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tumor2d README

⚠️ This package is no longer actively maintained.

DOI

Tumor2d simulation is not precisely according to but heavily based on the original source code found here from the paper

@article{JagiellaRic2017,
	Author = {N. Jagiella and D. Rickert and F. J. Theis and J. Hasenauer},
	Doi = {10.1016/j.cels.2016.12.002},
	Journal = {Cell Systems},
	Keywords = {parameter estimation, ABC, multi-scale modeling, agent-based models},
	Month = {Feb.},
	Number = {2},
	Pages = {194--206},
	Title = {Parallelization and high-performance computing enables automated statistical inference of multiscale models},
	Volume = {4},
	Year = {2017}}

Installation

It is required that

  • SWIG is installed,
    • either use your system package manager, or conda install swig if running anaconda
  • BLAS is installed
    • use your system package manager, if not installed. It should be already installed if you're running anaconda (e.g. the MKL or OpenBLAS)

Python requirements are:

  • numpy.

Then,

  • clone the repository git clone https://github.com/ICB-DCM/tumor2d
  • change into the repository directory cd tumor2d
  • and run python setup.py build_ext --inplace from within the repository
  • if the repo is in your PYTHONPATH, you should be able to use it now
  • if you want to install the package, run pip install .

Usage

The function tumor2d.simulate is the main entry point. To run it with the default parameters, do

from tumor2d import simulate
simulate()

It takes 8 parameters as input:

  • division_rate
  • initial_spheroid_radius
  • initial_quiescent_cell_fraction
  • division_depth
  • ecm_production_rate
  • ecm_degradation_rate
  • ecm_division_threshold
  • randseed

The function returns a dictionary containing the

  • growth_curve
  • extra_cellular_matrix_profile
  • proliferation_profile

which can be used as summary statistics for ABC-SMC inference with pyABC. In the documentation of pyABC, there is an example included, showing how to perform analysis for this model.

Distribution

Currently, it is not possible to make a package via python setup.py bdist_wheel reliably. The reason i, that build_ext has to be run before the other installation steps, so that the SWIG generated .py is properly included. There are indications online on how to achieve running SWIG first. However, these did not work so far. Meanwhile, it works to run python setup.py build_ext --inplace, possibly followed by python setup.py bdist_wheel, as the SWIG generated .py file is then already there.

Running the tests

Run pytest test.