11.719299 1.455462 +2211 4.410833 0.394632 NaN NaN +2212 4.750000 NaN 10.163340 1.981026 +Experimental matrix: +[[ 0.034776 nan nan] + [ nan 14.36961692 0.04480593] + [ 0.065016 nan nan] + [ 0.0756 nan nan] + [ nan 13.95113347 0.40711452] + [ 0.1134 nan nan] + [ nan 13.16048597 0.67704153] + [ 0.18144 nan nan] + [ nan 12.47592318 1.17594406] + [ 0.285768 nan nan] + [ nan 11.71929928 1.45546171] + [ 0.394632 nan nan] + [ nan 10.16334038 1.98102579]] +Time vector: [0. 0.28333333 1.195 1.61361111 1.91666667 2.36138889 + 2.7 3.28638889 3.61666667 3.81944444 4.05 4.41083333 + 4.75 ] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:40,079 - physiofit - INFO - mc : False +2024-05-27 14:34:40,079 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:40,079 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:40,080 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:40,632 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:40,633 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.7986449837570246 + x: [ 2.897e-02 5.903e-01 -5.570e+00 1.442e+01 + 2.557e+00 1.392e-01] + nit: 91 + nfev: 8770 + population: [[ 2.896e-02 5.900e-01 ... 2.571e+00 1.372e-01] + [ 2.883e-02 5.920e-01 ... 2.597e+00 1.268e-01] + ... + [ 2.878e-02 5.920e-01 ... 2.568e+00 1.403e-01] + [ 2.867e-02 5.921e-01 ... 2.576e+00 1.337e-01]] + population_energies: [ 2.799e+00 2.822e+00 ... 2.805e+00 2.832e+00] + jac: [-4.504e-03 -5.262e-04 -1.776e-06 -1.230e-05 + -1.292e-05 -1.155e-06] +2024-05-27 14:34:40,633 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.02896881143493269 +2024-05-27 14:34:40,633 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5903219618284823 +2024-05-27 14:34:40,633 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.5699552625007955 +2024-05-27 14:34:40,634 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.420978284686308 +2024-05-27 14:34:40,634 - physiofit.physiofit.base.fitter - INFO - Ace_q = 2.557342889043702 +2024-05-27 14:34:40,634 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.1391799047196647 +2024-05-27 14:34:40,638 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.028969 NaN NaN +0.283333 NaN 14.371215 0.162028 +1.195000 0.058654 NaN NaN +1.613611 0.075096 NaN NaN +1.916667 NaN 13.846936 0.402741 +2.361389 0.116769 NaN NaN +2.700000 NaN 13.348755 0.631471 +3.286389 0.201592 NaN NaN +3.616667 NaN 12.382720 1.075009 +3.819444 0.276144 NaN NaN +4.050000 NaN 11.708886 1.384388 +4.410833 0.391518 NaN NaN +4.750000 NaN 10.181285 2.085757 + +2024-05-27 14:34:40,643 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.7986449837570246 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.0014317405398003452 + +2024-05-27 14:34:40,643 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0014317405398003452 +2024-05-27 14:34:40,646 - physiofit - INFO - Results for ytfB: + optimal +ytfB X_0 0.028969 +ytfB growth_rate 0.590322 +ytfB Glc_q -5.569955 +ytfB Glc_M0 14.420978 +ytfB Ace_q 2.557343 +ytfB Ace_M0 0.139180 +2024-05-27 14:34:40,653 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:41,782 - physiofit - INFO - Running optimization for ytfJ +2024-05-27 14:34:41,785 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:41,785 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:41,789 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2213 0.050000 NaN 14.270841 0.016648 +2214 1.950000 NaN 14.258037 0.374827 +2215 2.833333 NaN 13.622252 0.678396 +2216 2.876944 0.149688 NaN NaN +2217 3.678056 0.249480 NaN NaN +2218 3.983333 NaN 12.259146 1.206936 +2219 4.092222 0.319032 NaN NaN +2220 4.565000 0.403704 NaN NaN +2221 4.883333 NaN 9.767681 1.425461 +2222 5.166667 NaN 9.289785 1.960331 +Experimental matrix: +[[ nan 14.2708408 0.01664808] + [ nan 14.25803698 0.37482729] + [ nan 13.62225198 0.67839603] + [ 0.149688 nan nan] + [ 0.24948 nan nan] + [ nan 12.25914639 1.20693557] + [ 0.319032 nan nan] + [ 0.403704 nan nan] + [ nan 9.76768106 1.42546091] + [ nan 9.28978451 1.96033051]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:41,790 - physiofit - INFO - mc : False +2024-05-27 14:34:41,790 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:41,790 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:41,790 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:42,242 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:42,243 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.179112711848294 + x: [ 3.022e-02 5.705e-01 -5.709e+00 1.467e+01 + 1.809e+00 1.761e-01] + nit: 82 + nfev: 7939 + population: [[ 3.049e-02 5.683e-01 ... 1.805e+00 1.789e-01] + [ 3.061e-02 5.683e-01 ... 1.818e+00 1.721e-01] + ... + [ 3.002e-02 5.725e-01 ... 1.783e+00 1.932e-01] + [ 3.206e-02 5.563e-01 ... 1.800e+00 1.663e-01]] + population_energies: [ 5.179e+00 5.207e+00 ... 5.275e+00 5.248e+00] + jac: [ 1.048e-02 2.344e-03 1.749e-03 4.449e-03 + -1.975e-03 -7.521e-03] +2024-05-27 14:34:42,243 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.030217081782672645 +2024-05-27 14:34:42,244 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5704897984539448 +2024-05-27 14:34:42,244 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.70946325197308 +2024-05-27 14:34:42,244 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.66813006708966 +2024-05-27 14:34:42,244 - physiofit.physiofit.base.fitter - INFO - Ace_q = 1.80852976541266 +2024-05-27 14:34:42,244 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.17609618842942043 +2024-05-27 14:34:42,248 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.659380 0.178868 +1.950000 NaN 14.050659 0.371686 +2.833333 NaN 13.447934 0.562605 +2.876944 0.155972 NaN NaN +3.678056 0.246337 NaN NaN +3.983333 NaN 12.036186 1.009791 +4.092222 0.311992 NaN NaN +4.565000 0.408582 NaN NaN +4.883333 NaN 10.067142 1.633505 +5.166667 NaN 9.206911 1.905992 + +2024-05-27 14:34:42,253 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.179112711848294 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.1211037126334654 + +2024-05-27 14:34:42,253 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.1211037126334654 +2024-05-27 14:34:42,256 - physiofit - INFO - Results for ytfJ: + optimal +ytfJ X_0 0.030217 +ytfJ growth_rate 0.570490 +ytfJ Glc_q -5.709463 +ytfJ Glc_M0 14.668130 +ytfJ Ace_q 1.808530 +ytfJ Ace_M0 0.176096 +2024-05-27 14:34:42,261 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:43,281 - physiofit - INFO - Running optimization for zwf1 +2024-05-27 14:34:43,283 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:43,284 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:43,287 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2223 0.000000 0.036288 NaN NaN +2224 0.066667 NaN 15.125933 0.011551 +2225 1.188889 0.066528 NaN NaN +2226 1.716667 NaN 15.385713 0.373333 +2227 2.276944 0.098280 NaN NaN +2228 2.800000 NaN 13.859049 0.844623 +2229 3.128333 0.137592 NaN NaN +2230 3.633333 NaN 12.661490 1.341033 +2231 3.771389 0.179928 NaN NaN +2232 4.266667 NaN 11.997464 1.965710 +2233 4.415556 0.255528 NaN NaN +2234 4.822778 0.367416 NaN NaN +2235 4.883333 NaN 10.566023 2.689767 +Experimental matrix: +[[3.62880000e-02 nan nan] + [ nan 1.51259334e+01 1.15510320e-02] + [6.65280000e-02 nan nan] + [ nan 1.53857135e+01 3.73332829e-01] + [9.82800000e-02 nan nan] + [ nan 1.38590491e+01 8.44622676e-01] + [1.37592000e-01 nan nan] + [ nan 1.26614900e+01 1.34103320e+00] + [1.79928000e-01 nan nan] + [ nan 1.19974639e+01 1.96571034e+00] + [2.55528000e-01 nan nan] + [3.67416000e-01 nan nan] + [ nan 1.05660230e+01 2.68976740e+00]] +Time vector: [0. 0.06666667 1.18888889 1.71666667 2.27694444 2.8 + 3.12833333 3.63333333 3.77138889 4.26666667 4.41555556 4.82277778 + 4.88333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:43,288 - physiofit - INFO - mc : False +2024-05-27 14:34:43,288 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:43,288 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:43,288 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:43,757 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:43,758 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 7.4074857055851115 + x: [ 2.757e-02 5.226e-01 -7.909e+00 1.539e+01 + 4.300e+00 4.696e-02] + nit: 88 + nfev: 8444 + population: [[ 2.781e-02 5.204e-01 ... 4.250e+00 5.701e-02] + [ 2.682e-02 5.297e-01 ... 4.260e+00 6.076e-02] + ... + [ 2.588e-02 5.348e-01 ... 4.381e+00 3.747e-02] + [ 2.688e-02 5.300e-01 ... 4.281e+00 6.682e-02]] + population_energies: [ 7.407e+00 7.502e+00 ... 7.625e+00 7.524e+00] + jac: [ 1.473e-02 5.368e-03 -5.048e-02 1.645e-03 + 1.642e-02 1.109e-02] +2024-05-27 14:34:43,759 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.027565032323480735 +2024-05-27 14:34:43,759 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5226436624547448 +2024-05-27 14:34:43,759 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.908784419245451 +2024-05-27 14:34:43,759 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 15.394883489567668 +2024-05-27 14:34:43,759 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.299716514333137 +2024-05-27 14:34:43,759 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.04696330935822449 +2024-05-27 14:34:43,763 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.000000 0.027565 NaN NaN +0.066667 NaN 15.380094 0.055004 +1.188889 0.051311 NaN NaN +1.716667 NaN 14.788915 0.376406 +2.276944 0.090611 NaN NaN +2.800000 NaN 14.009776 0.799996 +3.128333 0.141394 NaN NaN +3.633333 NaN 13.026133 1.334766 +3.771389 0.197876 NaN NaN +4.266667 NaN 11.933039 1.929041 +4.415556 0.277081 NaN NaN +4.822778 0.342798 NaN NaN +4.883333 NaN 10.457890 2.731026 + +2024-05-27 14:34:43,766 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 7.4074857055851115 +Number of measurements: 19 +Number of parameters to fit: 6 +Degrees of freedom: 13 +p-value = 0.12005009632858263 + +2024-05-27 14:34:43,766 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.12005009632858263 +2024-05-27 14:34:43,768 - physiofit - INFO - Results for zwf1: + optimal +zwf1 X_0 0.027565 +zwf1 growth_rate 0.522644 +zwf1 Glc_q -7.908784 +zwf1 Glc_M0 15.394883 +zwf1 Ace_q 4.299717 +zwf1 Ace_M0 0.046963 +2024-05-27 14:34:43,785 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:44,793 - physiofit - INFO - Running optimization for zwf2 +2024-05-27 14:34:44,795 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:44,795 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:44,799 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2236 1.950000 NaN 14.006952 0.409912 +2237 2.501389 0.098280 NaN NaN +2238 3.250000 NaN 12.806212 0.977467 +2239 3.341944 0.137592 NaN NaN +2240 3.997500 0.179928 NaN NaN +2241 4.083333 NaN 11.593317 1.524744 +2242 4.523333 0.255528 NaN NaN +2243 4.766667 NaN 10.886291 2.251556 +Experimental matrix: +[[ nan 14.00695241 0.40991201] + [ 0.09828 nan nan] + [ nan 12.80621156 0.97746737] + [ 0.137592 nan nan] + [ 0.179928 nan nan] + [ nan 11.59331748 1.52474443] + [ 0.255528 nan nan] + [ nan 10.88629115 2.25155624]] +Time vector: [1.95 2.50138889 3.25 3.34194444 3.9975 4.08333333 + 4.52333333 4.76666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:44,800 - physiofit - INFO - mc : False +2024-05-27 14:34:44,800 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:44,800 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:44,800 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:45,350 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:45,351 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1.363110211622025 + x: [ 2.787e-02 4.823e-01 -7.399e+00 1.451e+01 + 4.278e+00 2.446e-02] + nit: 108 + nfev: 10020 + population: [[ 2.811e-02 4.801e-01 ... 4.280e+00 1.958e-02] + [ 2.801e-02 4.811e-01 ... 4.292e+00 1.543e-02] + ... + [ 2.816e-02 4.796e-01 ... 4.259e+00 2.679e-02] + [ 2.831e-02 4.782e-01 ... 4.281e+00 2.152e-02]] + population_energies: [ 1.363e+00 1.367e+00 ... 1.367e+00 1.369e+00] + jac: [ 5.805e-03 1.879e-03 -1.968e-02 -4.679e-04 + 8.084e-03 -5.289e-05] +2024-05-27 14:34:45,351 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.027874635068561675 +2024-05-27 14:34:45,351 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.4823185173357819 +2024-05-27 14:34:45,351 - physiofit.physiofit.base.fitter - INFO - Glc_q = -7.399338314072396 +2024-05-27 14:34:45,351 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.513471136099655 +2024-05-27 14:34:45,351 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.278403561092146 +2024-05-27 14:34:45,351 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.02446242985115932 +2024-05-27 14:34:45,354 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.950000 NaN 13.845806 0.410516 +2.501389 0.093147 NaN NaN +3.250000 NaN 12.890694 0.962775 +3.341944 0.139714 NaN NaN +3.997500 0.191672 NaN NaN +4.083333 NaN 11.876338 1.549291 +4.523333 0.247004 NaN NaN +4.766667 NaN 10.679885 2.241097 + +2024-05-27 14:34:45,357 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1.363110211622025 +Number of measurements: 12 +Number of parameters to fit: 6 +Degrees of freedom: 6 +p-value = 0.031936028388322005 + +2024-05-27 14:34:45,357 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.031936028388322005 +2024-05-27 14:34:45,359 - physiofit - INFO - Results for zwf2: + optimal +zwf2 X_0 0.027875 +zwf2 growth_rate 0.482319 +zwf2 Glc_q -7.399338 +zwf2 Glc_M0 14.513471 +zwf2 Ace_q 4.278404 +zwf2 Ace_M0 0.024462 +2024-05-27 14:34:45,366 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:46,450 - physiofit - INFO - Running optimization for zwf3 +2024-05-27 14:34:46,452 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:46,453 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:46,458 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2244 0.050000 NaN 14.410233 0.021614 +2245 1.950000 NaN 14.295743 0.481247 +2246 2.833333 NaN 13.480224 0.845184 +2247 2.876944 0.130032 NaN NaN +2248 3.678056 0.211680 NaN NaN +2249 3.983333 NaN 12.255036 1.790165 +2250 4.092222 0.296352 NaN NaN +2251 4.565000 0.373464 NaN NaN +2252 4.883333 NaN 9.709284 2.600183 +2253 5.166667 NaN 9.155408 3.250767 +Experimental matrix: +[[ nan 14.4102332 0.02161391] + [ nan 14.29574287 0.48124696] + [ nan 13.4802244 0.84518409] + [ 0.130032 nan nan] + [ 0.21168 nan nan] + [ nan 12.25503587 1.79016455] + [ 0.296352 nan nan] + [ 0.373464 nan nan] + [ nan 9.70928393 2.60018285] + [ nan 9.15540773 3.25076702]] +Time vector: [0.05 1.95 2.83333333 2.87694444 3.67805556 3.98333333 + 4.09222222 4.565 4.88333333 5.16666667] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:46,458 - physiofit - INFO - mc : False +2024-05-27 14:34:46,458 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:46,459 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:46,459 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:46,934 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:46,934 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.765056338615922 + x: [ 2.450e-02 5.980e-01 -6.536e+00 1.467e+01 + 3.605e+00 1.437e-01] + nit: 90 + nfev: 8400 + population: [[ 2.450e-02 5.981e-01 ... 3.609e+00 1.428e-01] + [ 2.451e-02 5.978e-01 ... 3.609e+00 1.425e-01] + ... + [ 2.410e-02 6.026e-01 ... 3.595e+00 1.438e-01] + [ 2.475e-02 5.956e-01 ... 3.631e+00 1.400e-01]] + population_energies: [ 3.765e+00 3.768e+00 ... 3.782e+00 3.798e+00] + jac: [ 6.516e-03 1.198e-02 4.466e-02 2.463e-02 + 2.484e-02 -2.253e-02] +2024-05-27 14:34:46,935 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.024498601872422685 +2024-05-27 14:34:46,935 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.5980048801425469 +2024-05-27 14:34:46,935 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.535516373254823 +2024-05-27 14:34:46,935 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.673568396917831 +2024-05-27 14:34:46,935 - physiofit.physiofit.base.fitter - INFO - Ace_q = 3.60485692963896 +2024-05-27 14:34:46,935 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.14372601552736833 +2024-05-27 14:34:46,939 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +0.050000 NaN 14.665442 0.148208 +1.950000 NaN 14.081997 0.470024 +2.833333 NaN 13.483966 0.799886 +2.876944 0.136872 NaN NaN +3.678056 0.220989 NaN NaN +3.983333 NaN 12.042440 1.595003 +4.092222 0.283096 NaN NaN +4.565000 0.375594 NaN NaN +4.883333 NaN 9.975752 2.734945 +5.166667 NaN 9.058937 3.240642 + +2024-05-27 14:34:46,942 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.765056338615922 +Number of measurements: 16 +Number of parameters to fit: 6 +Degrees of freedom: 10 +p-value = 0.04267609689976896 + +2024-05-27 14:34:46,942 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.04267609689976896 +2024-05-27 14:34:46,945 - physiofit - INFO - Results for zwf3: + optimal +zwf3 X_0 0.024499 +zwf3 growth_rate 0.598005 +zwf3 Glc_q -6.535516 +zwf3 Glc_M0 14.673568 +zwf3 Ace_q 3.604857 +zwf3 Ace_M0 0.143726 +2024-05-27 14:34:46,953 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:47,979 - physiofit - INFO - Running optimization for zwf_6_1 +2024-05-27 14:34:47,981 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:47,982 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:47,989 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2254 1.350000 NaN 13.996275 0.227239 +2255 1.694722 0.068040 NaN NaN +2256 1.916667 NaN 13.766882 0.340786 +2257 2.300278 0.080136 NaN NaN +2258 2.698333 0.080136 NaN NaN +2259 2.866667 NaN 13.136295 0.624681 +2260 3.436111 0.105840 NaN NaN +2261 3.821111 0.123984 NaN NaN +2262 4.000000 NaN 12.746017 1.224357 +2263 4.201111 0.136080 NaN NaN +2264 4.598056 0.154224 NaN NaN +2265 4.800000 NaN 11.636858 1.836270 +2266 4.995000 0.189000 NaN NaN +2267 5.183333 NaN 11.221400 2.275297 +2268 5.375278 0.231336 NaN NaN +2269 5.583333 NaN 10.434113 2.766004 +Experimental matrix: +[[ nan 13.99627498 0.22723865] + [ 0.06804 nan nan] + [ nan 13.76688157 0.34078616] + [ 0.080136 nan nan] + [ 0.080136 nan nan] + [ nan 13.13629537 0.62468066] + [ 0.10584 nan nan] + [ 0.123984 nan nan] + [ nan 12.74601708 1.22435697] + [ 0.13608 nan nan] + [ 0.154224 nan nan] + [ nan 11.63685774 1.83627015] + [ 0.189 nan nan] + [ nan 11.2214 2.27529728] + [ 0.231336 nan nan] + [ nan 10.4341129 2.76600359]] +Time vector: [1.35 1.69472222 1.91666667 2.30027778 2.69833333 2.86666667 + 3.43611111 3.82111111 4. 4.20111111 4.59805556 4.8 + 4.995 5.18333333 5.37527778 5.58333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:47,990 - physiofit - INFO - mc : False +2024-05-27 14:34:47,990 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:47,990 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:47,991 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:48,558 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:48,559 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2.613519513880476 + x: [ 2.742e-02 3.911e-01 -6.832e+00 1.431e+01 + 4.868e+00 1.000e-06] + nit: 101 + nfev: 9404 + population: [[ 2.719e-02 3.929e-01 ... 4.891e+00 7.737e-05] + [ 2.688e-02 3.961e-01 ... 4.896e+00 7.297e-04] + ... + [ 2.695e-02 3.935e-01 ... 4.920e+00 2.084e-04] + [ 2.748e-02 3.893e-01 ... 4.883e+00 1.433e-03]] + population_energies: [ 2.614e+00 2.639e+00 ... 2.639e+00 2.646e+00] + jac: [ 7.589e-02 8.183e-03 -1.056e-02 2.477e-03 + 3.847e-04 7.501e+00] +2024-05-27 14:34:48,560 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.027423629878204337 +2024-05-27 14:34:48,560 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.39111736401413766 +2024-05-27 14:34:48,560 - physiofit.physiofit.base.fitter - INFO - Glc_q = -6.8324807913263115 +2024-05-27 14:34:48,560 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.313388826147113 +2024-05-27 14:34:48,560 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.868148337324374 +2024-05-27 14:34:48,560 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 1e-06 +2024-05-27 14:34:48,564 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.350000 NaN 13.980173 0.237418 +1.694722 0.053210 NaN NaN +1.916667 NaN 13.778634 0.381014 +2.300278 0.067430 NaN NaN +2.698333 0.078789 NaN NaN +2.866667 NaN 13.322418 0.706069 +3.436111 0.105144 NaN NaN +3.821111 0.122230 NaN NaN +4.000000 NaN 12.502449 1.290297 +4.201111 0.141816 NaN NaN +4.598056 0.165635 NaN NaN +4.800000 NaN 11.661155 1.889720 +4.995000 0.193453 NaN NaN +5.183333 NaN 11.154664 2.250595 +5.375278 0.224476 NaN NaN +5.583333 NaN 10.538609 2.689535 + +2024-05-27 14:34:48,568 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2.613519513880476 +Number of measurements: 23 +Number of parameters to fit: 6 +Degrees of freedom: 17 +p-value = 2.5515654904898116e-05 + +2024-05-27 14:34:48,569 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 2.5515654904898116e-05 +2024-05-27 14:34:48,571 - physiofit - INFO - Results for zwf_6_1: + optimal +zwf_6_1 X_0 0.027424 +zwf_6_1 growth_rate 0.391117 +zwf_6_1 Glc_q -6.832481 +zwf_6_1 Glc_M0 14.313389 +zwf_6_1 Ace_q 4.868148 +zwf_6_1 Ace_M0 0.000001 +2024-05-27 14:34:48,578 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:49,622 - physiofit - INFO - Running optimization for zwf_6_2 +2024-05-27 14:34:49,624 - physiofit - INFO - Run options for the fitter: +2024-05-27 14:34:49,625 - physiofit - INFO - sd : {'Ace': 0.2, 'Glc': 0.46, 'X': 0.02} +2024-05-27 14:34:49,628 - physiofit - INFO - model : Selected model: Steady-state batch model +Model data: + time X Glc Ace +2270 1.350000 NaN 13.627631 0.231857 +2271 1.694722 0.048384 NaN NaN +2272 1.916667 NaN 13.451641 0.328802 +2273 2.300278 0.080136 NaN NaN +2274 2.698333 0.087696 NaN NaN +2275 2.866667 NaN 13.525269 0.633879 +2276 3.436111 0.120960 NaN NaN +2277 3.821111 0.143640 NaN NaN +2278 4.000000 NaN 12.850514 1.233219 +2279 4.201111 0.173880 NaN NaN +2280 4.598056 0.202608 NaN NaN +2281 4.800000 NaN 11.811424 1.871694 +2282 4.995000 0.246456 NaN NaN +2283 5.183333 NaN 11.080644 2.139090 +2284 5.375278 0.273672 NaN NaN +2285 5.583333 NaN 10.181875 2.789569 +Experimental matrix: +[[ nan 13.62763065 0.23185682] + [ 0.048384 nan nan] + [ nan 13.45164104 0.32880228] + [ 0.080136 nan nan] + [ 0.087696 nan nan] + [ nan 13.52526928 0.63387936] + [ 0.12096 nan nan] + [ 0.14364 nan nan] + [ nan 12.8505141 1.23321918] + [ 0.17388 nan nan] + [ 0.202608 nan nan] + [ nan 11.81142414 1.87169375] + [ 0.246456 nan nan] + [ nan 11.08064357 2.13908975] + [ 0.273672 nan nan] + [ nan 10.18187462 2.78956891]] +Time vector: [1.35 1.69472222 1.91666667 2.30027778 2.69833333 2.86666667 + 3.43611111 3.82111111 4. 4.20111111 4.59805556 4.8 + 4.995 5.18333333 5.37527778 5.58333333] +Name vector: ['X', 'Glc', 'Ace'] +Biomass & Metabolites: ['Glc', 'Ace'] +Parameters to estimate: {'X_0': 1, 'growth_rate': 1, 'Glc_q': 1, 'Glc_M0': 1, 'Ace_q': 1, 'Ace_M0': 1} +Fixed parameters: None +Bounds: {'X_0': (0.001, 10), 'growth_rate': (0.001, 3), 'Glc_q': (-50, 50), 'Glc_M0': (1e-06, 50), 'Ace_q': (-50, 50), 'Ace_M0': (1e-06, 50)} + +2024-05-27 14:34:49,629 - physiofit - INFO - mc : False +2024-05-27 14:34:49,629 - physiofit - INFO - iterations : 100 +2024-05-27 14:34:49,629 - physiofit - INFO - debug_mode : False +2024-05-27 14:34:49,630 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-27 14:34:50,123 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ] + [0.02 0.46 0.2 ]] +2024-05-27 14:34:50,124 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3.0755437907473944 + x: [ 2.639e-02 4.421e-01 -5.727e+00 1.415e+01 + 4.219e+00 1.539e-03] + nit: 102 + nfev: 9522 + population: [[ 2.642e-02 4.417e-01 ... 4.199e+00 6.490e-03] + [ 2.658e-02 4.408e-01 ... 4.196e+00 6.290e-03] + ... + [ 2.635e-02 4.416e-01 ... 4.209e+00 1.353e-02] + [ 2.629e-02 4.419e-01 ... 4.222e+00 1.289e-02]] + population_energies: [ 3.076e+00 3.085e+00 ... 3.093e+00 3.101e+00] + jac: [-2.547e-03 -1.231e-03 3.640e-02 5.150e-03 + 5.653e-03 -1.084e-05] +2024-05-27 14:34:50,124 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.026388566337433025 +2024-05-27 14:34:50,124 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.44206119827839246 +2024-05-27 14:34:50,124 - physiofit.physiofit.base.fitter - INFO - Glc_q = -5.726500603094223 +2024-05-27 14:34:50,124 - physiofit.physiofit.base.fitter - INFO - Glc_M0 = 14.148564204546094 +2024-05-27 14:34:50,124 - physiofit.physiofit.base.fitter - INFO - Ace_q = 4.219134442027595 +2024-05-27 14:34:50,124 - physiofit.physiofit.base.fitter - INFO - Ace_M0 = 0.0015388728056567917 +2024-05-27 14:34:50,127 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X Glc Ace +Time +1.350000 NaN 13.869532 0.207122 +1.694722 0.055818 NaN NaN +1.916667 NaN 13.692789 0.337342 +2.300278 0.072951 NaN NaN +2.698333 0.086987 NaN NaN +2.866667 NaN 13.276515 0.644042 +3.436111 0.120530 NaN NaN +3.821111 0.142893 NaN NaN +4.000000 NaN 12.487032 1.225712 +4.201111 0.169030 NaN NaN +4.598056 0.201452 NaN NaN +4.800000 NaN 11.637091 1.851926 +4.995000 0.240093 NaN NaN +5.183333 NaN 11.110195 2.240129 +5.375278 0.284045 NaN NaN +5.583333 NaN 10.456389 2.721836 + +2024-05-27 14:34:50,132 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3.0755437907473944 +Number of measurements: 23 +Number of parameters to fit: 6 +Degrees of freedom: 17 +p-value = 8.305631350668445e-05 + +2024-05-27 14:34:50,133 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 8.305631350668445e-05 +2024-05-27 14:34:50,139 - physiofit - INFO - Results for zwf_6_2: + optimal +zwf_6_2 X_0 0.026389 +zwf_6_2 growth_rate 0.442061 +zwf_6_2 Glc_q -5.726501 +zwf_6_2 Glc_M0 14.148564 +zwf_6_2 Ace_q 4.219134 +zwf_6_2 Ace_M0 0.001539 +2024-05-27 14:34:50,149 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-27 14:34:51,173 - physiofit - INFO - Resulting dataframe: + experiments time X Glc Ace +0 WT1 0.000000 0.031752 NaN NaN +1 WT1 0.066667 NaN 15.153739 0.004196 +2 WT1 1.188889 0.061992 NaN NaN +3 WT1 1.716667 NaN 14.334846 0.348769 +4 WT1 2.276944 0.111888 NaN NaN +... ... ... ... ... ... +2281 zwf_6_2 4.800000 NaN 11.811424 1.871694 +2282 zwf_6_2 4.995000 0.246456 NaN NaN +2283 zwf_6_2 5.183333 NaN 11.080644 2.139090 +2284 zwf_6_2 5.375278 0.273672 NaN NaN +2285 zwf_6_2 5.583333 NaN 10.181875 2.789569 + +[2286 rows x 5 columns] diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/Ace.svg b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/Ace.svg new file mode 100644 index 0000000..8638892 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/Ace.svg @@ -0,0 +1,962 @@ + + + + + + + + 2024-05-27T14:30:18.097428 + image/svg+xml + + + Matplotlib v3.8.4, https://matplotlib.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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(0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/flux_results.tsv new file mode 100644 index 0000000..c2171f7 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.03306757094486952 +growth_rate 0.5419643549844086 +Glc_q -6.167780567684359 +Glc_M0 14.634651281615142 +Ace_q 2.4263461657652092 +Ace_M0 0.13013854762109056 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/plots.pdf b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/plots.pdf new file mode 100644 index 0000000..bc016f2 Binary files /dev/null and b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/plots.pdf differ diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/stat_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/stat_results.tsv new file mode 100644 index 0000000..90bbd57 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/modF/stat_results.tsv @@ -0,0 +1,18 @@ +================== +Khi² test results +================== + +khi2_value 4.349565 +number_of_measurements 16.000000 +number_of_params 6.000000 +Degrees_of_freedom 10.000000 +p_val 0.069797 + +At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.06979716848676583 + +================== +AIC test results +================== + +AIC 37.521212 +AICc 51.521212 \ No newline at end of file diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/nanE/Ace.svg b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/nanE/Ace.svg new file mode 100644 index 0000000..7f65eaf --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/nanE/Ace.svg @@ -0,0 +1,962 @@ + + + + + + + + 2024-05-27T14:30:19.541484 + image/svg+xml + + + Matplotlib v3.8.4, https://matplotlib.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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args: null + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yahJ/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yahJ/flux_results.tsv new file mode 100644 index 0000000..81b8ccb --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yahJ/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.015100250926870548 +growth_rate 0.7949229499198881 +Glc_q -5.210089654094659 +Glc_M0 14.18295285071596 +Ace_q 2.1064604924380497 +Ace_M0 0.29760079279234103 diff --git 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b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yajD/config_file.yml @@ -0,0 +1,24 @@ +iterations: 100 +mc: false +model: + args: null + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yajD/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yajD/flux_results.tsv new file mode 100644 index 0000000..da81655 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yajD/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.025876567875853723 +growth_rate 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b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ybiH/config_file.yml @@ -0,0 +1,24 @@ +iterations: 100 +mc: false +model: + args: null + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ybiH/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ybiH/flux_results.tsv new file mode 100644 index 0000000..41ef438 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ybiH/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.03503195010302243 +growth_rate 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(1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ybiU/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ybiU/flux_results.tsv new file mode 100644 index 0000000..184928c --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ybiU/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.025024968209125656 +growth_rate 0.5479308471185746 +Glc_q -8.626219694298719 +Glc_M0 15.652372243335185 +Ace_q 3.6161468233004364 +Ace_M0 0.08409969620563781 diff --git 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50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydbC/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydbC/flux_results.tsv new file mode 100644 index 0000000..7fd5e1f --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydbC/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.02013839129811845 +growth_rate 0.6411558913144022 +Glc_q -6.507989514857879 +Glc_M0 14.17350318542841 +Ace_q 2.7192257863224776 +Ace_M0 0.2701046730336295 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydbC/plots.pdf 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model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydcI/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydcI/flux_results.tsv new file mode 100644 index 0000000..ad5115c --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydcI/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.029295081101182882 +growth_rate 0.5747133580758487 +Glc_q -5.063916168867397 +Glc_M0 14.52770271465131 +Ace_q 2.276892720411388 +Ace_M0 0.1266323750197039 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydcI/plots.pdf 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bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydcJ/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydcJ/flux_results.tsv new file mode 100644 index 0000000..14e0670 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydcJ/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.014534128042810963 +growth_rate 0.7068826490773048 +Glc_q -5.4988128338735 +Glc_M0 13.062250567277271 +Ace_q 3.4168583758182716 +Ace_M0 0.41927569481249527 diff --git 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50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yddM/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yddM/flux_results.tsv new file mode 100644 index 0000000..170c842 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yddM/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.03301648186973496 +growth_rate 0.5714277916392163 +Glc_q -5.232462938869538 +Glc_M0 14.349296772796153 +Ace_q 2.4737514263624933 +Ace_M0 0.12409313333966647 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yddM/plots.pdf 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(1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydeI/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydeI/flux_results.tsv new file mode 100644 index 0000000..250a76f --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydeI/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.02919897078119934 +growth_rate 0.5083022843962759 +Glc_q -5.932988160167847 +Glc_M0 14.473192566952237 +Ace_q 3.0451071266955885 +Ace_M0 0.1246845554254861 diff --git 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50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiJ/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiJ/flux_results.tsv new file mode 100644 index 0000000..58cbc7d --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiJ/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.02420925198562736 +growth_rate 0.5853717464304172 +Glc_q -5.178436742274981 +Glc_M0 14.154890288857494 +Ace_q 3.0034338160979175 +Ace_M0 0.193965465471882 diff --git a/validation/models/Steady-state_model/physiofit_results/results/plots.pdf b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiJ/plots.pdf similarity index 57% rename from validation/models/Steady-state_model/physiofit_results/results/plots.pdf rename to validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiJ/plots.pdf index 036643f..f273f09 100644 Binary files a/validation/models/Steady-state_model/physiofit_results/results/plots.pdf and b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiJ/plots.pdf differ diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiJ/stat_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiJ/stat_results.tsv new file mode 100644 index 0000000..8c4cc62 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiJ/stat_results.tsv @@ -0,0 +1,18 @@ +================== +Khi² test results +================== + +khi2_value 1.124861 +number_of_measurements 12.000000 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50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiZ/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiZ/flux_results.tsv new file mode 100644 index 0000000..2f899df --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiZ/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.019932225253371832 +growth_rate 0.6624601111009357 +Glc_q -5.023935007134119 +Glc_M0 14.039569297087006 +Ace_q 2.5702118199000195 +Ace_M0 0.24195411801703268 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ydiZ/plots.pdf 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50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yeaG/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yeaG/flux_results.tsv new file mode 100644 index 0000000..c60c86f --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yeaG/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.02200682134349738 +growth_rate 0.6057844521460668 +Glc_q -8.397102292091693 +Glc_M0 14.304134858147691 +Ace_q 3.256054182133859 +Ace_M0 0.20176196964821042 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yeaG/plots.pdf 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(0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yebV/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yebV/flux_results.tsv new file mode 100644 index 0000000..8365801 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yebV/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.032229845007689745 +growth_rate 0.5890713430788245 +Glc_q -4.777848635981626 +Glc_M0 14.502115099718122 +Ace_q 2.136818201603816 +Ace_M0 0.1567262755063316 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yebV/plots.pdf 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50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yecA/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yecA/flux_results.tsv new file mode 100644 index 0000000..e13c826 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yecA/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.020670906307843993 +growth_rate 0.623816132789155 +Glc_q -5.199334453475143 +Glc_M0 14.286832169263267 +Ace_q 3.7015694804291623 +Ace_M0 0.11939837923249076 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yecA/plots.pdf 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args: null + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yfaT/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yfaT/flux_results.tsv new file mode 100644 index 0000000..269f05d --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yfaT/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.03652311808078611 +growth_rate 0.5111783885181634 +Glc_q -7.276889588840574 +Glc_M0 15.743122074061887 +Ace_q 2.5530721487930235 +Ace_M0 0.08039245181489119 diff --git 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args: null + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yfhm/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yfhm/flux_results.tsv new file mode 100644 index 0000000..0f4fc30 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yfhm/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.019596265615763244 +growth_rate 0.6051855967308594 +Glc_q -4.989136908487301 +Glc_M0 13.247964229004094 +Ace_q 2.5723823917563022 +Ace_M0 0.2979187004018037 diff --git 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b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ygaM/config_file.yml @@ -0,0 +1,24 @@ +iterations: 100 +mc: false +model: + args: null + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ygaM/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ygaM/flux_results.tsv new file mode 100644 index 0000000..364e9cb --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ygaM/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.019259399813305586 +growth_rate 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50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ygaU/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ygaU/flux_results.tsv new file mode 100644 index 0000000..1a31d28 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ygaU/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.019722310084158687 +growth_rate 0.6216809923575196 +Glc_q -7.5502596583353725 +Glc_M0 14.472002989234458 +Ace_q 4.420365981629611 +Ace_M0 0.16842313798872577 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ygaU/plots.pdf 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-0,0 +1,24 @@ +iterations: 100 +mc: false +model: + args: null + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yibL/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yibL/flux_results.tsv new file mode 100644 index 0000000..a9dd92c --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yibL/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.023227246620336425 +growth_rate 0.6195379710492022 +Glc_q -7.140410089044937 +Glc_M0 14.818033710927212 +Ace_q 2.55897929732318 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0.520386181512388 +Glc_q -5.542192507046417 +Glc_M0 14.642349628362123 +Ace_q 1.8700622819906971 +Ace_M0 0.1771956253263771 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yigI/plots.pdf b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yigI/plots.pdf new file mode 100644 index 0000000..48377d3 Binary files /dev/null and b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yigI/plots.pdf differ diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yigI/stat_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yigI/stat_results.tsv new file mode 100644 index 0000000..a160c4f --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yigI/stat_results.tsv @@ -0,0 +1,18 @@ +================== +Khi² test results +================== + +khi2_value 5.916988 +number_of_measurements 16.000000 +number_of_params 6.000000 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false +model: + args: null + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yiiD/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yiiD/flux_results.tsv new file mode 100644 index 0000000..06d64df --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yiiD/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.035167229488810146 +growth_rate 0.514572922543641 +Glc_q -6.017174024756494 +Glc_M0 14.677220468566825 +Ace_q 2.6614797557998466 +Ace_M0 0.07993328888298612 diff 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10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yjhU/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yjhU/flux_results.tsv new file mode 100644 index 0000000..c0306e1 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yjhU/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.035917200916423295 +growth_rate 0.5483029376051027 +Glc_q -4.486313124467216 +Glc_M0 14.399234491454841 +Ace_q 2.266886804420999 +Ace_M0 0.10035599367081743 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/yjhU/plots.pdf 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model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ykgG/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ykgG/flux_results.tsv new file mode 100644 index 0000000..30ae645 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ykgG/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.02637168679748064 +growth_rate 0.6132248413757002 +Glc_q -5.173751044730108 +Glc_M0 14.372875834431232 +Ace_q 2.3543488250184472 +Ace_M0 0.11890405233690547 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ykgG/plots.pdf 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+ model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ymbA/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ymbA/flux_results.tsv new file mode 100644 index 0000000..22a04e9 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ymbA/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.03368145328694123 +growth_rate 0.5604459977173624 +Glc_q -4.7679981762024894 +Glc_M0 14.266988203853256 +Ace_q 2.0475386921909324 +Ace_M0 0.20078597389861502 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ymbA/plots.pdf 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10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ytfB/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ytfB/flux_results.tsv new file mode 100644 index 0000000..c128b3c --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ytfB/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.02896881143493269 +growth_rate 0.5903219618284823 +Glc_q -5.5699552625007955 +Glc_M0 14.420978284686308 +Ace_q 2.557342889043702 +Ace_M0 0.1391799047196647 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/ytfB/plots.pdf 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4.868148337324374 +Ace_M0 1e-06 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_1/plots.pdf b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_1/plots.pdf new file mode 100644 index 0000000..afff53f Binary files /dev/null and b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_1/plots.pdf differ diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_1/stat_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_1/stat_results.tsv new file mode 100644 index 0000000..a431300 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_1/stat_results.tsv @@ -0,0 +1,18 @@ +================== +Khi² test results +================== + +khi2_value 2.613520 +number_of_measurements 23.000000 +number_of_params 6.000000 +Degrees_of_freedom 17.000000 +p_val 0.000026 + +At level of 95% confidence, 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b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_2/config_file.yml @@ -0,0 +1,24 @@ +iterations: 100 +mc: false +model: + args: null + bounds: + Ace_M0: (1e-06, 50) + Ace_q: (-50, 50) + Glc_M0: (1e-06, 50) + Glc_q: (-50, 50) + X_0: (0.001, 10) + growth_rate: (0.001, 3) + model_name: Steady-state batch model + parameters_to_estimate: + Ace_M0: 1 + Ace_q: 1 + Glc_M0: 1 + Glc_q: 1 + X_0: 1 + growth_rate: 1 +path_to_data: C:\Users\legregam\PycharmProjects\PhysioFit\versions publi\retour_reveiew\config_file.yml +sds: + Ace: 0.2 + Glc: 0.46 + X: 0.02 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_2/flux_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_2/flux_results.tsv new file mode 100644 index 0000000..5d17f65 --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_2/flux_results.tsv @@ -0,0 +1,7 @@ + optimal +X_0 0.026388566337433025 +growth_rate 0.44206119827839246 +Glc_q -5.726500603094223 +Glc_M0 14.148564204546094 +Ace_q 4.219134442027595 +Ace_M0 0.0015388728056567917 diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_2/plots.pdf b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_2/plots.pdf new file mode 100644 index 0000000..0d0c3cd Binary files /dev/null and b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_2/plots.pdf differ diff --git a/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_2/stat_results.tsv b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_2/stat_results.tsv new file mode 100644 index 0000000..20b2f0d --- /dev/null +++ b/validation/validation_results/Berges_2021/PhysioFit_v3.4.0/dataset_res/zwf_6_2/stat_results.tsv @@ -0,0 +1,18 @@ +================== +Khi² test results +================== + +khi2_value 3.075544 +number_of_measurements 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Value: 8.305631350668445e-05 + +================== +AIC test results +================== + +AIC 39.840080 +AICc 47.306746 \ No newline at end of file diff --git a/validation/validation_results/Berges_2021/results.xlsx b/validation/validation_results/Berges_2021/results.xlsx new file mode 100644 index 0000000..2482819 Binary files /dev/null and b/validation/validation_results/Berges_2021/results.xlsx differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-1.txt b/validation/validation_results/Peiro_2019/Peiro_2019/WT-1.txt new file mode 100644 index 0000000..ab0c44c --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/WT-1.txt @@ -0,0 +1,5 @@ +"time" "X" "DHA" +0 0.084 13.258820025773 +14.8430555555556 0.317 8.27391577990282 +19.3238888888889 0.628 3.81001812804928 + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-1_res/WT.