| Name | uq-physicell JSON |
| Version |
1.0.2
JSON |
| download |
| home_page | None |
| Summary | Project to perform uncertainty quantification of PhysiCell models |
| upload_time | 2024-10-09 15:00:40 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | MIT |
| keywords |
physicell
uncertainty quantification
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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](examples/SampleModel.ini#l1) and [physicell_model_2](examples/SampleModel.ini#l18) as shown in the config file [examples/SampleModel.ini](examples/SampleModel.ini#l20), 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](examples/SampleModel.ini#l18)
- 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](examples/SampleModel.ini#l20) model in the [examples/SampleModel.ini](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](examples/SampleModel.ini#l18) 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](examples/SampleModel.ini#l18)
- 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](examples/SampleModel.ini#l18)
- 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.
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