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Polarity Models Python

Code to run various polarity models. Requires Python 3.11 or later.

Models contained in src/models/. Code to run models in src/tasks/.

Run by doing python -m src.tasks.<filename_without_extension> from the main project directory.

Figures in paper are generated by tasks

  • gen_maintenance_fig.py
  • gen_polarisation_illustration_fig.py
  • gen_scribble_downreg_koffP.py
  • gen_scribble_downreg_rhop.py
  • gen_downregulation_scribble_and_pkc.py
  • gen_emergence_timeslice_fig.py
  • comparison_par3addition_goehring.py

Figures are blocked from displaying and a file is saved with the relevant figure for the above tasks. This can be toggled by commenting out matplotlib.use("Agg") at the bottom of the files.

The file src/figure_helper.py is used for commonly used colours and labels across figures.

The task run_example outlines the general way to run the new four-equation polarity model and how to change parameters.

Note that generated savedata filenames are not necessarily unique. It is possible that a change to initial condition or parameters might not change the filename. Be suspicious if you change something and it doesn't rerun the simulation.

Dependencies

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