COBRApy is a package for constraint-based modeling of metabolic networks.

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

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

memote – the genome-scale metabolic model test suite

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

The consensus GEM for Saccharomyces cerevisiae

Python package to study microbial communities using metabolic modeling.

Infer metabolic directions from moment differences of mass-weighted intensity distributions

SMETANA: a tool to analyse interactions in microbial communities

From annotated genomes to metabolic screening in large scale microbiotas

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

Curation and analysis of metabolic models

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

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

KEGG Module Evaluation Tool

Materials and presentation for the 2022 ISB Microbiome course.

Materials and presentation for the 2023 ISB Microbiome course.

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

Open source genome-scale metabolic models of human and model animals