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/WT-1_res/WT.pdf new file mode 100644 index 0000000..8a6e726 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/WT-1_res/WT.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-1_res/WT_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/WT-1_res/WT_log.txt new file mode 100644 index 0000000..ab5103f --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/WT-1_res/WT_log.txt @@ -0,0 +1,147 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 3.864778 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 19.32389 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 19.3238878888889 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 19.3238878888889 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -19.323888 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.84306 19.32389 + +$sys$data_meas + X DHA +[1,] 0.084 13.258820 +[2,] 0.317 8.273916 +[3,] 0.628 3.810018 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.08398438 13.19339977 0.15254553 -2.15938210 6.13510342 + +$result$lastp + X DHA mu qDHA tlag +-5.072896e-11 -8.441563e-10 -7.704156e-11 1.971126e-09 -1.022015e-08 + +$result$hci + X DHA mu qDHA tlag +0.007805687 1.766223363 0.006149800 0.749597619 0.787889647 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.3072598 + +$result$laststep + X DHA mu qDHA tlag +-5.072896e-11 -8.441563e-10 -7.704156e-11 1.971126e-09 -1.022015e-08 + +$result$normp +[1] 1.044308e-08 + +$result$res +[1] -0.007812001 0.013974754 -0.006010149 -0.130840516 0.254694010 -0.110126511 + +$result$prevres +[1] -0.007811976 0.013974709 -0.006010130 -0.130840514 0.254694013 -0.110126516 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] +[1,] 500.00000 0.000000 0.0000 0.000000 0.000000 +[2,] 1887.42219 0.000000 1380.3321 0.000000 -24.180598 +[3,] 3738.71909 0.000000 4141.1994 0.000000 -47.898379 +[4,] 0.00000 2.000000 0.0000 0.000000 0.000000 +[5,] -76.28949 1.759186 -34.2178 2.967110 1.313789 +[6,] -176.43777 1.692356 -129.9823 6.862156 2.584053 + +$result$retres +$result$retres$res +[1] -0.007811976 0.013974709 -0.006010130 -0.130840514 0.254694013 -0.110126516 + +$result$retres$sim + col +row X DHA + [1,] 0.08398438 13.193400 + [2,] 0.31702795 8.401263 + [3,] 0.62798798 3.754955 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] 1.562395e-05 0.06542026 +[2,] -2.794942e-05 -0.12734701 +[3,] 1.202026e-05 0.05506326 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-1_res/WT_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/WT-1_res/WT_res.txt new file mode 100644 index 0000000..bce6941 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/WT-1_res/WT_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.083984375997233 0.0839165273542344 0.0841263137828839 0.00227911629485606 0.0798678916288136 0.0882830283623536 +DHA 13.1933997678932 13.2314495900269 13.2428891572852 0.419759917127411 12.489038959901 14.0885942913112 +mu 0.152545528041564 0.152417604657689 0.152539341356651 0.00147745676793034 0.149279553878945 0.155210598432048 +qDHA -2.15938210481223 -2.16188431051137 -2.1685218965098 0.172008831167281 -2.47042809641739 -1.85338910290281 +tlag 6.13510341610688 6.11847092820189 6.12662802416664 0.205264345861409 5.70300593760095 6.49638833880479 +res 0.0944085708240221 1.13649716251624 0.483028301150402 1.5072898353465 0.00555125478815405 4.44617364680094 + + +Goodness of fit (khi2 test) + +khi2 value 0.0944085708240247 +data points 6 +fitted parameters 5 +degrees of freedom 1 +khi2 reduced value 0.0944085708240247 +p-value, i.e. P(X^2<=value) 0.241354351256143 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-2.txt b/validation/validation_results/Peiro_2019/Peiro_2019/WT-2.txt new file mode 100644 index 0000000..b9e4923 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/WT-2.txt @@ -0,0 +1,7 @@ +"time" "X" "DHA" +0 0.081 10.6491883966229 +14.8263888888889 0.301 7.00082201865763 +17.1905555555556 0.437 5.57998685911328 +18.9405555555556 0.583 3.76402486905013 +21.0272222222222 0.79 1.19028479195311 + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-2_res/WT-2.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/WT-2_res/WT-2.pdf new file mode 100644 index 0000000..06db5e0 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/WT-2_res/WT-2.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-2_res/WT-2_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/WT-2_res/WT-2_log.txt new file mode 100644 index 0000000..94986c3 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/WT-2_res/WT-2_log.txt @@ -0,0 +1,159 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 4.205444 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 21.02722 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 21.0272212222222 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 21.0272212222222 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -21.027221 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.82639 17.19056 18.94056 21.02722 + +$sys$data_meas + X DHA +[1,] 0.081 10.649188 +[2,] 0.301 7.000822 +[3,] 0.437 5.579987 +[4,] 0.583 3.764025 +[5,] 0.790 1.190285 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.08101565 10.73184352 0.15444261 -1.73121819 6.25250783 + +$result$lastp + X DHA mu qDHA tlag +-6.509145e-11 2.323074e-07 -4.126469e-09 -4.579631e-08 -3.570111e-07 + +$result$hci + X DHA mu qDHA tlag +0.011166380 2.323579561 0.005195454 0.768439055 0.998029519 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 2.172705 + +$result$laststep + X DHA mu qDHA tlag +-6.509145e-11 2.323074e-07 -4.126469e-09 -4.579631e-08 -3.570111e-07 + +$result$normp +[1] 4.284133e-07 + +$result$res + [1] 0.007823755 1.771890610 0.877883895 -4.043857098 1.763562139 0.165310252 0.011866072 -0.410119835 0.029881594 0.182744838 + +$result$prevres + [1] 0.007823787 1.771887724 0.877881877 -4.043857667 1.763564770 0.165309788 0.011866044 -0.410119742 0.029881782 0.182745138 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.00000 0.000000 0.00000 0.000000 0.000000 + [2,] 1879.53676 0.000000 1305.56100 0.000000 -23.517268 + [3,] 2707.84581 0.000000 2399.56566 0.000000 -33.881293 + [4,] 3548.15583 0.000000 3647.25715 0.000000 -44.395477 + [5,] 4897.36954 0.000000 5862.06821 0.000000 -61.277201 + [6,] 0.00000 2.000000 0.00000 0.000000 0.000000 + [7,] -60.09362 1.759440 -25.58354 2.812195 1.012382 + [8,] -95.66359 1.723851 -54.36661 4.476760 1.452175 + [9,] -131.63435 1.697972 -89.47636 6.160080 1.898419 +[10,] -189.26399 1.667622 -154.89200 8.856969 2.615004 + +$result$retres +$result$retres$res + [1] 0.007823787 1.771887724 0.877881877 -4.043857667 1.763564770 0.165309788 0.011866044 -0.410119742 0.029881782 0.182745138 + +$result$retres$sim + col +row X DHA + [1,] 0.08101565 10.731843 + [2,] 0.30454378 7.006755 + [3,] 0.43875576 5.374927 + [4,] 0.57491228 3.778966 + [5,] 0.79352713 1.281657 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -1.564757e-05 -0.082654894 +[2,] -3.543775e-03 -0.005933022 +[3,] -1.755764e-03 0.205059871 +[4,] 8.087715e-03 -0.014940891 +[5,] -3.527130e-03 -0.091372569 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-2_res/WT-2_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/WT-2_res/WT-2_res.txt new file mode 100644 index 0000000..45eebf7 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/WT-2_res/WT-2_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.081015647509301 0.0809817531715747 0.0810887177697038 0.00194912529610382 0.0767466354957448 0.0845020054231831 +DHA 10.731843522865 10.7005559184876 10.7042914673902 0.460809869759534 9.90438227416651 11.5188454536992 +mu 0.154442606901177 0.154385831189355 0.154348752845099 0.00100549200593106 0.152548138893721 0.156283073720438 +qDHA -1.73121819116858 -1.71954468023138 -1.73024270194734 0.153834834272414 -2.01154673459666 -1.45235693418483 +tlag 6.25250782761719 6.24455845990261 6.24228084749619 0.170944077230684 5.91149415754982 6.58363652519548 +res 23.6032244747501 5.01736336770977 4.41954207525 2.98394196128838 1.14852328747338 12.4358679254342 + + +Goodness of fit (khi2 test) + +khi2 value 23.6032244747701 +data points 10 +fitted parameters 5 +degrees of freedom 5 +khi2 reduced value 4.72064489495402 +p-value, i.e. P(X^2<=value) 0.999741264848601 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-3.txt b/validation/validation_results/Peiro_2019/Peiro_2019/WT-3.txt new file mode 100644 index 0000000..c43798f --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/WT-3.txt @@ -0,0 +1,7 @@ +"time" "X" "DHA" +0 0.093 15.6482220112906 +14.8097222222222 0.293 11.3628521058326 +17.2572222222222 0.439 9.25080966430236 +19.2905555555556 0.653 6.7848869288702 +22.0319444444444 0.888 2.69063540175899 + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-3_res/WT-3.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/WT-3_res/WT-3.pdf new file mode 100644 index 0000000..ae40235 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/WT-3_res/WT-3.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-3_res/WT-3_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/WT-3_res/WT-3_log.txt new file mode 100644 index 0000000..64bab9d --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/WT-3_res/WT-3_log.txt @@ -0,0 +1,159 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 4.406389 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 22.03194 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 22.0319434444444 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 22.0319434444444 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -22.031943 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.80972 17.25722 19.29056 22.03194 + +$sys$data_meas + X DHA +[1,] 0.093 15.648222 +[2,] 0.293 11.362852 +[3,] 0.439 9.250810 +[4,] 0.653 6.784887 +[5,] 0.888 2.690635 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.09305142 15.87690005 0.14596572 -1.94004556 6.44565611 + +$result$lastp + X DHA mu qDHA tlag + 3.870267e-12 3.819764e-08 -1.031311e-09 1.276478e-09 -9.702354e-08 + +$result$hci + X DHA mu qDHA tlag + 0.06385121 12.82822994 0.02299453 3.68361808 5.18746669 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 12.42657 + +$result$laststep + X DHA mu qDHA tlag + 3.870267e-12 3.819764e-08 -1.031311e-09 1.276478e-09 -9.702354e-08 + +$result$normp +[1] 1.042848e-07 + +$result$res + [1] 0.02570818 11.22798451 5.95555072 -23.14007145 8.62717748 0.45735608 -0.53158569 -0.33720117 0.17085260 0.18899001 + +$result$prevres + [1] 0.02570818 11.22798363 5.95555004 -23.14007174 8.62717833 0.45735600 -0.53158568 -0.33720114 0.17085263 0.18899003 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.00000 0.000000 0.00000 0.000000 0.000000 + [2,] 1695.06268 0.000000 1319.24727 0.000000 -23.022878 + [3,] 2422.91368 0.000000 2437.52756 0.000000 -32.908781 + [4,] 3260.13230 0.000000 3896.62774 0.000000 -44.280150 + [5,] 4864.26963 0.000000 7054.77766 0.000000 -66.068051 + [6,] 0.00000 2.000000 0.00000 0.000000 0.000000 + [7,] -61.73316 1.759693 -29.06193 2.960940 1.174347 + [8,] -98.75432 1.722858 -62.90976 4.736605 1.670149 + [9,] -141.17441 1.692843 -110.61478 6.771222 2.240583 +[10,] -222.21557 1.653203 -220.35485 10.658241 3.333744 + +$result$retres +$result$retres$res + [1] 0.02570818 11.22798363 5.95555004 -23.14007174 8.62717833 0.45735600 -0.53158568 -0.33720114 0.17085263 0.18899003 + +$result$retres$sim + col +row X DHA + [1,] 0.09305142 15.876900 + [2,] 0.31545597 11.097059 + [3,] 0.45091110 9.082209 + [4,] 0.60671986 6.870313 + [5,] 0.90525436 2.785130 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -5.141636e-05 -0.22867800 +[2,] -2.245597e-02 0.26579284 +[3,] -1.191110e-02 0.16860057 +[4,] 4.628014e-02 -0.08542632 +[5,] -1.725436e-02 -0.09449502 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/WT-3_res/WT-3_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/WT-3_res/WT-3_res.txt new file mode 100644 index 0000000..048a1f5 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/WT-3_res/WT-3_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0930514163600193 0.0935103548729223 0.0933640118479379 0.00181956719999285 0.0901724848728048 0.0971839924816152 +DHA 15.8769000505433 15.8552349505788 15.8966471158007 0.348029480622767 15.1548104512125 16.4848863343936 +mu 0.14596571721236 0.145926798320907 0.145953173444319 0.000740517463589375 0.144459833439989 0.147115517641408 +qDHA -1.94004555724344 -1.92889412302622 -1.91982671965598 0.11908474285592 -2.17764932734184 -1.71897259865288 +tlag 6.44565611313005 6.4748276999083 6.47382359846497 0.149004805386155 6.19595987516839 6.78395845325573 +res 772.098349965613 5.0744829034133 4.48298699248909 2.97302935476619 0.8382727724529 12.5800808428996 + + +Goodness of fit (khi2 test) + +khi2 value 772.098349965614 +data points 10 +fitted parameters 5 +degrees of freedom 5 +khi2 reduced value 154.419669993123 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-1.txt b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-1.txt new file mode 100644 index 0000000..d142da2 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-1.txt @@ -0,0 +1,7 @@ +"time" "X" "DHA" +0 0.08 13.0913526935729 +7.9825 0.11 12.6971558008413 +9.47666666666667 0.15 12.3892921375855 +23.8927777777778 0.45 10.0693075861087 +26.9761111111111 0.48 10.0428756478163 +47.8430555555556 1.09 3.36605161627835 diff --git a/validation/models/Steady-state_model_deg/original_results/dhaKLM.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-1_res/dhaKLM.pdf similarity index 100% rename from validation/models/Steady-state_model_deg/original_results/dhaKLM.pdf rename to validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-1_res/dhaKLM.pdf diff --git a/validation/models/Steady-state_model_deg/original_results/dhaKLM_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-1_res/dhaKLM_log.txt similarity index 100% rename from validation/models/Steady-state_model_deg/original_results/dhaKLM_log.txt rename to validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-1_res/dhaKLM_log.txt diff --git a/validation/models/Steady-state_model_deg/original_results/dhaKLM_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-1_res/dhaKLM_res.txt similarity index 100% rename from validation/models/Steady-state_model_deg/original_results/dhaKLM_res.txt rename to validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-1_res/dhaKLM_res.txt diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2.txt b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2.txt new file mode 100644 index 0000000..2073749 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2.txt @@ -0,0 +1,7 @@ +"time" "X" "DHA" +0 "0.05" 14.3031446996899 +7.9825 "NA" 12.4362147876673 +9.47666666666667 "0.08" 12.4110947820852 +23.8927777777778 "0.33" 10.8832536162944 +26.9761111111111 "0.42" 9.32203666988474 +47.8430555555556 "0.95" 3.98841228000199 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2_res/dhaKLM-2.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2_res/dhaKLM-2.pdf new file mode 100644 index 0000000..d7eee7a Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2_res/dhaKLM-2.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2_res/dhaKLM-2_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2_res/dhaKLM-2_log.txt new file mode 100644 index 0000000..4443fa7 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2_res/dhaKLM-2_log.txt @@ -0,0 +1,164 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 9.568611 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 47.84305 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 47.8430545555556 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 47.8430545555556 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -47.843055 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.000000 7.982500 9.476667 23.892778 26.976111 47.843056 + +$sys$data_meas + X DHA +[1,] 0.05 14.303145 +[2,] NA 12.436215 +[3,] 0.08 12.411095 +[4,] 0.33 10.883254 +[5,] 0.42 9.322037 +[6,] 0.95 3.988412 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 9.750530e-02 1.409737e+01 4.790937e-02 -3.300295e-01 9.999977e-07 + +$result$lastp + X DHA mu qDHA tlag +-1.871466e-07 -8.151318e-07 4.508631e-08 -8.700357e-08 -2.327027e-12 + +$result$hci + X DHA mu qDHA tlag + 0.20828045 15.89653634 0.01048925 1.94281779 47.26150504 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 22.98323 + +$result$laststep + X DHA mu qDHA tlag +-1.871466e-07 -8.151318e-07 4.508631e-08 -8.700357e-08 -2.327027e-12 + +$result$normp +[1] 8.420606e-07 + +$result$res + [1] 23.7526507 36.7674450 -11.8454612 -32.4649545 7.4562325 -0.4115396 0.8365423 0.4116899 -1.4819482 0.4438906 0.1592631 + +$result$prevres + [1] 23.7527442 36.7675596 -11.8453322 -32.4648296 7.4561178 -0.4115380 0.8365429 0.4116904 -1.4819495 0.4438889 0.1592627 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.000000 0.000000 0.000000 0.000000 -1.05432873 + [2,] 787.315266 0.000000 727.500496 0.000000 -3.67788201 + [3,] 1570.728686 0.000000 3659.290290 0.000000 -7.33753685 + [4,] 1820.771047 0.000000 4789.208304 0.000000 -8.50559029 + [5,] 4947.989342 0.000000 23082.174363 0.000000 -23.11414726 + [6,] 0.000000 2.000000 0.000000 0.000000 0.02905150 + [7,] -6.215349 1.866660 -2.600193 1.836293 0.08910302 + [8,] -7.624752 1.842707 -3.835900 2.252694 0.09491616 + [9,] -27.171884 1.626825 -38.570770 8.027794 0.17928205 +[10,] -33.258320 1.584042 -54.452626 9.826000 0.20633760 +[11,] -107.782852 1.322623 -352.975619 31.843892 0.54606077 + +$result$retres +$result$retres$res + [1] 23.7527442 36.7675596 -11.8453322 -32.4648296 7.4561178 -0.4115380 0.8365429 0.4116904 -1.4819495 0.4438889 0.1592627 + +$result$retres$sim + col +row X DHA + [1,] 0.09750549 14.097376 + [2,] 0.14292854 12.854486 + [3,] 0.15353512 12.616940 + [4,] 0.30630934 10.142279 + [5,] 0.35507034 9.543981 + [6,] 0.96491224 4.068044 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -0.04750549 0.20576901 +[2,] NA -0.41827146 +[3,] -0.07353512 -0.20584518 +[4,] 0.02369066 0.74097476 +[5,] 0.06492966 -0.22194447 +[6,] -0.01491224 -0.07963136 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2_res/dhaKLM-2_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2_res/dhaKLM-2_res.txt new file mode 100644 index 0000000..e25b47e --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-2_res/dhaKLM-2_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0975053013354361 0.0981728181732934 0.0979290597757943 0.00131595916578355 0.0961311432589941 0.101365268745504 +DHA 14.0973748763578 14.096693057126 14.087044565049 0.29255991210792 13.5538578507939 14.6808645274473 +mu 0.0479093707409472 0.0479416447001391 0.0479438137834448 0.000173212060887557 0.0476139473718224 0.0482687033078298 +qDHA -0.330029461852843 -0.334180479680254 -0.334619956751591 0.0377033375513963 -0.404752669356296 -0.263355788352113 +tlag 9.99997674888675e-07 0.17322325961121 1.00000000013978e-06 0.271971859797768 9.99999999357071e-07 0.964057768873543 +res 3169.37427905074 7.09541185539638 6.77717744951462 3.67619286102839 1.10420939523182 14.4002802722964 + + +Goodness of fit (khi2 test) + +khi2 value 3169.37427911163 +data points 11 +fitted parameters 5 +degrees of freedom 6 +khi2 reduced value 528.229046518606 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3.txt b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3.txt new file mode 100644 index 0000000..64240f2 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3.txt @@ -0,0 +1,8 @@ +"time" "X" "DHA" +0 0.027 17.5627155874568 +15 0.162 15.800197281975 +17 0.192 NA +19.25 NA 10.8452221132329 +21.25 0.27 10.2626211449951 +23.1666666666667 0.29 NA +39.1666666666667 0.63 7.33663599934672 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3_res/dhaKLM-3.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3_res/dhaKLM-3.pdf new file mode 100644 index 0000000..3f76bdc Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3_res/dhaKLM-3.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3_res/dhaKLM-3_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3_res/dhaKLM-3_log.txt new file mode 100644 index 0000000..c0c5f05 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3_res/dhaKLM-3_log.txt @@ -0,0 +1,168 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 7.833333 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + [7,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 39.16667 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 39.1666656666667 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 39.1666656666667 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -39.166666 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 15.00000 17.00000 19.25000 21.25000 23.16667 39.16667 + +$sys$data_meas + X DHA +[1,] 0.027 17.562716 +[2,] 0.162 15.800197 +[3,] 0.192 NA +[4,] NA 10.845222 +[5,] 0.270 10.262621 +[6,] 0.290 NA +[7,] 0.630 7.336636 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.07724170 16.67006630 0.05395751 -0.56476310 0.00000100 + +$result$lastp + X DHA mu qDHA tlag + 1.334234e-08 -2.968711e-07 -5.290279e-09 1.261482e-07 6.327383e-12 + +$result$hci + X DHA mu qDHA tlag + 0.118111992 10.902818556 0.009034885 2.045111768 29.825205919 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 13.06419 + +$result$laststep + X DHA mu qDHA tlag + 1.334234e-08 -2.968711e-07 -5.290279e-09 1.261482e-07 6.327383e-12 + +$result$normp +[1] 3.228806e-07 + +$result$res + [1] 25.1208487 5.7607913 0.6474499 -13.4422782 -10.1978994 4.6184360 -1.7852986 -4.2210691 3.7814618 3.9938955 -1.4484759 + +$result$prevres + [1] 25.1208420 5.7607832 0.6474419 -13.4422856 -10.1979061 4.6184470 -1.7852980 -4.2210687 3.7814620 3.9938956 -1.4484776 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.00000 0.000000 0.00000 0.000000 -0.94065611 + [2,] 1123.23785 0.000000 1301.41166 0.000000 -4.68139604 + [3,] 1251.23427 0.000000 1643.00642 0.000000 -5.21485555 + [4,] 1573.73206 0.000000 2583.10131 0.000000 -6.55895189 + [5,] 1745.19879 0.000000 3122.91504 0.000000 -7.27358566 + [6,] 4137.90107 0.000000 12518.38886 0.000000 -17.24581635 + [7,] 0.00000 2.000000 0.00000 0.000000 0.03938269 + [8,] -24.68454 1.756802 -16.50585 3.376061 0.17951688 + [9,] -35.70352 1.693437 -31.75028 4.883108 0.22267725 +[10,] -41.77480 1.664414 -41.67037 5.713467 0.24671490 +[11,] -136.46103 1.425626 -283.36966 18.663538 0.63092852 + +$result$retres +$result$retres$res + [1] 25.1208420 5.7607832 0.6474419 -13.4422856 -10.1979061 4.6184470 -1.7852980 -4.2210687 3.7814620 3.9938956 -1.4484776 + +$result$retres$sim + col +row X DHA + [1,] 0.07724168 16.670067 + [2,] 0.17352157 13.689663 + [3,] 0.19329488 13.249827 + [4,] 0.21824566 12.735953 + [5,] 0.24311543 12.259569 + [6,] 0.26960419 11.783134 + [7,] 0.63923689 6.612397 + + +$result$it +[1] 9 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -0.050241684 0.8926490 +[2,] -0.011521566 2.1105344 +[3,] -0.001294884 NA +[4,] NA -1.8907310 +[5,] 0.026884571 -1.9969478 +[6,] 0.020395812 NA +[7,] -0.009236894 0.7242388 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3_res/dhaKLM-3_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3_res/dhaKLM-3_res.txt new file mode 100644 index 0000000..3c3d175 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/dhaKLM-3_res/dhaKLM-3_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0772416973706733 0.0778632491388357 0.0774923508328956 0.00122688543637317 0.0762725722735735 0.0808625338956896 +DHA 16.670066295773 16.7025362306397 16.6992697739348 0.319164680392768 16.1323600517798 17.2913366903573 +mu 0.05395750720208 0.0540177624956764 0.0539841486742074 0.000262414360970296 0.0535432397033494 0.0545081814341308 +qDHA -0.564763097194313 -0.57723595069237 -0.572963400588731 0.0687060990169572 -0.700466541062389 -0.424019932872308 +tlag 9.99999996587064e-07 0.180699149211601 1.00000000008427e-06 0.283451062663298 9.99999999473644e-07 0.864530604574533 +res 1024.0383456486 9.4828537675685 8.31573645907641 4.70896741663336 3.39245175911229 19.686951482249 + + +Goodness of fit (khi2 test) + +khi2 value 1024.03834564831 +data points 11 +fitted parameters 5 +degrees of freedom 6 +khi2 reduced value 170.673057608052 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1.txt new file mode 100644 index 0000000..9fd9360 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1.txt @@ -0,0 +1,10 @@ +"time" "X" "DHA" +0 0.063 16.5538640791172 +14.3763888888889 0.72 7.24836138441197 +15.6263888888889 0.92 7.42765310019496 +16.6238888888889 1.04 5.27558367904497 +17.6238888888889 1.17 2.67542504347393 +18.1238888888889 1.28 1.45934074061066 +18.6238888888889 1.34 0.34217275393937 +19.1238888888889 1.4 0.260288165585422 + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1_res/fsaA-1.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1_res/fsaA-1.pdf new file mode 100644 index 0000000..bf99c51 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1_res/fsaA-1.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1_res/fsaA-1_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1_res/fsaA-1_log.txt new file mode 100644 index 0000000..c47d423 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1_res/fsaA-1_log.txt @@ -0,0 +1,177 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 3.824778 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + [7,] 0.002 0.5 + [8,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 19.12389 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 19.1238878888889 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 19.1238878888889 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -19.123888 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.37639 15.62639 16.62389 17.62389 18.12389 18.62389 19.12389 + +$sys$data_meas + X DHA +[1,] 0.063 16.5538641 +[2,] 0.720 7.2483614 +[3,] 0.920 7.4276531 +[4,] 1.040 5.2755837 +[5,] 1.170 2.6754250 +[6,] 1.280 1.4593407 +[7,] 1.340 0.3421728 +[8,] 1.400 0.2602882 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 1.036652e-01 1.676377e+01 1.375062e-01 -1.550075e+00 9.999998e-07 + +$result$lastp + X DHA mu qDHA tlag + 1.033792e-08 1.414520e-07 -5.621760e-09 2.817502e-08 6.918910e-13 + +$result$hci + X DHA mu qDHA tlag + 0.09608859 11.44145420 0.01260835 1.48850033 7.24421965 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 11.7394 + +$result$laststep + X DHA mu qDHA tlag + 1.033792e-08 1.414520e-07 -5.621760e-09 2.817502e-08 6.918910e-13 + +$result$normp +[1] 1.4471e-07 + +$result$res + [1] 20.3325780 14.2265221 -15.5915670 -10.2571083 -0.1165123 -13.4893589 1.1004700 18.8638328 0.4198117 1.1787707 -2.4962950 -1.2318821 0.5143278 1.0481942 1.2591089 -0.7346102 + +$result$prevres + [1] 20.3325729 14.2265150 -15.5915723 -10.2571115 -0.1165127 -13.4893575 1.1004733 18.8638384 0.4198114 1.1787708 -2.4962948 -1.2318820 0.5143279 1.0481942 1.2591088 -0.7346103 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.0000 0.000000 0.0000 0.000000 -3.2172302 + [2,] 3609.9550 0.000000 5380.0255 0.000000 -51.4584668 + [3,] 4286.9609 0.000000 6944.4985 0.000000 -61.1089150 + [4,] 4917.2061 0.000000 8473.9086 0.000000 -70.0928086 + [5,] 5642.0457 0.000000 10307.9210 0.000000 -80.4251070 + [6,] 6043.5997 0.000000 11354.8086 0.000000 -86.1490990 + [7,] 6473.7330 0.000000 12498.5000 0.000000 -92.2804773 + [8,] 6934.4796 0.000000 13747.4715 0.000000 -98.8482362 + [9,] 0.0000 2.000000 0.0000 0.000000 0.1450684 +[10,] -134.4164 1.766297 -132.9013 8.989432 2.1998765 +[11,] -163.3393 1.747316 -178.7578 10.923718 2.6091099 +[12,] -190.2361 1.732315 -224.5639 12.722510 2.9901030 +[13,] -221.1450 1.717407 -280.4467 14.789623 3.4283021 +[14,] -238.2592 1.710000 -312.7209 15.934178 3.6710682 +[15,] -256.5856 1.702626 -348.2422 17.159797 3.9311177 +[16,] -276.2103 1.695284 -387.3090 18.472250 4.2096807 + +$result$retres +$result$retres$res + [1] 20.3325729 14.2265150 -15.5915723 -10.2571115 -0.1165127 -13.4893575 1.1004733 18.8638384 0.4198114 1.1787708 -2.4962948 -1.2318820 0.5143279 1.0481942 1.2591088 -0.7346103 + +$result$retres$sim + col +row X DHA + [1,] 0.1036651 16.7637698 + [2,] 0.7484530 7.8377468 + [3,] 0.8888169 6.1795057 + [4,] 1.0194858 4.6596427 + [5,] 1.1697670 2.9325890 + [6,] 1.2530213 1.9834378 + [7,] 1.3422009 0.9717272 + [8,] 1.4377277 -0.1070170 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -0.0406651458 -0.2099057 +[2,] -0.0284530301 -0.5893854 +[3,] 0.0311831446 1.2481474 +[4,] 0.0205142230 0.6159410 +[5,] 0.0002330254 -0.2571639 +[6,] 0.0269787150 -0.5240971 +[7,] -0.0022009466 -0.6295544 +[8,] -0.0377276768 0.3673051 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1_res/fsaA-1_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1_res/fsaA-1_res.txt new file mode 100644 index 0000000..bf93b02 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-1_res/fsaA-1_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.103665156090248 0.104453538554777 0.104174338473252 0.00128647408414985 0.102410523047733 0.107063444584246 +DHA 16.7637699416875 16.67435889106 16.5932307284783 0.48187873609825 15.7887539461949 17.6197993344253 +mu 0.137506196416978 0.137588773154395 0.137565242179155 0.000444796310057704 0.136829101060917 0.138466692150395 +qDHA -1.55007545200465 -1.53464346538342 -1.52460753997153 0.0609139939928476 -1.65336741239841 -1.41906802536968 +tlag 9.99999826500897e-07 0.0646458367228709 0.0173409150375325 0.0831679146078303 9.99999999875406e-07 0.280225203164018 +res 1515.94751075913 12.3933120319842 11.6047594586931 5.42533144503074 3.16137843230262 23.8647862960788 + + +Goodness of fit (khi2 test) + +khi2 value 1515.94751075907 +data points 16 +fitted parameters 5 +degrees of freedom 11 +khi2 reduced value 137.813410069006 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2.txt new file mode 100644 index 0000000..8153c00 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2.txt @@ -0,0 +1,10 @@ +"time" "X" "DHA" +0 0.066 14.2759362214275 +14.3763888888889 0.57 5.03457025564164 +15.6263888888889 0.73 4.72889760563487 +16.6238888888889 0.94 3.69555628180219 +17.6238888888889 0.9 2.52848744476874 +18.1238888888889 1.07 1.99325612574553 +18.6238888888889 1.19 0.632275509837759 +19.1238888888889 1.31 0.0872919397395476 + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2_res/fsaA-2.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2_res/fsaA-2.pdf new file mode 100644 index 0000000..a699605 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2_res/fsaA-2.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2_res/fsaA-2_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2_res/fsaA-2_log.txt new file mode 100644 index 0000000..761a576 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2_res/fsaA-2_log.txt @@ -0,0 +1,177 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 3.824778 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + [7,] 0.002 0.5 + [8,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 19.12389 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 19.1238878888889 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 19.1238878888889 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -19.123888 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.37639 15.62639 16.62389 17.62389 18.12389 18.62389 19.12389 + +$sys$data_meas + X DHA +[1,] 0.066 14.27593622 +[2,] 0.570 5.03457026 +[3,] 0.730 4.72889761 +[4,] 0.940 3.69555628 +[5,] 0.900 2.52848744 +[6,] 1.070 1.99325613 +[7,] 1.190 0.63227551 +[8,] 1.310 0.08729194 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.06583399 13.25167718 0.16430430 -1.64922277 1.05599317 + +$result$lastp + X DHA mu qDHA tlag + 1.220466e-11 4.491477e-09 -9.619960e-11 7.236801e-11 -8.705452e-09 + +$result$hci + X DHA mu qDHA tlag + 0.09407791 20.16556554 0.02777980 3.53473360 9.15013396 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 21.37643 + +$result$laststep + X DHA mu qDHA tlag + 1.220466e-11 4.491477e-09 -9.619960e-11 7.236801e-11 -8.705452e-09 + +$result$normp +[1] 9.796576e-09 + +$result$res + [1] -0.08300306 8.70841012 -4.32839939 -45.09679408 50.77940486 8.65662613 -4.79496309 -14.26103195 -2.04851809 3.25312070 1.04667835 0.45503790 -0.31204416 -0.97991936 -0.13588572 -1.07542763 + +$result$prevres + [1] -0.08300307 8.70841002 -4.32839947 -45.09679413 50.77940485 8.65662614 -4.79496304 -14.26103187 -2.04851810 3.25312070 1.04667835 0.45503790 -0.31204416 -0.97991936 -0.13588572 -1.07542763 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.0000 0.000000 0.00000 0.000000 0.000000 + [2,] 4461.3488 0.000000 3912.31224 0.000000 -48.257555 + [3,] 5478.5010 0.000000 5255.12794 0.000000 -59.259896 + [4,] 6454.1612 0.000000 6614.84880 0.000000 -69.813425 + [5,] 7606.6994 0.000000 8296.86095 0.000000 -82.280211 + [6,] 8257.9925 0.000000 9279.07460 0.000000 -89.325123 + [7,] 8965.0499 0.000000 10368.66054 0.000000 -96.973227 + [8,] 9732.6462 0.000000 11576.80485 0.000000 -105.276169 + [9,] 0.0000 2.000000 0.00000 0.000000 0.000000 +[10,] -153.1752 1.766297 -90.92319 6.114476 1.850400 +[11,] -192.1559 1.747316 -127.30499 7.670517 2.269968 +[12,] -229.5157 1.732315 -164.94865 9.161851 2.672438 +[13,] -273.6214 1.717407 -212.31784 10.922471 3.147887 +[14,] -298.5355 1.710000 -240.29948 11.916996 3.416566 +[15,] -325.5763 1.702626 -271.56714 12.996418 3.708254 +[16,] -354.9260 1.695284 -306.47818 14.168006 4.024920 + +$result$retres +$result$retres$res + [1] -0.08300307 8.70841002 -4.32839947 -45.09679413 50.77940485 8.65662614 -4.79496304 -14.26103187 -2.04851810 3.25312070 1.04667835 0.45503790 -0.31204416 -0.97991936 -0.13588572 -1.07542763 + +$result$retres$sim + col +row X DHA + [1,] 0.06583399 13.2516772 + [2,] 0.58741682 6.6611306 + [3,] 0.72134320 5.2522368 + [4,] 0.84980641 3.9230752 + [5,] 1.00155881 2.3724654 + [6,] 1.08731325 1.5032964 + [7,] 1.18041007 0.5643326 + [8,] 1.28147794 -0.4504219 + + +$result$it +[1] 9 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] 0.0001660061 1.02425905 +[2,] -0.0174168200 -1.62656035 +[3,] 0.0086567989 -0.52333918 +[4,] 0.0901935883 -0.22751895 +[5,] -0.1015588097 0.15602208 +[6,] -0.0173132523 0.48995968 +[7,] 0.0095899261 0.06794286 +[8,] 0.0285220637 0.53771382 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2_res/fsaA-2_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2_res/fsaA-2_res.txt new file mode 100644 index 0000000..e5b3845 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-2_res/fsaA-2_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0658339938710197 0.0660658081821672 0.066180996516927 0.00166925391625312 0.0632361039132883 0.0692601657708497 +DHA 13.2516771755278 13.1103641031006 13.1180165522072 0.447738001561714 12.2761178513031 13.8915405531498 +mu 0.164304302259284 0.164272954265818 0.164279124810003 0.000600604788129164 0.163234712597118 0.165364103409441 +qDHA -1.64922276932891 -1.61013539602321 -1.61445831159137 0.0771666065468398 -1.75954433555692 -1.45471021746012 +tlag 1.05599317049447 1.07195906578892 1.07422048290871 0.167133369767811 0.782726114153107 1.42785463123473 +res 5026.46745020853 10.7460351794129 9.85792861140935 4.47836700222491 4.48876412536886 20.4844871441231 + + +Goodness of fit (khi2 test) + +khi2 value 5026.46745020854 +data points 16 +fitted parameters 5 +degrees of freedom 11 +khi2 reduced value 456.951586382595 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3.txt new file mode 100644 index 0000000..ac2ba6b --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3.txt @@ -0,0 +1,10 @@ +"time" "X" "DHA" +0 0.062 17.5152469392568 +14.3763888888889 0.73 7.99729257802944 +15.6263888888889 0.9 6.08084367279699 +16.6238888888889 1.12 4.21175038252713 +17.6238888888889 1.2 2.6456750309825 +18.1238888888889 1.29 1.49100616222069 +18.6238888888889 1.39 0.235434751787573 +19.1238888888889 1.44 0.380261944305956 + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3_res/fsaA-3.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3_res/fsaA-3.pdf new file mode 100644 index 0000000..2284905 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3_res/fsaA-3.