The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

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.

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!

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

KEGG Module Evaluation Tool

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

A manually curated database of human gut metabolic modules.

Genome-scale metabolic model of Methylococcus capsulatus.

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

Ⓜ️ Metabolic network completion

Genome-scale model of Yarrowia lipolytica.

Python implementation of mgpipe

Diversity-based enumeration of optimal context-specific metabolic networks

epigenome scale metabolic modeling for cancer metabolism

Enzymatic Link Prediction

A pathologic file generator (PLFG) is implemented to assist and facilitate the curation progress of every computationally predicted pathway genome database (PGDB).

University of Cambridge Part III Systems Biology course, practical exercises for learning flux balance analysis

Chemical reaction balancing web service