The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

memote – the genome-scale metabolic model test suite

The consensus GEM for Saccharomyces cerevisiae

The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Python package to study microbial communities using metabolic modeling.

Curation and analysis of metabolic models

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data

A Snakemake pipeline for the generation of MAGs, reconstruction of GEMs, and simulation of cross-feeding interactions within microbial communities from lab cultures, human gut, ocean, plant-associated, and bulk soil microbiomes

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

SMETANA: a tool to analyse interactions in microbial communities

From annotated genomes to metabolic screening in large scale microbiotas

The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.

Repository of tutorials for The COBRA Toolbox

Metabolic Atlas web app

A python library for programmatic usage of EBI InterPro Genome Properties.

A Universal Modeling Language for Metabolic Flux Analysis

Genome-scale metabolic model of Methylococcus capsulatus.

Toolkit for Modelling and Simulation of Gene Expressions and Metabolism

Dynamically load balanced FVA through a hybrid MPI/OpenMP.

Genome-scale model of Yarrowia lipolytica.

Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method

epigenome scale metabolic modeling for cancer metabolism

An R library for conducting analyses on COMPASS data.

An R package to identify orphan metabolites and evaluate the mass and charge balance of stoichiometric reactions. The package also includes functions to characterize and write models in TSV and SBML formats, extract all reactants, products, metabolite names and compartments from a metabolic reconstruction.

An R package to incorporate in a continuous way the gene-expression data as FBA flux boundaries in a metabolic model. Also, functions to calculate and plot the differences between model fluxes in different metabolic scenarios was included. This is an implementation of the algorithm described by Lee et al. (2012) in DOI: 10.1186/1752-0509-6-73.

A desktop app, web app and CLI to operate and find vulnerabilities in SBML metabolic networks.

Python wrapper for the DIMEdb REST API.