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

The consensus GEM for Saccharomyces cerevisiae

The generic genome-scale metabolic model of Homo sapiens

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.

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

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

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.

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

Collection of scripts to collect data from databases such as BRENDA, BiGG, and the chemical translation service, and update a model of CHO-K1 growth.