uq-physicell 1.0.1

Project to perform uncertainty quantification of PhysiCell models

Installation

Install the package using pip:

pip install uq_physicell

Examples

Here are some examples to help you get started with using the package:

1. Example 1: Basic Usage

   • Description: Print information of models physicell_model_1 and physicell_model_2 as shown in the config file examples/SampleModel.ini, without running the PhysiCell simulation.
   • Code:

     python examples/ex1_print.py
     

2. Example 2: Running PhysiCell Simulations

   • Description: Run PhysiCell simulations of physicell_model_2
   • Step 1: Compile the virus-macrophage example in the PhysiCell folder.
   • Code:

     make reset && make virus-macrophage-sample && make
     

   • Step 2: Change the path of the executable variable in physicell_model_2 model in the examples/SampleModel.ini file.
   • Code:

     executable = [new path]
     

   • Step 3: run the simulations.
   • Code:

     python examples/ex2_runModel.py
     

3. Example 3: Customizable Summary Function

   • Description: This example illustrates how to run PhysiCell simulations of physicell_model_2 with a customizable summary function that generates population time series.
   • Code:

     python examples/ex3_runModelCust.py
     

4. Example 4: Sensitivity Analysis as an unique task

   • Requirements: install SALib
   • Description: Run simulations to perfom sensitivity analysis (Sobol method) physicell_model_2
   • Code:

     python examples/ex4_runSA_singleTask.py
     

   • After simulate all samples you can perform the analysis: python example/SA_ex4_ex5.py

5. Example 5: Sensitivity Analysis as parallel tasks using MPI

   • Requirements: install SALib and mpi4py
   • Description: Run simulations to perfom sensitivity analysis (Sobol method) of physicell_model_2
   • Code:

     mpiexec -n 2 python -m mpi4py examples/ex5_runSA_MPI.py
     

   • After simulate all samples you can perform the analysis: python example/SA_ex4_ex5.py

Feel free to explore these examples to understand the capabilities of the package and how to use it effectively.