The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
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Updated
Jul 31, 2024 - MATLAB
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.
mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models
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.
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
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