This repository contains the code used in Bernstein DB, Dewhirst FE, Segre D. (2019) Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome. eLife. DOI: 10.7554/eLife.39733.
Figures/
All data and scripts necessary to recreat the figures from the original article
algorithm_functions/
MATLAB code used to implement out algorithm
combinatorial_theory_functions/
Code pertaining to the combinatorial equations we developed to describe our method
example_models/
Several metabolic network models in .mat format that are used by example_calculate_PM.m
example_results/
A directory to hold the results calculated with example_calculate_PM.m
metabolic_networks_mat/
All metabolic network models in .mat format used in the original article.
example_calculate_PM.m
Example script to run the functions in algorithm_functions/ and calculate the producibility metric (PM)