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3_res/fsaA-3_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3_res/fsaA-3_log.txt new file mode 100644 index 0000000..8961bb8 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3_res/fsaA-3_log.txt @@ -0,0 +1,177 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 3.824778 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + [7,] 0.002 0.5 + [8,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 19.12389 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 19.1238878888889 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 19.1238878888889 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -19.123888 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.37639 15.62639 16.62389 17.62389 18.12389 18.62389 19.12389 + +$sys$data_meas + X DHA +[1,] 0.062 17.5152469 +[2,] 0.730 7.9972926 +[3,] 0.900 6.0808437 +[4,] 1.120 4.2117504 +[5,] 1.200 2.6456750 +[6,] 1.290 1.4910062 +[7,] 1.390 0.2354348 +[8,] 1.440 0.3802619 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.1011976 17.3109523 0.1403347 -1.6239079 0.0000010 + +$result$lastp + X DHA mu qDHA tlag +-1.089960e-07 -1.358833e-07 6.067928e-08 -5.278680e-07 3.845813e-13 + +$result$hci + X DHA mu qDHA tlag + 0.12488667 14.85541800 0.01605765 1.91136670 9.39698396 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 15.28451 + +$result$laststep + X DHA mu qDHA tlag +-1.089960e-07 -1.358833e-07 6.067928e-08 -5.278680e-07 3.845813e-13 + +$result$normp +[1] 5.5917e-07 + +$result$res + [1] 19.59879929 15.48033464 3.43544777 -38.43348096 0.14515976 -1.23166795 -4.43762753 20.75776413 -0.40858931 -0.05933731 0.24311257 0.73448410 0.16598093 0.43691779 0.77199415 -1.84144416 + +$result$prevres + [1] 19.59885379 15.48041252 3.43550620 -38.43344532 0.14516436 -1.23168255 -4.43766415 20.75770238 -0.40858904 -0.05933957 0.24311087 0.73448313 0.16598101 0.43691854 0.77199568 -1.84144173 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.0000 0.000000 0.0000 0.000000 -3.2052562 + [2,] 3759.7730 0.000000 5469.9340 0.000000 -53.3945964 + [3,] 4480.6895 0.000000 7085.5591 0.000000 -63.6327260 + [4,] 5153.9365 0.000000 8670.4639 0.000000 -73.1938748 + [5,] 5930.4225 0.000000 10576.8911 0.000000 -84.2211788 + [6,] 6361.4911 0.000000 11667.5848 0.000000 -90.3430199 + [7,] 6823.8931 0.000000 12860.9555 0.000000 -96.9098435 + [8,] 7319.9060 0.000000 14166.1673 0.000000 -103.9539941 + [9,] 0.0000 2.000000 0.0000 0.000000 0.1483607 +[10,] -144.6775 1.766297 -140.2194 9.015929 2.3449103 +[11,] -176.3173 1.747316 -189.1704 10.987635 2.7911242 +[12,] -205.8351 1.732315 -238.2233 12.827114 3.2078590 +[13,] -239.8534 1.717407 -298.2380 14.947043 3.6885207 +[14,] -258.7292 1.710000 -332.9716 16.123337 3.9553698 +[15,] -278.9709 1.702626 -371.2543 17.384746 4.2416210 +[16,] -300.6777 1.695284 -413.4182 18.737457 4.5486846 + +$result$retres +$result$retres$res + [1] 19.59885379 15.48041252 3.43550620 -38.43344532 0.14516436 -1.23168255 -4.43766415 20.75770238 -0.40858904 -0.05933957 0.24311087 0.73448313 0.16598101 0.43691854 0.77199568 -1.84144173 + +$result$retres$sim + col +row X DHA + [1,] 0.1011977 17.3109524 + [2,] 0.7609608 7.9676228 + [3,] 0.9068710 6.2023991 + [4,] 1.0431331 4.5789919 + [5,] 1.2002903 2.7286655 + [6,] 1.2875366 1.7094654 + [7,] 1.3811247 0.6214326 + [8,] 1.4815154 -0.5404589 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -0.0391977076 0.20429452 +[2,] -0.0309608250 0.02966979 +[3,] -0.0068710124 -0.12155543 +[4,] 0.0768668906 -0.36724156 +[5,] -0.0002903287 -0.08299050 +[6,] 0.0024633651 -0.21845927 +[7,] 0.0088753283 -0.38599784 +[8,] -0.0415154048 0.92072086 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3_res/fsaA-3_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3_res/fsaA-3_res.txt new file mode 100644 index 0000000..2a8d68d --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-3_res/fsaA-3_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.10119759857541 0.101975874030175 0.101793587881668 0.00138564713999565 0.100101358307981 0.105650807294015 +DHA 17.3109522818836 17.2250276042452 17.2548688108746 0.440134284286943 16.3750937649157 18.0634513882808 +mu 0.140334739301992 0.140357943023686 0.140298398874269 0.00050500210968007 0.139557928243762 0.141421733794107 +qDHA -1.62390790041695 -1.59953672621546 -1.59246646129056 0.0518298216932858 -1.70710269727718 -1.50516959710166 +tlag 9.99999989925726e-07 0.0563777500096881 1.00000000002876e-06 0.0896754490969904 9.99999999875406e-07 0.317690150369604 +res 2569.77821653641 11.7682915688946 11.3151254732183 4.74906075488955 4.18868564670591 22.0965805118714 + + +Goodness of fit (khi2 test) + +khi2 value 2569.778216554 +data points 16 +fitted parameters 5 +degrees of freedom 11 +khi2 reduced value 233.616201504909 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4.txt new file mode 100644 index 0000000..5140c74 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4.txt @@ -0,0 +1,8 @@ +"time" "X" "DHA" +0 0.027 17.5627155874568 +15 0.258 13.2904139352901 +17 0.364 10.9558956583542 +19.25 0.53 NA +21.25 0.72 5.96190401715964 +23.1666666666667 1 2.89931114118383 + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4_res/fsaA-3.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4_res/fsaA-3.pdf new file mode 100644 index 0000000..c517653 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4_res/fsaA-3.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4_res/fsaA-3_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4_res/fsaA-3_log.txt new file mode 100644 index 0000000..3d3c203 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4_res/fsaA-3_log.txt @@ -0,0 +1,164 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 4.633333 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 23.16667 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 23.1666656666667 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 23.1666656666667 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -23.166666 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 15.00000 17.00000 19.25000 21.25000 23.16667 + +$sys$data_meas + X DHA +[1,] 0.027 17.562716 +[2,] 0.258 13.290414 +[3,] 0.364 10.955896 +[4,] 0.530 NA +[5,] 0.720 5.961904 +[6,] 1.000 2.899311 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.02703444 17.73037070 0.16433433 -2.08809692 1.21118548 + +$result$lastp + X DHA mu qDHA tlag + 2.865670e-09 -6.005188e-08 1.870534e-09 7.827219e-09 9.365951e-07 + +$result$hci + X DHA mu qDHA tlag +0.011137608 2.148339975 0.003575268 0.576105181 2.545256446 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 2.277067 + +$result$laststep + X DHA mu qDHA tlag + 2.865670e-09 -6.005188e-08 1.870534e-09 7.827219e-09 9.365951e-07 + +$result$normp +[1] 9.385572e-07 + +$result$res + [1] 0.01722169 1.31312420 -0.97975611 -2.99564627 3.95483804 -1.30039101 0.33531023 -1.14500972 0.53181943 0.56187831 -0.31309184 + +$result$prevres + [1] 0.01722026 1.31312708 -0.97975278 -2.99564256 3.95484183 -1.30038759 0.33531035 -1.14500990 0.53181919 0.56187791 -0.31309231 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.0000 0.000000 0.00000 0.000000 0.000000 + [2,] 4820.2635 0.000000 1796.86366 0.000000 -21.414921 + [3,] 6695.9125 0.000000 2858.09528 0.000000 -29.747841 + [4,] 9691.5029 0.000000 4726.24825 0.000000 -43.056311 + [5,] 13462.6364 0.000000 7293.22391 0.000000 -59.810276 + [6,] 18446.8257 0.000000 10949.19042 0.000000 -81.953468 + [7,] 0.0000 2.000000 0.00000 0.000000 0.000000 + [8,] -211.3203 1.756802 -53.73622 2.735949 1.039046 + [9,] -302.2550 1.726693 -90.76670 3.913274 1.441323 +[10,] -629.7520 1.664414 -253.73682 8.153354 2.892737 +[11,] -870.7516 1.637067 -392.60295 11.273558 3.961862 + +$result$retres +$result$retres$res + [1] 0.01722026 1.31312708 -0.97975278 -2.99564256 3.95484183 -1.30038759 0.33531035 -1.14500990 0.53181919 0.56187791 -0.31309231 + +$result$retres$sim + col +row X DHA + [1,] 0.02703444 17.730371 + [2,] 0.26062625 12.717909 + [3,] 0.36204049 11.221805 + [4,] 0.52400871 8.966306 + [5,] 0.72790968 6.242843 + [6,] 0.99739922 2.742765 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -3.444052e-05 -0.1676552 +[2,] -2.626254e-03 0.5725050 +[3,] 1.959506e-03 -0.2659096 +[4,] 5.991285e-03 NA +[5,] -7.909684e-03 -0.2809390 +[6,] 2.600775e-03 0.1565462 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4_res/fsaA-3_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4_res/fsaA-3_res.txt new file mode 100644 index 0000000..30c4d99 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaA-4_res/fsaA-3_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0270344433825737 0.0269930552972946 0.027166500422744 0.00173174893189778 0.023596565307493 0.0302311104792774 +DHA 17.7303707004261 17.7597082528982 17.7796281394468 0.384176579475149 16.9803332724885 18.6002085391542 +mu 0.164334333855806 0.164291093702129 0.164255093024368 0.000573995716233835 0.163148431389816 0.16526825319258 +qDHA -2.0880969217259 -2.08814051895832 -2.07799660744369 0.114518314549379 -2.32390803582977 -1.86806480120691 +tlag 1.21118548053599 1.18298879085431 1.22381685389095 0.39942133030086 0.332579368400487 1.86188429628994 +res 31.1102168920635 7.0059645472804 5.9876699276043 3.80881845528234 2.07410108223096 16.0523035841121 + + +Goodness of fit (khi2 test) + +khi2 value 31.1102168921245 +data points 11 +fitted parameters 5 +degrees of freedom 6 +khi2 reduced value 5.18503614868742 +p-value, i.e. P(X^2<=value) 0.99997584995084 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1.txt new file mode 100644 index 0000000..5445d4c --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1.txt @@ -0,0 +1,9 @@ +"time" "X" "DHA" +0 0.028 14.0966842707368 +14.9597222222222 0.267 10.3399875933251 +16.9097222222222 0.384 9.10355605334123 +19.0072222222222 0.502 7.81863285856706 +20.4572222222222 0.609 5.99444953033369 +22.4572222222222 0.761 3.34400873585295 +23.4605555555556 0.841 2.17964869377495 +24.4486111111111 0.921 1.58231022922151 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1_res/D-fsaB-1.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1_res/D-fsaB-1.pdf new file mode 100644 index 0000000..fb26689 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1_res/D-fsaB-1.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1_res/D-fsaB-1_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1_res/D-fsaB-1_log.txt new file mode 100644 index 0000000..6f4fc57 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1_res/D-fsaB-1_log.txt @@ -0,0 +1,177 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 4.889722 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + [7,] 0.002 0.5 + [8,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 24.44861 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 24.4486101111111 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 24.4486101111111 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -24.448610 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.95972 16.90972 19.00722 20.45722 22.45722 23.46056 24.44861 + +$sys$data_meas + X DHA +[1,] 0.028 14.096684 +[2,] 0.267 10.339988 +[3,] 0.384 9.103556 +[4,] 0.502 7.818633 +[5,] 0.609 5.994450 +[6,] 0.761 3.344009 +[7,] 0.841 2.179649 +[8,] 0.921 1.582310 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 4.947500e-02 1.469835e+01 1.206952e-01 -1.512040e+00 9.999999e-07 + +$result$lastp + X DHA mu qDHA tlag + 2.297589e-08 9.315038e-07 -2.085517e-08 8.081613e-09 -6.750156e-14 + +$result$hci + X DHA mu qDHA tlag + 0.070022226 7.239231051 0.009002339 1.403674344 12.035780766 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 8.672224 + +$result$laststep + X DHA mu qDHA tlag + 2.297589e-08 9.315038e-07 -2.085517e-08 8.081613e-09 -6.750156e-14 + +$result$normp +[1] 9.320555e-07 + +$result$res + [1] 10.73749936 16.98860195 -1.57792530 -5.71978084 -12.30850306 -8.53496131 -0.65003560 12.52631296 1.20334137 -0.86959261 -0.71282305 -1.18255315 -0.05074554 1.08098079 0.95322151 -0.55087727 + +$result$prevres + [1] 10.73748787 16.98857902 -1.57794658 -5.71979751 -12.30851409 -8.53495984 -0.65002515 12.52633447 1.20333951 -0.86959271 -0.71282290 -1.18255277 -0.05074506 1.08098131 0.95322197 -0.55087691 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.0000 0.000000 0.00000 0.000000 -1.34772974 + [2,] 3041.7110 0.000000 2251.26719 0.000000 -18.16325748 + [3,] 3848.8559 0.000000 3219.98384 0.000000 -22.98303837 + [4,] 4957.6619 0.000000 4662.09507 0.000000 -29.60415668 + [5,] 5905.8439 0.000000 5977.42587 0.000000 -35.26612601 + [6,] 7518.2460 0.000000 8353.30119 0.000000 -44.89441552 + [7,] 8486.1077 0.000000 9849.91324 0.000000 -50.67389994 + [8,] 9560.9210 0.000000 11564.83642 0.000000 -57.09203424 + [9,] 0.0000 2.000000 0.00000 0.000000 0.06753607 +[10,] -121.6919 1.757413 -58.72424 3.981841 0.85813897 +[11,] -159.7791 1.728041 -89.45431 5.228081 1.08337549 +[12,] -211.9922 1.696994 -136.91785 6.936530 1.39283807 +[13,] -256.5783 1.675858 -181.37036 8.395419 1.65749832 +[14,] -332.3135 1.647137 -263.50102 10.873526 2.10759434 +[15,] -377.7391 1.632914 -316.10952 12.359882 2.37778441 +[16,] -428.1620 1.619028 -377.01513 14.009754 2.67784081 + +$result$retres +$result$retres$res + [1] 10.73748787 16.98857902 -1.57794658 -5.71979751 -12.30851409 -8.53495984 -0.65002515 12.52633447 1.20333951 -0.86959271 -0.71282290 -1.18255277 -0.05074506 1.08098131 0.95322197 -0.55087691 + +$result$retres$sim + col +row X DHA + [1,] 0.04947498 14.698354 + [2,] 0.30097716 9.905191 + [3,] 0.38084411 8.747145 + [4,] 0.49056040 7.227356 + [5,] 0.58438297 5.969077 + [6,] 0.74393008 3.884499 + [7,] 0.83969995 2.656260 + [8,] 0.94605267 1.306872 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -0.021474976 -0.60166975 +[2,] -0.033977158 0.43479635 +[3,] 0.003155893 0.35641145 +[4,] 0.011439595 0.59127639 +[5,] 0.024617028 0.02537253 +[6,] 0.017069920 -0.54049065 +[7,] 0.001300050 -0.47661099 +[8,] -0.025052669 0.27543846 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1_res/D-fsaB-1_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1_res/D-fsaB-1_res.txt new file mode 100644 index 0000000..6df9dbe --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-1_res/D-fsaB-1_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0494749987201887 0.0504395983370219 0.0500745618674241 0.00130322568836968 0.0487176882183526 0.0529606427407315 +DHA 14.6983549569373 14.6946287436473 14.6866337795985 0.381922165916792 14.0625746233942 15.344142124614 +mu 0.120695234551369 0.120783589930155 0.120710798248742 0.000496634806827808 0.119919815586194 0.121667791036614 +qDHA -1.51203966794307 -1.51445843260799 -1.51425043007884 0.073334583343477 -1.64997475389869 -1.3888892267308 +tlag 9.99999884232494e-07 0.173520500457481 0.0568891168091444 0.214032252374957 9.99999999584666e-07 0.742773586116535 +res 827.28206671062 11.6669122108004 10.7869089865227 5.27810652813194 3.93012371941519 24.8356029696855 + + +Goodness of fit (khi2 test) + +khi2 value 827.282066712595 +data points 16 +fitted parameters 5 +degrees of freedom 11 +khi2 reduced value 75.2074606102359 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2.txt new file mode 100644 index 0000000..37b6e3f --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2.txt @@ -0,0 +1,8 @@ +"time" "X" "DHA" +0 0.06 13.5371602216208 +14.9930555555556 0.412 9.62837147580034 +15.9430555555556 0.475 8.69799577417337 +16.9430555555556 0.536 7.2835559192104 +18.0430555555556 0.61 6.05013999789047 +19.1097222222222 0.707 4.67525168691874 +20.1597222222222 0.806 3.38789832016416 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2_res/D-fsaB-2.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2_res/D-fsaB-2.pdf new file mode 100644 index 0000000..bf92fdc Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2_res/D-fsaB-2.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2_res/D-fsaB-2_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2_res/D-fsaB-2_log.txt new file mode 100644 index 0000000..eae8fb7 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2_res/D-fsaB-2_log.txt @@ -0,0 +1,171 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 4.031944 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + [7,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 20.15972 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 20.1597212222222 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 20.1597212222222 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -20.159721 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.99306 15.94306 16.94306 18.04306 19.10972 20.15972 + +$sys$data_meas + X DHA +[1,] 0.060 13.537160 +[2,] 0.412 9.628371 +[3,] 0.475 8.697996 +[4,] 0.536 7.283556 +[5,] 0.610 6.050140 +[6,] 0.707 4.675252 +[7,] 0.806 3.387898 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.0607619 14.2639116 0.1282692 -1.4668343 0.0000010 + +$result$lastp + X DHA mu qDHA tlag +-2.555552e-10 -1.405948e-07 2.305350e-10 3.579823e-08 0.000000e+00 + +$result$hci + X DHA mu qDHA tlag +0.015048774 1.781633788 0.003238336 0.418170583 2.072975088 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.78941 + +$result$laststep + X DHA mu qDHA tlag +-2.555552e-10 -1.405948e-07 2.305350e-10 3.579823e-08 0.000000e+00 + +$result$normp +[1] 1.450811e-07 + +$result$res + [1] 0.3809509 1.8805454 -2.6799683 -1.0427201 2.4107547 -1.0159593 0.3029658 1.4535027 -1.9612938 -1.4693115 -0.2413342 0.2480621 0.8320152 1.0004308 + +$result$prevres + [1] 0.3809511 1.8805456 -2.6799682 -1.0427201 2.4107548 -1.0159594 0.3029657 1.4535030 -1.9612937 -1.4693115 -0.2413342 0.2480620 0.8320150 1.0004306 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.0000 0.000000 0.00000 0.000000 -1.7590611 + [2,] 3421.2317 0.000000 3116.76436 0.000000 -26.6646810 + [3,] 3864.5932 0.000000 3743.74858 0.000000 -30.1201886 + [4,] 4393.4977 0.000000 4523.07176 0.000000 -34.2424092 + [5,] 5059.2681 0.000000 5546.62902 0.000000 -39.4313459 + [6,] 5801.0699 0.000000 6735.87175 0.000000 -45.2128623 + [7,] 6637.4315 0.000000 8130.47536 0.000000 -51.7313676 + [8,] 0.0000 2.000000 0.00000 0.000000 0.0804636 + [9,] -127.7926 1.756907 -76.85325 5.293658 1.1525893 +[10,] -146.9466 1.742540 -95.22185 6.087090 1.3005928 +[11,] -169.7732 1.727543 -118.48894 7.032657 1.4771645 +[12,] -198.4797 1.711196 -149.61313 8.221789 1.6994422 +[13,] -230.4375 1.695491 -186.39472 9.545605 1.9471183 +[14,] -266.4435 1.680173 -230.18038 11.037113 2.2263799 + +$result$retres +$result$retres$res + [1] 0.3809511 1.8805456 -2.6799682 -1.0427201 2.4107548 -1.0159594 0.3029657 1.4535030 -1.9612937 -1.4693115 -0.2413342 0.2480620 0.8320150 1.0004306 + +$result$retres$sim + col +row X DHA + [1,] 0.0607619 14.263912 + [2,] 0.4157611 8.647725 + [3,] 0.4696401 7.963340 + [4,] 0.5339146 7.162889 + [5,] 0.6148215 6.174171 + [6,] 0.7049681 5.091259 + [7,] 0.8066059 3.888114 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -0.0007619021 -0.7267515 +[2,] -0.0037610911 0.9806469 +[3,] 0.0053599363 0.7346557 +[4,] 0.0020854401 0.1206671 +[5,] -0.0048215095 -0.1240310 +[6,] 0.0020319188 -0.4160075 +[7,] -0.0006059313 -0.5002153 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2_res/D-fsaB-2_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2_res/D-fsaB-2_res.txt new file mode 100644 index 0000000..0e16c2a --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-2_res/D-fsaB-2_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.060761901867639 0.0614148080209154 0.061101126601452 0.00150185937960249 0.0592815737201235 0.0646520970874588 +DHA 14.2639115769643 14.2600390819833 14.3067319074736 0.429020241739314 13.419630925465 15.038669184579 +mu 0.128269246845908 0.128494074456596 0.128479529539133 0.000774025504180055 0.126904708339444 0.130105624661101 +qDHA -1.46683428782563 -1.47011781687191 -1.47215199879317 0.0985660316618392 -1.64442883998669 -1.27093289977056 +tlag 1.000000000001e-06 0.11209724770066 1.00000000011202e-06 0.171419109802355 9.99999999720669e-07 0.597589616610639 +res 28.8178774479281 9.8067134084551 8.99368520317207 4.66534518769336 3.28680890527192 20.9356779619399 + + +Goodness of fit (khi2 test) + +khi2 value 28.8178774479283 +data points 14 +fitted parameters 5 +degrees of freedom 9 +khi2 reduced value 3.20198638310314 +p-value, i.e. P(X^2<=value) 0.999304503558486 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3.txt new file mode 100644 index 0000000..c5be5ed --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3.txt @@ -0,0 +1,9 @@ +"time" "X" "DHA" +0 0.046 14.1576014285142 +14.6263888888889 0.318 9.43061765241843 +16.7263888888889 0.425 8.20310402661491 +18.6430555555556 0.544 6.56564011554499 +19.7597222222222 0.623 4.76455079734043 +20.7430555555556 0.713 4.33145366452681 +21.7763888888889 0.784 2.19236810158525 +23.1238888888889 0.898 1.39314945552377 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3_res/D-fsaB-3.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3_res/D-fsaB-3.pdf new file mode 100644 index 0000000..5b780e7 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3_res/D-fsaB-3.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3_res/D-fsaB-3_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3_res/D-fsaB-3_log.txt new file mode 100644 index 0000000..3b0a347 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3_res/D-fsaB-3_log.txt @@ -0,0 +1,177 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 4.624778 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + [7,] 0.002 0.5 + [8,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 23.12389 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 23.1238878888889 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 23.1238878888889 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -23.123888 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.62639 16.72639 18.64306 19.75972 20.74306 21.77639 23.12389 + +$sys$data_meas + X DHA +[1,] 0.046 14.157601 +[2,] 0.318 9.430618 +[3,] 0.425 8.203104 +[4,] 0.544 6.565640 +[5,] 0.623 4.764551 +[6,] 0.713 4.331454 +[7,] 0.784 2.192368 +[8,] 0.898 1.393149 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.05842196 14.41950206 0.11910185 -1.57553910 0.00000100 + +$result$lastp + X DHA mu qDHA tlag +-1.582717e-09 -4.273200e-08 1.302482e-09 -3.968487e-09 -4.440892e-16 + +$result$hci + X DHA mu qDHA tlag +0.045729971 4.972394616 0.006593376 0.986361106 6.835950775 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 5.642742 + +$result$laststep + X DHA mu qDHA tlag +-1.582717e-09 -4.273200e-08 1.302482e-09 -3.968487e-09 -4.440892e-16 + +$result$normp +[1] 4.29648e-08 + +$result$res + [1] 6.2109784 7.7631433 1.6525030 -2.9312447 -4.1571157 -10.9695292 -1.2168718 9.8128960 0.5238013 -0.4041967 -0.7670463 -0.6318819 0.8345235 -0.3992560 1.4213799 -0.6268178 + +$result$prevres + [1] 6.2109792 7.7631447 1.6525042 -2.9312440 -4.1571153 -10.9695291 -1.2168722 9.8128946 0.5238014 -0.4041967 -0.7670463 -0.6318819 0.8345235 -0.3992560 1.4213799 -0.6268178 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.0000 0.000000 0.00000 0.000000 -1.57044106 + [2,] 2854.4600 0.000000 2439.14244 0.000000 -19.86179923 + [3,] 3665.6167 0.000000 3581.99785 0.000000 -25.50595966 + [4,] 4605.6100 0.000000 5016.26350 0.000000 -32.04658691 + [5,] 5260.7426 0.000000 6073.00972 0.000000 -36.60510648 + [6,] 5914.3938 0.000000 7167.35741 0.000000 -41.15331868 + [7,] 6688.9769 0.000000 8509.84497 0.000000 -46.54299389 + [8,] 7853.4323 0.000000 10609.53794 0.000000 -54.64546506 + [9,] 0.0000 2.000000 0.00000 0.000000 0.08309833 +[10,] -119.0837 1.762484 -65.87131 4.415698 0.99083380 +[11,] -159.4921 1.730781 -103.77262 5.914066 1.26908396 +[12,] -206.2163 1.702344 -153.16191 7.646626 1.59158052 +[13,] -238.7381 1.685992 -190.42191 8.852555 1.81636754 +[14,] -271.1611 1.671723 -229.58211 10.054822 2.04065904 +[15,] -309.5576 1.656858 -278.25216 11.478584 2.30645935 +[16,] -367.2411 1.637673 -355.45738 13.617527 2.70606515 + +$result$retres +$result$retres$res + [1] 6.2109792 7.7631447 1.6525042 -2.9312440 -4.1571153 -10.9695291 -1.2168722 9.8128946 0.5238014 -0.4041967 -0.7670463 -0.6318819 0.8345235 -0.3992560 1.4213799 -0.6268178 + +$result$retres$sim + col +row X DHA + [1,] 0.05842196 14.419502 + [2,] 0.33352629 9.228519 + [3,] 0.42830501 7.819581 + [4,] 0.53813751 6.249699 + [5,] 0.61468577 5.181813 + [6,] 0.69106094 4.131826 + [7,] 0.78156626 2.903058 + [8,] 0.91762579 1.079741 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -0.012421958 -0.2619007 +[2,] -0.015526289 0.2020984 +[3,] -0.003305008 0.3835231 +[4,] 0.005862488 0.3159410 +[5,] 0.008314231 -0.4172617 +[6,] 0.021939058 0.1996280 +[7,] 0.002433744 -0.7106899 +[8,] -0.019625789 0.3134089 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3_res/D-fsaB-3_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3_res/D-fsaB-3_res.txt new file mode 100644 index 0000000..f7e49fc --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/fsaB-3_res/D-fsaB-3_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0584219567678786 0.0590848302063425 0.0588795648062363 0.00128046273171084 0.0573575255901198 0.0627239963091861 +DHA 14.4195020647707 14.4653805855053 14.4563039665496 0.387444380894254 13.7271172150581 15.1186083963495 +mu 0.119101852403693 0.119115052107508 0.119082062532718 0.000508703773331324 0.118206828655884 0.120017788336837 +qDHA -1.57553909929175 -1.59047012038485 -1.59424005690981 0.0767362692843871 -1.71684659588046 -1.45727507203689 +tlag 1.00000000013978e-06 0.0958290592575493 1.00000000008427e-06 0.162637248977771 9.99999999579115e-07 0.607845365169201 +res 350.245928945968 11.8021842940741 10.4614959675611 5.20506342031596 4.64617535160237 24.6205722530572 + + +Goodness of fit (khi2 test) + +khi2 value 350.24592894597 +data points 16 +fitted parameters 5 +degrees of freedom 11 +khi2 reduced value 31.8405389950882 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1.txt new file mode 100644 index 0000000..7793c1a --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1.txt @@ -0,0 +1,7 @@ +"time" "X" "DHA" +0 0.069 10.7824647055244 +14.8263888888889 0.217 7.78562963474239 +17.1905555555556 0.29 7.20165438888892 +18.9405555555556 0.368 6.42109764149892 +21.0272222222222 0.487 4.96363465828093 +22.8325 0.627 3.49118071820468 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1_res/gldA.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1_res/gldA.pdf new file mode 100644 index 0000000..11b9b43 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1_res/gldA.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1_res/gldA_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1_res/gldA_log.txt new file mode 100644 index 0000000..5d338e4 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1_res/gldA_log.txt @@ -0,0 +1,165 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.1000 0.1000 0.1000 0.1000 4.5665 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.0000 50.0000 50.0000 50.0000 22.8325 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 22.832499 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 22.832499 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -22.832499 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.82639 17.19056 18.94056 21.02722 22.83250 + +$sys$data_meas + X DHA +[1,] 0.069 10.782465 +[2,] 0.217 7.785630 +[3,] 0.290 7.201654 +[4,] 0.368 6.421098 +[5,] 0.487 4.963635 +[6,] 0.627 3.491181 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.06898978 10.72138123 0.13478269 -1.33196912 6.48662603 + +$result$lastp + X DHA mu qDHA tlag +-4.410241e-13 7.797880e-09 -4.126382e-10 8.596131e-10 -4.392326e-08 + +$result$hci + X DHA mu qDHA tlag +0.005900996 1.150405189 0.002688925 0.432399382 0.697377299 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.248194 + +$result$laststep + X DHA mu qDHA tlag +-4.410241e-13 7.797880e-09 -4.126382e-10 8.596131e-10 -4.392326e-08 + +$result$normp +[1] 4.462027e-08 + +$result$res + [1] -0.005107676 -2.348540831 0.986722647 0.820555474 1.346609299 -1.203791174 -0.122166948 0.541410613 -0.176082091 -0.352530029 -0.013365003 0.131664907 + +$result$prevres + [1] -0.005107676 -2.348541094 0.986722429 0.820555330 1.346609320 -1.203790914 -0.122166964 0.541410615 -0.176082086 -0.352530023 -0.013364998 0.131664908 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.00000 0.000000 0.00000 0.000000 0.0000000 + [2,] 1538.65474 0.000000 885.27799 0.000000 -14.3073792 + [3,] 2116.06288 0.000000 1562.63158 0.000000 -19.6764832 + [4,] 2678.95539 0.000000 2301.74216 0.000000 -24.9106117 + [5,] 3549.02701 0.000000 3560.21566 0.000000 -33.0010847 + [6,] 4526.70219 0.000000 5104.75446 0.000000 -42.0921232 + [7,] 0.00000 2.000000 0.00000 0.000000 0.0000000 + [8,] -39.87484 1.759440 -13.70528 2.065330 0.5417840 + [9,] -61.67348 1.723851 -28.38163 3.194398 0.7410226 +[10,] -82.83754 1.697972 -45.65732 4.290598 0.9353041 +[11,] -115.45634 1.667622 -76.71599 5.980100 1.2356645 +[12,] -152.02782 1.641803 -116.49990 7.874332 1.5732196 + +$result$retres +$result$retres$res + [1] -0.005107676 -2.348541094 0.986722429 0.820555330 1.346609320 -1.203790914 -0.122166964 0.541410615 -0.176082086 -0.352530023 -0.013364998 0.131664908 + +$result$retres$sim + col +row X DHA + [1,] 0.06898978 10.721381 + [2,] 0.21230292 8.056335 + [3,] 0.29197344 7.113613 + [4,] 0.36964111 6.244833 + [5,] 0.48969322 4.956952 + [6,] 0.62459242 3.557013 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] 1.021535e-05 0.061083482 +[2,] 4.697082e-03 -0.270705308 +[3,] -1.973445e-03 0.088041043 +[4,] -1.641111e-03 0.176265012 +[5,] -2.693219e-03 0.006682499 +[6,] 2.407582e-03 -0.065832454 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1_res/gldA_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1_res/gldA_res.txt new file mode 100644 index 0000000..68e7a15 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-1_res/gldA_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.068989784647161 0.0687222596688052 0.0687229304044487 0.00192291707840905 0.0648601865034956 0.0717843246927195 +DHA 10.7213812313874 10.7180188456507 10.7314900472384 0.417337693950481 9.92346537097431 11.5825743735661 +mu 0.134782689793713 0.134766320522449 0.134763342164069 0.000906073345190276 0.133066646169025 0.136434481320854 +qDHA -1.3319691234728 -1.34040256911252 -1.34852564947058 0.154724901464124 -1.66560680630161 -1.09284115497233 +tlag 6.48662603371609 6.45281776204799 6.47424267647132 0.242233497712172 5.99835153195706 6.83717669874311 +res 10.9059195942328 6.49648352558275 5.6383357206001 3.38434319929801 1.87327875582326 13.7240223994907 + + +Goodness of fit (khi2 test) + +khi2 value 10.9059195942329 +data points 12 +fitted parameters 5 +degrees of freedom 7 +khi2 reduced value 1.55798851346185 +p-value, i.e. P(X^2<=value) 0.857224264472426 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2.txt new file mode 100644 index 0000000..7efd6bf --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2.txt @@ -0,0 +1,6 @@ +"time" "X" "DHA" +0 0.06 14.1235979187275 +7.9825 0.08 13.4979136164267 +9.47666666666667 0.1 12.2682933135326 +23.8927777777778 0.74 7.41070962325223 +26.9761111111111 1.15 2.97111205772673 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2_res/gldA-3.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2_res/gldA-3.pdf new file mode 100644 index 0000000..a96c6c9 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2_res/gldA-3.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2_res/gldA-3_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2_res/gldA-3_log.txt new file mode 100644 index 0000000..d5e8e74 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2_res/gldA-3_log.txt @@ -0,0 +1,159 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 5.395222 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 26.97611 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 26.9761101111111 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 26.9761101111111 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -26.976110 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.000000 7.982500 9.476667 23.892778 26.976111 + +$sys$data_meas + X DHA +[1,] 0.06 14.123598 +[2,] 0.08 13.497914 +[3,] 0.10 12.268293 +[4,] 0.74 7.410710 +[5,] 1.15 2.971112 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.06001149 14.21384467 0.14119826 -1.06616709 6.07237311 + +$result$lastp + X DHA mu qDHA tlag +-7.349116e-12 -1.615983e-08 -6.280437e-10 1.250375e-08 -8.919968e-08 + +$result$hci + X DHA mu qDHA tlag +0.007518055 1.145302541 0.002613944 0.264931198 0.960991711 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.462792 + +$result$laststep + X DHA mu qDHA tlag +-7.349116e-12 -1.615983e-08 -6.280437e-10 1.250375e-08 -8.919968e-08 + +$result$normp +[1] 9.151209e-08 + +$result$res + [1] 0.005745292 -0.705071112 -1.475481095 1.518656553 -0.809973847 0.180493494 -0.741780919 1.103538393 -1.539740739 0.943823912 + +$result$prevres + [1] 0.005745295 -0.705071555 -1.475481596 1.518656077 -0.809973471 0.180493526 -0.741780878 1.103538433 -1.539740773 0.943823810 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.000000 0.000000 0.0000000 0.0000000 0.0000000 + [2,] 654.790075 0.000000 75.0582960 0.0000000 -5.5483757 + [3,] 808.587121 0.000000 165.1917010 0.0000000 -6.8515778 + [4,] 6190.792004 0.000000 6620.6127598 0.0000000 -52.4577897 + [5,] 9568.001409 0.000000 12002.7178262 0.0000000 -81.0746355 + [6,] 0.000000 2.000000 0.0000000 0.0000000 0.0000000 + [7,] -4.638524 1.866660 -0.2785207 0.2610892 0.1651738 + [8,] -9.195378 1.842707 -1.0188049 0.5175815 0.2021713 + [9,] -163.997954 1.626825 -122.7492115 9.2309748 1.4993368 +[10,] -260.438038 1.584042 -237.3059392 14.6593107 2.3136387 + +$result$retres +$result$retres$res + [1] 0.005745295 -0.705071555 -1.475481596 1.518656077 -0.809973471 0.180493526 -0.741780878 1.103538433 -1.539740773 0.943823810 + +$result$retres$sim + col +row X DHA + [1,] 0.06001149 14.213845 + [2,] 0.07858986 13.127023 + [3,] 0.09704904 12.820063 + [4,] 0.74303731 6.640839 + [5,] 1.14838005 3.443024 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -1.149059e-05 -0.09024676 +[2,] 1.410143e-03 0.37089044 +[3,] 2.950963e-03 -0.55176922 +[4,] -3.037312e-03 0.76987039 +[5,] 1.619947e-03 -0.47191190 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2_res/gldA-3_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2_res/gldA-3_res.txt new file mode 100644 index 0000000..38b7cb9 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-2_res/gldA-3_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0600114905832737 0.0601877132301364 0.0601655147111731 0.00216547727812987 0.0555072397804008 0.0641518875700595 +DHA 14.2138446657212 14.2488088505587 14.2795782655574 0.256721698098556 13.7879062016889 14.7196790604008 +mu 0.141198264365427 0.141136923057298 0.141190499329124 0.00068540932073921 0.139867056828168 0.142392346690478 +qDHA -1.06616709102181 -1.05998175444638 -1.05652306890586 0.0602300579371291 -1.17401812384623 -0.934407292041198 +tlag 6.07237311004816 6.08115159176512 6.07818615661994 0.264347147696452 5.58894901864727 6.57499036848368 +res 10.6987970412956 5.62020756951811 4.84179294555297 4.04450913060813 0.975933096868979 15.9562680957037 + + +Goodness of fit (khi2 test) + +khi2 value 10.6987970412967 +data points 10 +fitted parameters 5 +degrees of freedom 5 +khi2 reduced value 2.13975940825934 +p-value, i.e. P(X^2<=value) 0.942309957009672 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3.txt new file mode 100644 index 0000000..44e79ef --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3.txt @@ -0,0 +1,7 @@ +"time" "X" "DHA" +0 0.034 17.5627155874568 +15 0.24 15.6862441523715 +17 0.316 13.356815873554 +19.25 0.45 7.00377787734219 +21.25 0.61 7.80725476598394 +23.1666666666667 0.73 6.41513439487189 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3_res/gldA-4.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3_res/gldA-4.pdf new file mode 100644 index 0000000..15a2e7c Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3_res/gldA-4.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3_res/gldA-4_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3_res/gldA-4_log.txt new file mode 100644 index 0000000..8bda555 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3_res/gldA-4_log.txt @@ -0,0 +1,165 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 4.633333 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 23.16667 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 23.1666656666667 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 23.1666656666667 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -23.166666 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 15.00000 17.00000 19.25000 21.25000 23.16667 + +$sys$data_meas + X DHA +[1,] 0.034 17.562716 +[2,] 0.240 15.686244 +[3,] 0.316 13.356816 +[4,] 0.450 7.003778 +[5,] 0.610 7.807255 +[6,] 0.730 6.415134 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.03420641 18.48088143 0.13403534 -1.88096958 0.13994594 + +$result$lastp + X DHA mu qDHA tlag + 6.177488e-10 1.162895e-07 -1.559501e-09 -1.985928e-08 -1.091116e-07 + +$result$hci + X DHA mu qDHA tlag +0.03900654 7.78720951 0.01451203 2.24316982 8.80632549 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 8.25267 + +$result$laststep + X DHA mu qDHA tlag + 6.177488e-10 1.162895e-07 -1.559501e-09 -1.985928e-08 -1.091116e-07 + +$result$normp +[1] 1.607041e-07 + +$result$res + [1] 0.1032046 5.3410309 5.8758212 -3.4410993 -15.3251303 9.5256255 1.8363317 -4.7216584 -2.6648866 6.3697738 0.6213918 -1.5865372 + +$result$prevres + [1] 0.1032043 5.3410297 5.8758201 -3.4410999 -15.3251303 9.5256267 1.8363315 -4.7216584 -2.6648866 6.3697738 0.6213919 -1.5865371 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.0000 0.000000 0.00000 0.000000 0.0000000 + [2,] 3664.2558 0.000000 1862.57446 0.000000 -16.8001279 + [3,] 4790.7929 0.000000 2762.95517 0.000000 -21.9651518 + [4,] 6477.1167 0.000000 4234.00253 0.000000 -29.6967232 + [5,] 8468.4386 0.000000 6115.05213 0.000000 -38.8266706 + [6,] 10948.9901 0.000000 8624.09697 0.000000 -50.1996709 + [7,] 0.0000 2.000000 0.00000 0.000000 0.0000000 + [8,] -170.0387 1.756802 -57.45330 3.092242 0.8927766 + [9,] -229.8418 1.726693 -90.59562 4.179792 1.1650261 +[10,] -319.2056 1.693437 -146.74387 5.804919 1.5726051 +[11,] -424.5970 1.664414 -220.67023 7.721517 2.0539410 +[12,] -555.7648 1.637067 -321.53291 10.106871 2.6535664 + +$result$retres +$result$retres$res + [1] 0.1032043 5.3410297 5.8758201 -3.4410999 -15.3251303 9.5256267 1.8363315 -4.7216584 -2.6648866 6.3697738 0.6213919 -1.5865371 + +$result$retres$sim + col +row X DHA + [1,] 0.03420641 18.480881 + [2,] 0.25068206 13.325415 + [3,] 0.32775164 12.024373 + [4,] 0.44311780 10.188665 + [5,] 0.57934974 8.117951 + [6,] 0.74905125 5.621866 + + +$result$it +[1] 8 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA +[1,] -0.0002064085 -0.9181657 +[2,] -0.0106820594 2.3608292 +[3,] -0.0117516402 1.3324433 +[4,] 0.0068821998 -3.1848869 +[5,] 0.0306502605 -0.3106960 +[6,] -0.0190512534 0.7932685 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3_res/gldA-4_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3_res/gldA-4_res.txt new file mode 100644 index 0000000..ed426a4 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-3_res/gldA-4_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0342064091309346 0.0346940396149425 0.0344756478874127 0.00134806601551532 0.0328576092507059 0.0375209071867517 +DHA 18.4808814319206 18.4260007557944 18.4463783370803 0.363701221899381 17.7746055535404 19.0927634974624 +mu 0.13403534164682 0.134115096574819 0.134159984927141 0.000824004853408522 0.132441776397926 0.135645144957205 +qDHA -1.88096957809701 -1.86638832564419 -1.85797734748166 0.113521435167547 -2.07502563640809 -1.64730719628592 +tlag 0.139945944521637 0.252101788496525 0.120163813913486 0.279959233762751 9.99999999637402e-07 0.876481787517649 +res 476.745900055693 7.11214848385451 6.13732338082986 4.00941870684245 1.42586539498188 15.2945116830176 + + +Goodness of fit (khi2 test) + +khi2 value 476.745900055699 +data points 12 +fitted parameters 5 +degrees of freedom 7 +khi2 reduced value 68.1065571508141 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4.txt new file mode 100644 index 0000000..2ef30dc --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4.txt @@ -0,0 +1,10 @@ +"time" "X" "DHA" +0 0.045 14.2129532953121 +14.9597222222222 0.21 10.9278012102082 +16.9097222222222 0.289 10.4193437966785 +19.0072222222222 0.384 9.30863343422318 +20.4572222222222 0.465 8.07255293835911 +22.4572222222222 0.609 6.99145513313644 +23.4605555555556 0.693 6.07429758219554 +24.4486111111111 0.773 4.73668629253941 +25.4491666666667 0.876 3.04879265147842 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4_res/D-glda-1.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4_res/D-glda-1.pdf new file mode 100644 index 0000000..03607a0 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4_res/D-glda-1.