This repository accompanies the preprint "Entangled stoichiometric objectives shape microbial catabolism". The preprint can be found at https://doi.org/10.1101/2025.07.29.667445.

Description of the file structure: The code to run the simulations is in separate_cat_ana.py and PrecursorSeparator.py. The other python files in the main folder are used to perform the simulations, using input files in the folder input_files and outputting the results to the folder Results. The figures in the publications are in Plots, and were creates with the files in the folder plot_scripts. The genome scale models used for the simulations are in the folder Models.