Polarity Models Python

Code to run the model and generate the results for the manuscript "A mathematical model of epithelial apico-basal polarisation, and application to the endometrial cell polarity cycle".

Dependencies

Requires Python 3.11 or later.

• scipy (v1.15.2)
• matplotlib (v3.10.0)
• numpy (v2.2.3)

Quickstart

1. Clone the repository:

   git clone https://github.com/selareid/polarity_models_python.git
   cd polarity_models_python

2. Create and activate a virtual environment:

   python -m venv .venv
   source .venv/bin/activate      # on Windows: .venv\Scripts\activate

3. Install the package (and its dependencies):

   pip install -e .

Scripts

Model modules are contained in src/polarity/models/. The code to run the models and generate the results are contained in scripts/. The module src/polarity/figure_helper.py provides useful methods and definitions for the figure generation.

Results in paper are generated by the following scripts (in scripts/)

• run_parameter_sweep.py: parameter sweeps associated with establishment and sensitivity to loss
• run_downregulation_AP.py: parameter sweeps associated with polarity loss (calls methods in run_parameter_sweep.py so must be run from within scripts directory)
• par3add_parameter_search.py: runs the iterative parameter search The script scripts/run_example.py outlines the general way to run the model and change the parameters.

The figures for the manuscript are generated using the following notebooks:

• fig3,5-establishment_example.ipynb
• fig4,7-nullclines.ipynb
• fig6-parameter_sweep_plots.ipynb
• fig7-polarity_loss_plots.ipynb