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4_res/D-glda-1_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4_res/D-glda-1_log.txt new file mode 100644 index 0000000..f537154 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4_res/D-glda-1_log.txt @@ -0,0 +1,183 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 5.089833 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + [7,] 0.002 0.5 + [8,] 0.002 0.5 + [9,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 25.44917 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 25.4491656666667 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 25.4491656666667 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -25.449166 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.95972 16.90972 19.00722 20.45722 22.45722 23.46056 24.44861 25.44917 + +$sys$data_meas + X DHA + [1,] 0.045 14.212953 + [2,] 0.210 10.927801 + [3,] 0.289 10.419344 + [4,] 0.384 9.308633 + [5,] 0.465 8.072553 + [6,] 0.609 6.991455 + [7,] 0.693 6.074298 + [8,] 0.773 4.736686 + [9,] 0.876 3.048793 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.04505448 14.54163633 0.13040981 -1.32071004 2.61443482 + +$result$lastp + X DHA mu qDHA tlag +-2.124145e-11 3.716050e-08 -4.203081e-10 -5.597592e-09 -7.021379e-08 + +$result$hci + X DHA mu qDHA tlag +0.014211597 2.484487034 0.003544592 0.573480198 2.483607436 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 3.290605 + +$result$laststep + X DHA mu qDHA tlag +-2.124145e-11 3.716050e-08 -4.203081e-10 -5.597592e-09 -7.021379e-08 + +$result$normp +[1] 7.963912e-08 + +$result$res + [1] 0.02723821 7.69350724 0.82475785 -0.95566263 -1.68886805 -4.90864527 -5.02860612 1.93119562 4.56985493 0.65736606 0.18789438 -0.47488241 -0.45547337 0.18928824 -0.69180802 -0.66162402 0.02152173 1.13166778 + +$result$prevres + [1] 0.02723822 7.69350684 0.82475746 -0.95566297 -1.68886832 -4.90864537 -5.02860609 1.93119581 4.56985533 0.65736599 0.18789435 -0.47488243 -0.45547337 0.18928824 -0.69180800 -0.66162399 0.02152176 1.13166782 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.00000 0.000000 0.00000 0.000000 0.0000000 + [2,] 2501.27214 0.000000 1391.23372 0.000000 -14.6963394 + [3,] 3225.53426 0.000000 2077.45916 0.000000 -18.9517748 + [4,] 4240.29646 0.000000 3131.74919 0.000000 -24.9140567 + [5,] 5122.93450 0.000000 4118.31394 0.000000 -30.1000370 + [6,] 6649.53581 0.000000 5944.72754 0.000000 -39.0696532 + [7,] 7579.07806 0.000000 7118.35388 0.000000 -44.5312214 + [8,] 8621.36743 0.000000 8481.07518 0.000000 -50.6552405 + [9,] 9822.99408 0.000000 10105.96394 0.000000 -57.7154531 +[10,] 0.00000 2.000000 0.00000 0.000000 0.0000000 +[11,] -77.95385 1.757413 -27.59730 2.659304 0.5649844 +[12,] -105.75499 1.728041 -44.66021 3.607708 0.7265435 +[13,] -144.60892 1.696994 -72.12523 4.933164 0.9529420 +[14,] -178.34698 1.675858 -98.67486 6.084098 1.1498851 +[15,] -236.62384 1.647137 -149.18080 8.072145 1.4905454 +[16,] -272.07670 1.632914 -182.28156 9.281578 1.6979846 +[17,] -311.80971 1.619028 -221.17951 10.637023 1.9305926 +[18,] -357.59672 1.605087 -268.07605 12.198994 2.1987678 + +$result$retres +$result$retres$res + [1] 0.02723822 7.69350684 0.82475746 -0.95566297 -1.68886832 -4.90864537 -5.02860609 1.93119581 4.56985533 0.65736599 0.18789435 -0.47488243 -0.45547337 0.18928824 -0.69180800 -0.66162399 0.02152176 1.13166782 + +$result$retres$sim + col +row X DHA + [1,] 0.04505448 14.541636 + [2,] 0.22538701 11.021748 + [3,] 0.29064951 10.181903 + [4,] 0.38208867 9.080897 + [5,] 0.46162226 8.167197 + [6,] 0.59918271 6.645551 + [7,] 0.68294279 5.743486 + [8,] 0.77686239 4.747447 + [9,] 0.88513971 3.614627 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA + [1,] -5.447644e-05 -0.32868299 + [2,] -1.538701e-02 -0.09394718 + [3,] -1.649515e-03 0.23744121 + [4,] 1.911326e-03 0.22773668 + [5,] 3.377737e-03 -0.09464412 + [6,] 9.817291e-03 0.34590400 + [7,] 1.005721e-02 0.33081200 + [8,] -3.862392e-03 -0.01076088 + [9,] -9.139711e-03 -0.56583391 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4_res/D-glda-1_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4_res/D-glda-1_res.txt new file mode 100644 index 0000000..8514e91 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-4_res/D-glda-1_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0450544764230469 0.0449092256536221 0.0449524525575962 0.00212072986882959 0.0412194995523412 0.0493902170242986 +DHA 14.5416363252067 14.5553971015345 14.5893963995194 0.356158847689236 13.8870841651149 15.1895282918483 +mu 0.130409814850669 0.130419507489476 0.130433101109452 0.000502950602037081 0.129494751287199 0.131226874073985 +qDHA -1.32071003547717 -1.31817647125346 -1.32421239138969 0.0669234821968707 -1.43232730137367 -1.20204673562798 +tlag 2.61443482213558 2.58360381982727 2.60279188853769 0.361547523849596 1.93632978271239 3.31527137555848 +res 140.765069409892 13.0547838930341 12.518417086773 5.01512253238375 4.60998211275876 21.5465824952335 + + +Goodness of fit (khi2 test) + +khi2 value 140.765069409891 +data points 18 +fitted parameters 5 +degrees of freedom 13 +khi2 reduced value 10.8280822622993 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5.txt new file mode 100644 index 0000000..3d0bd3a --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5.txt @@ -0,0 +1,10 @@ +"time" "X" "DHA" +0 0.06 13.7578907103336 +14.9930555555556 0.362 9.81844827544029 +15.9430555555556 0.421 9.32281542341176 +16.9430555555556 0.478 8.66846976281463 +18.0430555555556 0.557 8.01774401849908 +19.1097222222222 0.663 6.63302615436167 +20.1597222222222 0.776 5.40230824441119 +21.1738888888889 0.868 3.75307065845186 +22.1605555555556 0.969 2.30001191511247 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5_res/D-glda-2.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5_res/D-glda-2.pdf new file mode 100644 index 0000000..9d2d696 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5_res/D-glda-2.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5_res/D-glda-2_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5_res/D-glda-2_log.txt new file mode 100644 index 0000000..b4f0dce --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5_res/D-glda-2_log.txt @@ -0,0 +1,183 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 4.432111 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + [7,] 0.002 0.5 + [8,] 0.002 0.5 + [9,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 22.16055 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 22.1605545555556 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 22.1605545555556 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -22.160555 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.99306 15.94306 16.94306 18.04306 19.10972 20.15972 21.17389 22.16056 + +$sys$data_meas + X DHA + [1,] 0.060 13.757891 + [2,] 0.362 9.818448 + [3,] 0.421 9.322815 + [4,] 0.478 8.668470 + [5,] 0.557 8.017744 + [6,] 0.663 6.633026 + [7,] 0.776 5.402308 + [8,] 0.868 3.753071 + [9,] 0.969 2.300012 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.06012364 14.49227791 0.13638705 -1.41494939 1.63837068 + +$result$lastp + X DHA mu qDHA tlag + 6.336364e-11 1.655875e-08 -7.446861e-11 -3.454918e-09 -2.274999e-09 + +$result$hci + X DHA mu qDHA tlag +0.021570630 4.127920354 0.005434956 0.891421220 2.730927730 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 4.994183 + +$result$laststep + X DHA mu qDHA tlag + 6.336364e-11 1.655875e-08 -7.446861e-11 -3.454918e-09 -2.274999e-09 + +$result$normp +[1] 1.706792e-08 + +$result$res + [1] 0.06182058 4.79836813 1.00100336 3.40667579 3.14363077 -5.75265261 -12.09799773 -2.33592622 9.34230049 1.46877440 -0.38080357 -0.60934458 -0.73300173 -1.20940337 -0.39804262 -0.12499295 0.77613687 1.04237165 + +$result$prevres + [1] 0.06182055 4.79836806 1.00100330 3.40667574 3.14363072 -5.75265263 -12.09799772 -2.33592618 9.34230057 1.46877437 -0.38080358 -0.60934459 -0.73300173 -1.20940337 -0.39804262 -0.12499294 0.77613689 1.04237167 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.0000 0.000000 0.00000 0.000000 0.0000000 + [2,] 3090.2714 0.000000 2481.27865 0.000000 -25.3404916 + [3,] 3517.7677 0.000000 3025.45520 0.000000 -28.8459983 + [4,] 4031.8030 0.000000 3709.95778 0.000000 -33.0611318 + [5,] 4684.4074 0.000000 4620.27501 0.000000 -38.4125444 + [6,] 5417.9578 0.000000 5691.24642 0.000000 -44.4277203 + [7,] 6252.1497 0.000000 6962.21313 0.000000 -51.2681658 + [8,] 7179.6063 0.000000 8432.78137 0.000000 -58.8733904 + [9,] 8213.7790 0.000000 10134.72299 0.000000 -67.3536954 +[10,] 0.0000 2.000000 0.00000 0.000000 0.0000000 +[11,] -103.2122 1.756907 -54.04408 4.385665 0.9979441 +[12,] -120.0374 1.742540 -68.30548 5.100595 1.1346721 +[13,] -140.2459 1.727543 -86.64048 5.959291 1.2990900 +[14,] -165.8755 1.711196 -111.54053 7.048336 1.5078441 +[15,] -194.6576 1.695491 -141.40318 8.271337 1.7425048 +[16,] -227.3634 1.680173 -177.44402 9.661063 2.0093735 +[17,] -263.7024 1.665509 -219.76812 11.205169 2.3060910 +[18,] -304.2008 1.651366 -269.39721 12.926016 2.6369611 + +$result$retres +$result$retres$res + [1] 0.06182055 4.79836806 1.00100330 3.40667574 3.14363072 -5.75265263 -12.09799772 -2.33592618 9.34230057 1.46877437 -0.38080358 -0.60934459 -0.73300173 -1.20940337 -0.39804262 -0.12499294 0.77613689 1.04237167 + +$result$retres$sim + col +row X DHA + [1,] 0.06012364 14.492278 + [2,] 0.37159674 9.628046 + [3,] 0.42300201 9.018143 + [4,] 0.48481335 8.301969 + [5,] 0.56328726 7.413042 + [6,] 0.65149469 6.434005 + [7,] 0.75180400 5.339812 + [8,] 0.86332815 4.141139 + [9,] 0.98768460 2.821198 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA + [1,] -0.0001236411 -0.73438718 + [2,] -0.0095967361 0.19040179 + [3,] -0.0020020066 0.30467229 + [4,] -0.0068133515 0.36650087 + [5,] -0.0062872614 0.60470168 + [6,] 0.0115053053 0.19902131 + [7,] 0.0241959954 0.06249647 + [8,] 0.0046718524 -0.38806844 + [9,] -0.0186846011 -0.52118583 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5_res/D-glda-2_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5_res/D-glda-2_res.txt new file mode 100644 index 0000000..413288e --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-5_res/D-glda-2_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0601236411605523 0.0601408486245085 0.0603084914087872 0.00188700247352134 0.0561677429788878 0.0634000741071823 +DHA 14.4922779111475 14.4074904457348 14.4349130723891 0.454535211327981 13.511732049235 15.1796795257047 +mu 0.136387051696441 0.136443262895319 0.136502845386586 0.00051603437882421 0.135276049410909 0.137286283681904 +qDHA -1.41494938966511 -1.39939492869667 -1.40919996374242 0.0996155902104774 -1.58190337606378 -1.21697453478575 +tlag 1.63837068350654 1.64503986821712 1.64706520264617 0.241079769184802 1.12060687759498 2.07708279592504 +res 324.244258000479 13.8765372453405 12.454075332971 6.15818550745244 4.77639986337492 26.6826322240496 + + +Goodness of fit (khi2 test) + +khi2 value 324.244258000474 +data points 18 +fitted parameters 5 +degrees of freedom 13 +khi2 reduced value 24.9418660000365 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6.txt new file mode 100644 index 0000000..84e0605 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6.txt @@ -0,0 +1,10 @@ +"time" "X" "DHA" +0 0.055 13.999950982541 +14.6263888888889 0.285 10.3636274201456 +16.7263888888889 0.39 9.07619614311147 +18.6430555555556 0.518 7.83289591910994 +19.7597222222222 0.604 5.06282454533187 +20.7430555555556 0.695 5.93472663360668 +21.7763888888889 0.781 4.87695150561304 +23.1238888888889 0.93 2.55848659002936 +24.1272222222222 1.043 1.34642761579538 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6_res/D-glda-3.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6_res/D-glda-3.pdf new file mode 100644 index 0000000..bff49f8 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6_res/D-glda-3.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6_res/D-glda-3_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6_res/D-glda-3_log.txt new file mode 100644 index 0000000..40c9122 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6_res/D-glda-3_log.txt @@ -0,0 +1,183 @@ +$sys +$sys$params + X DHA mu qDHA tlag +0.100000 0.100000 0.100000 0.100000 4.825444 + +$sys$to_est +[1] "X" "DHA" "mu" "qDHA" "tlag" + +$sys$nconc +[1] "X" "DHA" + +$sys$nflux +[1] "mu" "qDHA" + +$sys$metab +[1] "DHA" + +$sys$weight + col +row X DHA + [1,] 0.002 0.5 + [2,] 0.002 0.5 + [3,] 0.002 0.5 + [4,] 0.002 0.5 + [5,] 0.002 0.5 + [6,] 0.002 0.5 + [7,] 0.002 0.5 + [8,] 0.002 0.5 + [9,] 0.002 0.5 + +$sys$te_upc + X DHA mu qDHA tlag +50.00000 50.00000 50.00000 50.00000 24.12722 + +$sys$te_loc + X DHA mu qDHA tlag + 1e-06 1e-06 0e+00 -5e+01 1e-06 + +$sys$u + X DHA mu qDHA tlag +X <= 50 -1 0 0 0 0 +DHA <= 50 0 -1 0 0 0 +mu <= 50 0 0 -1 0 0 +qDHA <= 50 0 0 0 -1 0 +tlag <= 24.1272212222222 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 +mu >= 0 0 0 1 0 0 +qDHA >= -50 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 mu <= 50 qDHA <= 50 tlag <= 24.1272212222222 X >= 1e-06 DHA >= 1e-06 mu >= 0 qDHA >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -24.127221 0.000001 0.000001 0.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.62639 16.72639 18.64306 19.75972 20.74306 21.77639 23.12389 24.12722 + +$sys$data_meas + X DHA + [1,] 0.055 13.999951 + [2,] 0.285 10.363627 + [3,] 0.390 9.076196 + [4,] 0.518 7.832896 + [5,] 0.604 5.062825 + [6,] 0.695 5.934727 + [7,] 0.781 4.876952 + [8,] 0.930 2.558487 + [9,] 1.043 1.346428 + +$sys$nb_par +[1] 5 + +$sys$nb_conc +[1] 2 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA mu qDHA tlag + 0.05504532 14.25925046 0.13141571 -1.41548292 1.63743132 + +$result$lastp + X DHA mu qDHA tlag + 3.904621e-12 -9.534585e-09 1.835471e-10 5.273384e-11 2.877320e-08 + +$result$hci + X DHA mu qDHA tlag +0.019853481 3.630157798 0.004328987 0.708684546 2.824640197 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 4.596973 + +$result$laststep + X DHA mu qDHA tlag + 3.904621e-12 -9.534585e-09 1.835471e-10 5.273384e-11 2.877320e-08 + +$result$normp +[1] 3.03124e-08 + +$result$res + [1] 0.022661872 9.208787810 4.923702132 -1.809793276 -4.157906672 -8.571589703 -2.274972373 -1.564225639 7.253088283 0.518598948 -0.733967029 -0.578151865 -0.828102489 2.826285842 -0.789963948 -0.887589464 0.424527042 -0.001444059 + +$result$prevres + [1] 0.022661870 9.208788011 4.923702320 -1.809793124 -4.157906557 -8.571589634 -2.274972368 -1.564225748 7.253088062 0.518598967 -0.733967028 -0.578151866 -0.828102492 2.826285838 -0.789963952 -0.887589469 0.424527038 -0.001444063 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] + [1,] 500.00000 0.000000 0.00000 0.000000 0.000000 + [2,] 2756.07041 0.000000 1970.53901 0.000000 -19.936918 + [3,] 3631.98340 0.000000 3016.64027 0.000000 -26.273115 + [4,] 4672.33526 0.000000 4373.68002 0.000000 -33.798834 + [5,] 5410.85188 0.000000 5397.58107 0.000000 -39.141130 + [6,] 6157.26073 0.000000 6475.43886 0.000000 -44.540518 + [7,] 7052.82486 0.000000 7818.44737 0.000000 -51.018868 + [8,] 8419.16702 0.000000 9957.59311 0.000000 -60.902741 + [9,] 9605.77670 0.000000 11891.54640 0.000000 -69.486462 +[10,] 0.00000 2.000000 0.00000 0.000000 0.000000 +[11,] -93.34879 1.762484 -42.97214 3.630149 0.814551 +[12,] -129.08278 1.730781 -71.21709 5.019773 1.070539 +[13,] -171.43079 1.702344 -109.43241 6.666603 1.374629 +[14,] -201.45314 1.685992 -139.02466 7.834113 1.590514 +[15,] -231.77319 1.671723 -170.68114 9.013200 1.808716 +[16,] -268.12898 1.656858 -210.68426 10.427004 2.070532 +[17,] -323.56040 1.637673 -275.37446 12.582622 2.469997 +[18,] -371.67438 1.623532 -334.64556 14.453680 2.816927 + +$result$retres +$result$retres$res + [1] 0.022661870 9.208788011 4.923702320 -1.809793124 -4.157906557 -8.571589634 -2.274972368 -1.564225748 7.253088062 0.518598967 -0.733967028 -0.578151866 -0.828102492 2.826285838 -0.789963952 -0.887589469 0.424527038 -0.001444063 + +$result$retres$sim + col +row X DHA + [1,] 0.05504532 14.259250 + [2,] 0.30341758 9.996644 + [3,] 0.39984740 8.787120 + [4,] 0.51438041 7.418845 + [5,] 0.59568419 6.475967 + [6,] 0.67785682 5.539745 + [7,] 0.77645006 4.433157 + [8,] 0.92687155 2.770750 + [9,] 1.05750618 1.345706 + + +$result$it +[1] 7 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA + [1,] -4.532374e-05 -0.2592994833 + [2,] -1.841758e-02 0.3669835139 + [3,] -9.847405e-03 0.2890759330 + [4,] 3.619586e-03 0.4140512459 + [5,] 8.315813e-03 -1.4131429189 + [6,] 1.714318e-02 0.3949819762 + [7,] 4.549945e-03 0.4437947343 + [8,] 3.128451e-03 -0.2122635188 + [9,] -1.450618e-02 0.0007220314 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6_res/D-glda-3_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6_res/D-glda-3_res.txt new file mode 100644 index 0000000..7f3cbaa --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/gldA-6_res/D-glda-3_res.txt @@ -0,0 +1,20 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0550453237445943 0.0546785605108354 0.05459569943043 0.00193235664107294 0.0510560445674656 0.0584952477531036 +DHA 14.2592504563031 14.2980377627785 14.2768448833424 0.354150253890284 13.7133974022684 14.9614724017181 +mu 0.131415709939746 0.131430708293024 0.131385359301529 0.000426984039699259 0.130730571357717 0.132245652433613 +qDHA -1.41548291617722 -1.4202766977216 -1.42119362904337 0.0710043706874336 -1.55878298092127 -1.2944821293005 +tlag 1.63743132108884 1.58416930165662 1.59134145607296 0.283878416224151 0.999896994607547 2.07571767672873 +res 274.718050417427 13.3981969823358 12.9060071821115 5.41738897457715 5.64574924724565 26.6467164592764 + + +Goodness of fit (khi2 test) + +khi2 value 274.718050417423 +data points 18 +fitted parameters 5 +degrees of freedom 13 +khi2 reduced value 21.1321577244171 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1.txt new file mode 100644 index 0000000..4681e38 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1.txt @@ -0,0 +1,10 @@ +"time" "X" "DHA" "Glycerol" +0 0.045 14.0814024982631 0.300831918534606 +14.9597222222222 0.113 11.7205045924564 0.54654723848679 +16.9097222222222 0.141 11.3992813973551 0.585712734932434 +19.0072222222222 0.177 11.0175424097334 0.673240634156931 +20.4572222222222 0.203 10.7612558534851 0.62189095025365 +22.4572222222222 0.254 10.0242726355685 0.632956075215561 +23.4605555555556 0.281 9.50965752744699 0.287462779752611 +24.4486111111111 0.309 9.32328283408138 0.476408191505266 +25.4491666666667 0.347 8.91729885347106 0.582449292132955 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1_res/D-glpk-1.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1_res/D-glpk-1.pdf new file mode 100644 index 0000000..748ff18 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1_res/D-glpk-1.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1_res/D-glpk-1_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1_res/D-glpk-1_log.txt new file mode 100644 index 0000000..7230cf6 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1_res/D-glpk-1_log.txt @@ -0,0 +1,196 @@ +$sys +$sys$params + X DHA Glycerol mu qDHA qGlycerol tlag + 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 5.089833 + +$sys$to_est +[1] "X" "DHA" "Glycerol" "mu" "qDHA" "qGlycerol" "tlag" + +$sys$nconc +[1] "X" "DHA" "Glycerol" + +$sys$nflux +[1] "mu" "qDHA" "qGlycerol" + +$sys$metab +[1] "DHA" "Glycerol" + +$sys$weight + col +row X DHA Glycerol + [1,] 0.002 0.5 0.5 + [2,] 0.002 0.5 0.5 + [3,] 0.002 0.5 0.5 + [4,] 0.002 0.5 0.5 + [5,] 0.002 0.5 0.5 + [6,] 0.002 0.5 0.5 + [7,] 0.002 0.5 0.5 + [8,] 0.002 0.5 0.5 + [9,] 0.002 0.5 0.5 + +$sys$te_upc + X DHA Glycerol mu qDHA qGlycerol tlag + 50.00000 50.00000 50.00000 50.00000 50.00000 50.00000 25.44917 + +$sys$te_loc + X DHA Glycerol mu qDHA qGlycerol tlag + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 1e-06 + +$sys$u + X DHA Glycerol mu qDHA qGlycerol tlag +X <= 50 -1 0 0 0 0 0 0 +DHA <= 50 0 -1 0 0 0 0 0 +Glycerol <= 50 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 -1 0 0 0 +qDHA <= 50 0 0 0 0 -1 0 0 +qGlycerol <= 50 0 0 0 0 0 -1 0 +tlag <= 25.4491656666667 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 0 0 +Glycerol >= 1e-06 0 0 1 0 0 0 0 +mu >= 0 0 0 0 1 0 0 0 +qDHA >= -50 0 0 0 0 1 0 0 +qGlycerol >= -50 0 0 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 Glycerol <= 50 mu <= 50 qDHA <= 50 qGlycerol <= 50 tlag <= 25.4491656666667 X >= 1e-06 DHA >= 1e-06 Glycerol >= 1e-06 mu >= 0 qDHA >= -50 qGlycerol >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -25.449166 0.000001 0.000001 0.000001 0.000000 -50.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.95972 16.90972 19.00722 20.45722 22.45722 23.46056 24.44861 25.44917 + +$sys$data_meas + X DHA Glycerol + [1,] 0.045 14.081402 0.3008319 + [2,] 0.113 11.720505 0.5465472 + [3,] 0.141 11.399281 0.5857127 + [4,] 0.177 11.017542 0.6732406 + [5,] 0.203 10.761256 0.6218910 + [6,] 0.254 10.024273 0.6329561 + [7,] 0.281 9.509658 0.2874628 + [8,] 0.309 9.323283 0.4764082 + [9,] 0.347 8.917299 0.5824493 + +$sys$nb_par +[1] 7 + +$sys$nb_conc +[1] 3 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA Glycerol mu qDHA qGlycerol tlag + 0.04500254 14.10385379 0.49028187 0.10552944 -0.87707903 0.02124541 6.11823255 + +$result$lastp + X DHA Glycerol mu qDHA qGlycerol tlag +-3.787305e-10 1.271866e-08 7.484999e-08 -2.415353e-10 -3.727995e-09 -4.859047e-08 -1.186458e-07 + +$result$hci + X DHA Glycerol mu qDHA qGlycerol tlag +0.002089249 0.374125111 0.350896486 0.001150862 0.189723845 0.197473678 0.477514352 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5009375 + +$result$laststep + X DHA Glycerol mu qDHA qGlycerol tlag +-3.787305e-10 1.271866e-08 7.484999e-08 -2.415353e-10 -3.727995e-09 -4.859047e-08 -1.186458e-07 + +$result$normp +[1] 1.490511e-07 + +$result$res + [1] 0.001268725 0.703161381 -0.226724484 -0.815987798 0.682177333 -0.806536218 -0.212012560 1.205486248 -0.454531515 0.044902577 0.228098961 0.043952857 -0.176760428 -0.415488022 -0.094895541 0.295458083 -0.006451671 0.070982183 0.378899909 -0.084585703 -0.152391487 -0.313426623 -0.199052052 -0.201846295 0.500490451 0.135015158 -0.063103358 + +$result$prevres + [1] 0.001268914 0.703161268 -0.226724589 -0.815987885 0.682177268 -0.806536238 -0.212012548 1.205486298 -0.454531417 0.044902552 0.228098955 0.043952854 -0.176760428 -0.415488019 -0.094895535 0.295458091 -0.006451660 0.070982195 0.378899759 -0.084585789 -0.152391549 -0.313426653 -0.199052056 -0.201846254 0.500490518 0.135015254 -0.063103231 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] + [1,] 500.0000000 0.000000 0 0.0000000 0.000000 0.000000 0.000000000 + [2,] 1271.1096758 0.000000 0 505.7611527 0.000000 0.000000 -6.036617696 + [3,] 1561.5402776 0.000000 0 758.3533174 0.000000 0.000000 -7.415899550 + [4,] 1948.4237189 0.000000 0 1130.1583161 0.000000 0.000000 -9.253244881 + [5,] 2270.5869980 0.000000 0 1465.1891723 0.000000 0.000000 -10.783228162 + [6,] 2804.1410519 0.000000 0 2061.8736860 0.000000 0.000000 -13.317125830 + [7,] 3117.3350265 0.000000 0 2432.9195754 0.000000 0.000000 -14.804513052 + [8,] 3459.9267911 0.000000 0 2854.1404893 0.000000 0.000000 -16.431513104 + [9,] 3845.2380007 0.000000 0 3345.1305317 0.000000 0.000000 -18.261391760 +[10,] 0.0000000 2.000000 0 0.0000000 0.000000 0.000000 0.000000000 +[11,] -24.8251254 1.757413 0 -5.7559737 1.273766 0.000000 0.191030328 +[12,] -33.9873983 1.728041 0 -9.9062364 1.743878 0.000000 0.233320492 +[13,] -46.1270408 1.696994 0 -16.5461184 2.366758 0.000000 0.289680798 +[14,] -56.1976867 1.675858 0 -22.8715193 2.883478 0.000000 0.336627678 +[15,] -72.8254062 1.647137 0 -34.6524938 3.736639 0.000000 0.414399033 +[16,] -82.5644519 1.632914 0 -42.2152720 4.236346 0.000000 0.460058797 +[17,] -93.2041094 1.619028 0 -50.9648466 4.782262 0.000000 0.510009656 +[18,] -105.1569022 1.605087 0 -61.3407065 5.395554 0.000000 0.566194414 +[19,] 0.0000000 0.000000 2 0.0000000 0.000000 0.000000 0.000000000 +[20,] 0.6209670 0.000000 2 0.1424760 0.000000 1.315344 -0.004861229 +[21,] 0.8548479 0.000000 2 0.2461485 0.000000 1.810756 -0.005971951 +[22,] 1.1664013 0.000000 2 0.4126989 0.000000 2.470694 -0.007451547 +[23,] 1.4258362 0.000000 2 0.5718612 0.000000 3.020234 -0.008683627 +[24,] 1.8555020 0.000000 2 0.8691363 0.000000 3.930361 -0.010724150 +[25,] 2.1077140 0.000000 2 1.0603813 0.000000 4.464601 -0.011921928 +[26,] 2.3835998 0.000000 2 1.2819361 0.000000 5.048988 -0.013232135 +[27,] 2.6938871 0.000000 2 1.5450050 0.000000 5.706244 -0.014705718 + +$result$retres +$result$retres$res + [1] 0.001268914 0.703161268 -0.226724589 -0.815987885 0.682177268 -0.806536238 -0.212012548 1.205486298 -0.454531417 0.044902552 0.228098955 0.043952854 -0.176760428 -0.415488019 -0.094895535 0.295458091 -0.006451660 0.070982195 0.378899759 -0.084585789 -0.152391549 -0.313426653 -0.199052056 -0.201846254 0.500490518 0.135015254 -0.063103231 + +$result$retres$sim + col +row X DHA Glycerol + [1,] 0.04500254 14.103854 0.4902818 + [2,] 0.11440632 11.834554 0.5042543 + [3,] 0.14054655 11.421258 0.5095170 + [4,] 0.17536802 10.929162 0.5165273 + [5,] 0.20436435 10.553512 0.5223649 + [6,] 0.25238693 9.976825 0.5320329 + [7,] 0.28057597 9.657387 0.5377080 + [8,] 0.31141097 9.320057 0.5439158 + [9,] 0.34609094 8.952790 0.5508977 + + +$result$it +[1] 5 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA Glycerol + [1,] -2.537828e-06 -0.02245128 -0.18944988 + [2,] -1.406323e-03 -0.11404948 0.04229289 + [3,] 4.534492e-04 -0.02197643 0.07619577 + [4,] 1.631976e-03 0.08838021 0.15671333 + [5,] -1.364355e-03 0.20774401 0.09952603 + [6,] 1.613072e-03 0.04744777 0.10092313 + [7,] 4.240251e-04 -0.14772905 -0.25024526 + [8,] -2.410973e-03 0.00322583 -0.06750763 + [9,] 9.090628e-04 -0.03549110 0.03155162 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1_res/D-glpk-1_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1_res/D-glpk-1_res.txt new file mode 100644 index 0000000..7bdc2f9 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-1_res/D-glpk-1_res.txt @@ -0,0 +1,22 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0450025374490971 0.0450443421417446 0.0449320802742777 0.00207336069276686 0.0416880829999906 0.0489947531761939 +DHA 14.1038537869745 14.1174662089285 14.165809166652 0.361364979079222 13.4838163993762 14.8231653592358 +Glycerol 0.490281873041256 0.514103199617701 0.482320240485182 0.276283456860286 0.0597206497712045 1.09313457033971 +mu 0.105529441877674 0.105366906148864 0.105352666617534 0.000968668039814353 0.103705208358592 0.107476946950758 +qDHA -0.877079032752942 -0.892238117210015 -0.883362986743698 0.175844488800696 -1.21971734669937 -0.556934380989461 +qGlycerol 0.0212454057175085 0.0368377610393723 0.0269318489907992 0.172976254740446 -0.266839261077128 0.373865098180041 +tlag 6.11823255097713 6.09083271729701 6.13539411576757 0.482625851659735 5.25280346458756 6.96605945865371 +res 5.0187667904824 18.8307060143376 18.2210018584026 5.79584783688944 9.24740098881365 30.6783328853486 + + +Goodness of fit (khi2 test) + +khi2 value 5.01876679048264 +data points 27 +fitted parameters 7 +degrees of freedom 20 +khi2 reduced value 0.250938339524132 +p-value, i.e. P(X^2<=value) 0.000285548437322021 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2.txt new file mode 100644 index 0000000..4545e0e --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2.txt @@ -0,0 +1,13 @@ +"time" "X" "DHA" "Glycerol" +0 0.051 13.7742591988714 0.255859883369191 +14.9930555555556 0.15 11.2560361818776 0.529660022921786 +15.9430555555556 0.166 10.934139152399 0.387501793619758 +16.9430555555556 0.183 11.6088218366363 0.705550980455042 +18.0430555555556 0.206 10.6660605593739 0.817858993134583 +19.1097222222222 0.235 10.2388751622393 0.489520046409934 +20.1597222222222 0.27 9.59513934328659 0.679338451342444 +21.1738888888889 0.297 9.71668762579136 0.806720583105409 +22.1605555555556 0.33 8.97919072240849 0.493777897415975 +23.1486111111111 0.377 9.00570119388197 1.00713844113837 +24.1486111111111 0.414 7.94328290440636 0.689018769499229 +25.1491666666667 0.44 5.75519349966588 0.473915318454737 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2_res/D-glpk-2.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2_res/D-glpk-2.pdf new file mode 100644 index 0000000..3365c51 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2_res/D-glpk-2.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2_res/D-glpk-2_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2_res/D-glpk-2_log.txt new file mode 100644 index 0000000..8ce8097 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2_res/D-glpk-2_log.txt @@ -0,0 +1,217 @@ +$sys +$sys$params + X DHA Glycerol mu qDHA qGlycerol tlag + 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 5.029833 + +$sys$to_est +[1] "X" "DHA" "Glycerol" "mu" "qDHA" "qGlycerol" "tlag" + +$sys$nconc +[1] "X" "DHA" "Glycerol" + +$sys$nflux +[1] "mu" "qDHA" "qGlycerol" + +$sys$metab +[1] "DHA" "Glycerol" + +$sys$weight + col +row X DHA Glycerol + [1,] 0.002 0.5 0.5 + [2,] 0.002 0.5 0.5 + [3,] 0.002 0.5 0.5 + [4,] 0.002 0.5 0.5 + [5,] 0.002 0.5 0.5 + [6,] 0.002 0.5 0.5 + [7,] 0.002 0.5 0.5 + [8,] 0.002 0.5 0.5 + [9,] 0.002 0.5 0.5 + [10,] 0.002 0.5 0.5 + [11,] 0.002 0.5 0.5 + [12,] 0.002 0.5 0.5 + +$sys$te_upc + X DHA Glycerol mu qDHA qGlycerol tlag + 50.00000 50.00000 50.00000 50.00000 50.00000 50.00000 25.14917 + +$sys$te_loc + X DHA Glycerol mu qDHA qGlycerol tlag + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 1e-06 + +$sys$u + X DHA Glycerol mu qDHA qGlycerol tlag +X <= 50 -1 0 0 0 0 0 0 +DHA <= 50 0 -1 0 0 0 0 0 +Glycerol <= 50 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 -1 0 0 0 +qDHA <= 50 0 0 0 0 -1 0 0 +qGlycerol <= 50 0 0 0 0 0 -1 0 +tlag <= 25.1491656666667 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 0 0 +Glycerol >= 1e-06 0 0 1 0 0 0 0 +mu >= 0 0 0 0 1 0 0 0 +qDHA >= -50 0 0 0 0 1 0 0 +qGlycerol >= -50 0 0 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 Glycerol <= 50 mu <= 50 qDHA <= 50 qGlycerol <= 50 tlag <= 25.1491656666667 X >= 1e-06 DHA >= 1e-06 Glycerol >= 1e-06 mu >= 0 qDHA >= -50 qGlycerol >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -25.149166 0.000001 0.000001 0.000001 0.000000 -50.000000 -50.000000 0.000001 + +$sys$times + [1] 0.00000 14.99306 15.94306 16.94306 18.04306 19.10972 20.15972 21.17389 22.16056 23.14861 24.14861 25.14917 + +$sys$data_meas + X DHA Glycerol + [1,] 0.051 13.774259 0.2558599 + [2,] 0.150 11.256036 0.5296600 + [3,] 0.166 10.934139 0.3875018 + [4,] 0.183 11.608822 0.7055510 + [5,] 0.206 10.666061 0.8178590 + [6,] 0.235 10.238875 0.4895200 + [7,] 0.270 9.595139 0.6793385 + [8,] 0.297 9.716688 0.8067206 + [9,] 0.330 8.979191 0.4937779 +[10,] 0.377 9.005701 1.0071384 +[11,] 0.414 7.943283 0.6890188 +[12,] 0.440 5.755193 0.4739153 + +$sys$nb_par +[1] 7 + +$sys$nb_conc +[1] 3 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA Glycerol mu qDHA qGlycerol tlag + 0.05111086 14.35691852 0.44929403 0.10806955 -1.25803554 0.08379412 4.93809959 + +$result$lastp + X DHA Glycerol mu qDHA qGlycerol tlag + 8.451124e-11 -1.208879e-07 -3.200179e-08 5.107975e-10 5.098360e-08 1.702590e-08 9.648461e-08 + +$result$hci + X DHA Glycerol mu qDHA qGlycerol tlag +0.008558520 1.414103272 1.314248130 0.003128495 0.581463557 0.599819707 1.628992063 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 2.093713 + +$result$laststep + X DHA Glycerol mu qDHA qGlycerol tlag + 8.451124e-11 -1.208879e-07 -3.200179e-08 5.107975e-10 5.098360e-08 1.702590e-08 9.648461e-08 + +$result$normp +[1] 1.668435e-07 + +$result$res + [1] 0.05542810 0.75347762 0.94404357 2.02417725 2.32981187 0.69912283 -2.59787202 -0.76143556 -0.63774200 -5.61608533 -3.24441564 7.02286800 1.16531864 0.45566881 0.53178986 -1.45455659 -0.32213633 -0.25712582 0.18924854 -0.93404591 -0.38697934 -1.44825926 -0.43372300 2.73056281 0.38686830 -0.00504331 0.30467609 -0.30170960 -0.48971059 0.20688132 -0.12870503 -0.33590351 0.34154005 -0.62773633 0.07323625 0.57560637 + +$result$prevres + [1] 0.055428058 0.753477891 0.944043838 2.024177500 2.329812086 0.699123008 -2.597871887 -0.761435486 -0.637742002 -5.616085431 -3.244415851 7.022867644 1.165318884 0.455668906 0.531789938 -1.454556528 -0.322136299 -0.257125812 0.189248520 -0.934045959 -0.386979420 -1.448259376 -0.433723147 2.730562623 0.386868363 -0.005043275 0.304676124 -0.301709582 -0.489710575 0.206881329 -0.128705033 -0.335903526 0.341540029 -0.627736366 0.073236207 0.575606305 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] + [1,] 500.000000 0.000000 0 0.000000 0.000000 0.000000 0.00000000 + [2,] 1482.140658 0.000000 0 761.697892 0.000000 0.000000 -8.18664455 + [3,] 1642.391660 0.000000 0 923.800514 0.000000 0.000000 -9.07179535 + [4,] 1829.829993 0.000000 0 1122.753641 0.000000 0.000000 -10.10711612 + [5,] 2060.810953 0.000000 0 1380.342559 0.000000 0.000000 -11.38294578 + [6,] 2312.603075 0.000000 0 1675.073378 0.000000 0.000000 -12.77372647 + [7,] 2590.489344 0.000000 0 2015.375242 0.000000 0.000000 -14.30863889 + [8,] 2890.551553 0.000000 0 2398.652219 0.000000 0.000000 -15.96604073 + [9,] 3215.799352 0.000000 0 2830.721766 0.000000 0.000000 -17.76255586 +[10,] 3578.181398 0.000000 0 3330.409650 0.000000 0.000000 -19.76418302 +[11,] 3986.542188 0.000000 0 3914.249016 0.000000 0.000000 -22.01977504 +[12,] 4441.773918 0.000000 0 4588.374427 0.000000 0.000000 -24.53425998 +[13,] 0.000000 2.000000 0 0.000000 0.000000 0.000000 0.00000000 +[14,] -44.139971 1.756907 0 -13.511263 1.793297 0.000000 0.36170231 +[15,] -51.210893 1.742540 0 -17.403909 2.080571 0.000000 0.39979464 +[16,] -59.461089 1.727543 0 -22.368958 2.415756 0.000000 0.44435850 +[17,] -69.603841 1.711196 0 -29.033332 2.827831 0.000000 0.49928531 +[18,] -80.636643 1.695491 0 -36.909329 3.276066 0.000000 0.55917149 +[19,] -92.790163 1.680173 0 -46.259360 3.769833 0.000000 0.62527391 +[20,] -105.892452 1.665509 0 -57.046802 4.302147 0.000000 0.69666076 +[21,] -120.074776 1.651366 0 -69.464993 4.878339 0.000000 0.77404815 +[22,] -135.857032 1.637323 0 -84.097942 5.519533 0.000000 0.86027954 +[23,] -153.622227 1.623232 0 -101.490759 6.241289 0.000000 0.95746052 +[24,] -173.407009 1.609254 0 -121.891889 7.045095 0.000000 1.06580436 +[25,] 0.000000 0.000000 2 0.000000 0.000000 0.000000 0.00000000 +[26,] 3.046097 0.000000 2 0.921763 0.000000 1.857990 -0.02539078 +[27,] 3.543114 0.000000 2 1.189461 0.000000 2.161150 -0.02813606 +[28,] 4.124452 0.000000 2 1.531572 0.000000 2.515741 -0.03134710 +[29,] 4.840836 0.000000 2 1.991671 0.000000 2.952705 -0.03530407 +[30,] 5.621766 0.000000 2 2.536439 0.000000 3.429040 -0.03961756 +[31,] 6.483627 0.000000 2 3.184269 0.000000 3.954738 -0.04437807 +[32,] 7.414267 0.000000 2 3.932857 0.000000 4.522389 -0.04951848 +[33,] 8.423019 0.000000 2 4.795832 0.000000 5.137685 -0.05509035 +[34,] 9.546942 0.000000 2 5.814055 0.000000 5.823231 -0.06129837 +[35,] 10.813468 0.000000 2 7.025830 0.000000 6.595758 -0.06829406 +[36,] 12.225364 0.000000 2 8.448874 0.000000 7.456955 -0.07609271 + +$result$retres +$result$retres$res + [1] 0.055428058 0.753477891 0.944043838 2.024177500 2.329812086 0.699123008 -2.597871887 -0.761435486 -0.637742002 -5.616085431 -3.244415851 7.022867644 1.165318884 0.455668906 0.531789938 -1.454556528 -0.322136299 -0.257125812 0.189248520 -0.934045959 -0.386979420 -1.448259376 -0.433723147 2.730562623 0.386868363 -0.005043275 0.304676124 -0.301709582 -0.489710575 0.206881329 -0.128705033 -0.335903526 0.341540029 -0.627736366 0.073236207 0.575606305 + +$result$retres$sim + col +row X DHA Glycerol + [1,] 0.05111086 14.356919 0.4492941 + [2,] 0.15150696 11.483871 0.5271384 + [3,] 0.16788809 11.200034 0.5398399 + [4,] 0.18704835 10.881544 0.5546962 + [5,] 0.21065962 10.504992 0.5730037 + [6,] 0.23639825 10.110312 0.5929607 + [7,] 0.26480426 9.689764 0.6149859 + [8,] 0.29547713 9.249665 0.6387688 + [9,] 0.32872452 8.785701 0.6645479 + [10,] 0.36576783 8.281572 0.6932703 + [11,] 0.40751117 7.726421 0.7256369 + [12,] 0.45404574 7.120475 0.7617185 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA Glycerol + [1,] -0.0001108561 -0.58265944 -0.193434181 + [2,] -0.0015069558 -0.22783445 0.002521638 + [3,] -0.0018880877 -0.26589497 -0.152338062 + [4,] -0.0040483550 0.72727826 0.150854791 + [5,] -0.0046596242 0.16106815 0.244855288 + [6,] -0.0013982460 0.12856291 -0.103440665 + [7,] 0.0051957438 -0.09462426 0.064352516 + [8,] 0.0015228710 0.46702298 0.167951763 + [9,] 0.0012754840 0.19348971 -0.170770014 +[10,] 0.0112321709 0.72412969 0.313868183 +[11,] 0.0064888317 0.21686157 -0.036618103 +[12,] -0.0140457353 -1.36528131 -0.287803153 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2_res/D-glpk-2_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2_res/D-glpk-2_res.txt new file mode 100644 index 0000000..7c054cc --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-2_res/D-glpk-2_res.txt @@ -0,0 +1,22 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0511108562004676 0.0511939922522261 0.0511810338573276 0.00189186866651619 0.0472268602692051 0.0542501888971008 +DHA 14.3569185199813 14.3719865390796 14.3753333757809 0.348234375961597 13.579646369394 14.9964821801432 +Glycerol 0.449294032804528 0.470231977718012 0.467973192707047 0.262622406742114 9.99999999990418e-07 1.0013710347605 +mu 0.10806955418439 0.108082788597986 0.108139148804545 0.000806629525150612 0.106338353379792 0.109603813502381 +qDHA -1.25803553656555 -1.26269050518536 -1.27112167913857 0.140895261832525 -1.49663498191492 -0.971226490818428 +qGlycerol 0.0837941184803682 0.0781650837234851 0.0770773544464657 0.131883199737226 -0.186831676988799 0.316189853176714 +tlag 4.93809959259634 4.94887217571172 4.96184833935501 0.370317226420569 4.17573095721658 5.61094973555035 +res 127.125394872208 27.3965794046326 25.4817032225022 7.01766805118311 16.9594816122794 41.1305764657002 + + +Goodness of fit (khi2 test) + +khi2 value 127.125394872208 +data points 36 +fitted parameters 7 +degrees of freedom 29 +khi2 reduced value 4.38363430593821 +p-value, i.e. P(X^2<=value) 0.99999999999997 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3.txt new file mode 100644 index 0000000..0f451d7 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3.txt @@ -0,0 +1,10 @@ +"time" "X" "DHA" "Glycerol" +0 0.048 14.0735116140636 0.670952670518386 +14.6263888888889 0.136 11.2992686962907 0.76472240518105 +16.7263888888889 0.173 10.7457605359433 0.632853910068234 +18.6430555555556 0.215 10.4286813845375 0.732544272535647 +19.7597222222222 0.242 9.37826448211913 1.27536068364415 +20.7430555555556 0.272 10.0601468442621 1.22112106980703 +21.7763888888889 0.298 8.88568128310554 1.12856385385065 +23.1238888888889 0.344 6.37327502357548 0.991637036151033 +24.1272222222222 0.379 6.25350686930036 1.28277568349065 diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3_res/D-glpk-3.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3_res/D-glpk-3.pdf new file mode 100644 index 0000000..47a3d00 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3_res/D-glpk-3.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3_res/D-glpk-3_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3_res/D-glpk-3_log.txt new file mode 100644 index 0000000..e961ba8 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3_res/D-glpk-3_log.txt @@ -0,0 +1,196 @@ +$sys +$sys$params + X DHA Glycerol mu qDHA qGlycerol tlag + 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 4.825444 + +$sys$to_est +[1] "X" "DHA" "Glycerol" "mu" "qDHA" "qGlycerol" "tlag" + +$sys$nconc +[1] "X" "DHA" "Glycerol" + +$sys$nflux +[1] "mu" "qDHA" "qGlycerol" + +$sys$metab +[1] "DHA" "Glycerol" + +$sys$weight + col +row X DHA Glycerol + [1,] 0.002 0.5 0.5 + [2,] 0.002 0.5 0.5 + [3,] 0.002 0.5 0.5 + [4,] 0.002 0.5 0.5 + [5,] 0.002 0.5 0.5 + [6,] 0.002 0.5 0.5 + [7,] 0.002 0.5 0.5 + [8,] 0.002 0.5 0.5 + [9,] 0.002 0.5 0.5 + +$sys$te_upc + X DHA Glycerol mu qDHA qGlycerol tlag + 50.00000 50.00000 50.00000 50.00000 50.00000 50.00000 24.12722 + +$sys$te_loc + X DHA Glycerol mu qDHA qGlycerol tlag + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 1e-06 + +$sys$u + X DHA Glycerol mu qDHA qGlycerol tlag +X <= 50 -1 0 0 0 0 0 0 +DHA <= 50 0 -1 0 0 0 0 0 +Glycerol <= 50 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 -1 0 0 0 +qDHA <= 50 0 0 0 0 -1 0 0 +qGlycerol <= 50 0 0 0 0 0 -1 0 +tlag <= 24.1272212222222 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 0 0 +Glycerol >= 1e-06 0 0 1 0 0 0 0 +mu >= 0 0 0 0 1 0 0 0 +qDHA >= -50 0 0 0 0 1 0 0 +qGlycerol >= -50 0 0 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 Glycerol <= 50 mu <= 50 qDHA <= 50 qGlycerol <= 50 tlag <= 24.1272212222222 X >= 1e-06 DHA >= 1e-06 Glycerol >= 1e-06 mu >= 0 qDHA >= -50 qGlycerol >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -24.127221 0.000001 0.000001 0.000001 0.000000 -50.