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Source codes to simulate tumor growth in interaction with immune cell in a size and space structured tumor-immune interaction model and to perform sensitivity analysis of the stationary profile.

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tumorgrowth - Analysis of the equilibrium phase in immune-controlled tumors to predict best strategies for cancer treatment

Source codes to simulate tumor growth in interaction with immune cell in a size and space structured tumor-immune interaction model and to perform sensitivity analysis of the stationary profile.

System requirements

Hardware requirements

The source codes can be runned on a standard computer (in the case of the sensitivity analysis it can be beneficial to have enough cpus in order to be able to exploit the parallel computation )

Software requirements

OS requirements

the source codes are supported by all OS

Python Dependencies

the following python version must be installed to run to source codes:

  • python 3.7

the sources codes depend on the following Python packages

  • fipy (version 3.3)
  • gmsh (version 3.0.6)
  • scipy (version 1.5.3)
  • matplotlib (version 3.2.1)
  • numpy (version 1.19.1)
  • pandas (version 1.1.0)
  • seaborn (version 0.10.1)
  • h5py (version 2.10.0)
  • pygpc (version 0.2.7.5)
  • cma (version 3.0.3)

The organization of the code

  1. Simulations of the evolution problem
  • the file 2DTumorImmuneInteraction.py
  • the file 2DTumorImmuneInteraction_withRealParameters.py
  1. Estimation the model parameters
  • the file params_estimation.py
  1. The power-dichotomy algorithm
  • the file power_dichotomy_algorithm.py
  • the file power_dichotomy_algorithm_withRealParameters.py
  • the file power_dichotomy_algorithm_withRealParameters_multSimu.py
  • the file power_dichotomy_algorithm_withRealParameters_multSimu_matrix.py
  1. The global sensitivity analysis of the tumor mass at equilibrium
  • the file sensitivity_analysis_withRealParameters.py
  • the file sensitivity_analysis_results_postprocessing.py

License

This project is covered under the Creative Commons Zero v1.0 Universal.

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Source codes to simulate tumor growth in interaction with immune cell in a size and space structured tumor-immune interaction model and to perform sensitivity analysis of the stationary profile.

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