genome-scale-models
There are 44 repositories under genome-scale-models topic.
SysBioChalmers/RAVEN
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
SysBioChalmers/Human-GEM
The generic genome-scale metabolic model of Homo sapiens
SysBioChalmers/yeast-GEM
The consensus GEM for Saccharomyces cerevisiae
kishwarshafin/helen
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
cdanielmachado/smetana
SMETANA: a tool to analyse interactions in microbial communities
jclachance/BOFdat
Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data
cdanielmachado/embl_gems
EMBL GEMs: A collection of GEnome-scale Models for bacterial species
ChristianLieven/memote-m-capsulatus
Genome-scale metabolic model of Methylococcus capsulatus.
lobolab/mergem
mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models
cdanielmachado/cooccurrence
Supplementary data for co-occurrence manuscript
SysBioChalmers/ecModels
A container for all enzyme constrained models created by GECKO.
m-jahn/genome-scale-models
Genome scale metabolic models in SBML format
SysBioChalmers/Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.
CABSEL/DeltaFBA
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.
cdanielmachado/designmc
Designing microbial communities
niupuhua1234/TRIMER
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.
BigDataInSilicoBiologyGroup/IgemRNA
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.
LiLabTsinghua/Yeast-MetaTwin
The metabolic twin model of yeast
pwendering/COMMIT
COMMIT: Community-dependent gap-filling considering metabolite leakage
SysBioChalmers/Streptomyces_coelicolor-GEM
Genome-scale model of Streptomyces coelicolor.
binfalse/GEMtractor
Trim, extract, and convert GEMs
dcoukos/CHO_model_updates
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.
franciscozorrilla/Chalmers-iGEM2018
COM-dFBA is a MATLAB based COMmunity Dynamic Flux Balance Analysis framework developed by the Chalmers iGEM 2018 team. For this work, we were nominated for best modeling at the Giant Jamboree.
iAMB-RWTH-Aachen/Opol-GSMM
Genome scale metabolic model for Ogataea polymorpha NCYC495.
SysBioChalmers/EnzymeConstrained_humanModels
Collection of scripts for enhancing humanGEM based models with kinetic and proteomics constraints and specialized simulation utilities.
SysBioInra/rbatools
Programming interface to resource allocation modelling with the Resource Balance Analysis (RBA) method. This is version 1.0.3
SystemsBioinformatics/cbmpy-metadraft
CBMPy Metadraft: a flexible and extensible genome-scale model reconstruction tool
computer-aided-biotech/iMN22HE
Methanoperedens nitroreducens genome-scale metabolic model.
sriram-lab/MetOncoFit
Common biochemical and topological attributes of metabolic genes recurrently dysregulated in tumors.
SysBioChalmers/Kluyveromyces_marxianus-GEM
The consensus GEM for Kluyveromyces marxianus
SysBioChalmers/overflow
Supplementary code and results from doi:10.1101/2020.02.20.957662
SysBioChalmers/pcLactis
Proteome-constrained model of Lactococcus lactis
SysBioChalmers/rhto-GEM
Genome-scale metabolic model of Rhodotorula toruloides
sysbiomics/Cordyceps_militaris-GEM
Genome-scale metabolic model of Cordyceps militaris