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.62639 16.72639 18.64306 19.75972 20.74306 21.77639 23.12389 24.12722 + +$sys$data_meas + X DHA Glycerol + [1,] 0.048 14.073512 0.6709527 + [2,] 0.136 11.299269 0.7647224 + [3,] 0.173 10.745761 0.6328539 + [4,] 0.215 10.428681 0.7325443 + [5,] 0.242 9.378264 1.2753607 + [6,] 0.272 10.060147 1.2211211 + [7,] 0.298 8.885681 1.1285639 + [8,] 0.344 6.373275 0.9916370 + [9,] 0.379 6.253507 1.2827757 + +$sys$nb_par +[1] 7 + +$sys$nb_conc +[1] 3 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA Glycerol mu qDHA qGlycerol tlag + 0.04814897 14.62074934 0.60361269 0.10589166 -1.70749744 0.20666578 4.56390760 + +$result$lastp + X DHA Glycerol mu qDHA qGlycerol tlag +-4.141889e-10 -8.804796e-09 1.585090e-09 -3.225573e-10 1.339486e-08 -2.010229e-09 -1.333697e-07 + +$result$hci + X DHA Glycerol mu qDHA qGlycerol tlag +0.005101329 0.964073883 0.912526248 0.002714558 0.441003063 0.459439303 1.092314084 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.223978 + +$result$laststep + X DHA Glycerol mu qDHA qGlycerol tlag +-4.141889e-10 -8.804796e-09 1.585090e-09 -3.225573e-10 1.339486e-08 -2.010229e-09 -1.333697e-07 + +$result$normp +[1] 1.34355e-07 + +$result$res + [1] 0.07448527 1.87342528 0.77446080 -0.58684342 -0.66703991 -2.46156166 -0.02019751 -0.17100780 1.58997303 1.09447545 0.31961975 -0.09821808 -1.07216491 -0.02286964 -2.39338862 -1.19369307 2.17373636 1.04738618 -0.13467996 0.03531859 0.43490003 0.38883247 -0.59203613 -0.38046586 -0.07480552 0.37742460 -0.05448823 + +$result$prevres + [1] 0.07448548 1.87342512 0.77446066 -0.58684352 -0.66703999 -2.46156170 -0.02019751 -0.17100772 1.58997318 1.09447546 0.31961977 -0.09821806 -1.07216490 -0.02286964 -2.39338862 -1.19369308 2.17373633 1.04738614 -0.13467997 0.03531859 0.43490003 0.38883247 -0.59203613 -0.38046586 -0.07480552 0.37742461 -0.05448822 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] + [1,] 500.000000 0.000000 0 0.000000 0.000000 0.000000 0.00000000 + [2,] 1451.192491 0.000000 0 703.100023 0.000000 0.000000 -7.39901279 + [3,] 1812.592438 0.000000 0 1061.473983 0.000000 0.000000 -9.24163729 + [4,] 2220.466073 0.000000 0 1505.246134 0.000000 0.000000 -11.32121134 + [5,] 2499.180307 0.000000 0 1828.557337 0.000000 0.000000 -12.74225657 + [6,] 2773.443246 0.000000 0 2160.538133 0.000000 0.000000 -14.14060656 + [7,] 3094.143021 0.000000 0 2564.312043 0.000000 0.000000 -15.77571820 + [8,] 3568.695007 0.000000 0 3189.142858 0.000000 0.000000 -18.19525678 + [9,] 3968.723928 0.000000 0 3738.353241 0.000000 0.000000 -20.23483397 +[10,] 0.000000 2.000000 0 0.000000 0.000000 0.000000 0.00000000 +[11,] -59.205443 1.762484 0 -17.038307 1.669508 0.000000 0.45259497 +[12,] -81.248185 1.730781 0 -29.142497 2.291082 0.000000 0.56227023 +[13,] -106.011613 1.702344 0 -45.195437 2.989375 0.000000 0.68609641 +[14,] -122.885557 1.685992 0 -57.381646 3.465196 0.000000 0.77073102 +[15,] -139.461763 1.671723 0 -70.210008 3.932621 0.000000 0.85402570 +[16,] -158.816337 1.656858 0 -86.151568 4.478392 0.000000 0.95143518 +[17,] -187.412476 1.637673 0 -111.390228 5.284762 0.000000 1.09559392 +[18,] -211.486404 1.623532 0 -134.020545 5.963612 0.000000 1.21712726 +[19,] 0.000000 0.000000 2 0.000000 0.000000 0.000000 0.00000000 +[20,] 7.425663 0.000000 2 2.112431 0.000000 1.730030 -0.05776178 +[21,] 10.246999 0.000000 2 3.627282 0.000000 2.387345 -0.07214658 +[22,] 13.431141 0.000000 2 5.643842 0.000000 3.129186 -0.08838116 +[23,] 15.606977 0.000000 2 7.178479 0.000000 3.636112 -0.09947482 +[24,] 17.748062 0.000000 2 8.796597 0.000000 4.134942 -0.11039130 +[25,] 20.251665 0.000000 2 10.810345 0.000000 4.718231 -0.12315611 +[26,] 23.956344 0.000000 2 14.003685 0.000000 5.581346 -0.14204469 +[27,] 27.079245 0.000000 2 16.871215 0.000000 6.308920 -0.15796703 + +$result$retres +$result$retres$res + [1] 0.07448548 1.87342512 0.77446066 -0.58684352 -0.66703999 -2.46156170 -0.02019751 -0.17100772 1.58997318 1.09447546 0.31961977 -0.09821806 -1.07216490 -0.02286964 -2.39338862 -1.19369308 2.17373633 1.04738614 -0.13467997 0.03531859 0.43490003 0.38883247 -0.59203613 -0.38046586 -0.07480552 0.37742461 -0.05448822 + +$result$retres$sim + col +row X DHA Glycerol + [1,] 0.04814897 14.620749 0.6036127 + [2,] 0.13974685 11.459079 0.7823817 + [3,] 0.17454892 10.696652 0.8503039 + [4,] 0.21382631 9.892599 0.9269605 + [5,] 0.24066592 9.366830 0.9793426 + [6,] 0.26707688 8.863453 1.0308881 + [7,] 0.29795960 8.288835 1.0911611 + [8,] 0.34365798 7.460143 1.1803493 + [9,] 0.38217995 6.777200 1.2555316 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA Glycerol + [1,] -1.489710e-04 -0.54723773 0.06733998 + [2,] -3.746850e-03 -0.15980989 -0.01765929 + [3,] -1.548921e-03 0.04910903 -0.21745002 + [4,] 1.173687e-03 0.53608245 -0.19441624 + [5,] 1.334080e-03 0.01143482 0.29601807 + [6,] 4.923123e-03 1.19669431 0.19023293 + [7,] 4.039502e-05 0.59684654 0.03740276 + [8,] 3.420154e-04 -1.08686817 -0.18871230 + [9,] -3.179946e-03 -0.52369307 0.02724411 + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3_res/D-glpk-3_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3_res/D-glpk-3_res.txt new file mode 100644 index 0000000..5104182 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-3_res/D-glpk-3_res.txt @@ -0,0 +1,22 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0481489705479765 0.0482483990739572 0.0481419291196979 0.00205326589739546 0.0444817891485042 0.0525311124706163 +DHA 14.6207493368783 14.684994792291 14.6569934966234 0.356984542436588 14.0746533949489 15.4081012143701 +Glycerol 0.603612689244077 0.617235928723363 0.633250446910361 0.311223799178272 0.0812192282976252 1.28502949585431 +mu 0.105891657061089 0.106032338378713 0.106108333774686 0.0010669138298903 0.103961043219184 0.10805582055453 +qDHA -1.70749744379887 -1.74537235141077 -1.74068076655014 0.17089307035022 -2.0583311791444 -1.40577250307307 +qGlycerol 0.206665775372396 0.183790078286421 0.157320433398645 0.173985885870766 -0.159680379434711 0.502509513410297 +tlag 4.56390760177401 4.60084812616122 4.62048835789407 0.440993086513035 3.76629048170903 5.48645886727176 +res 29.9624294893085 20.7412252052354 19.6044852761173 7.15858535404646 10.3403868260638 34.4160793704011 + + +Goodness of fit (khi2 test) + +khi2 value 29.9624294893085 +data points 27 +fitted parameters 7 +degrees of freedom 20 +khi2 reduced value 1.49812147446542 +p-value, i.e. P(X^2<=value) 0.929535270885032 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4.txt new file mode 100644 index 0000000..9cab46b --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4.txt @@ -0,0 +1,10 @@ +"time" "X" "DHA" "Glycerol" +0 0.045 14.0814024982631 0.300831918534606 +14.9597222222222 0.113 11.7205045924564 0.54654723848679 +16.9097222222222 0.141 11.3992813973551 0.585712734932434 +19.0072222222222 0.177 11.0175424097334 0.673240634156931 +20.4572222222222 0.203 10.7612558534851 NA +22.4572222222222 0.254 10.0242726355685 NA +23.4605555555556 0.281 9.50965752744699 NA +24.4486111111111 0.309 9.32328283408138 NA +25.4491666666667 0.347 8.91729885347106 NA diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4_res/D-glpk-1-1.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4_res/D-glpk-1-1.pdf new file mode 100644 index 0000000..42752cc Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4_res/D-glpk-1-1.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4_res/D-glpk-1-1_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4_res/D-glpk-1-1_log.txt new file mode 100644 index 0000000..35cdfa7 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4_res/D-glpk-1-1_log.txt @@ -0,0 +1,191 @@ +$sys +$sys$params + X DHA Glycerol mu qDHA qGlycerol tlag + 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 5.089833 + +$sys$to_est +[1] "X" "DHA" "Glycerol" "mu" "qDHA" "qGlycerol" "tlag" + +$sys$nconc +[1] "X" "DHA" "Glycerol" + +$sys$nflux +[1] "mu" "qDHA" "qGlycerol" + +$sys$metab +[1] "DHA" "Glycerol" + +$sys$weight + col +row X DHA Glycerol + [1,] 0.002 0.5 0.5 + [2,] 0.002 0.5 0.5 + [3,] 0.002 0.5 0.5 + [4,] 0.002 0.5 0.5 + [5,] 0.002 0.5 0.5 + [6,] 0.002 0.5 0.5 + [7,] 0.002 0.5 0.5 + [8,] 0.002 0.5 0.5 + [9,] 0.002 0.5 0.5 + +$sys$te_upc + X DHA Glycerol mu qDHA qGlycerol tlag + 50.00000 50.00000 50.00000 50.00000 50.00000 50.00000 25.44917 + +$sys$te_loc + X DHA Glycerol mu qDHA qGlycerol tlag + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 1e-06 + +$sys$u + X DHA Glycerol mu qDHA qGlycerol tlag +X <= 50 -1 0 0 0 0 0 0 +DHA <= 50 0 -1 0 0 0 0 0 +Glycerol <= 50 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 -1 0 0 0 +qDHA <= 50 0 0 0 0 -1 0 0 +qGlycerol <= 50 0 0 0 0 0 -1 0 +tlag <= 25.4491656666667 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 0 0 +Glycerol >= 1e-06 0 0 1 0 0 0 0 +mu >= 0 0 0 0 1 0 0 0 +qDHA >= -50 0 0 0 0 1 0 0 +qGlycerol >= -50 0 0 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 Glycerol <= 50 mu <= 50 qDHA <= 50 qGlycerol <= 50 tlag <= 25.4491656666667 X >= 1e-06 DHA >= 1e-06 Glycerol >= 1e-06 mu >= 0 qDHA >= -50 qGlycerol >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -25.449166 0.000001 0.000001 0.000001 0.000000 -50.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.95972 16.90972 19.00722 20.45722 22.45722 23.46056 24.44861 25.44917 + +$sys$data_meas + X DHA Glycerol + [1,] 0.045 14.081402 0.3008319 + [2,] 0.113 11.720505 0.5465472 + [3,] 0.141 11.399281 0.5857127 + [4,] 0.177 11.017542 0.6732406 + [5,] 0.203 10.761256 NA + [6,] 0.254 10.024273 NA + [7,] 0.281 9.509658 NA + [8,] 0.309 9.323283 NA + [9,] 0.347 8.917299 NA + +$sys$nb_par +[1] 7 + +$sys$nb_conc +[1] 3 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA Glycerol mu qDHA qGlycerol tlag + 0.04500249 14.10385349 0.31528201 0.10552952 -0.87707929 0.30203189 6.11823356 + +$result$lastp + X DHA Glycerol mu qDHA qGlycerol tlag +-6.325442e-11 -9.770057e-10 7.907712e-09 -3.075188e-11 1.194373e-09 -1.167120e-08 -1.827053e-08 + +$result$hci + X DHA Glycerol mu qDHA qGlycerol tlag +0.002307970 0.413295962 0.531018911 0.001271352 0.209587996 0.637212486 0.527503116 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 0.5415761 + +$result$laststep + X DHA Glycerol mu qDHA qGlycerol tlag +-6.325442e-11 -9.770057e-10 7.907712e-09 -3.075188e-11 1.194373e-09 -1.167120e-08 -1.827053e-08 + +$result$normp +[1] 2.312892e-08 + +$result$res + [1] 0.001242971 0.703127540 -0.226755837 -0.816013203 0.682158777 -0.806540312 -0.212006614 1.205504321 -0.454498516 0.044901986 0.228099160 0.043953150 -0.176760098 -0.415487722 -0.094895394 0.295458091 -0.006451852 0.070981749 0.028900178 -0.065254851 0.006044029 0.030310644 + +$result$prevres + [1] 0.001243003 0.703127526 -0.226755850 -0.816013214 0.682158769 -0.806540314 -0.212006612 1.205504328 -0.454498503 0.044901988 0.228099162 0.043953151 -0.176760097 -0.415487722 -0.094895395 0.295458089 -0.006451854 0.070981746 0.028900162 -0.065254852 0.006044033 0.030310657 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] + [1,] 500.00000 0.000000 0 0.000000 0.000000 0.000000 0.00000000 + [2,] 1271.11039 0.000000 0 505.760802 0.000000 0.000000 -6.03661839 + [3,] 1561.54138 0.000000 0 758.352916 0.000000 0.000000 -7.41590148 + [4,] 1948.42540 0.000000 0 1130.157910 0.000000 0.000000 -9.25324873 + [5,] 2270.58920 0.000000 0 1465.188814 0.000000 0.000000 -10.78323381 + [6,] 2804.14419 0.000000 0 2061.873505 0.000000 0.000000 -13.31713478 + [7,] 3117.33875 0.000000 0 2432.919551 0.000000 0.000000 -14.80452411 + [8,] 3459.93118 0.000000 0 2854.140678 0.000000 0.000000 -16.43152659 + [9,] 3845.24316 0.000000 0 3345.131011 0.000000 0.000000 -18.26140810 +[10,] 0.00000 2.000000 0 0.000000 0.000000 0.000000 0.00000000 +[11,] -24.82514 1.757413 0 -5.755970 1.273765 0.000000 0.19103028 +[12,] -33.98742 1.728041 0 -9.906231 1.743877 0.000000 0.23332046 +[13,] -46.12708 1.696994 0 -16.546112 2.366756 0.000000 0.28968081 +[14,] -56.19773 1.675858 0 -22.871513 2.883477 0.000000 0.33662773 +[15,] -72.82548 1.647137 0 -34.652490 3.736638 0.000000 0.41439915 +[16,] -82.56454 1.632914 0 -42.215270 4.236344 0.000000 0.46005897 +[17,] -93.20421 1.619028 0 -50.964847 4.782260 0.000000 0.51000988 +[18,] -105.15702 1.605087 0 -61.340712 5.395553 0.000000 0.56619471 +[19,] 0.00000 0.000000 2 0.000000 0.000000 0.000000 0.00000000 +[20,] 8.82786 0.000000 2 2.025480 0.000000 1.315343 -0.06910868 +[21,] 12.15278 0.000000 2 3.499320 0.000000 1.810754 -0.08489905 +[22,] 16.58193 0.000000 2 5.867051 0.000000 2.470692 -0.10593345 + +$result$retres +$result$retres$res + [1] 0.001243003 0.703127526 -0.226755850 -0.816013214 0.682158769 -0.806540314 -0.212006612 1.205504328 -0.454498503 0.044901988 0.228099162 0.043953151 -0.176760097 -0.415487722 -0.094895395 0.295458089 -0.006451854 0.070981746 0.028900162 -0.065254852 0.006044033 0.030310657 + +$result$retres$sim + col +row X DHA Glycerol + [1,] 0.04500249 14.103853 0.3152820 + [2,] 0.11440626 11.834554 0.5139198 + [3,] 0.14054649 11.421258 0.5887348 + [4,] 0.17536797 10.929162 0.6883960 + [5,] 0.20436432 10.553512 0.7713853 + [6,] 0.25238692 9.976825 0.9088289 + [7,] 0.28057599 9.657387 0.9895077 + [8,] 0.31141101 9.320057 1.0777594 + [9,] 0.34609100 8.952790 1.1770157 + + +$result$it +[1] 5 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA Glycerol + [1,] -2.486006e-06 -0.022450994 -0.014450081 + [2,] -1.406255e-03 -0.114049581 0.032627426 + [3,] 4.535117e-04 -0.021976576 -0.003022017 + [4,] 1.632026e-03 0.088380049 -0.015155328 + [5,] -1.364318e-03 0.207743861 NA + [6,] 1.613081e-03 0.047447698 NA + [7,] 4.240132e-04 -0.147729045 NA + [8,] -2.411009e-03 0.003225927 NA + [9,] 9.089970e-04 -0.035490873 NA + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4_res/D-glpk-1-1_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4_res/D-glpk-1-1_res.txt new file mode 100644 index 0000000..3a0590b --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-4_res/D-glpk-1-1_res.txt @@ -0,0 +1,22 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0450024859425211 0.0448057811215065 0.0445905860252323 0.00193952012658467 0.0417583222025195 0.0486982478194059 +DHA 14.103853491474 14.1041194932431 14.0585543544471 0.359083675638618 13.4301591593521 14.8422279950641 +Glycerol 0.315282007595211 0.387895865430342 0.360087249933307 0.258215208932059 9.99999999999677e-07 0.979840537653153 +mu 0.105529516455517 0.105541650711018 0.105585441606164 0.00100281697629446 0.103692318161457 0.107307711455078 +qDHA -0.877079287203017 -0.870427005444213 -0.84416494829487 0.181964808211137 -1.20548529005424 -0.584201936995363 +qGlycerol 0.302031889764397 0.276513370225183 0.29840355820568 0.158823402503167 -0.0199261801754614 0.569876124900674 +tlag 6.11823355959417 6.06902665542346 6.03444585117464 0.426455595169712 5.36220662084291 6.88841450436507 +res 4.39957069514549 19.9756350111056 19.3007267853561 6.69620353605287 9.02998488345278 34.0892694425993 + + +Goodness of fit (khi2 test) + +khi2 value 4.39957069514552 +data points 22 +fitted parameters 7 +degrees of freedom 15 +khi2 reduced value 0.293304713009701 +p-value, i.e. P(X^2<=value) 0.00389510806471667 +conclusion At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5.txt new file mode 100644 index 0000000..3bf7970 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5.txt @@ -0,0 +1,13 @@ +"time" "X" "DHA" "Glycerol" +0 0.051 13.7742591988714 0.255859883369191 +14.9930555555556 0.15 11.2560361818776 0.529660022921786 +15.9430555555556 0.166 10.934139152399 NA +16.9430555555556 0.183 11.6088218366363 0.705550980455042 +18.0430555555556 0.206 10.6660605593739 0.817858993134583 +19.1097222222222 0.235 10.2388751622393 NA +20.1597222222222 0.27 9.59513934328659 NA +21.1738888888889 0.297 9.71668762579136 0.806720583105409 +22.1605555555556 0.33 8.97919072240849 NA +23.1486111111111 0.377 9.00570119388197 1.00713844113837 +24.1486111111111 0.414 7.94328290440636 NA +25.1491666666667 0.44 5.75519349966588 NA diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5_res/D-glpk-2-2.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5_res/D-glpk-2-2.pdf new file mode 100644 index 0000000..e1f1014 Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5_res/D-glpk-2-2.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5_res/D-glpk-2-2_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5_res/D-glpk-2-2_log.txt new file mode 100644 index 0000000..e9e4231 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5_res/D-glpk-2-2_log.txt @@ -0,0 +1,211 @@ +$sys +$sys$params + X DHA Glycerol mu qDHA qGlycerol tlag + 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 5.029833 + +$sys$to_est +[1] "X" "DHA" "Glycerol" "mu" "qDHA" "qGlycerol" "tlag" + +$sys$nconc +[1] "X" "DHA" "Glycerol" + +$sys$nflux +[1] "mu" "qDHA" "qGlycerol" + +$sys$metab +[1] "DHA" "Glycerol" + +$sys$weight + col +row X DHA Glycerol + [1,] 0.002 0.5 0.5 + [2,] 0.002 0.5 0.5 + [3,] 0.002 0.5 0.5 + [4,] 0.002 0.5 0.5 + [5,] 0.002 0.5 0.5 + [6,] 0.002 0.5 0.5 + [7,] 0.002 0.5 0.5 + [8,] 0.002 0.5 0.5 + [9,] 0.002 0.5 0.5 + [10,] 0.002 0.5 0.5 + [11,] 0.002 0.5 0.5 + [12,] 0.002 0.5 0.5 + +$sys$te_upc + X DHA Glycerol mu qDHA qGlycerol tlag + 50.00000 50.00000 50.00000 50.00000 50.00000 50.00000 25.14917 + +$sys$te_loc + X DHA Glycerol mu qDHA qGlycerol tlag + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 1e-06 + +$sys$u + X DHA Glycerol mu qDHA qGlycerol tlag +X <= 50 -1 0 0 0 0 0 0 +DHA <= 50 0 -1 0 0 0 0 0 +Glycerol <= 50 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 -1 0 0 0 +qDHA <= 50 0 0 0 0 -1 0 0 +qGlycerol <= 50 0 0 0 0 0 -1 0 +tlag <= 25.1491656666667 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 0 0 +Glycerol >= 1e-06 0 0 1 0 0 0 0 +mu >= 0 0 0 0 1 0 0 0 +qDHA >= -50 0 0 0 0 1 0 0 +qGlycerol >= -50 0 0 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 Glycerol <= 50 mu <= 50 qDHA <= 50 qGlycerol <= 50 tlag <= 25.1491656666667 X >= 1e-06 DHA >= 1e-06 Glycerol >= 1e-06 mu >= 0 qDHA >= -50 qGlycerol >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -25.149166 0.000001 0.000001 0.000001 0.000000 -50.000000 -50.000000 0.000001 + +$sys$times + [1] 0.00000 14.99306 15.94306 16.94306 18.04306 19.10972 20.15972 21.17389 22.16056 23.14861 24.14861 25.14917 + +$sys$data_meas + X DHA Glycerol + [1,] 0.051 13.774259 0.2558599 + [2,] 0.150 11.256036 0.5296600 + [3,] 0.166 10.934139 NA + [4,] 0.183 11.608822 0.7055510 + [5,] 0.206 10.666061 0.8178590 + [6,] 0.235 10.238875 NA + [7,] 0.270 9.595139 NA + [8,] 0.297 9.716688 0.8067206 + [9,] 0.330 8.979191 NA +[10,] 0.377 9.005701 1.0071384 +[11,] 0.414 7.943283 NA +[12,] 0.440 5.755193 NA + +$sys$nb_par +[1] 7 + +$sys$nb_conc +[1] 3 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA Glycerol mu qDHA qGlycerol tlag + 0.05111068 14.35691770 0.32708063 0.10806971 -1.25803617 0.24448849 4.93809176 + +$result$lastp + X DHA Glycerol mu qDHA qGlycerol tlag + 8.311278e-11 -1.184272e-07 -1.687232e-08 5.038568e-10 4.990033e-08 1.306489e-08 9.512860e-08 + +$result$hci + X DHA Glycerol mu qDHA qGlycerol tlag +0.009664306 1.596831440 1.846881410 0.003532734 0.656599829 1.059996596 1.839457199 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 2.337484 + +$result$laststep + X DHA Glycerol mu qDHA qGlycerol tlag + 8.311278e-11 -1.184272e-07 -1.687232e-08 5.038568e-10 4.990033e-08 1.306489e-08 9.512860e-08 + +$result$normp +[1] 1.613076e-07 + +$result$res + [1] 0.05533884 0.75339476 0.94396408 2.02410313 2.32974628 0.69906870 -2.59791117 -0.76145611 -0.63773981 -5.61605500 -3.24435037 7.02297580 1.16531701 0.45566921 0.53179045 -1.45455584 -0.32213548 -0.25712496 0.18924931 -0.93404535 -0.38697912 -1.44825955 -0.43372401 2.73056084 0.14244148 0.04909790 -0.14187175 -0.25965511 0.14639116 0.06359632 + +$result$prevres + [1] 0.05533880 0.75339504 0.94396434 2.02410338 2.32974650 0.69906888 -2.59791104 -0.76145604 -0.63773982 -5.61605509 -3.24435058 7.02297545 1.16531725 0.45566930 0.53179053 -1.45455578 -0.32213545 -0.25712495 0.18924930 -0.93404539 -0.38697920 -1.44825966 -0.43372415 2.73056066 0.14244152 0.04909791 -0.14187175 -0.25965511 0.14639114 0.06359628 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] + [1,] 500.000000 0.000000 0 0.000000 0.000000 0.000000 0.00000000 + [2,] 1482.144213 0.000000 0 761.697652 0.000000 0.000000 -8.18664729 + [3,] 1642.395842 0.000000 0 923.800296 0.000000 0.000000 -9.07179973 + [4,] 1829.834934 0.000000 0 1122.753484 0.000000 0.000000 -10.10712255 + [5,] 2060.816868 0.000000 0 1380.342524 0.000000 0.000000 -11.38295496 + [6,] 2312.610093 0.000000 0 1675.073536 0.000000 0.000000 -12.77373887 + [7,] 2590.497626 0.000000 0 2015.375683 0.000000 0.000000 -14.30865511 + [8,] 2890.561247 0.000000 0 2398.653042 0.000000 0.000000 -15.96606132 + [9,] 3215.810628 0.000000 0 2830.723091 0.000000 0.000000 -17.76258148 +[10,] 3578.194489 0.000000 0 3330.411635 0.000000 0.000000 -19.76421455 +[11,] 3986.557389 0.000000 0 3914.251865 0.000000 0.000000 -22.01981356 +[12,] 4441.791542 0.000000 0 4588.378384 0.000000 0.000000 -24.53430670 +[13,] 0.000000 2.000000 0 0.000000 0.000000 0.000000 0.00000000 +[14,] -44.140089 1.756907 0 -13.511267 1.793295 0.000000 0.36170210 +[15,] -51.211032 1.742540 0 -17.403914 2.080569 0.000000 0.39979447 +[16,] -59.461254 1.727543 0 -22.368964 2.415753 0.000000 0.44435838 +[17,] -69.604040 1.711196 0 -29.033341 2.827828 0.000000 0.49928527 +[18,] -80.636880 1.695491 0 -36.909342 3.276063 0.000000 0.55917154 +[19,] -92.790445 1.680173 0 -46.259380 3.769830 0.000000 0.62527406 +[20,] -105.892784 1.665509 0 -57.046831 4.302143 0.000000 0.69666105 +[21,] -120.075165 1.651366 0 -69.465033 4.878336 0.000000 0.77404859 +[22,] -135.857486 1.637323 0 -84.097998 5.519530 0.000000 0.86028016 +[23,] -153.622757 1.623232 0 -101.490835 6.241286 0.000000 0.95746136 +[24,] -173.407628 1.609254 0 -121.891992 7.045092 0.000000 1.06580547 +[25,] 0.000000 0.000000 2 0.000000 0.000000 0.000000 0.00000000 +[26,] 8.887706 0.000000 2 2.689454 0.000000 1.857988 -0.07408333 +[27,] 12.034059 0.000000 2 4.468711 0.000000 2.515738 -0.09146226 +[28,] 14.124281 0.000000 2 5.811155 0.000000 2.952702 -0.10300764 +[29,] 21.632877 0.000000 2 11.475011 0.000000 4.522385 -0.14448149 +[30,] 27.855469 0.000000 2 16.963840 0.000000 5.823227 -0.17885207 + +$result$retres +$result$retres$res + [1] 0.05533880 0.75339504 0.94396434 2.02410338 2.32974650 0.69906888 -2.59791104 -0.76145604 -0.63773982 -5.61605509 -3.24435058 7.02297545 1.16531725 0.45566930 0.53179053 -1.45455578 -0.32213545 -0.25712495 0.18924930 -0.93404539 -0.38697920 -1.44825966 -0.43372415 2.73056066 0.14244152 0.04909791 -0.14187175 -0.25965511 0.14639114 0.06359628 + +$result$retres$sim + col +row X DHA Glycerol + [1,] 0.05111068 14.356918 0.3270806 + [2,] 0.15150679 11.483871 0.5542090 + [3,] 0.16788793 11.200034 0.5912684 + [4,] 0.18704821 10.881544 0.6346151 + [5,] 0.21065949 10.504993 0.6880314 + [6,] 0.23639814 10.110313 0.7462605 + [7,] 0.26480418 9.689764 0.8105242 + [8,] 0.29547709 9.249665 0.8799162 + [9,] 0.32872452 8.785701 0.9551326 + [10,] 0.36576789 8.281571 1.0389366 + [11,] 0.40751130 7.726421 1.1333736 + [12,] 0.45404595 7.120474 1.2386500 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA Glycerol + [1,] -0.0001106776 -0.58265862 -0.07122076 + [2,] -0.0015067901 -0.22783465 -0.02454896 + [3,] -0.0018879287 -0.26589526 NA + [4,] -0.0040482068 0.72727789 0.07093587 + [5,] -0.0046594930 0.16106772 0.12982755 + [6,] -0.0013981378 0.12856247 NA + [7,] 0.0051958221 -0.09462465 NA + [8,] 0.0015229121 0.46702270 -0.07319557 + [9,] 0.0012754796 0.19348960 NA +[10,] 0.0112321102 0.72412983 -0.03179814 +[11,] 0.0064887012 0.21686208 NA +[12,] -0.0140459509 -1.36528033 NA + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5_res/D-glpk-2-2_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5_res/D-glpk-2-2_res.txt new file mode 100644 index 0000000..63c9c84 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-5_res/D-glpk-2-2_res.txt @@ -0,0 +1,22 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0511106776748352 0.0512490413644941 0.0512238952376381 0.00199830954608348 0.0476007035031269 0.0551452126054435 +DHA 14.3569177033443 14.3277512684651 14.3220689659663 0.331073864756904 13.7635522389463 15.0250419556152 +Glycerol 0.327080625699182 0.393564230145264 0.375679103841157 0.257547475017896 9.99999999990418e-07 0.940495725659274 +mu 0.108069708630597 0.108109655362258 0.10810121213378 0.000760369950425512 0.106564359188691 0.109373017797517 +qDHA -1.2580361671529 -1.25531612781469 -1.23762277479637 0.130047696427947 -1.52508533115349 -1.03257198732805 +qGlycerol 0.244488493203686 0.237437873347698 0.251681340709351 0.12226759826379 -0.0273687698869204 0.44511561361588 +tlag 4.93809176192419 4.96118262314815 5.01286331257586 0.396287091016278 4.20106445819352 5.63529176125285 +res 125.668168082834 28.7980591390272 28.3784694914379 7.37531272086986 16.6592901328427 43.9352405737179 + + +Goodness of fit (khi2 test) + +khi2 value 125.668168082834 +data points 30 +fitted parameters 7 +degrees of freedom 23 +khi2 reduced value 5.46383339490584 +p-value, i.e. P(X^2<=value) 1 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6.txt new file mode 100644 index 0000000..a71d79a --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6.txt @@ -0,0 +1,10 @@ +"time" "X" "DHA" "Glycerol" +0 0.048 14.0735116140636 NA +14.6263888888889 0.136 11.2992686962907 NA +16.7263888888889 0.173 10.7457605359433 0.632853910068234 +18.6430555555556 0.215 10.4286813845375 0.732544272535647 +19.7597222222222 0.242 9.37826448211913 1.27536068364415 +20.7430555555556 0.272 10.0601468442621 NA +21.7763888888889 0.298 8.88568128310554 NA +23.1238888888889 0.344 6.37327502357548 NA +24.1272222222222 0.379 6.25350686930036 NA diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6_res/D-glpk-3-3.pdf b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6_res/D-glpk-3-3.pdf new file mode 100644 index 0000000..4a15deb Binary files /dev/null and b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6_res/D-glpk-3-3.pdf differ diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6_res/D-glpk-3-3_log.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6_res/D-glpk-3-3_log.txt new file mode 100644 index 0000000..3406a96 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6_res/D-glpk-3-3_log.txt @@ -0,0 +1,190 @@ +$sys +$sys$params + X DHA Glycerol mu qDHA qGlycerol tlag + 0.100000 0.100000 0.100000 0.100000 0.100000 0.100000 4.825444 + +$sys$to_est +[1] "X" "DHA" "Glycerol" "mu" "qDHA" "qGlycerol" "tlag" + +$sys$nconc +[1] "X" "DHA" "Glycerol" + +$sys$nflux +[1] "mu" "qDHA" "qGlycerol" + +$sys$metab +[1] "DHA" "Glycerol" + +$sys$weight + col +row X DHA Glycerol + [1,] 0.002 0.5 0.5 + [2,] 0.002 0.5 0.5 + [3,] 0.002 0.5 0.5 + [4,] 0.002 0.5 0.5 + [5,] 0.002 0.5 0.5 + [6,] 0.002 0.5 0.5 + [7,] 0.002 0.5 0.5 + [8,] 0.002 0.5 0.5 + [9,] 0.002 0.5 0.5 + +$sys$te_upc + X DHA Glycerol mu qDHA qGlycerol tlag + 50.00000 50.00000 50.00000 50.00000 50.00000 50.00000 24.12722 + +$sys$te_loc + X DHA Glycerol mu qDHA qGlycerol tlag + 1e-06 1e-06 1e-06 0e+00 -5e+01 -5e+01 1e-06 + +$sys$u + X DHA Glycerol mu qDHA qGlycerol tlag +X <= 50 -1 0 0 0 0 0 0 +DHA <= 50 0 -1 0 0 0 0 0 +Glycerol <= 50 0 0 -1 0 0 0 0 +mu <= 50 0 0 0 -1 0 0 0 +qDHA <= 50 0 0 0 0 -1 0 0 +qGlycerol <= 50 0 0 0 0 0 -1 0 +tlag <= 24.1272212222222 0 0 0 0 0 0 -1 +X >= 1e-06 1 0 0 0 0 0 0 +DHA >= 1e-06 0 1 0 0 0 0 0 +Glycerol >= 1e-06 0 0 1 0 0 0 0 +mu >= 0 0 0 0 1 0 0 0 +qDHA >= -50 0 0 0 0 1 0 0 +qGlycerol >= -50 0 0 0 0 0 1 0 +tlag >= 1e-06 0 0 0 0 0 0 1 + +$sys$co + X <= 50 DHA <= 50 Glycerol <= 50 mu <= 50 qDHA <= 50 qGlycerol <= 50 tlag <= 24.1272212222222 X >= 1e-06 DHA >= 1e-06 Glycerol >= 1e-06 mu >= 0 qDHA >= -50 qGlycerol >= -50 tlag >= 1e-06 + -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -50.000000 -24.127221 0.000001 0.000001 0.000001 0.000000 -50.000000 -50.000000 0.000001 + +$sys$times +[1] 0.00000 14.62639 16.72639 18.64306 19.75972 20.74306 21.77639 23.12389 24.12722 + +$sys$data_meas + X DHA Glycerol + [1,] 0.048 14.073512 NA + [2,] 0.136 11.299269 NA + [3,] 0.173 10.745761 0.6328539 + [4,] 0.215 10.428681 0.7325443 + [5,] 0.242 9.378264 1.2753607 + [6,] 0.272 10.060147 NA + [7,] 0.298 8.885681 NA + [8,] 0.344 6.373275 NA + [9,] 0.379 6.253507 NA + +$sys$nb_par +[1] 7 + +$sys$nb_conc +[1] 3 + +$sys$deg + DHA +0.008643483 + +$sys$lag +[1] TRUE + + +$result +$result$par + X DHA Glycerol mu qDHA qGlycerol tlag + 0.04815128 14.62071962 0.00000100 0.10589308 -1.70752385 0.58794782 4.56459218 + +$result$lastp + X DHA Glycerol mu qDHA qGlycerol tlag +-4.248144e-10 -8.162887e-09 0.000000e+00 -3.317272e-10 1.329093e-08 -5.133870e-09 -1.369256e-07 + +$result$hci + X DHA Glycerol mu qDHA qGlycerol tlag +0.006198151 1.171329571 5.402416981 0.003298222 0.535821071 3.492552685 1.327105348 + +$result$ci_p +[1] 0.95 + +$result$sd_res +[1] 1.446334 + +$result$laststep + X DHA Glycerol mu qDHA qGlycerol tlag +-4.248144e-10 -8.162887e-09 0.000000e+00 -3.317272e-10 1.329093e-08 -5.133870e-09 -1.369256e-07 + +$result$normp +[1] 1.379078e-07 + +$result$res + [1] 0.07564212 1.87272053 0.77384199 -0.58730916 -0.66737242 -2.46174334 -0.02018058 -0.17065797 1.59063558 1.09441600 0.31967183 -0.09817465 -1.07213450 -0.02284980 -2.39338033 -1.19369959 2.17370564 1.04733317 0.13787004 0.37465069 -0.41293726 + +$result$prevres + [1] 0.07564233 1.87272036 0.77384185 -0.58730926 -0.66737250 -2.46174338 -0.02018058 -0.17065788 1.59063574 1.09441602 0.31967186 -0.09817463 -1.07213449 -0.02284980 -2.39338033 -1.19369960 2.17370562 1.04733314 0.13787004 0.37465070 -0.41293725 + +$result$jacobian + [,1] [,2] [,3] [,4] [,5] [,6] [,7] + [1,] 500.00000 0.000000 0 0.00000 0.000000 0.000000 0.0000000 + [2,] 1451.10812 0.000000 0 703.04510 0.000000 0.000000 -7.3990378 + [3,] 1812.49249 0.000000 0 1061.40671 0.000000 0.000000 -9.2416963 + [4,] 2220.34971 0.000000 0 1505.16639 0.000000 0.000000 -11.3213145 + [5,] 2499.05331 0.000000 0 1828.46991 0.000000 0.000000 -12.7423930 + [6,] 2773.30621 0.000000 0 2160.44378 0.000000 0.000000 -14.1407778 + [7,] 3093.99470 0.000000 0 2564.21034 0.000000 0.000000 -15.7759325 + [8,] 3568.53079 0.000000 0 3189.03172 0.000000 0.000000 -18.1955389 + [9,] 3968.54699 0.000000 0 3738.23538 0.000000 0.000000 -20.2351767 +[10,] 0.00000 2.000000 0 0.00000 0.000000 0.000000 0.0000000 +[11,] -59.20043 1.762484 0 -17.03638 1.669421 0.000000 0.4525984 +[12,] -81.24231 1.730781 0 -29.13993 2.290991 0.000000 0.5622760 +[13,] -106.00484 1.702344 0 -45.19221 2.989281 0.000000 0.6861052 +[14,] -122.87820 1.685992 0 -57.37802 3.465101 0.000000 0.7707421 +[15,] -139.45386 1.671723 0 -70.20601 3.932526 0.000000 0.8540391 +[16,] -158.80782 1.656858 0 -86.14717 4.478298 0.000000 0.9514514 +[17,] -187.40310 1.637673 0 -111.38531 5.284670 0.000000 1.0956146 +[18,] -211.47634 1.623532 0 -134.01525 5.963523 0.000000 1.2171519 +[19,] 29.14929 0.000000 2 10.31825 0.000000 2.387246 -0.2052499 +[20,] 38.20744 0.000000 2 16.05487 0.000000 3.129082 -0.2514363 +[21,] 44.39720 0.000000 2 20.42057 0.000000 3.636006 -0.2829972 + +$result$retres +$result$retres$res + [1] 0.07564233 1.87272036 0.77384185 -0.58730926 -0.66737250 -2.46174338 -0.02018058 -0.17065788 1.59063574 1.09441602 0.31967186 -0.09817463 -1.07213449 -0.02284980 -2.39338033 -1.19369960 2.17370562 1.04733314 0.13787004 0.37465070 -0.41293725 + +$result$retres$sim + col +row X DHA Glycerol + [1,] 0.04815128 14.620720 0.0000010 + [2,] 0.13974544 11.459105 0.5085572 + [3,] 0.17454768 10.696673 0.7017889 + [4,] 0.21382538 9.892614 0.9198696 + [5,] 0.24066526 9.366840 1.0688921 + [6,] 0.26707651 8.863457 1.2155347 + [7,] 0.29795964 8.288831 1.3870064 + [8,] 0.34365868 7.460128 1.6407402 + [9,] 0.38218127 6.777173 1.8546283 + + +$result$it +[1] 6 + +$result$btit +[1] 0 + +$result$history +NULL + +$result$error +[1] 0 + +$result$mes +[1] "" + +$result$resi + X DHA Glycerol + [1,] -1.512847e-04 -0.54720801 NA + [2,] -3.745441e-03 -0.15983593 NA + [3,] -1.547684e-03 0.04908732 -0.06893502 + [4,] 1.174619e-03 0.53606725 -0.18732535 + [5,] 1.334745e-03 0.01142490 0.20646863 + [6,] 4.923487e-03 1.19669016 NA + [7,] 4.036116e-05 0.59684980 NA + [8,] 3.413158e-04 -1.08685281 NA + [9,] -3.181271e-03 -0.52366657 NA + + diff --git a/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6_res/D-glpk-3-3_res.txt b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6_res/D-glpk-3-3_res.txt new file mode 100644 index 0000000..186c761 --- /dev/null +++ b/validation/validation_results/Peiro_2019/Peiro_2019/glpK-6_res/D-glpk-3-3_res.txt @@ -0,0 +1,22 @@ +Results (100 mc iterations) + +optimal mean median sd CI_2.5 CI_97.5 +X 0.0481512842431644 0.0478844765575888 0.0478005769614705 0.00196293447882858 0.0438882290613688 0.0513589433105651 +DHA 14.6207196152768 14.6127750522687 14.6692525866881 0.370389093164758 13.9254202677183 15.4148706721253 +Glycerol 9.99999999945489e-07 0.204554066446801 0.153539210171973 0.232103584096328 9.99999999889978e-07 0.700464476228444 +mu 0.105893083612739 0.105929740892444 0.105879543643278 0.00103818257804967 0.103834114030702 0.10779389916801 +qDHA -1.70752385358733 -1.70430666543956 -1.71434437379926 0.165776097144497 -2.03798351400866 -1.3763883741876 +qGlycerol 0.587947821016814 0.490988634900593 0.511440783093983 0.135994268754431 0.177419785173857 0.723175060844689 +tlag 4.56459218427717 4.51068611794609 4.52284066093798 0.422545477720155 3.61516672108182 5.22633963391124 +res 29.2863353031364 18.651773318998 17.2571489024905 6.41036825953788 9.48247522144485 33.1829340662785 + + +Goodness of fit (khi2 test) + +khi2 value 29.2863353031366 +data points 21 +fitted parameters 7 +degrees of freedom 14 +khi2 reduced value 2.09188109308118 +p-value, i.e. P(X^2<=value) 0.99044359026528 +conclusion At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/dataset_1.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/dataset_1.tsv new file mode 100644 index 0000000..dbb5858 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/dataset_1.tsv @@ -0,0 +1,130 @@ +experiments time X DHA +WT-1 0.000000 0.084000 13.258820 +WT-1 14.843056 0.317000 8.273916 +WT-1 19.323889 0.628000 3.810018 +WT-2 0.000000 0.081000 10.649188 +WT-2 14.826389 0.301000 7.000822 +WT-2 17.190556 0.437000 5.579987 +WT-2 18.940556 0.583000 3.764025 +WT-2 21.027222 0.790000 1.190285 +WT-3 0.000000 0.093000 15.648222 +WT-3 14.809722 0.293000 11.362852 +WT-3 17.257222 0.439000 9.250810 +WT-3 19.290556 0.653000 6.784887 +WT-3 22.031944 0.888000 2.690635 +delta_gldA-1 0.000000 0.069000 10.782465 +delta_gldA-1 14.826389 0.217000 7.785630 +delta_gldA-1 17.190556 0.290000 7.201654 +delta_gldA-1 18.940556 0.368000 6.421098 +delta_gldA-1 21.027222 0.487000 4.963635 +delta_gldA-1 22.832500 0.627000 3.491181 +delta_gldA-2 0.000000 0.060000 14.123598 +delta_gldA-2 7.982500 0.080000 13.497914 +delta_gldA-2 9.476667 0.100000 12.268293 +delta_gldA-2 23.892778 0.740000 7.410710 +delta_gldA-2 26.976111 1.150000 2.971112 +delta_gldA-3 0.000000 0.034000 17.562716 +delta_gldA-3 15.000000 0.240000 15.686244 +delta_gldA-3 17.000000 0.316000 13.356816 +delta_gldA-3 19.250000 0.450000 7.003778 +delta_gldA-3 21.250000 0.610000 7.807255 +delta_gldA-3 23.166667 0.730000 6.415134 +delta_dhaKLM-1 0.000000 0.080000 13.091353 +delta_dhaKLM-1 7.982500 0.110000 12.697156 +delta_dhaKLM-1 9.476667 0.150000 12.389292 +delta_dhaKLM-1 23.892778 0.450000 10.069308 +delta_dhaKLM-1 26.976111 0.480000 10.042876 +delta_dhaKLM-1 47.843056 1.090000 3.366052 +delta_dhaKLM-2 0.000000 0.050000 14.303145 +delta_dhaKLM-2 7.982500 NA 12.436215 +delta_dhaKLM-2 9.476667 0.080000 12.411095 +delta_dhaKLM-2 23.892778 0.330000 10.883254 +delta_dhaKLM-2 26.976111 0.420000 9.322037 +delta_dhaKLM-2 47.843056 0.950000 3.988412 +delta_dhaKLM-3 0.000000 0.027000 17.562716 +delta_dhaKLM-3 15.000000 0.162000 15.800197 +delta_dhaKLM-3 17.000000 0.192000 18.841635 +delta_dhaKLM-3 19.250000 10.845222 +delta_dhaKLM-3 21.250000 0.270000 10.262621 +delta_dhaKLM-3 23.166667 0.290000 12.005897 +delta_dhaKLM-3 39.166667 0.630000 7.336636 +delta_fsaB-1 0.000000 0.028000 14.096684 +delta_fsaB-1 14.959722 0.267000 10.339988 +delta_fsaB-1 16.909722 0.384000 9.103556 +delta_fsaB-1 19.007222 0.502000 7.818633 +delta_fsaB-1 20.457222 0.609000 5.994450 +delta_fsaB-1 22.457222 0.761000 3.344009 +delta_fsaB-1 23.460556 0.841000 2.179649 +delta_fsaB-1 24.448611 0.921000 1.582310 +delta_fsaB-2 0.000000 0.060000 13.537160 +delta_fsaB-2 14.993056 0.412000 9.628371 +delta_fsaB-2 15.943056 0.475000 8.697996 +delta_fsaB-2 16.943056 0.536000 7.283556 +delta_fsaB-2 18.043056 0.610000 6.050140 +delta_fsaB-2 19.109722 0.707000 4.675252 +delta_fsaB-2 20.159722 0.806000 3.387898 +delta_fsaB-3 0.000000 0.046000 14.157601 +delta_fsaB-3 14.626389 0.318000 9.430618 +delta_fsaB-3 16.726389 0.425000 8.203104 +delta_fsaB-3 18.643056 0.544000 6.565640 +delta_fsaB-3 19.759722 0.623000 4.764551 +delta_fsaB-3 20.743056 0.713000 4.331454 +delta_fsaB-3 21.776389 0.784000 2.192368 +delta_fsaB-3 23.123889 0.898000 1.393149 +delta_gldA-4 0.000000 0.045000 14.212953 +delta_gldA-4 14.959722 0.210000 10.927801 +delta_gldA-4 16.909722 0.289000 10.419344 +delta_gldA-4 19.007222 0.384000 9.308633 +delta_gldA-4 20.457222 0.465000 8.072553 +delta_gldA-4 22.457222 0.609000 6.991455 +delta_gldA-4 23.460556 0.693000 6.074298 +delta_gldA-4 24.448611 0.773000 4.736686 +delta_gldA-4 25.449167 0.876000 3.048793 +delta_gldA-5 0.000000 0.060000 13.757891 +delta_gldA-5 14.993056 0.362000 9.818448 +delta_gldA-5 15.943056 0.421000 9.322815 +delta_gldA-5 16.943056 0.478000 8.668470 +delta_gldA-5 18.043056 0.557000 8.017744 +delta_gldA-5 19.109722 0.663000 6.633026 +delta_gldA-5 20.159722 0.776000 5.402308 +delta_gldA-5 21.173889 0.868000 3.753071 +delta_gldA-5 22.160556 0.969000 2.300012 +delta_gldA-6 0.000000 0.055000 13.999951 +delta_gldA-6 14.626389 0.285000 10.363627 +delta_gldA-6 16.726389 0.390000 9.076196 +delta_gldA-6 18.643056 0.518000 7.832896 +delta_gldA-6 19.759722 0.604000 5.062825 +delta_gldA-6 20.743056 0.695000 5.934727 +delta_gldA-6 21.776389 0.781000 4.876952 +delta_gldA-6 23.123889 0.930000 2.558487 +delta_gldA-6 24.127222 1.043000 1.346428 +delta_fsaA-1 0.000000 0.063000 16.553864 +delta_fsaA-1 14.376389 0.720000 7.248361 +delta_fsaA-1 15.626389 0.920000 7.427653 +delta_fsaA-1 16.623889 1.040000 5.275584 +delta_fsaA-1 17.623889 1.170000 2.675425 +delta_fsaA-1 18.123889 1.280000 1.459341 +delta_fsaA-1 18.623889 1.340000 0.342173 +delta_fsaA-1 19.123889 1.400000 0.260288 +delta_fsaA-2 0.000000 0.066000 14.275936 +delta_fsaA-2 14.376389 0.570000 5.034570 +delta_fsaA-2 15.626389 0.730000 4.728898 +delta_fsaA-2 16.623889 0.940000 3.695556 +delta_fsaA-2 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+1,23 @@ +iterations: 100 +mc: false +model: + args: + Degradation constants: + DHA: 0.008643483 + bounds: + DHA_M0: (8, 20) + DHA_q: (-20, -0.01) + X_0: (0.001, 0.5) + growth_rate: (0.001, 0.5) + t_lag: (1e-06, 24) + model_name: Steady-state batch model with lag phase and degradation of metabolites + parameters_to_estimate: + DHA_M0: 15 + DHA_q: -5 + X_0: 0.05 + growth_rate: 0.1 + t_lag: 4 +path_to_data: C:\Users\millard\Documents\GIT\PhysioFit\test_data\Peiro_2019\PhysioFit_v3\results\dataset_1.tsv +sds: + DHA: 0.5 + X: 0.002 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/WT-2/flux_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/WT-2/flux_results.tsv new file mode 100644 index 0000000..6360410 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/WT-2/flux_results.tsv @@ -0,0 +1,6 @@ + optimal +X_0 0.08101245686660968 +growth_rate 0.1544407136031919 +t_lag 6.252090332986083 +DHA_q -1.740625754992438 +DHA_M0 10.76786553606676 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/WT-2/plots.pdf b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/WT-2/plots.pdf new file mode 100644 index 0000000..10eda39 Binary files /dev/null and b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/WT-2/plots.pdf differ diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/WT-2/stat_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/WT-2/stat_results.tsv new file mode 100644 index 0000000..84614c7 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/WT-2/stat_results.tsv @@ -0,0 +1,11 @@ +================== +Khi² test results +================== + +khi2_value 23.610551 +number_of_measurements 10.000000 +number_of_params 5.000000 +Degrees_of_freedom 5.000000 +p_val 0.999742 + +At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. 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+DHA_M0 14.18865505779821 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-2/plots.pdf b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-2/plots.pdf new file mode 100644 index 0000000..c8ad769 Binary files /dev/null and b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-2/plots.pdf differ diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-2/stat_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-2/stat_results.tsv new file mode 100644 index 0000000..41fe023 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-2/stat_results.tsv @@ -0,0 +1,11 @@ +================== +Khi² test results +================== + +khi2_value 10.705831 +number_of_measurements 10.000000 +number_of_params 5.000000 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-0.01) + X_0: (0.001, 0.5) + growth_rate: (0.001, 0.5) + t_lag: (1e-06, 24) + model_name: Steady-state batch model with lag phase and degradation of metabolites + parameters_to_estimate: + DHA_M0: 15 + DHA_q: -5 + X_0: 0.05 + growth_rate: 0.1 + t_lag: 4 +path_to_data: C:\Users\millard\Documents\GIT\PhysioFit\test_data\Peiro_2019\PhysioFit_v3\results\dataset_1.tsv +sds: + DHA: 0.5 + X: 0.002 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-4/flux_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-4/flux_results.tsv new file mode 100644 index 0000000..466d308 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-4/flux_results.tsv @@ -0,0 +1,6 @@ + optimal +X_0 0.04504759792169657 +growth_rate 0.13040943875764308 +t_lag 2.6132012583067166 +DHA_q -1.3207594751715286 +DHA_M0 14.542048361047478 diff --git 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1.000000 + +At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. 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+ growth_rate: (0.001, 0.5) + t_lag: (1e-06, 24) + model_name: Steady-state batch model with lag phase and degradation of metabolites + parameters_to_estimate: + DHA_M0: 15 + DHA_q: -5 + X_0: 0.05 + growth_rate: 0.1 + t_lag: 4 +path_to_data: C:\Users\millard\Documents\GIT\PhysioFit\test_data\Peiro_2019\PhysioFit_v3\results\dataset_1.tsv +sds: + DHA: 0.5 + X: 0.002 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-5/flux_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-5/flux_results.tsv new file mode 100644 index 0000000..ac64d7a --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-5/flux_results.tsv @@ -0,0 +1,6 @@ + optimal +X_0 0.06030507967627017 +growth_rate 0.1363997142021091 +t_lag 1.6621886311392635 +DHA_q -1.414648965103136 +DHA_M0 14.487505239599836 diff --git 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1.000000 + +At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. 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DHA_M0: (8, 20) + DHA_q: (-20, -0.01) + X_0: (0.001, 0.5) + growth_rate: (0.001, 0.5) + t_lag: (1e-06, 24) + model_name: Steady-state batch model with lag phase and degradation of metabolites + parameters_to_estimate: + DHA_M0: 15 + DHA_q: -5 + X_0: 0.05 + growth_rate: 0.1 + t_lag: 4 +path_to_data: C:\Users\millard\Documents\GIT\PhysioFit\test_data\Peiro_2019\PhysioFit_v3\results\dataset_1.tsv +sds: + DHA: 0.5 + X: 0.002 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-6/flux_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-6/flux_results.tsv new file mode 100644 index 0000000..e287aa8 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-6/flux_results.tsv @@ -0,0 +1,6 @@ + optimal +X_0 0.05522674647164361 +growth_rate 0.13142353874244778 +t_lag 1.6637177124358915 +DHA_q -1.45264510434267 +DHA_M0 14.462439760855087 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-6/plots.pdf b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-6/plots.pdf new file mode 100644 index 0000000..4dfd610 Binary files /dev/null and b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-6/plots.pdf differ diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-6/stat_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-6/stat_results.tsv new file mode 100644 index 0000000..eca7338 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/delta_gldA-6/stat_results.tsv @@ -0,0 +1,11 @@ +================== +Khi² test results +================== + +khi2_value 275.045735 +number_of_measurements 18.000000 +number_of_params 5.000000 +Degrees_of_freedom 13.000000 +p_val 1.000000 + +At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/log.txt b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/log.txt new file mode 100644 index 0000000..c270478 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/log.txt @@ -0,0 +1,2390 @@ +2024-05-21 22:57:02,135 - physiofit - INFO - Running optimization for WT-1 +2024-05-21 22:57:02,144 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:02,144 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:02,153 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +0 0.000000 0.084 13.258820 +1 14.843056 0.317 8.273916 +2 19.323889 0.628 3.810018 +Experimental matrix: +[[ 0.084 13.25882 ] + [ 0.317 8.273916] + [ 0.628 3.810018]] +Time vector: [ 0. 