Genome-scale metabolic models (GSMMs) are comprehensive representations of an organism’s metabolic network, capturing all known metabolic reactions and their associated genes, enzymes, and metabolites. These models provide a powerful framework for simulating cellular metabolism, predicting growth under different conditions, and understanding metabolic interactions within microbial communities.

This repository leverages GSMMs to study E. coli metabolism, analyze metabolic diversity within gut microbiota using AGORA models, and construct community models to explore microbial interactions.

Contents

1. E. coli Model Analysis

   Model Inspection

   Model Simulation

   Model Pertubation

2. Agora Models Analysis

   Model Clustering

   Community Modeling