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

The generic genome-scale metabolic model of Homo sapiens

The consensus GEM for Saccharomyces cerevisiae

H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)

SMETANA: a tool to analyse interactions in microbial communities

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

EMBL GEMs: A collection of GEnome-scale Models for bacterial species

Genome-scale metabolic model of Methylococcus capsulatus.

mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models

Supplementary data for co-occurrence manuscript

A container for all enzyme constrained models created by GECKO.

Genome-scale model of Yarrowia lipolytica.

Genome scale metabolic models in SBML format

TRIMER is a package for building integrated metabolic–regulatory models base on Bayesian network. TRIMER can be used for knockout phenotype prediction and knock flux prediction.

Designing microbial communities

DeltaFBA is a set of MATLAB functions that employs constraint-based modeling, in combination with differential gene expression data, to evaluate changes in the intracellular flux distribution between two conditions.

Genome-scale model of Streptomyces coelicolor.

COMMIT: Community-dependent gap-filling considering metabolite leakage

IgemRNA is an open access toolbox for transcriptome data statistical and biochemical network topology-based analysis. IgemRNA was developed in the MATLAB environment in order to take advantage of the up-to-date and most commonly distributed GSM modelling tool Cobra Toolbox 3.0 and spreadsheet file capabilities.

Trim, extract, and convert GEMs