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Use the provided installer (Installer.nb) in the base directory (recommended approach).
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Put the MASSToolbox folder (the folder containing MASS.m) somewhere where Mathematica can find it (check for example http://stackoverflow.com/questions/4641512/how-to-install-new-packages-for-mathematica for how to do this). That is the preferred method if you are planning to stay up-to-date with package developments.
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Add 'AppendTo[$Path, FileName[{$HomeDirectory,"path/to/the/folder/that/contains/the/MASStoolboxFolder"}]];' in a Notebook before initialization (<<MASStoolbox`).
Optional requirements:
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http://sbml.org/Software/MathSBML for importing/exporting MASS models to http://sbml.org/Main_Page.
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http://gurobi.com/ and https://github.com/phantomas1234/GurobiML in order to solve LP, MILP and QP problems via GurobiSolve (it mimicks Mathematica's own LinearProgramming function). Free academic licenses are http://www.gurobi.com/products/licensing-and-pricing/academic-licensing.
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http://www.gnu.org/software/glpk/ in order to use GLPKStandalone as a replacement for Mathematica's own LinearProgramming function (e.g. fba[model, "Biomass", Solver -> GLPKStandalone]). Make sure that GLPK's standalone solver glpsol is on your system's Path.
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http://www-01.ibm.com/software/integration/optimization/cplex-optimizer/ in order to use CPLEXStandalone as a replacement for Mathematica's own LinearProgramming function (e.g. fba[model, "Biomass", Solver -> CPLEXStandalone]). Academic licenses are http://www-01.ibm.com/support/docview.wss?uid=swg21419058. Make sure that the cplex command-line executable is on your system's path.
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http://www.gams.com/ for solving NLP optimization problems defined in Mathematica (following the functionality of FindMinimum and Minimize) via the interface function GAMS[...] and GAMSForm[...]. Make sure that the gams executable is on your system's Path. Alternatively, NLP problems can be submitted to http://www.neos-server.org/neos/. Make sure that you put http://www.neos-server.org/neos/NeosClient.py on your system's Path (and you'll need http://www.python.org/ to be installed for that purpose). Please, check the tutorial notebooks for more information.
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https://github.com/phantomas1234/MyStyle (for Plot and other style definitions ...).
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http://openbabel.org/wiki/Main_Page (excellent Chemoinformatics toolkit for drawing compounds etc.).
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http://www.chemaxon.com/products/marvin/ necessary for pH corrections etc. Academic licences are http://www.chemaxon.com/my-chemaxon/my-academic-license/.
The toolbox has been tested rigorously against the http://sbml.org/Facilities/Online_SBML_Test_Suite, however, the following restrictions apply:
- SBML models with versions > l2v3 are not supported (as http://sbml.org/Software/MathSBML does not provide support for them)
- Autocatalytic reactions (e.g. a + b -> 2 a; see http://en.wikipedia.org/wiki/Autocatalytic_reaction) are not supported
- Events are not supported
- Constant species are treated as boundary conditions
- Model structure ** Construct
- Structural properties ** Conservation analysis
- COBRA ** FBA ** FVA
- Visualization ** Plot time course data ** Tiled phase portraits ** Visualize data on pathway maps
- QC/QA ** Check elemental balancing ** Check stoichiometric consistency
- Import/Export ** SBML
- Sensitivity analysis package
- k-Cone analysis
- Flux sampling
- Export models as matlab structs amendable for the Cobra Toolbox
Detailed documentation of the software package is provided ...
... Please cite the following publication if ...
Jamshidi, N., & Palsson, B. Ø. (2010). Mass Action Stoichiometric Simulation Models: Incorporating Kinetics and Regulation into Stoichiometric Models. Biophysical Journal, 98(2), 175–185. doi:10.1016/j.bpj.2009.09.064
Jamshidi, N., & Palsson, B. Ø. (2008). Formulating genome-scale kinetic models in the post-genome era Molecular Systems Biology, 4, 171. doi:10.1038/msb.2008.8