Agent Based Model For Axolotl Limb Regeneration

The important files are:

• requirements.txt - Python package dependencies

src/

• abm.py - Main simulation code
• config.py - Default parameter configuration src/utils
• Contains plotting and data post-processing functions

scripts/

• run_sim.py - Runs a simulation with chosen parameters
• run_cases.py - Runs the cases from figure 3A, 3B, 3C, S2A, S2B
• stress_test.py - Runs poking experiments as seen in figure 5
• param_optimization_pso.py - Runs particle swarm optimization (PSO) pipeline, various parameters can be set
• read_pso_optim.py - Allows the user to check the status of a PSO run with simple visualizations
• pso_figs.py - Generates the scatter plots seen in figure 7