14.843056 19.323889] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:02,170 - physiofit - INFO - mc : False +2024-05-21 22:57:02,170 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:02,170 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:02,172 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:03,418 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:03,466 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 0.09444195172173199 + x: [ 8.398e-02 1.525e-01 6.135e+00 -2.160e+00 + 1.319e+01] + nit: 111 + nfev: 8472 + population: [[ 8.398e-02 1.525e-01 ... -2.160e+00 1.319e+01] + [ 8.393e-02 1.525e-01 ... -2.161e+00 1.320e+01] + ... + [ 8.397e-02 1.525e-01 ... -2.159e+00 1.319e+01] + [ 8.402e-02 1.525e-01 ... -2.159e+00 1.319e+01]] + population_energies: [ 9.444e-02 9.530e-02 ... 9.474e-02 9.508e-02] + jac: [-7.837e-02 -5.039e-02 -1.462e-02 -7.139e-02 + -7.902e-03] +2024-05-21 22:57:03,493 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.08398213978883132 +2024-05-21 22:57:03,496 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.15254484060411577 +2024-05-21 22:57:03,497 - physiofit.physiofit.base.fitter - INFO - t_lag = 6.134875880688067 +2024-05-21 22:57:03,497 - physiofit.physiofit.base.fitter - INFO - DHA_q = -2.1604246183747784 +2024-05-21 22:57:03,497 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 13.194801524159024 +2024-05-21 22:57:03,529 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.083982 13.194802 +14.843056 0.317029 8.400896 +19.323889 0.627987 3.752512 + +2024-05-21 22:57:03,546 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 0.09444195172173199 +Number of measurements: 6 +Number of parameters to fit: 5 +Degrees of freedom: 1 +p-value = 0.24139569023998605 + +2024-05-21 22:57:03,557 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.24139569023998605 +2024-05-21 22:57:03,588 - physiofit - INFO - Results for WT-1: + optimal +WT-1 X_0 0.083982 +WT-1 growth_rate 0.152545 +WT-1 t_lag 6.134876 +WT-1 DHA_q -2.160425 +WT-1 DHA_M0 13.194802 +2024-05-21 22:57:03,626 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:05,320 - physiofit - INFO - Running optimization for WT-2 +2024-05-21 22:57:05,326 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:05,332 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:05,334 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +3 0.000000 0.081 10.649188 +4 14.826389 0.301 7.000822 +5 17.190556 0.437 5.579987 +6 18.940556 0.583 3.764025 +7 21.027222 0.790 1.190285 +Experimental matrix: +[[ 0.081 10.649188] + [ 0.301 7.000822] + [ 0.437 5.579987] + [ 0.583 3.764025] + [ 0.79 1.190285]] +Time vector: [ 0. 14.826389 17.190556 18.940556 21.027222] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:05,334 - physiofit - INFO - mc : False +2024-05-21 22:57:05,334 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:05,334 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:05,334 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:06,135 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:06,135 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 23.610551164831477 + x: [ 8.101e-02 1.544e-01 6.252e+00 -1.741e+00 + 1.077e+01] + nit: 79 + nfev: 6252 + population: [[ 8.101e-02 1.545e-01 ... -1.746e+00 1.077e+01] + [ 8.109e-02 1.545e-01 ... -1.746e+00 1.079e+01] + ... + [ 8.147e-02 1.547e-01 ... -1.746e+00 1.070e+01] + [ 8.109e-02 1.546e-01 ... -1.745e+00 1.076e+01]] + population_energies: [ 2.361e+01 2.364e+01 ... 2.380e+01 2.365e+01] + jac: [ 1.435e-01 1.895e-01 3.009e-03 5.429e-03 + 4.177e-01] +2024-05-21 22:57:06,135 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.08101245686660968 +2024-05-21 22:57:06,135 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.1544407136031919 +2024-05-21 22:57:06,135 - physiofit.physiofit.base.fitter - INFO - t_lag = 6.252090332986083 +2024-05-21 22:57:06,135 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.740625754992438 +2024-05-21 22:57:06,135 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 10.76786553606676 +2024-05-21 22:57:06,155 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.081012 10.767866 +14.826389 0.304546 7.025125 +17.190556 0.438758 5.384818 +18.940556 0.574913 3.780470 +21.027222 0.793525 1.269934 + +2024-05-21 22:57:06,166 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 23.610551164831477 +Number of measurements: 10 +Number of parameters to fit: 5 +Degrees of freedom: 5 +p-value = 0.9997421006139489 + +2024-05-21 22:57:06,170 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 0.9997421006139489 + +2024-05-21 22:57:06,170 - physiofit - INFO - Results for WT-2: + optimal +WT-2 X_0 0.081012 +WT-2 growth_rate 0.154441 +WT-2 t_lag 6.252090 +WT-2 DHA_q -1.740626 +WT-2 DHA_M0 10.767866 +2024-05-21 22:57:06,203 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:07,864 - physiofit - INFO - Running optimization for WT-3 +2024-05-21 22:57:07,880 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:07,880 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:07,880 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +8 0.000000 0.093 15.648222 +9 14.809722 0.293 11.362852 +10 17.257222 0.439 9.250810 +11 19.290556 0.653 6.784887 +12 22.031944 0.888 2.690635 +Experimental matrix: +[[ 0.093 15.648222] + [ 0.293 11.362852] + [ 0.439 9.25081 ] + [ 0.653 6.784887] + [ 0.888 2.690635]] +Time vector: [ 0. 14.809722 17.257222 19.290556 22.031944] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:07,895 - physiofit - INFO - mc : False +2024-05-21 22:57:07,895 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:07,895 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:07,895 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:08,551 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:08,565 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 772.1904219346994 + x: [ 9.314e-02 1.460e-01 6.453e+00 -1.969e+00 + 1.600e+01] + nit: 54 + nfev: 4305 + population: [[ 9.241e-02 1.461e-01 ... -1.935e+00 1.604e+01] + [ 9.298e-02 1.458e-01 ... -2.107e+00 1.610e+01] + ... + [ 9.172e-02 1.466e-01 ... -1.947e+00 1.587e+01] + [ 9.240e-02 1.465e-01 ... -1.874e+00 1.563e+01]] + population_energies: [ 7.722e+02 7.753e+02 ... 7.756e+02 7.777e+02] + jac: [-4.291e-01 -5.595e-01 6.940e-01 -6.605e-01 + 1.355e+00] +2024-05-21 22:57:08,566 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.0931413105528343 +2024-05-21 22:57:08,566 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.14597772686712146 +2024-05-21 22:57:08,566 - physiofit.physiofit.base.fitter - INFO - t_lag = 6.453455195699607 +2024-05-21 22:57:08,566 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.9690189130018338 +2024-05-21 22:57:08,566 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 15.9971774661078 +2024-05-21 22:57:08,584 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.093141 15.997177 +14.809722 0.315433 11.161648 +17.257222 0.450892 9.118927 +19.290556 0.606709 6.875783 +22.031944 0.905267 2.731871 + +2024-05-21 22:57:08,596 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 772.1904219346994 +Number of measurements: 10 +Number of parameters to fit: 5 +Degrees of freedom: 5 +p-value = 1.0 + +2024-05-21 22:57:08,596 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:08,612 - physiofit - INFO - Results for WT-3: + optimal +WT-3 X_0 0.093141 +WT-3 growth_rate 0.145978 +WT-3 t_lag 6.453455 +WT-3 DHA_q -1.969019 +WT-3 DHA_M0 15.997177 +2024-05-21 22:57:08,657 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:10,172 - physiofit - INFO - Running optimization for delta_dhaKLM-1 +2024-05-21 22:57:10,177 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:10,177 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:10,189 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +13 0.000000 0.08 13.091353 +14 7.982500 0.11 12.697156 +15 9.476667 0.15 12.389292 +16 23.892778 0.45 10.069308 +17 26.976111 0.48 10.042876 +18 47.843056 1.09 3.366052 +Experimental matrix: +[[ 0.08 13.091353] + [ 0.11 12.697156] + [ 0.15 12.389292] + [ 0.45 10.069308] + [ 0.48 10.042876] + [ 1.09 3.366052]] +Time vector: [ 0. 7.9825 9.476667 23.892778 26.976111 47.843056] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:10,189 - physiofit - INFO - mc : False +2024-05-21 22:57:10,189 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:10,189 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:10,199 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:10,721 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:10,726 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4483.904893800401 + x: [ 1.263e-01 4.543e-02 1.000e-06 -3.303e-01 + 1.459e+01] + nit: 46 + nfev: 3711 + population: [[ 1.275e-01 4.527e-02 ... -2.815e-01 1.461e+01] + [ 1.290e-01 4.523e-02 ... -3.029e-01 1.339e+01] + ... + [ 1.283e-01 4.526e-02 ... -2.814e-01 1.283e+01] + [ 1.286e-01 4.518e-02 ... -3.831e-01 1.249e+01]] + population_energies: [ 4.484e+03 4.525e+03 ... 4.520e+03 4.576e+03] + jac: [ 1.020e+00 1.327e+01 1.331e+02 -6.005e+00 + 1.793e+01] +2024-05-21 22:57:10,728 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.12631844703097023 +2024-05-21 22:57:10,728 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.045429086733159686 +2024-05-21 22:57:10,729 - physiofit.physiofit.base.fitter - INFO - t_lag = 1e-06 +2024-05-21 22:57:10,729 - physiofit.physiofit.base.fitter - INFO - DHA_q = -0.33032841938660523 +2024-05-21 22:57:10,732 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.588257841364994 +2024-05-21 22:57:10,738 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.126318 14.588258 +7.982500 0.181534 13.226897 +9.476667 0.194284 12.965052 +23.892778 0.373992 10.209257 +26.976111 0.430224 9.537157 +47.843056 1.110174 3.375662 + +2024-05-21 22:57:10,739 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4483.904893800401 +Number of measurements: 12 +Number of parameters to fit: 5 +Degrees of freedom: 7 +p-value = 1.0 + +2024-05-21 22:57:10,739 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:10,752 - physiofit - INFO - Results for delta_dhaKLM-1: + optimal +delta_dhaKLM-1 X_0 0.126318 +delta_dhaKLM-1 growth_rate 0.045429 +delta_dhaKLM-1 t_lag 0.000001 +delta_dhaKLM-1 DHA_q -0.330328 +delta_dhaKLM-1 DHA_M0 14.588258 +2024-05-21 22:57:10,771 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:12,290 - physiofit - INFO - Running optimization for delta_dhaKLM-2 +2024-05-21 22:57:12,308 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:12,309 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:12,319 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +19 0.000000 0.05 14.303145 +20 7.982500 NaN 12.436215 +21 9.476667 0.08 12.411095 +22 23.892778 0.33 10.883254 +23 26.976111 0.42 9.322037 +24 47.843056 0.95 3.988412 +Experimental matrix: +[[ 0.05 14.303145] + [ nan 12.436215] + [ 0.08 12.411095] + [ 0.33 10.883254] + [ 0.42 9.322037] + [ 0.95 3.988412]] +Time vector: [ 0. 7.9825 9.476667 23.892778 26.976111 47.843056] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:12,322 - physiofit - INFO - mc : False +2024-05-21 22:57:12,322 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:12,322 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:12,322 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:12,867 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:12,879 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 3169.3746521833023 + x: [ 9.751e-02 4.791e-02 1.000e-06 -3.303e-01 + 1.410e+01] + nit: 47 + nfev: 3954 + population: [[ 9.828e-02 4.771e-02 ... -3.065e-01 1.342e+01] + [ 1.001e-01 4.758e-02 ... -3.248e-01 1.301e+01] + ... + [ 9.939e-02 4.764e-02 ... -3.716e-01 1.451e+01] + [ 1.002e-01 4.759e-02 ... -3.444e-01 1.399e+01]] + population_energies: [ 3.169e+03 3.219e+03 ... 3.188e+03 3.208e+03] + jac: [ 1.126e+01 4.725e+01 1.110e+02 -2.737e-01 + 4.889e-02] +2024-05-21 22:57:12,883 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.097505693317561 +2024-05-21 22:57:12,884 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.04790931465098734 +2024-05-21 22:57:12,884 - physiofit.physiofit.base.fitter - INFO - t_lag = 1e-06 +2024-05-21 22:57:12,885 - physiofit.physiofit.base.fitter - INFO - DHA_q = -0.33032022940239014 +2024-05-21 22:57:12,886 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.100032487611825 +2024-05-21 22:57:12,893 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.097506 14.100032 +7.982500 NaN 12.856698 +9.476667 0.153535 12.619059 +23.892778 0.306310 10.143270 +26.976111 0.355071 9.544653 +47.843056 0.964914 4.065160 + +2024-05-21 22:57:12,899 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 3169.3746521833023 +Number of measurements: 11 +Number of parameters to fit: 5 +Degrees of freedom: 6 +p-value = 1.0 + +2024-05-21 22:57:12,905 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:12,908 - physiofit - INFO - Results for delta_dhaKLM-2: + optimal +delta_dhaKLM-2 X_0 0.097506 +delta_dhaKLM-2 growth_rate 0.047909 +delta_dhaKLM-2 t_lag 0.000001 +delta_dhaKLM-2 DHA_q -0.330320 +delta_dhaKLM-2 DHA_M0 14.100032 +2024-05-21 22:57:12,921 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:14,336 - physiofit - INFO - Running optimization for delta_dhaKLM-3 +2024-05-21 22:57:14,352 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:14,352 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:14,352 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +25 0.000000 0.027 17.562716 +26 15.000000 0.162 15.800197 +27 17.000000 0.192 18.841635 +28 19.250000 NaN 10.845222 +29 21.250000 0.270 10.262621 +30 23.166667 0.290 12.005897 +31 39.166667 0.630 7.336636 +Experimental matrix: +[[ 0.027 17.562716] + [ 0.162 15.800197] + [ 0.192 18.841635] + [ nan 10.845222] + [ 0.27 10.262621] + [ 0.29 12.005897] + [ 0.63 7.336636]] +Time vector: [ 0. 15. 17. 19.25 21.25 23.166667 39.166667] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:14,366 - physiofit - INFO - mc : False +2024-05-21 22:57:14,367 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:14,371 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:14,371 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:14,918 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:14,918 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1128.4815734442434 + x: [ 7.722e-02 5.397e-02 1.000e-06 -6.216e-01 + 1.775e+01] + nit: 51 + nfev: 4116 + population: [[ 7.688e-02 5.411e-02 ... -6.161e-01 1.775e+01] + [ 7.866e-02 5.338e-02 ... -4.610e-01 1.659e+01] + ... + [ 7.745e-02 5.385e-02 ... -6.004e-01 1.769e+01] + [ 7.742e-02 5.401e-02 ... -6.632e-01 1.829e+01]] + population_energies: [ 1.128e+03 1.157e+03 ... 1.130e+03 1.135e+03] + jac: [ 3.660e+00 1.455e+01 1.044e+02 -2.879e+00 + -3.579e+00] +2024-05-21 22:57:14,927 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.0772190917387903 +2024-05-21 22:57:14,927 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.05396632422548781 +2024-05-21 22:57:14,928 - physiofit.physiofit.base.fitter - INFO - t_lag = 1e-06 +2024-05-21 22:57:14,928 - physiofit.physiofit.base.fitter - INFO - DHA_q = -0.621550466139007 +2024-05-21 22:57:14,928 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 17.752998480288184 +2024-05-21 22:57:14,935 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.077219 17.752998 +15.000000 0.173494 14.545279 +17.000000 0.193267 14.070179 +19.250000 NaN 13.514532 +21.250000 0.243090 12.998884 +23.166667 0.269580 12.482678 +39.166667 0.639271 6.854722 + +2024-05-21 22:57:14,937 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1128.4815734442434 +Number of measurements: 13 +Number of parameters to fit: 5 +Degrees of freedom: 8 +p-value = 1.0 + +2024-05-21 22:57:14,937 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:14,952 - physiofit - INFO - Results for delta_dhaKLM-3: + optimal +delta_dhaKLM-3 X_0 0.077219 +delta_dhaKLM-3 growth_rate 0.053966 +delta_dhaKLM-3 t_lag 0.000001 +delta_dhaKLM-3 DHA_q -0.621550 +delta_dhaKLM-3 DHA_M0 17.752998 +2024-05-21 22:57:14,968 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:16,390 - physiofit - INFO - Running optimization for delta_fsaA-1 +2024-05-21 22:57:16,390 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:16,390 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:16,412 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +32 0.000000 0.063 16.553864 +33 14.376389 0.720 7.248361 +34 15.626389 0.920 7.427653 +35 16.623889 1.040 5.275584 +36 17.623889 1.170 2.675425 +37 18.123889 1.280 1.459341 +38 18.623889 1.340 0.342173 +39 19.123889 1.400 0.260288 +Experimental matrix: +[[ 0.063 16.553864] + [ 0.72 7.248361] + [ 0.92 7.427653] + [ 1.04 5.275584] + [ 1.17 2.675425] + [ 1.28 1.459341] + [ 1.34 0.342173] + [ 1.4 0.260288]] +Time vector: [ 0. 14.376389 15.626389 16.623889 17.623889 18.123889 18.623889 + 19.123889] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:16,417 - physiofit - INFO - mc : False +2024-05-21 22:57:16,418 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:16,418 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:16,418 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:17,284 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:17,284 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 1516.0083030882479 + x: [ 1.037e-01 1.375e-01 1.000e-06 -1.563e+00 + 1.687e+01] + nit: 80 + nfev: 6225 + population: [[ 1.040e-01 1.374e-01 ... -1.548e+00 1.688e+01] + [ 1.044e-01 1.374e-01 ... -1.437e+00 1.567e+01] + ... + [ 1.056e-01 1.365e-01 ... -1.623e+00 1.788e+01] + [ 1.030e-01 1.379e-01 ... -1.567e+00 1.717e+01]] + population_energies: [ 1.516e+03 1.556e+03 ... 1.533e+03 1.520e+03] + jac: [-1.130e+00 -3.334e+00 2.897e+02 -3.208e-01 + 1.079e+00] +2024-05-21 22:57:17,284 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.10366788986323168 +2024-05-21 22:57:17,284 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.13750469867298099 +2024-05-21 22:57:17,284 - physiofit.physiofit.base.fitter - INFO - t_lag = 1e-06 +2024-05-21 22:57:17,304 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.5627846879898855 +2024-05-21 22:57:17,306 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 16.872735246802225 +2024-05-21 22:57:17,311 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.103668 16.872735 +14.376389 0.748457 7.876770 +15.626389 0.888820 6.205198 +16.623889 1.019487 4.673084 +17.623889 1.169767 2.932082 +18.123889 1.253020 1.975255 +18.623889 1.342199 0.955356 +19.123889 1.437724 -0.132126 + +2024-05-21 22:57:17,319 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 1516.0083030882479 +Number of measurements: 16 +Number of parameters to fit: 5 +Degrees of freedom: 11 +p-value = 1.0 + +2024-05-21 22:57:17,319 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:17,330 - physiofit - INFO - Results for delta_fsaA-1: + optimal +delta_fsaA-1 X_0 0.103668 +delta_fsaA-1 growth_rate 0.137505 +delta_fsaA-1 t_lag 0.000001 +delta_fsaA-1 DHA_q -1.562785 +delta_fsaA-1 DHA_M0 16.872735 +2024-05-21 22:57:17,352 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:18,837 - physiofit - INFO - Running optimization for delta_fsaA-2 +2024-05-21 22:57:18,864 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:18,867 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:18,879 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +40 0.000000 0.066 14.275936 +41 14.376389 0.570 5.034570 +42 15.626389 0.730 4.728898 +43 16.623889 0.940 3.695556 +44 17.623889 0.900 2.528487 +45 18.123889 1.070 1.993256 +46 18.623889 1.190 0.632276 +47 19.123889 1.310 0.087292 +Experimental matrix: +[[ 0.066 14.275936] + [ 0.57 5.03457 ] + [ 0.73 4.728898] + [ 0.94 3.695556] + [ 0.9 2.528487] + [ 1.07 1.993256] + [ 1.19 0.632276] + [ 1.31 0.087292]] +Time vector: [ 0. 14.376389 15.626389 16.623889 17.623889 18.123889 18.623889 + 19.123889] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:18,883 - physiofit - INFO - mc : False +2024-05-21 22:57:18,883 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:18,883 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:18,883 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:19,699 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:19,703 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5027.271818120154 + x: [ 6.560e-02 1.643e-01 1.033e+00 -1.589e+00 + 1.287e+01] + nit: 72 + nfev: 5631 + population: [[ 6.525e-02 1.646e-01 ... -1.537e+00 1.289e+01] + [ 6.714e-02 1.641e-01 ... -1.969e+00 1.552e+01] + ... + [ 6.018e-02 1.666e-01 ... -2.160e+00 1.469e+01] + [ 6.467e-02 1.665e-01 ... -1.631e+00 1.330e+01]] + population_energies: [ 5.027e+03 5.066e+03 ... 5.135e+03 5.043e+03] + jac: [-6.278e-01 -6.803e-01 -1.331e+00 1.118e+00 + -3.975e+00] +2024-05-21 22:57:19,705 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.06560161943293889 +2024-05-21 22:57:19,706 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.16429028175153318 +2024-05-21 22:57:19,707 - physiofit.physiofit.base.fitter - INFO - t_lag = 1.0330209786301892 +2024-05-21 22:57:19,708 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.5893576421087818 +2024-05-21 22:57:19,708 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 12.87186523833506 +2024-05-21 22:57:19,712 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.065602 12.871865 +14.376389 0.587447 6.506041 +15.626389 0.721368 5.147302 +16.623889 0.849823 3.865619 +17.623889 1.001565 2.370545 +18.123889 1.087312 1.532561 +18.623889 1.180400 0.627323 +19.123889 1.281459 -0.350945 + +2024-05-21 22:57:19,716 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5027.271818120154 +Number of measurements: 16 +Number of parameters to fit: 5 +Degrees of freedom: 11 +p-value = 1.0 + +2024-05-21 22:57:19,716 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:19,726 - physiofit - INFO - Results for delta_fsaA-2: + optimal +delta_fsaA-2 X_0 0.065602 +delta_fsaA-2 growth_rate 0.164290 +delta_fsaA-2 t_lag 1.033021 +delta_fsaA-2 DHA_q -1.589358 +delta_fsaA-2 DHA_M0 12.871865 +2024-05-21 22:57:19,733 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:21,474 - physiofit - INFO - Running optimization for delta_fsaA-3 +2024-05-21 22:57:21,486 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:21,500 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:21,516 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +48 0.000000 0.062 17.515247 +49 14.376389 0.730 7.997293 +50 15.626389 0.900 6.080844 +51 16.623889 1.120 4.211750 +52 17.623889 1.200 2.645675 +53 18.123889 1.290 1.491006 +54 18.623889 1.390 0.235435 +55 19.123889 1.440 0.380262 +Experimental matrix: +[[ 0.062 17.515247] + [ 0.73 7.997293] + [ 0.9 6.080844] + [ 1.12 4.21175 ] + [ 1.2 2.645675] + [ 1.29 1.491006] + [ 1.39 0.235435] + [ 1.44 0.380262]] +Time vector: [ 0. 14.376389 15.626389 16.623889 17.623889 18.123889 18.623889 + 19.123889] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:21,534 - physiofit - INFO - mc : False +2024-05-21 22:57:21,534 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:21,534 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:21,534 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:22,325 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:22,332 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 2570.0921063776627 + x: [ 1.012e-01 1.403e-01 1.000e-06 -1.653e+00 + 1.756e+01] + nit: 77 + nfev: 6000 + population: [[ 1.002e-01 1.409e-01 ... -1.656e+00 1.755e+01] + [ 9.961e-02 1.414e-01 ... -1.731e+00 1.719e+01] + ... + [ 1.016e-01 1.402e-01 ... -1.637e+00 1.743e+01] + [ 9.893e-02 1.416e-01 ... -1.799e+00 1.798e+01]] + population_energies: [ 2.570e+03 2.600e+03 ... 2.574e+03 2.596e+03] + jac: [-1.510e+00 -2.570e+00 2.787e+02 -3.215e+00 + 2.169e+00] +2024-05-21 22:57:22,333 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.10119991550299652 +2024-05-21 22:57:22,334 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.1403333823758422 +2024-05-21 22:57:22,335 - physiofit.physiofit.base.fitter - INFO - t_lag = 1e-06 +2024-05-21 22:57:22,335 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.6531282904914373 +2024-05-21 22:57:22,336 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 17.557143351255746 +2024-05-21 22:57:22,336 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.101200 17.557143 +14.376389 0.760963 8.053249 +15.626389 0.906872 6.256878 +16.623889 1.043133 4.604748 +17.623889 1.200289 2.721614 +18.123889 1.287534 1.684318 +18.623889 1.381121 0.576950 +19.123889 1.481511 -0.605605 + +2024-05-21 22:57:22,353 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 2570.0921063776627 +Number of measurements: 16 +Number of parameters to fit: 5 +Degrees of freedom: 11 +p-value = 1.0 + +2024-05-21 22:57:22,353 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:22,370 - physiofit - INFO - Results for delta_fsaA-3: + optimal +delta_fsaA-3 X_0 0.101200 +delta_fsaA-3 growth_rate 0.140333 +delta_fsaA-3 t_lag 0.000001 +delta_fsaA-3 DHA_q -1.653128 +delta_fsaA-3 DHA_M0 17.557143 +2024-05-21 22:57:22,396 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:23,841 - physiofit - INFO - Running optimization for delta_fsaA-4 +2024-05-21 22:57:23,841 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:23,841 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:23,852 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +56 0.000000 0.027 17.562716 +57 15.000000 0.258 13.290414 +58 17.000000 0.364 10.955896 +59 19.250000 0.530 NaN +60 21.250000 0.720 5.961904 +61 23.166667 1.000 2.899311 +Experimental matrix: +[[ 0.027 17.562716] + [ 0.258 13.290414] + [ 0.364 10.955896] + [ 0.53 nan] + [ 0.72 5.961904] + [ 1. 2.899311]] +Time vector: [ 0. 15. 17. 19.25 21.25 23.166667] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:23,852 - physiofit - INFO - mc : False +2024-05-21 22:57:23,852 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:23,852 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:23,852 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:24,836 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:24,836 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 31.124607638607696 + x: [ 2.707e-02 1.643e-01 1.219e+00 -2.076e+00 + 1.769e+01] + nit: 89 + nfev: 6840 + population: [[ 2.705e-02 1.644e-01 ... -2.076e+00 1.769e+01] + [ 2.729e-02 1.644e-01 ... -2.088e+00 1.763e+01] + ... + [ 2.731e-02 1.646e-01 ... -2.080e+00 1.779e+01] + [ 2.691e-02 1.643e-01 ... -2.078e+00 1.755e+01]] + population_energies: [ 3.112e+01 3.132e+01 ... 3.150e+01 3.151e+01] + jac: [ 1.143e+01 5.580e+00 6.458e-02 1.987e+00 + -1.089e-01] +2024-05-21 22:57:24,836 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.027067476506084036 +2024-05-21 22:57:24,836 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.1643337865438809 +2024-05-21 22:57:24,836 - physiofit.physiofit.base.fitter - INFO - t_lag = 1.2185260101651696 +2024-05-21 22:57:24,836 - physiofit.physiofit.base.fitter - INFO - DHA_q = -2.075932203899009 +2024-05-21 22:57:24,836 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 17.6924222955485 +2024-05-21 22:57:24,851 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.027067 17.692422 +15.000000 0.260628 12.701555 +17.000000 0.362043 11.213169 +19.250000 0.524011 NaN +21.250000 0.727913 6.261144 +23.166667 0.997402 2.780546 + +2024-05-21 22:57:24,851 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 31.124607638607696 +Number of measurements: 11 +Number of parameters to fit: 5 +Degrees of freedom: 6 +p-value = 0.9999760023248065 + +2024-05-21 22:57:24,867 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 0.9999760023248065 + +2024-05-21 22:57:24,873 - physiofit - INFO - Results for delta_fsaA-4: + optimal +delta_fsaA-4 X_0 0.027067 +delta_fsaA-4 growth_rate 0.164334 +delta_fsaA-4 t_lag 1.218526 +delta_fsaA-4 DHA_q -2.075932 +delta_fsaA-4 DHA_M0 17.692422 +2024-05-21 22:57:24,890 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:26,470 - physiofit - INFO - Running optimization for delta_fsaB-1 +2024-05-21 22:57:26,490 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:26,490 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:26,502 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +62 0.000000 0.028 14.096684 +63 14.959722 0.267 10.339988 +64 16.909722 0.384 9.103556 +65 19.007222 0.502 7.818633 +66 20.457222 0.609 5.994450 +67 22.457222 0.761 3.344009 +68 23.460556 0.841 2.179649 +69 24.448611 0.921 1.582310 +Experimental matrix: +[[ 0.028 14.096684] + [ 0.267 10.339988] + [ 0.384 9.103556] + [ 0.502 7.818633] + [ 0.609 5.99445 ] + [ 0.761 3.344009] + [ 0.841 2.179649] + [ 0.921 1.58231 ]] +Time vector: [ 0. 14.959722 16.909722 19.007222 20.457222 22.457222 23.460556 + 24.448611] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:26,506 - physiofit - INFO - mc : False +2024-05-21 22:57:26,506 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:26,508 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:26,508 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:27,257 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:27,259 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 828.2362884776034 + x: [ 4.948e-02 1.207e-01 7.279e-03 -1.509e+00 + 1.482e+01] + nit: 78 + nfev: 5979 + population: [[ 4.951e-02 1.208e-01 ... -1.515e+00 1.482e+01] + [ 4.921e-02 1.215e-01 ... -1.450e+00 1.410e+01] + ... + [ 4.842e-02 1.218e-01 ... -1.470e+00 1.444e+01] + [ 4.912e-02 1.212e-01 ... -1.498e+00 1.478e+01]] + population_energies: [ 8.282e+02 8.409e+02 ... 8.386e+02 8.313e+02] + jac: [ 2.640e+03 3.623e+03 4.846e+01 3.002e+01 + 6.679e+00] +2024-05-21 22:57:27,264 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.049477696542675545 +2024-05-21 22:57:27,264 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.12073750967780922 +2024-05-21 22:57:27,264 - physiofit.physiofit.base.fitter - INFO - t_lag = 0.007279319646611711 +2024-05-21 22:57:27,264 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.5090431419714003 +2024-05-21 22:57:27,264 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.824308223379592 +2024-05-21 22:57:27,268 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.049478 14.824308 +14.959722 0.300919 10.023548 +16.909722 0.380802 8.865637 +19.007222 0.490550 7.346506 +20.457222 0.584407 6.089045 +22.457222 0.744023 4.006173 +23.460556 0.839841 2.779074 +24.448611 0.946251 1.431022 + +2024-05-21 22:57:27,274 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 828.2362884776034 +Number of measurements: 16 +Number of parameters to fit: 5 +Degrees of freedom: 11 +p-value = 1.0 + +2024-05-21 22:57:27,274 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:27,279 - physiofit - INFO - Results for delta_fsaB-1: + optimal +delta_fsaB-1 X_0 0.049478 +delta_fsaB-1 growth_rate 0.120738 +delta_fsaB-1 t_lag 0.007279 +delta_fsaB-1 DHA_q -1.509043 +delta_fsaB-1 DHA_M0 14.824308 +2024-05-21 22:57:27,288 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:28,585 - physiofit - INFO - Running optimization for delta_fsaB-2 +2024-05-21 22:57:28,592 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:28,592 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:28,602 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +70 0.000000 0.060 13.537160 +71 14.993056 0.412 9.628371 +72 15.943056 0.475 8.697996 +73 16.943056 0.536 7.283556 +74 18.043056 0.610 6.050140 +75 19.109722 0.707 4.675252 +76 20.159722 0.806 3.387898 +Experimental matrix: +[[ 0.06 13.53716 ] + [ 0.412 9.628371] + [ 0.475 8.697996] + [ 0.536 7.283556] + [ 0.61 6.05014 ] + [ 0.707 4.675252] + [ 0.806 3.387898]] +Time vector: [ 0. 14.993056 15.943056 16.943056 18.043056 19.109722 20.159722] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:28,608 - physiofit - INFO - mc : False +2024-05-21 22:57:28,608 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:28,608 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:28,608 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:29,503 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:29,503 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 28.817923110225674 + x: [ 6.076e-02 1.283e-01 1.000e-06 -1.467e+00 + 1.426e+01] + nit: 85 + nfev: 6666 + population: [[ 6.095e-02 1.283e-01 ... -1.463e+00 1.426e+01] + [ 6.063e-02 1.287e-01 ... -1.430e+00 1.411e+01] + ... + [ 6.088e-02 1.283e-01 ... -1.449e+00 1.425e+01] + [ 6.082e-02 1.285e-01 ... -1.498e+00 1.436e+01]] + population_energies: [ 2.882e+01 2.943e+01 ... 2.908e+01 2.912e+01] + jac: [ 4.019e+00 2.280e+00 2.434e+00 -4.088e-03 + 2.311e-03] +2024-05-21 22:57:29,503 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.06076259192441902 +2024-05-21 22:57:29,503 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.1282686324090951 +2024-05-21 22:57:29,503 - physiofit.physiofit.base.fitter - INFO - t_lag = 1e-06 +2024-05-21 22:57:29,503 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.466896935362664 +2024-05-21 22:57:29,503 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.26421842190499 +2024-05-21 22:57:29,518 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.060763 14.264218 +14.993056 0.415762 8.647808 +15.943056 0.469641 7.963395 +16.943056 0.533915 7.162911 +18.043056 0.614822 6.174153 +19.109722 0.704968 5.091198 +20.159722 0.806605 3.888005 + +2024-05-21 22:57:29,518 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 28.817923110225674 +Number of measurements: 14 +Number of parameters to fit: 5 +Degrees of freedom: 9 +p-value = 0.9993045158716359 + +2024-05-21 22:57:29,518 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 0.9993045158716359 + +2024-05-21 22:57:29,539 - physiofit - INFO - Results for delta_fsaB-2: + optimal +delta_fsaB-2 X_0 0.060763 +delta_fsaB-2 growth_rate 0.128269 +delta_fsaB-2 t_lag 0.000001 +delta_fsaB-2 DHA_q -1.466897 +delta_fsaB-2 DHA_M0 14.264218 +2024-05-21 22:57:29,568 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:30,985 - physiofit - INFO - Running optimization for delta_fsaB-3 +2024-05-21 22:57:31,004 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:31,005 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:31,013 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +77 0.000000 0.046 14.157601 +78 14.626389 0.318 9.430618 +79 16.726389 0.425 8.203104 +80 18.643056 0.544 6.565640 +81 19.759722 0.623 4.764551 +82 20.743056 0.713 4.331454 +83 21.776389 0.784 2.192368 +84 23.123889 0.898 1.393149 +Experimental matrix: +[[ 0.046 14.157601] + [ 0.318 9.430618] + [ 0.425 8.203104] + [ 0.544 6.56564 ] + [ 0.623 4.764551] + [ 0.713 4.331454] + [ 0.784 2.192368] + [ 0.898 1.393149]] +Time vector: [ 0. 14.626389 16.726389 18.643056 19.759722 20.743056 21.776389 + 23.123889] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:31,017 - physiofit - INFO - mc : False +2024-05-21 22:57:31,017 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:31,017 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:31,018 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:31,869 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:31,869 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 350.24566494921953 + x: [ 5.842e-02 1.191e-01 1.000e-06 -1.576e+00 + 1.442e+01] + nit: 82 + nfev: 6567 + population: [[ 5.820e-02 1.193e-01 ... -1.613e+00 1.461e+01] + [ 5.810e-02 1.194e-01 ... -1.508e+00 1.403e+01] + ... + [ 5.787e-02 1.196e-01 ... -1.630e+00 1.454e+01] + [ 5.822e-02 1.194e-01 ... -1.532e+00 1.450e+01]] + population_energies: [ 3.502e+02 3.519e+02 ... 3.522e+02 3.536e+02] + jac: [-2.758e-01 -9.238e-02 4.304e+01 -3.382e-03 + -7.276e-04] +2024-05-21 22:57:31,869 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.058421995949459155 +2024-05-21 22:57:31,884 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.11910181444356989 +2024-05-21 22:57:31,885 - physiofit.physiofit.base.fitter - INFO - t_lag = 1e-06 +2024-05-21 22:57:31,886 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.5755397067740617 +2024-05-21 22:57:31,886 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.419490571229199 +2024-05-21 22:57:31,887 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.058422 14.419491 +14.626389 0.333526 9.228507 +16.726389 0.428305 7.819568 +18.643056 0.538138 6.249686 +19.759722 0.614686 5.181799 +20.743056 0.691061 4.131812 +21.776389 0.781566 2.903044 +23.123889 0.917626 1.079726 + +2024-05-21 22:57:31,887 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 350.24566494921953 +Number of measurements: 16 +Number of parameters to fit: 5 +Degrees of freedom: 11 +p-value = 1.0 + +2024-05-21 22:57:31,903 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:31,903 - physiofit - INFO - Results for delta_fsaB-3: + optimal +delta_fsaB-3 X_0 0.058422 +delta_fsaB-3 growth_rate 0.119102 +delta_fsaB-3 t_lag 0.000001 +delta_fsaB-3 DHA_q -1.575540 +delta_fsaB-3 DHA_M0 14.419491 +2024-05-21 22:57:31,936 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:33,346 - physiofit - INFO - Running optimization for delta_gldA-1 +2024-05-21 22:57:33,350 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:33,350 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:33,366 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +85 0.000000 0.069 10.782465 +86 14.826389 0.217 7.785630 +87 17.190556 0.290 7.201654 +88 18.940556 0.368 6.421098 +89 21.027222 0.487 4.963635 +90 22.832500 0.627 3.491181 +Experimental matrix: +[[ 0.069 10.782465] + [ 0.217 7.78563 ] + [ 0.29 7.201654] + [ 0.368 6.421098] + [ 0.487 4.963635] + [ 0.627 3.491181]] +Time vector: [ 0. 14.826389 17.190556 18.940556 21.027222 22.8325 ] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:33,369 - physiofit - INFO - mc : False +2024-05-21 22:57:33,369 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:33,369 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:33,369 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:34,153 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:34,156 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 10.905927952332291 + x: [ 6.899e-02 1.348e-01 6.487e+00 -1.332e+00 + 1.072e+01] + nit: 74 + nfev: 5937 + population: [[ 6.880e-02 1.347e-01 ... -1.327e+00 1.071e+01] + [ 6.898e-02 1.347e-01 ... -1.324e+00 1.065e+01] + ... + [ 6.855e-02 1.349e-01 ... -1.315e+00 1.069e+01] + [ 6.895e-02 1.346e-01 ... -1.343e+00 1.073e+01]] + population_energies: [ 1.091e+01 1.102e+01 ... 1.098e+01 1.109e+01] + jac: [-7.246e-01 -1.004e-01 9.429e-03 1.086e-02 + 3.507e-03] +2024-05-21 22:57:34,156 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.06898932912056423 +2024-05-21 22:57:34,156 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.1347828313241592 +2024-05-21 22:57:34,156 - physiofit.physiofit.base.fitter - INFO - t_lag = 6.486593019467831 +2024-05-21 22:57:34,156 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.3319332582499752 +2024-05-21 22:57:34,156 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 10.721400146665719 +2024-05-21 22:57:34,156 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.068989 10.721400 +14.826389 0.212303 8.056388 +17.190556 0.291973 7.113687 +18.940556 0.369641 6.244926 +21.027222 0.489693 4.957076 +22.832500 0.624593 3.557170 + +2024-05-21 22:57:34,179 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 10.905927952332291 +Number of measurements: 12 +Number of parameters to fit: 5 +Degrees of freedom: 7 +p-value = 0.8572246384893225 + +2024-05-21 22:57:34,181 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.8572246384893225 +2024-05-21 22:57:34,188 - physiofit - INFO - Results for delta_gldA-1: + optimal +delta_gldA-1 X_0 0.068989 +delta_gldA-1 growth_rate 0.134783 +delta_gldA-1 t_lag 6.486593 +delta_gldA-1 DHA_q -1.331933 +delta_gldA-1 DHA_M0 10.721400 +2024-05-21 22:57:34,217 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:35,666 - physiofit - INFO - Running optimization for delta_gldA-2 +2024-05-21 22:57:35,671 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:35,672 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:35,675 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +91 0.000000 0.06 14.123598 +92 7.982500 0.08 13.497914 +93 9.476667 0.10 12.268293 +94 23.892778 0.74 7.410710 +95 26.976111 1.15 2.971112 +Experimental matrix: +[[ 0.06 14.123598] + [ 0.08 13.497914] + [ 0.1 12.268293] + [ 0.74 7.41071 ] + [ 1.15 2.971112]] +Time vector: [ 0. 7.9825 9.476667 23.892778 26.976111] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:35,675 - physiofit - INFO - mc : False +2024-05-21 22:57:35,686 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:35,687 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:35,687 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:36,532 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:36,551 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 10.705831413852872 + x: [ 6.001e-02 1.412e-01 6.072e+00 -1.062e+00 + 1.419e+01] + nit: 81 + nfev: 6336 + population: [[ 5.996e-02 1.411e-01 ... -1.065e+00 1.419e+01] + [ 5.993e-02 1.412e-01 ... -1.055e+00 1.422e+01] + ... + [ 6.024e-02 1.412e-01 ... -1.051e+00 1.417e+01] + [ 5.981e-02 1.412e-01 ... -1.079e+00 1.421e+01]] + population_energies: [ 1.071e+01 1.076e+01 ... 