An agent-based model of recombination and prosocial behavior in bacteria

By Cassandra Areff, Yumi Briones, Alyssa Pradhan, and Danielle Share

GOAL

We aim to replicate the agent-based model of prosocial behavior and recombination in bacteria by Lee et al. (2023) using Python packages. We will run a minimal subset of parameter combinations and compare our findings to the original paper.

DIRECTORY STRUCTURE

Most important:

• run_sim.py is our simulation with parallel computing features
• gens_50 contains run_sim.py results for 50 generations
• gens_500 contains run_sim.py results for 500 generations
• 241212_vis generates visualizations from gens_50

Less important:

• test_sims are test simulation results
• abm.ipynb is the initial version of our simulation in notebook format, without parallel computing features
• test_visualizations contains test code for visualizations

REFERENCES

P. A. Lee, O. T. Eldakar, J. P. Gogarten, and C. P. Andam. Recombination as an enforcement mechanism of prosocial behavior in cooperating bacteria. Iscience, 26(8), 2023.