The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

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

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

memote – the genome-scale metabolic model test suite

Ⓜ️ Metabolic network completion

A Reference Pathways Mapper for turning metagenomic functional profiles into pathway/module profiles.

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

Genome-scale model of Yarrowia lipolytica.

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!

KEGG Module Evaluation Tool

An R interface to the omixer-rpm for turning metagenomic functional profiles into pathway/module profiles

A manually curated database of human gut metabolic modules.

Genome-scale metabolic model of Methylococcus capsulatus.

Genome-scale metabolic model of Rhodotorula toruloides

epigenome scale metabolic modeling for cancer metabolism

CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)

Metabolic pathway inference using non-negative matrix factorization with community detection

Tool for the reconstruction of context-specific metabolic models based on omics data from several sources

Diversity-based enumeration of optimal context-specific metabolic networks

Utility to simplify obtaining information from genome-scale models as well as their manipulation. This implementation is available only for working with COBRApy.