1.077e+01 1.078e+01] + jac: [-9.700e-02 -1.281e-01 -3.690e-03 4.040e-01 + -4.905e-01] +2024-05-21 22:57:36,553 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.06001232038317879 +2024-05-21 22:57:36,553 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.14119805714783704 +2024-05-21 22:57:36,553 - physiofit.physiofit.base.fitter - INFO - t_lag = 6.072439494227819 +2024-05-21 22:57:36,553 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.0621670462582433 +2024-05-21 22:57:36,553 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.18865505779821 +2024-05-21 22:57:36,569 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.060012 14.188655 +7.982500 0.078590 13.104039 +9.476667 0.097049 12.797892 +23.892778 0.743038 6.638806 +26.976111 1.148380 3.452386 + +2024-05-21 22:57:36,575 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 10.705831413852872 +Number of measurements: 10 +Number of parameters to fit: 5 +Degrees of freedom: 5 +p-value = 0.9424652861082232 + +2024-05-21 22:57:36,575 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.9424652861082232 +2024-05-21 22:57:36,584 - physiofit - INFO - Results for delta_gldA-2: + optimal +delta_gldA-2 X_0 0.060012 +delta_gldA-2 growth_rate 0.141198 +delta_gldA-2 t_lag 6.072439 +delta_gldA-2 DHA_q -1.062167 +delta_gldA-2 DHA_M0 14.188655 +2024-05-21 22:57:36,605 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:38,100 - physiofit - INFO - Running optimization for delta_gldA-3 +2024-05-21 22:57:38,100 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:38,117 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:38,117 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +96 0.000000 0.034 17.562716 +97 15.000000 0.240 15.686244 +98 17.000000 0.316 13.356816 +99 19.250000 0.450 7.003778 +100 21.250000 0.610 7.807255 +101 23.166667 0.730 6.415134 +Experimental matrix: +[[ 0.034 17.562716] + [ 0.24 15.686244] + [ 0.316 13.356816] + [ 0.45 7.003778] + [ 0.61 7.807255] + [ 0.73 6.415134]] +Time vector: [ 0. 15. 17. 19.25 21.25 23.166667] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:38,117 - physiofit - INFO - mc : False +2024-05-21 22:57:38,117 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:38,117 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:38,117 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:38,735 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:38,735 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 476.7850629052052 + x: [ 3.441e-02 1.341e-01 1.880e-01 -1.898e+00 + 1.855e+01] + nit: 57 + nfev: 4536 + population: [[ 3.431e-02 1.342e-01 ... -1.917e+00 1.853e+01] + [ 3.306e-02 1.347e-01 ... -1.942e+00 1.909e+01] + ... + [ 3.456e-02 1.345e-01 ... -2.001e+00 1.883e+01] + [ 3.528e-02 1.330e-01 ... -1.890e+00 1.833e+01]] + population_energies: [ 4.768e+02 4.829e+02 ... 4.781e+02 4.801e+02] + jac: [ 1.400e-01 6.587e-02 4.977e-01 -4.709e-01 + 7.176e-01] +2024-05-21 22:57:38,735 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.03441350960780874 +2024-05-21 22:57:38,735 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.13405402036286584 +2024-05-21 22:57:38,735 - physiofit.physiofit.base.fitter - INFO - t_lag = 0.18795109020994832 +2024-05-21 22:57:38,752 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.8980697786084149 +2024-05-21 22:57:38,752 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 18.545495500417697 +2024-05-21 22:57:38,752 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.034414 18.545496 +15.000000 0.250652 13.359112 +17.000000 0.327724 12.047851 +19.250000 0.443099 10.197208 +21.250000 0.579347 8.109153 +23.166667 0.749075 5.591699 + +2024-05-21 22:57:38,752 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 476.7850629052052 +Number of measurements: 12 +Number of parameters to fit: 5 +Degrees of freedom: 7 +p-value = 1.0 + +2024-05-21 22:57:38,752 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:38,767 - physiofit - INFO - Results for delta_gldA-3: + optimal +delta_gldA-3 X_0 0.034414 +delta_gldA-3 growth_rate 0.134054 +delta_gldA-3 t_lag 0.187951 +delta_gldA-3 DHA_q -1.898070 +delta_gldA-3 DHA_M0 18.545496 +2024-05-21 22:57:38,793 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:39,946 - physiofit - INFO - Running optimization for delta_gldA-4 +2024-05-21 22:57:39,954 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:39,954 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:39,956 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +102 0.000000 0.045 14.212953 +103 14.959722 0.210 10.927801 +104 16.909722 0.289 10.419344 +105 19.007222 0.384 9.308633 +106 20.457222 0.465 8.072553 +107 22.457222 0.609 6.991455 +108 23.460556 0.693 6.074298 +109 24.448611 0.773 4.736686 +110 25.449167 0.876 3.048793 +Experimental matrix: +[[ 0.045 14.212953] + [ 0.21 10.927801] + [ 0.289 10.419344] + [ 0.384 9.308633] + [ 0.465 8.072553] + [ 0.609 6.991455] + [ 0.693 6.074298] + [ 0.773 4.736686] + [ 0.876 3.048793]] +Time vector: [ 0. 14.959722 16.909722 19.007222 20.457222 22.457222 23.460556 + 24.448611 25.449167] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:39,956 - physiofit - INFO - mc : False +2024-05-21 22:57:39,956 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:39,956 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:39,956 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:40,802 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:40,802 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 140.7650975846098 + x: [ 4.505e-02 1.304e-01 2.613e+00 -1.321e+00 + 1.454e+01] + nit: 84 + nfev: 6615 + population: [[ 4.500e-02 1.305e-01 ... -1.346e+00 1.454e+01] + [ 4.520e-02 1.307e-01 ... -1.282e+00 1.448e+01] + ... + [ 4.461e-02 1.309e-01 ... -1.294e+00 1.436e+01] + [ 4.472e-02 1.304e-01 ... -1.367e+00 1.461e+01]] + population_energies: [ 1.408e+02 1.416e+02 ... 1.423e+02 1.415e+02] + jac: [ 1.227e+01 1.160e+01 -7.227e-02 1.133e-02 + 8.251e-03] +2024-05-21 22:57:40,802 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.04504759792169657 +2024-05-21 22:57:40,817 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.13040943875764308 +2024-05-21 22:57:40,818 - physiofit.physiofit.base.fitter - INFO - t_lag = 2.6132012583067166 +2024-05-21 22:57:40,819 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.3207594751715286 +2024-05-21 22:57:40,820 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.542048361047478 +2024-05-21 22:57:40,822 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.045048 14.542048 +14.959722 0.225388 11.021970 +16.909722 0.290650 10.182094 +19.007222 0.382089 9.081048 +20.457222 0.461623 8.167315 +22.457222 0.599183 6.645614 +23.460556 0.682943 5.743515 +24.448611 0.776862 4.747441 +25.449167 0.885139 3.614579 + +2024-05-21 22:57:40,831 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 140.7650975846098 +Number of measurements: 18 +Number of parameters to fit: 5 +Degrees of freedom: 13 +p-value = 1.0 + +2024-05-21 22:57:40,841 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:40,846 - physiofit - INFO - Results for delta_gldA-4: + optimal +delta_gldA-4 X_0 0.045048 +delta_gldA-4 growth_rate 0.130409 +delta_gldA-4 t_lag 2.613201 +delta_gldA-4 DHA_q -1.320759 +delta_gldA-4 DHA_M0 14.542048 +2024-05-21 22:57:40,866 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:42,216 - physiofit - INFO - Running optimization for delta_gldA-5 +2024-05-21 22:57:42,216 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:42,216 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:42,237 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +111 0.000000 0.060 13.757891 +112 14.993056 0.362 9.818448 +113 15.943056 0.421 9.322815 +114 16.943056 0.478 8.668470 +115 18.043056 0.557 8.017744 +116 19.109722 0.663 6.633026 +117 20.159722 0.776 5.402308 +118 21.173889 0.868 3.753071 +119 22.160556 0.969 2.300012 +Experimental matrix: +[[ 0.06 13.757891] + [ 0.362 9.818448] + [ 0.421 9.322815] + [ 0.478 8.66847 ] + [ 0.557 8.017744] + [ 0.663 6.633026] + [ 0.776 5.402308] + [ 0.868 3.753071] + [ 0.969 2.300012]] +Time vector: [ 0. 14.993056 15.943056 16.943056 18.043056 19.109722 20.159722 + 21.173889 22.160556] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:42,237 - physiofit - INFO - mc : False +2024-05-21 22:57:42,237 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:42,237 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:42,237 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:42,966 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:42,975 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 324.2545085805191 + x: [ 6.031e-02 1.364e-01 1.662e+00 -1.415e+00 + 1.449e+01] + nit: 76 + nfev: 5877 + population: [[ 6.032e-02 1.364e-01 ... -1.406e+00 1.449e+01] + [ 6.311e-02 1.371e-01 ... -1.341e+00 1.404e+01] + ... + [ 5.944e-02 1.359e-01 ... -1.450e+00 1.396e+01] + [ 6.040e-02 1.364e-01 ... -1.432e+00 1.443e+01]] + population_energies: [ 3.243e+02 3.302e+02 ... 3.392e+02 3.252e+02] + jac: [ 5.066e-02 5.912e-02 7.635e-01 -1.126e-01 + -7.414e-02] +2024-05-21 22:57:42,977 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.06030507967627017 +2024-05-21 22:57:42,977 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.1363997142021091 +2024-05-21 22:57:42,977 - physiofit.physiofit.base.fitter - INFO - t_lag = 1.6621886311392635 +2024-05-21 22:57:42,977 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.414648965103136 +2024-05-21 22:57:42,977 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.487505239599836 +2024-05-21 22:57:42,984 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.060305 14.487505 +14.993056 0.371572 9.626709 +15.943056 0.422979 9.016961 +16.943056 0.484793 8.300963 +18.043056 0.563272 7.412246 +19.109722 0.651485 6.433429 +20.159722 0.751803 5.339469 +21.173889 0.863338 4.141037 +22.160556 0.987709 2.821345 + +2024-05-21 22:57:43,000 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 324.2545085805191 +Number of measurements: 18 +Number of parameters to fit: 5 +Degrees of freedom: 13 +p-value = 1.0 + +2024-05-21 22:57:43,004 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:43,004 - physiofit - INFO - Results for delta_gldA-5: + optimal +delta_gldA-5 X_0 0.060305 +delta_gldA-5 growth_rate 0.136400 +delta_gldA-5 t_lag 1.662189 +delta_gldA-5 DHA_q -1.414649 +delta_gldA-5 DHA_M0 14.487505 +2024-05-21 22:57:43,026 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:44,368 - physiofit - INFO - Running optimization for delta_gldA-6 +2024-05-21 22:57:44,375 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:57:44,375 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5} +2024-05-21 22:57:44,379 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA +120 0.000000 0.055 13.999951 +121 14.626389 0.285 10.363627 +122 16.726389 0.390 9.076196 +123 18.643056 0.518 7.832896 +124 19.759722 0.604 5.062825 +125 20.743056 0.695 5.934727 +126 21.776389 0.781 4.876952 +127 23.123889 0.930 2.558487 +128 24.127222 1.043 1.346428 +Experimental matrix: +[[ 0.055 13.999951] + [ 0.285 10.363627] + [ 0.39 9.076196] + [ 0.518 7.832896] + [ 0.604 5.062825] + [ 0.695 5.934727] + [ 0.781 4.876952] + [ 0.93 2.558487] + [ 1.043 1.346428]] +Time vector: [ 0. 14.626389 16.726389 18.643056 19.759722 20.743056 21.776389 + 23.123889 24.127222] +Name vector: ['X', 'DHA'] +Biomass & Metabolites: ['DHA'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -5, 'DHA_M0': 15} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 24), 'DHA_q': (-20, -0.01), 'DHA_M0': (8, 20)} + +2024-05-21 22:57:44,379 - physiofit - INFO - mc : False +2024-05-21 22:57:44,388 - physiofit - INFO - iterations : 100 +2024-05-21 22:57:44,388 - physiofit - INFO - debug_mode : False +2024-05-21 22:57:44,394 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:57:45,081 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ] + [0.002 0.5 ]] +2024-05-21 22:57:45,081 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 275.04573494701475 + x: [ 5.523e-02 1.314e-01 1.664e+00 -1.453e+00 + 1.446e+01] + nit: 62 + nfev: 5019 + population: [[ 5.534e-02 1.312e-01 ... -1.446e+00 1.447e+01] + [ 5.664e-02 1.316e-01 ... -1.470e+00 1.454e+01] + ... + [ 5.532e-02 1.315e-01 ... -1.547e+00 1.468e+01] + [ 5.420e-02 1.320e-01 ... -1.492e+00 1.465e+01]] + population_energies: [ 2.750e+02 2.802e+02 ... 2.787e+02 2.789e+02] + jac: [-7.110e-01 -7.060e-01 7.409e-01 -4.365e+00 + 2.341e+00] +2024-05-21 22:57:45,081 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.05522674647164361 +2024-05-21 22:57:45,081 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.13142353874244778 +2024-05-21 22:57:45,081 - physiofit.physiofit.base.fitter - INFO - t_lag = 1.6637177124358915 +2024-05-21 22:57:45,081 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.45264510434267 +2024-05-21 22:57:45,081 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.462439760855087 +2024-05-21 22:57:45,089 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA +Time +0.000000 0.055227 14.462440 +14.626389 0.303399 10.110393 +16.726389 0.399829 8.871846 +18.643056 0.514364 7.470094 +19.759722 0.595671 6.503865 +20.743056 0.677847 5.544281 +21.776389 0.776445 4.409906 +23.123889 0.926875 2.705473 +24.127222 1.057519 1.244196 + +2024-05-21 22:57:45,099 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 275.04573494701475 +Number of measurements: 18 +Number of parameters to fit: 5 +Degrees of freedom: 13 +p-value = 1.0 + +2024-05-21 22:57:45,099 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 1.0 + +2024-05-21 22:57:45,101 - physiofit - INFO - Results for delta_gldA-6: + optimal +delta_gldA-6 X_0 0.055227 +delta_gldA-6 growth_rate 0.131424 +delta_gldA-6 t_lag 1.663718 +delta_gldA-6 DHA_q -1.452645 +delta_gldA-6 DHA_M0 14.462440 +2024-05-21 22:57:45,822 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:57:47,389 - physiofit - INFO - Resulting dataframe: + experiments time X DHA +0 WT-1 0.000000 0.084 13.258820 +1 WT-1 14.843056 0.317 8.273916 +2 WT-1 19.323889 0.628 3.810018 +3 WT-2 0.000000 0.081 10.649188 +4 WT-2 14.826389 0.301 7.000822 +.. ... ... ... ... +124 delta_gldA-6 19.759722 0.604 5.062825 +125 delta_gldA-6 20.743056 0.695 5.934727 +126 delta_gldA-6 21.776389 0.781 4.876952 +127 delta_gldA-6 23.123889 0.930 2.558487 +128 delta_gldA-6 24.127222 1.043 1.346428 + +[129 rows x 4 columns] +2024-05-21 22:59:36,152 - physiofit - INFO - Running optimization for delta_glpK-1 +2024-05-21 22:59:36,163 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:36,172 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:36,194 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +0 0.000000 0.045 14.081402 0.300832 +1 14.959722 0.113 11.720505 0.546547 +2 16.909722 0.141 11.399281 0.585713 +3 19.007222 0.177 11.017542 0.673241 +4 20.457222 0.203 10.761256 0.621891 +5 22.457222 0.254 10.024273 0.632956 +6 23.460556 0.281 9.509658 0.287463 +7 24.448611 0.309 9.323283 0.476408 +8 25.449167 0.347 8.917299 0.582449 +Experimental matrix: +[[ 0.045 14.081402 0.30083192] + [ 0.113 11.720505 0.54654724] + [ 0.141 11.399281 0.58571273] + [ 0.177 11.017542 0.67324063] + [ 0.203 10.761256 0.62189095] + [ 0.254 10.024273 0.63295607] + [ 0.281 9.509658 0.28746278] + [ 0.309 9.323283 0.47640819] + [ 0.347 8.917299 0.58244929]] +Time vector: [ 0. 14.959722 16.909722 19.007222 20.457222 22.457222 23.460556 + 24.448611 25.449167] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:36,213 - physiofit - INFO - mc : False +2024-05-21 22:59:36,213 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:36,213 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:36,219 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:59:39,082 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 22:59:39,102 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.028578582731186 + x: [ 4.492e-02 1.055e-01 6.098e+00 -8.759e-01 + 1.410e+01 3.776e-02 4.621e-01] + nit: 135 + nfev: 14416 + population: [[ 4.490e-02 1.055e-01 ... 3.471e-02 4.575e-01] + [ 4.480e-02 1.054e-01 ... 6.348e-02 4.278e-01] + ... + [ 4.485e-02 1.054e-01 ... 3.374e-02 4.396e-01] + [ 4.500e-02 1.055e-01 ... 3.053e-02 4.728e-01]] + population_energies: [ 5.029e+00 5.163e+00 ... 5.091e+00 5.058e+00] + jac: [ 3.568e-01 1.534e-01 -1.838e-01 1.628e-01 + 6.548e-02 6.274e-01 -1.920e-01] +2024-05-21 22:59:39,110 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.044922984929789515 +2024-05-21 22:59:39,110 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.10551061469771877 +2024-05-21 22:59:39,110 - physiofit.physiofit.base.fitter - INFO - t_lag = 6.098381306162389 +2024-05-21 22:59:39,110 - physiofit.physiofit.base.fitter - INFO - DHA_q = -0.8759316235630559 +2024-05-21 22:59:39,110 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.10408301231402 +2024-05-21 22:59:39,135 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.03775678539393264 +2024-05-21 22:59:39,138 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.4621062694285036 +2024-05-21 22:59:39,155 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.044923 14.104083 0.462106 +14.959722 0.114424 11.834635 0.486977 +16.909722 0.140564 11.421589 0.496331 +19.007222 0.175382 10.929834 0.508791 +20.457222 0.204376 10.554472 0.519166 +22.457222 0.252391 9.978272 0.536348 +23.460556 0.280576 9.659124 0.546434 +24.448611 0.311405 9.322117 0.557466 +25.449167 0.346078 8.955216 0.569874 + +2024-05-21 22:59:39,219 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.028578582731186 +Number of measurements: 27 +Number of parameters to fit: 7 +Degrees of freedom: 20 +p-value = 0.0002899136257538129 + +2024-05-21 22:59:39,219 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0002899136257538129 +2024-05-21 22:59:39,254 - physiofit - INFO - Results for delta_glpK-1: + optimal +delta_glpK-1 X_0 0.044923 +delta_glpK-1 growth_rate 0.105511 +delta_glpK-1 t_lag 6.098381 +delta_glpK-1 DHA_q -0.875932 +delta_glpK-1 DHA_M0 14.104083 +delta_glpK-1 Glycerol_q 0.037757 +delta_glpK-1 Glycerol_M0 0.462106 +2024-05-21 22:59:39,281 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:59:41,393 - physiofit - INFO - Running optimization for delta_glpK-2 +2024-05-21 22:59:41,402 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:41,405 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:41,407 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +9 0.000000 0.051 13.774259 0.255860 +10 14.993056 0.150 11.256036 0.529660 +11 15.943056 0.166 10.934139 0.387502 +12 16.943056 0.183 11.608822 0.705551 +13 18.043056 0.206 10.666061 0.817859 +14 19.109722 0.235 10.238875 0.489520 +15 20.159722 0.270 9.595139 0.679338 +16 21.173889 0.297 9.716688 0.806721 +17 22.160556 0.330 8.979191 0.493778 +18 23.148611 0.377 9.005701 1.007138 +19 24.148611 0.414 7.943283 0.689019 +20 25.149167 0.440 5.755193 0.473915 +Experimental matrix: +[[ 0.051 13.774259 0.25585988] + [ 0.15 11.256036 0.52966002] + [ 0.166 10.934139 0.38750179] + [ 0.183 11.608822 0.70555098] + [ 0.206 10.666061 0.81785899] + [ 0.235 10.238875 0.48952005] + [ 0.27 9.595139 0.67933845] + [ 0.297 9.716688 0.80672058] + [ 0.33 8.979191 0.4937779 ] + [ 0.377 9.005701 1.00713844] + [ 0.414 7.943283 0.68901877] + [ 0.44 5.755193 0.47391532]] +Time vector: [ 0. 14.993056 15.943056 16.943056 18.043056 19.109722 20.159722 + 21.173889 22.160556 23.148611 24.148611 25.149167] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:41,426 - physiofit - INFO - mc : False +2024-05-21 22:59:41,428 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:41,428 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:41,428 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:59:43,504 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 127.1324348264809 + x: [ 5.121e-02 1.081e-01 4.957e+00 -1.264e+00 + 1.437e+01 7.844e-02 4.638e-01] + nit: 115 + nfev: 12724 + population: [[ 5.077e-02 1.079e-01 ... 4.939e-02 5.090e-01] + [ 5.035e-02 1.078e-01 ... 4.349e-02 4.917e-01] + ... + [ 5.077e-02 1.077e-01 ... 7.443e-02 5.250e-01] + [ 5.228e-02 1.084e-01 ... 2.397e-02 6.714e-01]] + population_energies: [ 1.271e+02 1.278e+02 ... 1.282e+02 1.315e+02] + jac: [ 9.944e-01 1.079e+00 2.730e-01 -1.558e-02 + 2.680e-01 2.075e-01 3.895e-01] +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.051206956921290465 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.10808036846990784 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - t_lag = 4.957249169251253 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.2636285397208482 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.371071585278978 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.07844133415314852 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.46378336742393567 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.051207 14.371072 0.463783 +14.993056 0.151494 11.492566 0.536569 +15.943056 0.167876 11.207829 0.548458 +16.943056 0.187037 10.888299 0.562364 +18.043056 0.210649 10.510483 0.579502 +19.109722 0.236389 10.114440 0.598183 +20.159722 0.264797 9.692401 0.618800 +21.173889 0.295473 9.250705 0.641064 +22.160556 0.328723 8.785023 0.665196 +23.148611 0.365770 8.278991 0.692083 +24.148611 0.407518 7.721706 0.722383 +25.149167 0.454058 7.113390 0.756160 + +2024-05-21 22:59:43,540 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 127.1324348264809 +Number of measurements: 36 +Number of parameters to fit: 7 +Degrees of freedom: 29 +p-value = 0.9999999999999701 + +2024-05-21 22:59:43,549 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 0.9999999999999701 + +2024-05-21 22:59:43,556 - physiofit - INFO - Results for delta_glpK-2: + optimal +delta_glpK-2 X_0 0.051207 +delta_glpK-2 growth_rate 0.108080 +delta_glpK-2 t_lag 4.957249 +delta_glpK-2 DHA_q -1.263629 +delta_glpK-2 DHA_M0 14.371072 +delta_glpK-2 Glycerol_q 0.078441 +delta_glpK-2 Glycerol_M0 0.463783 +2024-05-21 22:59:43,573 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:59:45,688 - physiofit - INFO - Running optimization for delta_glpK-3 +2024-05-21 22:59:45,697 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:45,697 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:45,707 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +21 0.000000 0.048 14.073512 0.670953 +22 14.626389 0.136 11.299269 0.764722 +23 16.726389 0.173 10.745761 0.632854 +24 18.643056 0.215 10.428681 0.732544 +25 19.759722 0.242 9.378264 1.275361 +26 20.743056 0.272 10.060147 1.221121 +27 21.776389 0.298 8.885681 1.128564 +28 23.123889 0.344 6.373275 0.991637 +29 24.127222 0.379 6.253507 1.282776 +Experimental matrix: +[[ 0.048 14.073512 0.67095267] + [ 0.136 11.299269 0.7647224 ] + [ 0.173 10.745761 0.63285391] + [ 0.215 10.428681 0.73254427] + [ 0.242 9.378264 1.27536068] + [ 0.272 10.060147 1.22112107] + [ 0.298 8.885681 1.12856385] + [ 0.344 6.373275 0.99163704] + [ 0.379 6.253507 1.28277568]] +Time vector: [ 0. 14.626389 16.726389 18.643056 19.759722 20.743056 21.776389 + 23.123889 24.127222] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:45,710 - physiofit - INFO - mc : False +2024-05-21 22:59:45,710 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:45,710 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:45,710 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:59:47,586 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 22:59:47,596 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 29.96242346782853 + x: [ 4.815e-02 1.059e-01 4.565e+00 -1.707e+00 + 1.462e+01 2.071e-01 6.025e-01] + nit: 108 + nfev: 11789 + population: [[ 4.815e-02 1.059e-01 ... 1.768e-01 6.370e-01] + [ 4.810e-02 1.061e-01 ... 2.053e-01 6.342e-01] + ... + [ 4.851e-02 1.064e-01 ... 2.008e-01 5.668e-01] + [ 4.847e-02 1.057e-01 ... 1.137e-01 7.550e-01]] + population_energies: [ 2.996e+01 3.007e+01 ... 3.071e+01 3.098e+01] + jac: [ 2.696e-01 2.232e-01 1.688e-02 7.370e-02 + 1.246e-02 -1.424e-02 -2.424e-02] +2024-05-21 22:59:47,596 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.048154009772729135 +2024-05-21 22:59:47,596 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.1058924886852867 +2024-05-21 22:59:47,604 - physiofit.physiofit.base.fitter - INFO - t_lag = 4.565029781771143 +2024-05-21 22:59:47,605 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.7067834475510337 +2024-05-21 22:59:47,605 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.619542649531503 +2024-05-21 22:59:47,605 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.207128540570602 +2024-05-21 22:59:47,605 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.6024747770798531 +2024-05-21 22:59:47,605 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.048154 14.619543 0.602475 +14.626389 0.139746 11.458709 0.781631 +16.726389 0.174548 10.696524 0.849705 +18.643056 0.213826 9.892738 0.926533 +19.759722 0.240666 9.367149 0.979032 +20.743056 0.267077 8.863946 1.030693 +21.776389 0.297960 8.289532 1.091101 +23.123889 0.343658 7.461138 1.180489 +24.127222 0.382181 6.778444 1.255840 + +2024-05-21 22:59:47,621 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 29.96242346782853 +Number of measurements: 27 +Number of parameters to fit: 7 +Degrees of freedom: 20 +p-value = 0.9295351725802049 + +2024-05-21 22:59:47,621 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.9295351725802049 +2024-05-21 22:59:47,638 - physiofit - INFO - Results for delta_glpK-3: + optimal +delta_glpK-3 X_0 0.048154 +delta_glpK-3 growth_rate 0.105892 +delta_glpK-3 t_lag 4.565030 +delta_glpK-3 DHA_q -1.706783 +delta_glpK-3 DHA_M0 14.619543 +delta_glpK-3 Glycerol_q 0.207129 +delta_glpK-3 Glycerol_M0 0.602475 +2024-05-21 22:59:47,654 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:59:49,879 - physiofit - INFO - Running optimization for delta_glpK-4 +2024-05-21 22:59:49,886 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:49,887 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:49,894 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +30 0.000000 0.045 14.081402 0.300832 +31 14.959722 0.113 11.720505 0.546547 +32 16.909722 0.141 11.399281 0.585713 +33 19.007222 0.177 11.017542 0.673241 +34 20.457222 0.203 10.761256 NaN +35 22.457222 0.254 10.024273 NaN +36 23.460556 0.281 9.509658 NaN +37 24.448611 0.309 9.323283 NaN +38 25.449167 0.347 8.917299 NaN +Experimental matrix: +[[ 0.045 14.081402 0.30083192] + [ 0.113 11.720505 0.54654724] + [ 0.141 11.399281 0.58571273] + [ 0.177 11.017542 0.67324063] + [ 0.203 10.761256 nan] + [ 0.254 10.024273 nan] + [ 0.281 9.509658 nan] + [ 0.309 9.323283 nan] + [ 0.347 8.917299 nan]] +Time vector: [ 0. 14.959722 16.909722 19.007222 20.457222 22.457222 23.460556 + 24.448611 25.449167] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:49,909 - physiofit - INFO - mc : False +2024-05-21 22:59:49,909 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:49,909 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:49,909 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:59:52,255 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 22:59:52,260 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.401068570458678 + x: [ 4.502e-02 1.055e-01 6.122e+00 -8.737e-01 + 1.410e+01 3.202e-01 3.034e-01] + nit: 125 + nfev: 13494 + population: [[ 4.509e-02 1.055e-01 ... 3.211e-01 3.037e-01] + [ 4.497e-02 1.055e-01 ... 2.328e-01 3.439e-01] + ... + [ 4.521e-02 1.055e-01 ... 2.848e-01 3.385e-01] + [ 4.525e-02 1.055e-01 ... 2.815e-01 3.106e-01]] + population_energies: [ 4.401e+00 4.463e+00 ... 4.421e+00 4.460e+00] + jac: [ 6.103e-02 4.192e-02 3.501e-02 1.493e-01 + -3.438e-02 1.363e-01 2.483e-02] +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.04501657927047147 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.10553281714740584 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - t_lag = 6.121737712989762 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - DHA_q = -0.8737292288631839 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.09750351625617 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.32020690230153914 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.3033883198828303 +2024-05-21 22:59:52,303 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.045017 14.097504 0.303388 +14.959722 0.114403 11.831258 0.513920 +16.909722 0.140544 11.418845 0.593235 +19.007222 0.175365 10.927894 0.698892 +20.457222 0.204362 10.553177 NaN +22.457222 0.252386 9.978010 NaN +23.460556 0.280576 9.659452 NaN +24.448611 0.311412 9.323079 NaN +25.449167 0.346093 8.956881 NaN + +2024-05-21 22:59:52,340 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.401068570458678 +Number of measurements: 22 +Number of parameters to fit: 7 +Degrees of freedom: 15 +p-value = 0.0039025682239525006 + +2024-05-21 22:59:52,354 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0039025682239525006 +2024-05-21 22:59:52,421 - physiofit - INFO - Results for delta_glpK-4: + optimal +delta_glpK-4 X_0 0.045017 +delta_glpK-4 growth_rate 0.105533 +delta_glpK-4 t_lag 6.121738 +delta_glpK-4 DHA_q -0.873729 +delta_glpK-4 DHA_M0 14.097504 +delta_glpK-4 Glycerol_q 0.320207 +delta_glpK-4 Glycerol_M0 0.303388 +2024-05-21 22:59:52,460 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:59:54,656 - physiofit - INFO - Running optimization for delta_glpK-5 +2024-05-21 22:59:54,662 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:54,662 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:54,690 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +39 0.000000 0.051 13.774259 0.255860 +40 14.993056 0.150 11.256036 0.529660 +41 15.943056 0.166 10.934139 NaN +42 16.943056 0.183 11.608822 0.705551 +43 18.043056 0.206 10.666061 0.817859 +44 19.109722 0.235 10.238875 NaN +45 20.159722 0.270 9.595139 NaN +46 21.173889 0.297 9.716688 0.806721 +47 22.160556 0.330 8.979191 NaN +48 23.148611 0.377 9.005701 1.007138 +49 24.148611 0.414 7.943283 NaN +50 25.149167 0.440 5.755193 NaN +Experimental matrix: +[[ 0.051 13.774259 0.25585988] + [ 0.15 11.256036 0.52966002] + [ 0.166 10.934139 nan] + [ 0.183 11.608822 0.70555098] + [ 0.206 10.666061 0.81785899] + [ 0.235 10.238875 nan] + [ 0.27 9.595139 nan] + [ 0.297 9.716688 0.80672058] + [ 0.33 8.979191 nan] + [ 0.377 9.005701 1.00713844] + [ 0.414 7.943283 nan] + [ 0.44 5.755193 nan]] +Time vector: [ 0. 14.993056 15.943056 16.943056 18.043056 19.109722 20.159722 + 21.173889 22.160556 23.148611 24.148611 25.149167] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:54,714 - physiofit - INFO - mc : False +2024-05-21 22:59:54,714 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:54,714 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:54,714 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:59:56,521 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 22:59:56,533 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 125.70267666044796 + x: [ 5.106e-02 1.081e-01 4.928e+00 -1.252e+00 + 1.434e+01 2.758e-01 2.606e-01] + nit: 93 + nfev: 10302 + population: [[ 5.008e-02 1.082e-01 ... 3.230e-01 2.745e-01] + [ 5.130e-02 1.079e-01 ... 1.955e-01 3.211e-01] + ... + [ 5.247e-02 1.082e-01 ... 1.399e-01 3.257e-01] + [ 4.992e-02 1.085e-01 ... 2.107e-01 4.445e-01]] + population_energies: [ 1.257e+02 1.268e+02 ... 1.276e+02 1.271e+02] + jac: [ 5.023e-01 6.587e-01 -1.471e-01 -2.438e-01 + -4.320e-01 -1.215e-01 -9.693e-01] +2024-05-21 22:59:56,539 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.051060363040208286 +2024-05-21 22:59:56,540 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.10806470880089496 +2024-05-21 22:59:56,540 - physiofit.physiofit.base.fitter - INFO - t_lag = 4.928162900177404 +2024-05-21 22:59:56,540 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.251823280656221 +2024-05-21 22:59:56,540 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.338469212302549 +2024-05-21 22:59:56,546 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.27583188578238643 +2024-05-21 22:59:56,546 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.2605955010887979 +2024-05-21 22:59:56,564 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.051060 14.338469 0.260596 +14.993056 0.151513 11.472588 0.516997 +15.943056 0.167893 11.189775 NaN +16.943056 0.187053 10.872463 0.607714 +18.043056 0.210664 10.497342 0.667980 +19.109722 0.236402 10.104200 NaN +20.159722 0.264807 9.685327 NaN +21.173889 0.295479 9.247019 0.884467 +22.160556 0.328725 8.784979 NaN +23.148611 0.365767 8.282977 1.063874 +24.148611 0.407508 7.730207 NaN +25.149167 0.454040 7.126897 NaN + +2024-05-21 22:59:56,576 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 125.70267666044796 +Number of measurements: 30 +Number of parameters to fit: 7 +Degrees of freedom: 23 +p-value = 0.9999999999999997 + +2024-05-21 22:59:56,577 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 0.9999999999999997 + +2024-05-21 22:59:56,587 - physiofit - INFO - Results for delta_glpK-5: + optimal +delta_glpK-5 X_0 0.051060 +delta_glpK-5 growth_rate 0.108065 +delta_glpK-5 t_lag 4.928163 +delta_glpK-5 DHA_q -1.251823 +delta_glpK-5 DHA_M0 14.338469 +delta_glpK-5 Glycerol_q 0.275832 +delta_glpK-5 Glycerol_M0 0.260596 +2024-05-21 22:59:56,611 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:59:58,744 - physiofit - INFO - Running optimization for delta_glpK-6 +2024-05-21 22:59:58,765 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:58,765 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:58,773 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +51 0.000000 0.048 14.073512 NaN +52 14.626389 0.136 11.299269 NaN +53 16.726389 0.173 10.745761 0.632854 +54 18.643056 0.215 10.428681 0.732544 +55 19.759722 0.242 9.378264 1.275361 +56 20.743056 0.272 10.060147 NaN +57 21.776389 0.298 8.885681 NaN +58 23.123889 0.344 6.373275 NaN +59 24.127222 0.379 6.253507 NaN +Experimental matrix: +[[ 0.048 14.073512 nan] + [ 0.136 11.299269 nan] + [ 0.173 10.745761 0.63285391] + [ 0.215 10.428681 0.73254427] + [ 0.242 9.378264 1.27536068] + [ 0.272 10.060147 nan] + [ 0.298 8.885681 nan] + [ 0.344 6.373275 nan] + [ 0.379 6.253507 nan]] +Time vector: [ 0. 14.626389 16.726389 18.643056 19.759722 20.743056 21.776389 + 23.123889 24.127222] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:58,813 - physiofit - INFO - mc : False +2024-05-21 22:59:58,814 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:58,814 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:58,820 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 23:00:00,837 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 23:00:00,837 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 29.37035530509316 + x: [ 4.790e-02 1.058e-01 4.507e+00 -1.704e+00 + 1.461e+01 4.914e-01 1.448e-01] + nit: 123 + nfev: 13284 + population: [[ 4.781e-02 1.060e-01 ... 4.591e-01 1.332e-01] + [ 4.755e-02 1.062e-01 ... 1.821e-01 6.071e-01] + ... + [ 4.866e-02 1.057e-01 ... 5.772e-01 2.322e-03] + [ 4.781e-02 1.056e-01 ... 5.795e-01 3.191e-02]] + population_energies: [ 2.937e+01 3.072e+01 ... 2.953e+01 2.962e+01] + jac: [-1.015e+00 -7.891e-01 -6.406e-01 -5.797e-01 + -3.651e-01 -1.826e-01 3.776e-01] +2024-05-21 23:00:00,837 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.04790422952436111 +2024-05-21 23:00:00,837 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.105840155318471 +2024-05-21 23:00:00,854 - physiofit.physiofit.base.fitter - INFO - t_lag = 4.507329034622728 +2024-05-21 23:00:00,854 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.7042300990532426 +2024-05-21 23:00:00,854 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.612967773171455 +2024-05-21 23:00:00,854 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.4913765713848028 +2024-05-21 23:00:00,860 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.14475229839161888 +2024-05-21 23:00:00,867 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.047904 14.612968 NaN +14.626389 0.139799 11.449871 NaN +16.726389 0.174595 10.688497 0.732932 +18.643056 0.213862 9.885646 0.915233 +19.759722 0.240692 9.360709 1.039796 +20.743056 0.267093 8.858159 NaN +21.776389 0.297961 8.284522 NaN +23.123889 0.343636 7.457304 NaN +24.127222 0.382136 6.775624 NaN + +2024-05-21 23:00:00,873 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 29.37035530509316 +Number of measurements: 21 +Number of parameters to fit: 7 +Degrees of freedom: 14 +p-value = 0.9906919073378274 + +2024-05-21 23:00:00,873 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 0.9906919073378274 + +2024-05-21 23:00:00,889 - physiofit - INFO - Results for delta_glpK-6: + optimal +delta_glpK-6 X_0 0.047904 +delta_glpK-6 growth_rate 0.105840 +delta_glpK-6 t_lag 4.507329 +delta_glpK-6 DHA_q -1.704230 +delta_glpK-6 DHA_M0 14.612968 +delta_glpK-6 Glycerol_q 0.491377 +delta_glpK-6 Glycerol_M0 0.144752 +2024-05-21 23:00:00,916 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 23:00:03,071 - physiofit - INFO - Resulting dataframe: + experiments time X DHA Glycerol +0 delta_glpK-1 0.000000 0.045 14.081402 0.300832 +1 delta_glpK-1 14.959722 0.113 11.720505 0.546547 +2 delta_glpK-1 16.909722 0.141 11.399281 0.585713 +3 delta_glpK-1 19.007222 0.177 11.017542 0.673241 +4 delta_glpK-1 20.457222 0.203 10.761256 0.621891 +5 delta_glpK-1 22.457222 0.254 10.024273 0.632956 +6 delta_glpK-1 23.460556 0.281 9.509658 0.287463 +7 delta_glpK-1 24.448611 0.309 9.323283 0.476408 +8 delta_glpK-1 25.449167 0.347 8.917299 0.582449 +9 delta_glpK-2 0.000000 0.051 13.774259 0.255860 +10 delta_glpK-2 14.993056 0.150 11.256036 0.529660 +11 delta_glpK-2 15.943056 0.166 10.934139 0.387502 +12 delta_glpK-2 16.943056 0.183 11.608822 0.705551 +13 delta_glpK-2 18.043056 0.206 10.666061 0.817859 +14 delta_glpK-2 19.109722 0.235 10.238875 0.489520 +15 delta_glpK-2 20.159722 0.270 9.595139 0.679338 +16 delta_glpK-2 21.173889 0.297 9.716688 0.806721 +17 delta_glpK-2 22.160556 0.330 8.979191 0.493778 +18 delta_glpK-2 23.148611 0.377 9.005701 1.007138 +19 delta_glpK-2 24.148611 0.414 7.943283 0.689019 +20 delta_glpK-2 25.149167 0.440 5.755193 0.473915 +21 delta_glpK-3 0.000000 0.048 14.073512 0.670953 +22 delta_glpK-3 14.626389 0.136 11.299269 0.764722 +23 delta_glpK-3 16.726389 0.173 10.745761 0.632854 +24 delta_glpK-3 18.643056 0.215 10.428681 0.732544 +25 delta_glpK-3 19.759722 0.242 9.378264 1.275361 +26 delta_glpK-3 20.743056 0.272 10.060147 1.221121 +27 delta_glpK-3 21.776389 0.298 8.885681 1.128564 +28 delta_glpK-3 23.123889 0.344 6.373275 0.991637 +29 delta_glpK-3 24.127222 0.379 6.253507 1.282776 +30 delta_glpK-4 0.000000 0.045 14.081402 0.300832 +31 delta_glpK-4 14.959722 0.113 11.720505 0.546547 +32 delta_glpK-4 16.909722 0.141 11.399281 0.585713 +33 delta_glpK-4 19.007222 0.177 11.017542 0.673241 +34 delta_glpK-4 20.457222 0.203 10.761256 NaN +35 delta_glpK-4 22.457222 0.254 10.024273 NaN +36 delta_glpK-4 23.460556 0.281 9.509658 NaN +37 delta_glpK-4 24.448611 0.309 9.323283 NaN +38 delta_glpK-4 25.449167 0.347 8.917299 NaN +39 delta_glpK-5 0.000000 0.051 13.774259 0.255860 +40 delta_glpK-5 14.993056 0.150 11.256036 0.529660 +41 delta_glpK-5 15.943056 0.166 10.934139 NaN +42 delta_glpK-5 16.943056 0.183 11.608822 0.705551 +43 delta_glpK-5 18.043056 0.206 10.666061 0.817859 +44 delta_glpK-5 19.109722 0.235 10.238875 NaN +45 delta_glpK-5 20.159722 0.270 9.595139 NaN +46 delta_glpK-5 21.173889 0.297 9.716688 0.806721 +47 delta_glpK-5 22.160556 0.330 8.979191 NaN +48 delta_glpK-5 23.148611 0.377 9.005701 1.007138 +49 delta_glpK-5 24.148611 0.414 7.943283 NaN +50 delta_glpK-5 25.149167 0.440 5.755193 NaN +51 delta_glpK-6 0.000000 0.048 14.073512 NaN +52 delta_glpK-6 14.626389 0.136 11.299269 NaN +53 delta_glpK-6 16.726389 0.173 10.745761 0.632854 +54 delta_glpK-6 18.643056 0.215 10.428681 0.732544 +55 delta_glpK-6 19.759722 0.242 9.378264 1.275361 +56 delta_glpK-6 20.743056 0.272 10.060147 NaN +57 delta_glpK-6 21.776389 0.298 8.885681 NaN +58 delta_glpK-6 23.123889 0.344 6.373275 NaN +59 delta_glpK-6 24.127222 0.379 6.253507 NaN diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/summary.csv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/summary.csv new file mode 100644 index 0000000..3091956 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_1_res/summary.csv @@ -0,0 +1,96 @@ +experiments,parameter name,optimal +WT-1,X_0,0.08398213978883132 +WT-1,growth_rate,0.15254484060411577 +WT-1,t_lag,6.134875880688067 +WT-1,DHA_q,-2.1604246183747784 +WT-1,DHA_M0,13.194801524159024 +WT-2,X_0,0.08101245686660968 +WT-2,growth_rate,0.1544407136031919 +WT-2,t_lag,6.252090332986083 +WT-2,DHA_q,-1.740625754992438 +WT-2,DHA_M0,10.76786553606676 +WT-3,X_0,0.0931413105528343 +WT-3,growth_rate,0.14597772686712146 +WT-3,t_lag,6.453455195699607 +WT-3,DHA_q,-1.9690189130018338 +WT-3,DHA_M0,15.9971774661078 +delta_dhaKLM-1,X_0,0.12631844703097023 +delta_dhaKLM-1,growth_rate,0.045429086733159686 +delta_dhaKLM-1,t_lag,1e-06 +delta_dhaKLM-1,DHA_q,-0.33032841938660523 +delta_dhaKLM-1,DHA_M0,14.588257841364994 +delta_dhaKLM-2,X_0,0.097505693317561 +delta_dhaKLM-2,growth_rate,0.04790931465098734 +delta_dhaKLM-2,t_lag,1e-06 +delta_dhaKLM-2,DHA_q,-0.33032022940239014 +delta_dhaKLM-2,DHA_M0,14.100032487611825 +delta_dhaKLM-3,X_0,0.0772190917387903 +delta_dhaKLM-3,growth_rate,0.05396632422548781 +delta_dhaKLM-3,t_lag,1e-06 +delta_dhaKLM-3,DHA_q,-0.621550466139007 +delta_dhaKLM-3,DHA_M0,17.752998480288184 +delta_fsaA-1,X_0,0.10366788986323168 +delta_fsaA-1,growth_rate,0.13750469867298099 +delta_fsaA-1,t_lag,1e-06 +delta_fsaA-1,DHA_q,-1.5627846879898855 +delta_fsaA-1,DHA_M0,16.872735246802225 +delta_fsaA-2,X_0,0.06560161943293889 +delta_fsaA-2,growth_rate,0.16429028175153318 +delta_fsaA-2,t_lag,1.0330209786301892 +delta_fsaA-2,DHA_q,-1.5893576421087818 +delta_fsaA-2,DHA_M0,12.87186523833506 +delta_fsaA-3,X_0,0.10119991550299652 +delta_fsaA-3,growth_rate,0.1403333823758422 +delta_fsaA-3,t_lag,1e-06 +delta_fsaA-3,DHA_q,-1.6531282904914373 +delta_fsaA-3,DHA_M0,17.557143351255746 +delta_fsaA-4,X_0,0.027067476506084036 +delta_fsaA-4,growth_rate,0.1643337865438809 +delta_fsaA-4,t_lag,1.2185260101651696 +delta_fsaA-4,DHA_q,-2.075932203899009 +delta_fsaA-4,DHA_M0,17.6924222955485 +delta_fsaB-1,X_0,0.049477696542675545 +delta_fsaB-1,growth_rate,0.12073750967780922 +delta_fsaB-1,t_lag,0.007279319646611711 +delta_fsaB-1,DHA_q,-1.5090431419714003 +delta_fsaB-1,DHA_M0,14.824308223379592 +delta_fsaB-2,X_0,0.06076259192441902 +delta_fsaB-2,growth_rate,0.1282686324090951 +delta_fsaB-2,t_lag,1e-06 +delta_fsaB-2,DHA_q,-1.466896935362664 +delta_fsaB-2,DHA_M0,14.26421842190499 +delta_fsaB-3,X_0,0.058421995949459155 +delta_fsaB-3,growth_rate,0.11910181444356989 +delta_fsaB-3,t_lag,1e-06 +delta_fsaB-3,DHA_q,-1.5755397067740617 +delta_fsaB-3,DHA_M0,14.419490571229199 +delta_gldA-1,X_0,0.06898932912056423 +delta_gldA-1,growth_rate,0.1347828313241592 +delta_gldA-1,t_lag,6.486593019467831 +delta_gldA-1,DHA_q,-1.3319332582499752 +delta_gldA-1,DHA_M0,10.721400146665719 +delta_gldA-2,X_0,0.06001232038317879 +delta_gldA-2,growth_rate,0.14119805714783704 +delta_gldA-2,t_lag,6.072439494227819 +delta_gldA-2,DHA_q,-1.0621670462582433 +delta_gldA-2,DHA_M0,14.18865505779821 +delta_gldA-3,X_0,0.03441350960780874 +delta_gldA-3,growth_rate,0.13405402036286584 +delta_gldA-3,t_lag,0.18795109020994832 +delta_gldA-3,DHA_q,-1.8980697786084149 +delta_gldA-3,DHA_M0,18.545495500417697 +delta_gldA-4,X_0,0.04504759792169657 +delta_gldA-4,growth_rate,0.13040943875764308 +delta_gldA-4,t_lag,2.6132012583067166 +delta_gldA-4,DHA_q,-1.3207594751715286 +delta_gldA-4,DHA_M0,14.542048361047478 +delta_gldA-5,X_0,0.06030507967627017 +delta_gldA-5,growth_rate,0.1363997142021091 +delta_gldA-5,t_lag,1.6621886311392635 +delta_gldA-5,DHA_q,-1.414648965103136 +delta_gldA-5,DHA_M0,14.487505239599836 +delta_gldA-6,X_0,0.05522674647164361 +delta_gldA-6,growth_rate,0.13142353874244778 +delta_gldA-6,t_lag,1.6637177124358915 +delta_gldA-6,DHA_q,-1.45264510434267 +delta_gldA-6,DHA_M0,14.462439760855087 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-1/DHA.svg b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-1/DHA.svg new file mode 100644 index 0000000..2e04f30 --- /dev/null +++ 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b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-3/flux_results.tsv new file mode 100644 index 0000000..7a0825a --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-3/flux_results.tsv @@ -0,0 +1,8 @@ + optimal +X_0 0.048154009772729135 +growth_rate 0.1058924886852867 +t_lag 4.565029781771143 +DHA_q -1.7067834475510337 +DHA_M0 14.619542649531503 +Glycerol_q 0.207128540570602 +Glycerol_M0 0.6024747770798531 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-3/plots.pdf b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-3/plots.pdf new file mode 100644 index 0000000..dbb7e35 Binary files /dev/null and b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-3/plots.pdf differ diff --git a/validation/models/Monod_model/physiofit_results/stat_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-3/stat_results.tsv similarity index 61% rename from validation/models/Monod_model/physiofit_results/stat_results.tsv rename to validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-3/stat_results.tsv index 3a29a52..21247fd 100644 --- a/validation/models/Monod_model/physiofit_results/stat_results.tsv +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-3/stat_results.tsv @@ -2,10 +2,10 @@ Khi² test results ================== -khi2_value 12.599171 +khi2_value 29.962423 number_of_measurements 27.000000 number_of_params 7.000000 Degrees_of_freedom 20.000000 -p_val 0.106088 +p_val 0.929535 -At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. 