metabolic-models
There are 109 repositories under metabolic-models topic.
opencobra/cobrapy
COBRApy is a package for constraint-based modeling of metabolic networks.
opencobra/cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
franciscozorrilla/metaGEM
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
jotech/gapseq
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
opencobra/memote
memote – the genome-scale metabolic model test suite
SysBioChalmers/RAVEN
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
SysBioChalmers/yeast-GEM
The consensus GEM for Saccharomyces cerevisiae
micom-dev/micom
Python package to study microbial communities using metabolic modeling.
tubanlee/MM
Infer metabolic directions from moment differences of mass-weighted intensity distributions
cdanielmachado/smetana
SMETANA: a tool to analyse interactions in microbial communities
AuReMe/metage2metabo
From annotated genomes to metabolic screening in large scale microbiotas
cnapy-org/CNApy
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!
zhanglab/psamm
Curation and analysis of metabolic models
SBRG/cobrame
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Gibbons-Lab/isb_course_2022
Materials and presentation for the 2022 ISB Microbiome course.
jclachance/BOFdat
Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data
Matteopaluh/KEMET
KEGG Module Evaluation Tool
resendislab/corda
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
Gibbons-Lab/isb_course_2023
Materials and presentation for the 2023 ISB Microbiome course.
m-jahn/fluctuator
R package to Import and Modify SVG (XML) Graphic Files
MetabolicAtlas/MetabolicAtlas
Open source genome-scale metabolic models of human and model animals
VirtualMetabolicHuman/AGORA
The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.
opencobra/COBRA.tutorials
Repository of tutorials for The COBRA Toolbox
klamt-lab/autopacmen
Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method
mauriceling/advancesyntoolkit
Toolkit for Modelling and Simulation of Gene Expressions and Metabolism
sirno/misosoup
Minimal Supplying Community Search with constraint-based optimization methods.
YosefLab/compassR
An R library for conducting analyses on COMPASS data.
ChristianLieven/memote-m-capsulatus
Genome-scale metabolic model of Methylococcus capsulatus.
rcolpo/pgp_reconstruction
Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models
micom-dev/q2-micom
A Qiime plugin for MICOM.
COBREXA/COBREXA.jl
COnstraint Based Reconstruction and EXascale Analysis (in Julia)
Micromeda/pygenprop
A python library for programmatic usage of EBI InterPro Genome Properties.
modsim/FluxML
A Universal Modeling Language for Metabolic Flux Analysis
SysBioChalmers/Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.
korem-lab/pymgpipe
Python implementation of mgpipe