Pseudopod Competition as a decision-making mechanism

Code for the paper on pseudopod splitting during chemotaxis.

Project structure

The project is structured as follows:

├── README.md 
├── psxc/ # Folder containing the code related to the dynamical model and RL training.
├── scripts/ # Folder containing scripts to evaluate and create figures.
├── pyproject.toml  # Package setup for psxc (needed to run scripts)
└── requirements.txt # Project dependencies

Setup

Create a virtual environment and install the requiered packages (Note: we use jaxlib for GPU)

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

If you need to run it on a GPU, you can install jax as

pip install jax[cuda12]

Likewise, you need to install this library locally in order to run the scripts

pip install -e .