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a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-4/stat_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-4/stat_results.tsv new file mode 100644 index 0000000..752dbf7 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-4/stat_results.tsv @@ -0,0 +1,11 @@ +================== +Khi² test results +================== + +khi2_value 4.401069 +number_of_measurements 22.000000 +number_of_params 7.000000 +Degrees_of_freedom 15.000000 +p_val 0.003903 + +At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. 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a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-5/flux_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-5/flux_results.tsv new file mode 100644 index 0000000..4d302df --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-5/flux_results.tsv @@ -0,0 +1,8 @@ + optimal +X_0 0.051060363040208286 +growth_rate 0.10806470880089496 +t_lag 4.928162900177404 +DHA_q -1.251823280656221 +DHA_M0 14.338469212302549 +Glycerol_q 0.27583188578238643 +Glycerol_M0 0.2605955010887979 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-5/plots.pdf b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-5/plots.pdf new file mode 100644 index 0000000..365c9a0 Binary files /dev/null and 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0000000..275f769 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-6/config_file.yml @@ -0,0 +1,29 @@ +iterations: 100 +mc: false +model: + args: + Degradation constants: + DHA: 0.008643483 + Glycerol: 0 + bounds: + DHA_M0: (8, 20) + DHA_q: (-20, -0.001) + Glycerol_M0: (1e-06, 20) + Glycerol_q: (1e-06, 20) + X_0: (0.001, 0.5) + growth_rate: (0.001, 0.5) + t_lag: (1e-06, 40) + model_name: Steady-state batch model with lag phase and degradation of metabolites + parameters_to_estimate: + DHA_M0: 15 + DHA_q: -3 + Glycerol_M0: 0.1 + Glycerol_q: 2 + X_0: 0.05 + growth_rate: 0.1 + t_lag: 4 +path_to_data: C:\Users\millard\Documents\GIT\PhysioFit\test_data\Peiro_2019\PhysioFit_v3\results_2\dataset_2.tsv +sds: + DHA: 0.5 + Glycerol: 0.5 + X: 0.002 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-6/flux_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-6/flux_results.tsv new file mode 100644 index 0000000..63e9a1f --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-6/flux_results.tsv @@ -0,0 +1,8 @@ + optimal +X_0 0.04790422952436111 +growth_rate 0.105840155318471 +t_lag 4.507329034622728 +DHA_q -1.7042300990532426 +DHA_M0 14.612967773171455 +Glycerol_q 0.4913765713848028 +Glycerol_M0 0.14475229839161888 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-6/plots.pdf b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-6/plots.pdf new file mode 100644 index 0000000..475b783 Binary files /dev/null and b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-6/plots.pdf differ diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-6/stat_results.tsv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-6/stat_results.tsv new file mode 100644 index 0000000..e2a0a6c --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/delta_glpK-6/stat_results.tsv @@ -0,0 +1,11 @@ +================== +Khi² test results +================== + +khi2_value 29.370355 +number_of_measurements 21.000000 +number_of_params 7.000000 +Degrees_of_freedom 14.000000 +p_val 0.990692 + +At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 0.9906919073378274 diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/log.txt b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/log.txt new file mode 100644 index 0000000..95b77e7 --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/log.txt @@ -0,0 +1,695 @@ +2024-05-21 22:59:36,152 - physiofit - INFO - Running optimization for delta_glpK-1 +2024-05-21 22:59:36,163 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:36,172 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:36,194 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +0 0.000000 0.045 14.081402 0.300832 +1 14.959722 0.113 11.720505 0.546547 +2 16.909722 0.141 11.399281 0.585713 +3 19.007222 0.177 11.017542 0.673241 +4 20.457222 0.203 10.761256 0.621891 +5 22.457222 0.254 10.024273 0.632956 +6 23.460556 0.281 9.509658 0.287463 +7 24.448611 0.309 9.323283 0.476408 +8 25.449167 0.347 8.917299 0.582449 +Experimental matrix: +[[ 0.045 14.081402 0.30083192] + [ 0.113 11.720505 0.54654724] + [ 0.141 11.399281 0.58571273] + [ 0.177 11.017542 0.67324063] + [ 0.203 10.761256 0.62189095] + [ 0.254 10.024273 0.63295607] + [ 0.281 9.509658 0.28746278] + [ 0.309 9.323283 0.47640819] + [ 0.347 8.917299 0.58244929]] +Time vector: [ 0. 14.959722 16.909722 19.007222 20.457222 22.457222 23.460556 + 24.448611 25.449167] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:36,213 - physiofit - INFO - mc : False +2024-05-21 22:59:36,213 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:36,213 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:36,219 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:59:39,082 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 22:59:39,102 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 5.028578582731186 + x: [ 4.492e-02 1.055e-01 6.098e+00 -8.759e-01 + 1.410e+01 3.776e-02 4.621e-01] + nit: 135 + nfev: 14416 + population: [[ 4.490e-02 1.055e-01 ... 3.471e-02 4.575e-01] + [ 4.480e-02 1.054e-01 ... 6.348e-02 4.278e-01] + ... + [ 4.485e-02 1.054e-01 ... 3.374e-02 4.396e-01] + [ 4.500e-02 1.055e-01 ... 3.053e-02 4.728e-01]] + population_energies: [ 5.029e+00 5.163e+00 ... 5.091e+00 5.058e+00] + jac: [ 3.568e-01 1.534e-01 -1.838e-01 1.628e-01 + 6.548e-02 6.274e-01 -1.920e-01] +2024-05-21 22:59:39,110 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.044922984929789515 +2024-05-21 22:59:39,110 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.10551061469771877 +2024-05-21 22:59:39,110 - physiofit.physiofit.base.fitter - INFO - t_lag = 6.098381306162389 +2024-05-21 22:59:39,110 - physiofit.physiofit.base.fitter - INFO - DHA_q = -0.8759316235630559 +2024-05-21 22:59:39,110 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.10408301231402 +2024-05-21 22:59:39,135 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.03775678539393264 +2024-05-21 22:59:39,138 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.4621062694285036 +2024-05-21 22:59:39,155 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.044923 14.104083 0.462106 +14.959722 0.114424 11.834635 0.486977 +16.909722 0.140564 11.421589 0.496331 +19.007222 0.175382 10.929834 0.508791 +20.457222 0.204376 10.554472 0.519166 +22.457222 0.252391 9.978272 0.536348 +23.460556 0.280576 9.659124 0.546434 +24.448611 0.311405 9.322117 0.557466 +25.449167 0.346078 8.955216 0.569874 + +2024-05-21 22:59:39,219 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 5.028578582731186 +Number of measurements: 27 +Number of parameters to fit: 7 +Degrees of freedom: 20 +p-value = 0.0002899136257538129 + +2024-05-21 22:59:39,219 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0002899136257538129 +2024-05-21 22:59:39,254 - physiofit - INFO - Results for delta_glpK-1: + optimal +delta_glpK-1 X_0 0.044923 +delta_glpK-1 growth_rate 0.105511 +delta_glpK-1 t_lag 6.098381 +delta_glpK-1 DHA_q -0.875932 +delta_glpK-1 DHA_M0 14.104083 +delta_glpK-1 Glycerol_q 0.037757 +delta_glpK-1 Glycerol_M0 0.462106 +2024-05-21 22:59:39,281 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:59:41,393 - physiofit - INFO - Running optimization for delta_glpK-2 +2024-05-21 22:59:41,402 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:41,405 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:41,407 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +9 0.000000 0.051 13.774259 0.255860 +10 14.993056 0.150 11.256036 0.529660 +11 15.943056 0.166 10.934139 0.387502 +12 16.943056 0.183 11.608822 0.705551 +13 18.043056 0.206 10.666061 0.817859 +14 19.109722 0.235 10.238875 0.489520 +15 20.159722 0.270 9.595139 0.679338 +16 21.173889 0.297 9.716688 0.806721 +17 22.160556 0.330 8.979191 0.493778 +18 23.148611 0.377 9.005701 1.007138 +19 24.148611 0.414 7.943283 0.689019 +20 25.149167 0.440 5.755193 0.473915 +Experimental matrix: +[[ 0.051 13.774259 0.25585988] + [ 0.15 11.256036 0.52966002] + [ 0.166 10.934139 0.38750179] + [ 0.183 11.608822 0.70555098] + [ 0.206 10.666061 0.81785899] + [ 0.235 10.238875 0.48952005] + [ 0.27 9.595139 0.67933845] + [ 0.297 9.716688 0.80672058] + [ 0.33 8.979191 0.4937779 ] + [ 0.377 9.005701 1.00713844] + [ 0.414 7.943283 0.68901877] + [ 0.44 5.755193 0.47391532]] +Time vector: [ 0. 14.993056 15.943056 16.943056 18.043056 19.109722 20.159722 + 21.173889 22.160556 23.148611 24.148611 25.149167] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:41,426 - physiofit - INFO - mc : False +2024-05-21 22:59:41,428 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:41,428 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:41,428 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:59:43,504 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 127.1324348264809 + x: [ 5.121e-02 1.081e-01 4.957e+00 -1.264e+00 + 1.437e+01 7.844e-02 4.638e-01] + nit: 115 + nfev: 12724 + population: [[ 5.077e-02 1.079e-01 ... 4.939e-02 5.090e-01] + [ 5.035e-02 1.078e-01 ... 4.349e-02 4.917e-01] + ... + [ 5.077e-02 1.077e-01 ... 7.443e-02 5.250e-01] + [ 5.228e-02 1.084e-01 ... 2.397e-02 6.714e-01]] + population_energies: [ 1.271e+02 1.278e+02 ... 1.282e+02 1.315e+02] + jac: [ 9.944e-01 1.079e+00 2.730e-01 -1.558e-02 + 2.680e-01 2.075e-01 3.895e-01] +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.051206956921290465 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.10808036846990784 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - t_lag = 4.957249169251253 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.2636285397208482 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.371071585278978 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.07844133415314852 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.46378336742393567 +2024-05-21 22:59:43,523 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.051207 14.371072 0.463783 +14.993056 0.151494 11.492566 0.536569 +15.943056 0.167876 11.207829 0.548458 +16.943056 0.187037 10.888299 0.562364 +18.043056 0.210649 10.510483 0.579502 +19.109722 0.236389 10.114440 0.598183 +20.159722 0.264797 9.692401 0.618800 +21.173889 0.295473 9.250705 0.641064 +22.160556 0.328723 8.785023 0.665196 +23.148611 0.365770 8.278991 0.692083 +24.148611 0.407518 7.721706 0.722383 +25.149167 0.454058 7.113390 0.756160 + +2024-05-21 22:59:43,540 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 127.1324348264809 +Number of measurements: 36 +Number of parameters to fit: 7 +Degrees of freedom: 29 +p-value = 0.9999999999999701 + +2024-05-21 22:59:43,549 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 0.9999999999999701 + +2024-05-21 22:59:43,556 - physiofit - INFO - Results for delta_glpK-2: + optimal +delta_glpK-2 X_0 0.051207 +delta_glpK-2 growth_rate 0.108080 +delta_glpK-2 t_lag 4.957249 +delta_glpK-2 DHA_q -1.263629 +delta_glpK-2 DHA_M0 14.371072 +delta_glpK-2 Glycerol_q 0.078441 +delta_glpK-2 Glycerol_M0 0.463783 +2024-05-21 22:59:43,573 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:59:45,688 - physiofit - INFO - Running optimization for delta_glpK-3 +2024-05-21 22:59:45,697 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:45,697 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:45,707 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +21 0.000000 0.048 14.073512 0.670953 +22 14.626389 0.136 11.299269 0.764722 +23 16.726389 0.173 10.745761 0.632854 +24 18.643056 0.215 10.428681 0.732544 +25 19.759722 0.242 9.378264 1.275361 +26 20.743056 0.272 10.060147 1.221121 +27 21.776389 0.298 8.885681 1.128564 +28 23.123889 0.344 6.373275 0.991637 +29 24.127222 0.379 6.253507 1.282776 +Experimental matrix: +[[ 0.048 14.073512 0.67095267] + [ 0.136 11.299269 0.7647224 ] + [ 0.173 10.745761 0.63285391] + [ 0.215 10.428681 0.73254427] + [ 0.242 9.378264 1.27536068] + [ 0.272 10.060147 1.22112107] + [ 0.298 8.885681 1.12856385] + [ 0.344 6.373275 0.99163704] + [ 0.379 6.253507 1.28277568]] +Time vector: [ 0. 14.626389 16.726389 18.643056 19.759722 20.743056 21.776389 + 23.123889 24.127222] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:45,710 - physiofit - INFO - mc : False +2024-05-21 22:59:45,710 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:45,710 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:45,710 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:59:47,586 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 22:59:47,596 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 29.96242346782853 + x: [ 4.815e-02 1.059e-01 4.565e+00 -1.707e+00 + 1.462e+01 2.071e-01 6.025e-01] + nit: 108 + nfev: 11789 + population: [[ 4.815e-02 1.059e-01 ... 1.768e-01 6.370e-01] + [ 4.810e-02 1.061e-01 ... 2.053e-01 6.342e-01] + ... + [ 4.851e-02 1.064e-01 ... 2.008e-01 5.668e-01] + [ 4.847e-02 1.057e-01 ... 1.137e-01 7.550e-01]] + population_energies: [ 2.996e+01 3.007e+01 ... 3.071e+01 3.098e+01] + jac: [ 2.696e-01 2.232e-01 1.688e-02 7.370e-02 + 1.246e-02 -1.424e-02 -2.424e-02] +2024-05-21 22:59:47,596 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.048154009772729135 +2024-05-21 22:59:47,596 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.1058924886852867 +2024-05-21 22:59:47,604 - physiofit.physiofit.base.fitter - INFO - t_lag = 4.565029781771143 +2024-05-21 22:59:47,605 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.7067834475510337 +2024-05-21 22:59:47,605 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.619542649531503 +2024-05-21 22:59:47,605 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.207128540570602 +2024-05-21 22:59:47,605 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.6024747770798531 +2024-05-21 22:59:47,605 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.048154 14.619543 0.602475 +14.626389 0.139746 11.458709 0.781631 +16.726389 0.174548 10.696524 0.849705 +18.643056 0.213826 9.892738 0.926533 +19.759722 0.240666 9.367149 0.979032 +20.743056 0.267077 8.863946 1.030693 +21.776389 0.297960 8.289532 1.091101 +23.123889 0.343658 7.461138 1.180489 +24.127222 0.382181 6.778444 1.255840 + +2024-05-21 22:59:47,621 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 29.96242346782853 +Number of measurements: 27 +Number of parameters to fit: 7 +Degrees of freedom: 20 +p-value = 0.9295351725802049 + +2024-05-21 22:59:47,621 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.9295351725802049 +2024-05-21 22:59:47,638 - physiofit - INFO - Results for delta_glpK-3: + optimal +delta_glpK-3 X_0 0.048154 +delta_glpK-3 growth_rate 0.105892 +delta_glpK-3 t_lag 4.565030 +delta_glpK-3 DHA_q -1.706783 +delta_glpK-3 DHA_M0 14.619543 +delta_glpK-3 Glycerol_q 0.207129 +delta_glpK-3 Glycerol_M0 0.602475 +2024-05-21 22:59:47,654 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:59:49,879 - physiofit - INFO - Running optimization for delta_glpK-4 +2024-05-21 22:59:49,886 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:49,887 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:49,894 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +30 0.000000 0.045 14.081402 0.300832 +31 14.959722 0.113 11.720505 0.546547 +32 16.909722 0.141 11.399281 0.585713 +33 19.007222 0.177 11.017542 0.673241 +34 20.457222 0.203 10.761256 NaN +35 22.457222 0.254 10.024273 NaN +36 23.460556 0.281 9.509658 NaN +37 24.448611 0.309 9.323283 NaN +38 25.449167 0.347 8.917299 NaN +Experimental matrix: +[[ 0.045 14.081402 0.30083192] + [ 0.113 11.720505 0.54654724] + [ 0.141 11.399281 0.58571273] + [ 0.177 11.017542 0.67324063] + [ 0.203 10.761256 nan] + [ 0.254 10.024273 nan] + [ 0.281 9.509658 nan] + [ 0.309 9.323283 nan] + [ 0.347 8.917299 nan]] +Time vector: [ 0. 14.959722 16.909722 19.007222 20.457222 22.457222 23.460556 + 24.448611 25.449167] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:49,909 - physiofit - INFO - mc : False +2024-05-21 22:59:49,909 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:49,909 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:49,909 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:59:52,255 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 22:59:52,260 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 4.401068570458678 + x: [ 4.502e-02 1.055e-01 6.122e+00 -8.737e-01 + 1.410e+01 3.202e-01 3.034e-01] + nit: 125 + nfev: 13494 + population: [[ 4.509e-02 1.055e-01 ... 3.211e-01 3.037e-01] + [ 4.497e-02 1.055e-01 ... 2.328e-01 3.439e-01] + ... + [ 4.521e-02 1.055e-01 ... 2.848e-01 3.385e-01] + [ 4.525e-02 1.055e-01 ... 2.815e-01 3.106e-01]] + population_energies: [ 4.401e+00 4.463e+00 ... 4.421e+00 4.460e+00] + jac: [ 6.103e-02 4.192e-02 3.501e-02 1.493e-01 + -3.438e-02 1.363e-01 2.483e-02] +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.04501657927047147 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.10553281714740584 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - t_lag = 6.121737712989762 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - DHA_q = -0.8737292288631839 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.09750351625617 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.32020690230153914 +2024-05-21 22:59:52,274 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.3033883198828303 +2024-05-21 22:59:52,303 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.045017 14.097504 0.303388 +14.959722 0.114403 11.831258 0.513920 +16.909722 0.140544 11.418845 0.593235 +19.007222 0.175365 10.927894 0.698892 +20.457222 0.204362 10.553177 NaN +22.457222 0.252386 9.978010 NaN +23.460556 0.280576 9.659452 NaN +24.448611 0.311412 9.323079 NaN +25.449167 0.346093 8.956881 NaN + +2024-05-21 22:59:52,340 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 4.401068570458678 +Number of measurements: 22 +Number of parameters to fit: 7 +Degrees of freedom: 15 +p-value = 0.0039025682239525006 + +2024-05-21 22:59:52,354 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 0.0039025682239525006 +2024-05-21 22:59:52,421 - physiofit - INFO - Results for delta_glpK-4: + optimal +delta_glpK-4 X_0 0.045017 +delta_glpK-4 growth_rate 0.105533 +delta_glpK-4 t_lag 6.121738 +delta_glpK-4 DHA_q -0.873729 +delta_glpK-4 DHA_M0 14.097504 +delta_glpK-4 Glycerol_q 0.320207 +delta_glpK-4 Glycerol_M0 0.303388 +2024-05-21 22:59:52,460 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:59:54,656 - physiofit - INFO - Running optimization for delta_glpK-5 +2024-05-21 22:59:54,662 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:54,662 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:54,690 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +39 0.000000 0.051 13.774259 0.255860 +40 14.993056 0.150 11.256036 0.529660 +41 15.943056 0.166 10.934139 NaN +42 16.943056 0.183 11.608822 0.705551 +43 18.043056 0.206 10.666061 0.817859 +44 19.109722 0.235 10.238875 NaN +45 20.159722 0.270 9.595139 NaN +46 21.173889 0.297 9.716688 0.806721 +47 22.160556 0.330 8.979191 NaN +48 23.148611 0.377 9.005701 1.007138 +49 24.148611 0.414 7.943283 NaN +50 25.149167 0.440 5.755193 NaN +Experimental matrix: +[[ 0.051 13.774259 0.25585988] + [ 0.15 11.256036 0.52966002] + [ 0.166 10.934139 nan] + [ 0.183 11.608822 0.70555098] + [ 0.206 10.666061 0.81785899] + [ 0.235 10.238875 nan] + [ 0.27 9.595139 nan] + [ 0.297 9.716688 0.80672058] + [ 0.33 8.979191 nan] + [ 0.377 9.005701 1.00713844] + [ 0.414 7.943283 nan] + [ 0.44 5.755193 nan]] +Time vector: [ 0. 14.993056 15.943056 16.943056 18.043056 19.109722 20.159722 + 21.173889 22.160556 23.148611 24.148611 25.149167] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:54,714 - physiofit - INFO - mc : False +2024-05-21 22:59:54,714 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:54,714 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:54,714 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 22:59:56,521 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 22:59:56,533 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 125.70267666044796 + x: [ 5.106e-02 1.081e-01 4.928e+00 -1.252e+00 + 1.434e+01 2.758e-01 2.606e-01] + nit: 93 + nfev: 10302 + population: [[ 5.008e-02 1.082e-01 ... 3.230e-01 2.745e-01] + [ 5.130e-02 1.079e-01 ... 1.955e-01 3.211e-01] + ... + [ 5.247e-02 1.082e-01 ... 1.399e-01 3.257e-01] + [ 4.992e-02 1.085e-01 ... 2.107e-01 4.445e-01]] + population_energies: [ 1.257e+02 1.268e+02 ... 1.276e+02 1.271e+02] + jac: [ 5.023e-01 6.587e-01 -1.471e-01 -2.438e-01 + -4.320e-01 -1.215e-01 -9.693e-01] +2024-05-21 22:59:56,539 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.051060363040208286 +2024-05-21 22:59:56,540 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.10806470880089496 +2024-05-21 22:59:56,540 - physiofit.physiofit.base.fitter - INFO - t_lag = 4.928162900177404 +2024-05-21 22:59:56,540 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.251823280656221 +2024-05-21 22:59:56,540 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.338469212302549 +2024-05-21 22:59:56,546 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.27583188578238643 +2024-05-21 22:59:56,546 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.2605955010887979 +2024-05-21 22:59:56,564 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.051060 14.338469 0.260596 +14.993056 0.151513 11.472588 0.516997 +15.943056 0.167893 11.189775 NaN +16.943056 0.187053 10.872463 0.607714 +18.043056 0.210664 10.497342 0.667980 +19.109722 0.236402 10.104200 NaN +20.159722 0.264807 9.685327 NaN +21.173889 0.295479 9.247019 0.884467 +22.160556 0.328725 8.784979 NaN +23.148611 0.365767 8.282977 1.063874 +24.148611 0.407508 7.730207 NaN +25.149167 0.454040 7.126897 NaN + +2024-05-21 22:59:56,576 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 125.70267666044796 +Number of measurements: 30 +Number of parameters to fit: 7 +Degrees of freedom: 23 +p-value = 0.9999999999999997 + +2024-05-21 22:59:56,577 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 0.9999999999999997 + +2024-05-21 22:59:56,587 - physiofit - INFO - Results for delta_glpK-5: + optimal +delta_glpK-5 X_0 0.051060 +delta_glpK-5 growth_rate 0.108065 +delta_glpK-5 t_lag 4.928163 +delta_glpK-5 DHA_q -1.251823 +delta_glpK-5 DHA_M0 14.338469 +delta_glpK-5 Glycerol_q 0.275832 +delta_glpK-5 Glycerol_M0 0.260596 +2024-05-21 22:59:56,611 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 22:59:58,744 - physiofit - INFO - Running optimization for delta_glpK-6 +2024-05-21 22:59:58,765 - physiofit - INFO - Run options for the fitter: +2024-05-21 22:59:58,765 - physiofit - INFO - sd : {'X': 0.002, 'DHA': 0.5, 'Glycerol': 0.5} +2024-05-21 22:59:58,773 - physiofit - INFO - model : Selected model: Steady-state batch model with lag phase and degradation of metabolites +Model data: + time X DHA Glycerol +51 0.000000 0.048 14.073512 NaN +52 14.626389 0.136 11.299269 NaN +53 16.726389 0.173 10.745761 0.632854 +54 18.643056 0.215 10.428681 0.732544 +55 19.759722 0.242 9.378264 1.275361 +56 20.743056 0.272 10.060147 NaN +57 21.776389 0.298 8.885681 NaN +58 23.123889 0.344 6.373275 NaN +59 24.127222 0.379 6.253507 NaN +Experimental matrix: +[[ 0.048 14.073512 nan] + [ 0.136 11.299269 nan] + [ 0.173 10.745761 0.63285391] + [ 0.215 10.428681 0.73254427] + [ 0.242 9.378264 1.27536068] + [ 0.272 10.060147 nan] + [ 0.298 8.885681 nan] + [ 0.344 6.373275 nan] + [ 0.379 6.253507 nan]] +Time vector: [ 0. 14.626389 16.726389 18.643056 19.759722 20.743056 21.776389 + 23.123889 24.127222] +Name vector: ['X', 'DHA', 'Glycerol'] +Biomass & Metabolites: ['DHA', 'Glycerol'] +Parameters to estimate: {'X_0': 0.05, 'growth_rate': 0.1, 't_lag': 4, 'DHA_q': -3, 'DHA_M0': 15, 'Glycerol_q': 2, 'Glycerol_M0': 0.1} +Fixed parameters: {'Degradation constants': {'DHA': 0.008643483, 'Glycerol': 0}} +Bounds: {'X_0': (0.001, 0.5), 'growth_rate': (0.001, 0.5), 't_lag': (1e-06, 40), 'DHA_q': (-20, -0.001), 'DHA_M0': (8, 20), 'Glycerol_q': (1e-06, 20), 'Glycerol_M0': (1e-06, 20)} + +2024-05-21 22:59:58,813 - physiofit - INFO - mc : False +2024-05-21 22:59:58,814 - physiofit - INFO - iterations : 100 +2024-05-21 22:59:58,814 - physiofit - INFO - debug_mode : False +2024-05-21 22:59:58,820 - physiofit.physiofit.base.fitter - INFO - +Running optimization... + +2024-05-21 23:00:00,837 - physiofit.physiofit.base.fitter - INFO - SD matrix: [[0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ] + [0.002 0.5 0.5 ]] +2024-05-21 23:00:00,837 - physiofit.physiofit.base.fitter - INFO - Optimization results: message: Optimization terminated successfully. + success: True + fun: 29.37035530509316 + x: [ 4.790e-02 1.058e-01 4.507e+00 -1.704e+00 + 1.461e+01 4.914e-01 1.448e-01] + nit: 123 + nfev: 13284 + population: [[ 4.781e-02 1.060e-01 ... 4.591e-01 1.332e-01] + [ 4.755e-02 1.062e-01 ... 1.821e-01 6.071e-01] + ... + [ 4.866e-02 1.057e-01 ... 5.772e-01 2.322e-03] + [ 4.781e-02 1.056e-01 ... 5.795e-01 3.191e-02]] + population_energies: [ 2.937e+01 3.072e+01 ... 2.953e+01 2.962e+01] + jac: [-1.015e+00 -7.891e-01 -6.406e-01 -5.797e-01 + -3.651e-01 -1.826e-01 3.776e-01] +2024-05-21 23:00:00,837 - physiofit.physiofit.base.fitter - INFO - X_0 = 0.04790422952436111 +2024-05-21 23:00:00,837 - physiofit.physiofit.base.fitter - INFO - growth_rate = 0.105840155318471 +2024-05-21 23:00:00,854 - physiofit.physiofit.base.fitter - INFO - t_lag = 4.507329034622728 +2024-05-21 23:00:00,854 - physiofit.physiofit.base.fitter - INFO - DHA_q = -1.7042300990532426 +2024-05-21 23:00:00,854 - physiofit.physiofit.base.fitter - INFO - DHA_M0 = 14.612967773171455 +2024-05-21 23:00:00,854 - physiofit.physiofit.base.fitter - INFO - Glycerol_q = 0.4913765713848028 +2024-05-21 23:00:00,860 - physiofit.physiofit.base.fitter - INFO - Glycerol_M0 = 0.14475229839161888 +2024-05-21 23:00:00,867 - physiofit.physiofit.base.fitter - INFO - Simulated data: + X DHA Glycerol +Time +0.000000 0.047904 14.612968 NaN +14.626389 0.139799 11.449871 NaN +16.726389 0.174595 10.688497 0.732932 +18.643056 0.213862 9.885646 0.915233 +19.759722 0.240692 9.360709 1.039796 +20.743056 0.267093 8.858159 NaN +21.776389 0.297961 8.284522 NaN +23.123889 0.343636 7.457304 NaN +24.127222 0.382136 6.775624 NaN + +2024-05-21 23:00:00,873 - physiofit.physiofit.base.fitter - INFO - khi2 test results: +khi2 value: 29.37035530509316 +Number of measurements: 21 +Number of parameters to fit: 7 +Degrees of freedom: 14 +p-value = 0.9906919073378274 + +2024-05-21 23:00:00,873 - physiofit.physiofit.base.fitter - INFO - At level of 95% confidence, the model does not fit the data good enough with respect to the provided measurement SD. Value: 0.9906919073378274 + +2024-05-21 23:00:00,889 - physiofit - INFO - Results for delta_glpK-6: + optimal +delta_glpK-6 X_0 0.047904 +delta_glpK-6 growth_rate 0.105840 +delta_glpK-6 t_lag 4.507329 +delta_glpK-6 DHA_q -1.704230 +delta_glpK-6 DHA_M0 14.612968 +delta_glpK-6 Glycerol_q 0.491377 +delta_glpK-6 Glycerol_M0 0.144752 +2024-05-21 23:00:00,916 - physiofit.physiofit.base.io - WARNING - Monte Carlo analysis has not been done, confidence intervals will not be computed +2024-05-21 23:00:03,071 - physiofit - INFO - Resulting dataframe: + experiments time X DHA Glycerol +0 delta_glpK-1 0.000000 0.045 14.081402 0.300832 +1 delta_glpK-1 14.959722 0.113 11.720505 0.546547 +2 delta_glpK-1 16.909722 0.141 11.399281 0.585713 +3 delta_glpK-1 19.007222 0.177 11.017542 0.673241 +4 delta_glpK-1 20.457222 0.203 10.761256 0.621891 +5 delta_glpK-1 22.457222 0.254 10.024273 0.632956 +6 delta_glpK-1 23.460556 0.281 9.509658 0.287463 +7 delta_glpK-1 24.448611 0.309 9.323283 0.476408 +8 delta_glpK-1 25.449167 0.347 8.917299 0.582449 +9 delta_glpK-2 0.000000 0.051 13.774259 0.255860 +10 delta_glpK-2 14.993056 0.150 11.256036 0.529660 +11 delta_glpK-2 15.943056 0.166 10.934139 0.387502 +12 delta_glpK-2 16.943056 0.183 11.608822 0.705551 +13 delta_glpK-2 18.043056 0.206 10.666061 0.817859 +14 delta_glpK-2 19.109722 0.235 10.238875 0.489520 +15 delta_glpK-2 20.159722 0.270 9.595139 0.679338 +16 delta_glpK-2 21.173889 0.297 9.716688 0.806721 +17 delta_glpK-2 22.160556 0.330 8.979191 0.493778 +18 delta_glpK-2 23.148611 0.377 9.005701 1.007138 +19 delta_glpK-2 24.148611 0.414 7.943283 0.689019 +20 delta_glpK-2 25.149167 0.440 5.755193 0.473915 +21 delta_glpK-3 0.000000 0.048 14.073512 0.670953 +22 delta_glpK-3 14.626389 0.136 11.299269 0.764722 +23 delta_glpK-3 16.726389 0.173 10.745761 0.632854 +24 delta_glpK-3 18.643056 0.215 10.428681 0.732544 +25 delta_glpK-3 19.759722 0.242 9.378264 1.275361 +26 delta_glpK-3 20.743056 0.272 10.060147 1.221121 +27 delta_glpK-3 21.776389 0.298 8.885681 1.128564 +28 delta_glpK-3 23.123889 0.344 6.373275 0.991637 +29 delta_glpK-3 24.127222 0.379 6.253507 1.282776 +30 delta_glpK-4 0.000000 0.045 14.081402 0.300832 +31 delta_glpK-4 14.959722 0.113 11.720505 0.546547 +32 delta_glpK-4 16.909722 0.141 11.399281 0.585713 +33 delta_glpK-4 19.007222 0.177 11.017542 0.673241 +34 delta_glpK-4 20.457222 0.203 10.761256 NaN +35 delta_glpK-4 22.457222 0.254 10.024273 NaN +36 delta_glpK-4 23.460556 0.281 9.509658 NaN +37 delta_glpK-4 24.448611 0.309 9.323283 NaN +38 delta_glpK-4 25.449167 0.347 8.917299 NaN +39 delta_glpK-5 0.000000 0.051 13.774259 0.255860 +40 delta_glpK-5 14.993056 0.150 11.256036 0.529660 +41 delta_glpK-5 15.943056 0.166 10.934139 NaN +42 delta_glpK-5 16.943056 0.183 11.608822 0.705551 +43 delta_glpK-5 18.043056 0.206 10.666061 0.817859 +44 delta_glpK-5 19.109722 0.235 10.238875 NaN +45 delta_glpK-5 20.159722 0.270 9.595139 NaN +46 delta_glpK-5 21.173889 0.297 9.716688 0.806721 +47 delta_glpK-5 22.160556 0.330 8.979191 NaN +48 delta_glpK-5 23.148611 0.377 9.005701 1.007138 +49 delta_glpK-5 24.148611 0.414 7.943283 NaN +50 delta_glpK-5 25.149167 0.440 5.755193 NaN +51 delta_glpK-6 0.000000 0.048 14.073512 NaN +52 delta_glpK-6 14.626389 0.136 11.299269 NaN +53 delta_glpK-6 16.726389 0.173 10.745761 0.632854 +54 delta_glpK-6 18.643056 0.215 10.428681 0.732544 +55 delta_glpK-6 19.759722 0.242 9.378264 1.275361 +56 delta_glpK-6 20.743056 0.272 10.060147 NaN +57 delta_glpK-6 21.776389 0.298 8.885681 NaN +58 delta_glpK-6 23.123889 0.344 6.373275 NaN +59 delta_glpK-6 24.127222 0.379 6.253507 NaN diff --git a/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/summary.csv b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/summary.csv new file mode 100644 index 0000000..01b83da --- /dev/null +++ b/validation/validation_results/Peiro_2019/PhysioFit_v3.4.0/results/dataset_2_res/summary.csv @@ -0,0 +1,43 @@ +experiments,parameter name,optimal +delta_glpK-1,X_0,0.044922984929789515 +delta_glpK-1,growth_rate,0.10551061469771877 +delta_glpK-1,t_lag,6.098381306162389 +delta_glpK-1,DHA_q,-0.8759316235630559 +delta_glpK-1,DHA_M0,14.10408301231402 +delta_glpK-1,Glycerol_q,0.03775678539393264 +delta_glpK-1,Glycerol_M0,0.4621062694285036 +delta_glpK-2,X_0,0.051206956921290465 +delta_glpK-2,growth_rate,0.10808036846990784 +delta_glpK-2,t_lag,4.957249169251253 +delta_glpK-2,DHA_q,-1.2636285397208482 +delta_glpK-2,DHA_M0,14.371071585278978 +delta_glpK-2,Glycerol_q,0.07844133415314852 +delta_glpK-2,Glycerol_M0,0.46378336742393567 +delta_glpK-3,X_0,0.048154009772729135 +delta_glpK-3,growth_rate,0.1058924886852867 +delta_glpK-3,t_lag,4.565029781771143 +delta_glpK-3,DHA_q,-1.7067834475510337 +delta_glpK-3,DHA_M0,14.619542649531503 +delta_glpK-3,Glycerol_q,0.207128540570602 +delta_glpK-3,Glycerol_M0,0.6024747770798531 +delta_glpK-4,X_0,0.04501657927047147 +delta_glpK-4,growth_rate,0.10553281714740584 +delta_glpK-4,t_lag,6.121737712989762 +delta_glpK-4,DHA_q,-0.8737292288631839 +delta_glpK-4,DHA_M0,14.09750351625617 +delta_glpK-4,Glycerol_q,0.32020690230153914 +delta_glpK-4,Glycerol_M0,0.3033883198828303 +delta_glpK-5,X_0,0.051060363040208286 +delta_glpK-5,growth_rate,0.10806470880089496 +delta_glpK-5,t_lag,4.928162900177404 +delta_glpK-5,DHA_q,-1.251823280656221 +delta_glpK-5,DHA_M0,14.338469212302549 +delta_glpK-5,Glycerol_q,0.27583188578238643 +delta_glpK-5,Glycerol_M0,0.2605955010887979 +delta_glpK-6,X_0,0.04790422952436111 +delta_glpK-6,growth_rate,0.105840155318471 +delta_glpK-6,t_lag,4.507329034622728 +delta_glpK-6,DHA_q,-1.7042300990532426 +delta_glpK-6,DHA_M0,14.612967773171455 +delta_glpK-6,Glycerol_q,0.4913765713848028 +delta_glpK-6,Glycerol_M0,0.14475229839161888 diff --git a/validation/validation_results/Peiro_2019/results.xlsx b/validation/validation_results/Peiro_2019/results.xlsx new file mode 100644 index 0000000..eef99db Binary files /dev/null and b/validation/validation_results/Peiro_2019/results.xlsx differ diff --git a/validation/models/Monod_model/data.tsv b/validation/validation_results/Zentou_2019/data.tsv similarity index 100% rename from validation/models/Monod_model/data.tsv rename to validation/validation_results/Zentou_2019/data.tsv diff --git a/validation/models/Monod_model/physiofit_results/P_ethanol.svg b/validation/validation_results/Zentou_2019/data_res/A/P_ethanol.svg similarity index 67% rename from validation/models/Monod_model/physiofit_results/P_ethanol.svg rename to validation/validation_results/Zentou_2019/data_res/A/P_ethanol.svg index ed76125..30486d5 100644 --- a/validation/models/Monod_model/physiofit_results/P_ethanol.svg +++ b/validation/validation_results/Zentou_2019/data_res/A/P_ethanol.svg @@ -6,11 +6,11 @@ - 2023-03-24T17:10:16.451106 + 2024-05-23T22:04:27.387693 image/svg+xml - Matplotlib v3.7.1, https://matplotlib.org/ + Matplotlib v3.8.3, https://matplotlib.org/ @@ -39,7 +39,7 @@ z - - - - - - - - - - - + + + + + + + + + + - - - + + - - + @@ -137,7 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/validation/validation_results/Zentou_2019/data_res/A/config_file.yml b/validation/validation_results/Zentou_2019/data_res/A/config_file.yml new file mode 100644 index 0000000..5a06d00 --- /dev/null +++ b/validation/validation_results/Zentou_2019/data_res/A/config_file.yml @@ -0,0 +1,26 @@ +iterations: 100 +mc: true +model: + args: null + bounds: + P_ethanol_p_0: (0.001, 10) + P_ethanol_y_P: (0.01, 2) + S_GlcEq_km: (1, 150) + S_GlcEq_qsmax: (0.1, 20) + S_GlcEq_s_0: (10, 200) + X_0: (0.1, 5) + y_BM: (0.01, 1) + model_name: Dynamic Monod model (1 substrate, 1 product) + parameters_to_estimate: + P_ethanol_p_0: 5 + P_ethanol_y_P: 1 + S_GlcEq_km: 1 + S_GlcEq_qsmax: 6 + S_GlcEq_s_0: 100 + X_0: 1 + y_BM: 1 +path_to_data: C:\Users\millard\Desktop\Zentou_2019\data.tsv +sds: + P_ethanol: 3 + S_GlcEq: 7 + X: 1 diff --git a/validation/validation_results/Zentou_2019/data_res/A/flux_results.tsv b/validation/validation_results/Zentou_2019/data_res/A/flux_results.tsv new file mode 100644 index 0000000..458dd72 --- /dev/null +++ b/validation/validation_results/Zentou_2019/data_res/A/flux_results.tsv @@ -0,0 +1,8 @@ + optimal mean sd median CI_2.5 CI_97.5 +X_0 1.076488984128511 1.0939732724353661 0.3251555783637284 1.0686044783935 0.5271183156805785 1.751535320374794 +y_BM 0.2723190413825765 0.27425003875368215 0.01573486865842605 0.2732104336024527 0.24658775300003885 0.30813747719959567 +S_GlcEq_km 8.253192906951384 11.781233623497569 20.228660071676217 8.223679849933523 1.0 43.688836325619924 +S_GlcEq_qsmax 0.6318248561937452 0.6729516964861937 0.22659384873124322 0.62208453210428 0.47880966950242654 1.0882208427817857 +S_GlcEq_s_0 74.29652433941904 74.05739523685425 3.1833892498391436 74.00584605498133 68.22933357181026 80.0608659805935 +P_ethanol_y_P 0.4244849150963135 0.41722140609831476 0.03337042158640167 0.4165269454637047 0.35376399359482663 0.4775121702187669 +P_ethanol_p_0 0.18238818583104965 0.8867525439851033 0.912478998547139 0.7123230263446669 0.001 2.7831008931512473 diff --git a/validation/validation_results/Zentou_2019/data_res/A/plots.pdf b/validation/validation_results/Zentou_2019/data_res/A/plots.pdf new file mode 100644 index 0000000..c0559ac Binary files /dev/null and b/validation/validation_results/Zentou_2019/data_res/A/plots.pdf differ diff --git a/validation/validation_results/Zentou_2019/data_res/A/stat_results.tsv b/validation/validation_results/Zentou_2019/data_res/A/stat_results.tsv new file mode 100644 index 0000000..4c685c7 --- /dev/null +++ b/validation/validation_results/Zentou_2019/data_res/A/stat_results.tsv @@ -0,0 +1,11 @@ +================== +Khi² test results +================== + +khi2_value 5.834382e-01 +number_of_measurements 2.700000e+01 +number_of_params 7.000000e+00 +Degrees_of_freedom 2.000000e+01 +p_val 9.437135e-13 + +At level of 95% confidence, the model fits the data good enough with respect to the provided measurement SD. Value: 9.437134576541502e-13 \ No newline at end of file diff --git a/validation/validation_results/Zentou_2019/data_res/log.txt b/validation/validation_results/Zentou_2019/data_res/log.txt new file mode 100644 index 0000000..e69de29 diff --git a/validation/validation_results/Zentou_2019/data_res/summary.csv b/validation/validation_results/Zentou_2019/data_res/summary.csv new file mode 100644 index 0000000..332ec64 --- /dev/null +++ b/validation/validation_results/Zentou_2019/data_res/summary.csv @@ -0,0 +1,8 @@ +experiments,parameter name,optimal,mean,sd,median,CI_2.5,CI_97.5 +A,X_0,1.076488984128511,1.0939732724353661,0.3251555783637284,1.0686044783935,0.5271183156805785,1.751535320374794 +A,y_BM,0.2723190413825765,0.27425003875368215,0.01573486865842605,0.2732104336024527,0.24658775300003885,0.30813747719959567 +A,S_GlcEq_km,8.253192906951384,11.781233623497569,20.228660071676217,8.223679849933523,1.0,43.688836325619924 +A,S_GlcEq_qsmax,0.6318248561937452,0.6729516964861937,0.22659384873124322,0.62208453210428,0.47880966950242654,1.0882208427817857 +A,S_GlcEq_s_0,74.29652433941904,74.05739523685425,3.1833892498391436,74.00584605498133,68.22933357181026,80.0608659805935 +A,P_ethanol_y_P,0.4244849150963135,0.41722140609831476,0.03337042158640167,0.4165269454637047,0.35376399359482663,0.4775121702187669 +A,P_ethanol_p_0,0.18238818583104965,0.8867525439851033,0.912478998547139,0.7123230263446669,0.001,2.7831008931512473