metabolic-models

There are 6 repositories under metabolic-models topic.

opencobra / cobrapy
COBRApy is a package for constraint-based modeling of metabolic networks.
modeling metabolic-models metabolic-network metabolism flux bioinformatics biochemistry computational-biology systems-biology cell-design strain-engineering python cobra sbml sbml-model sbml-simulation
Language:Python 442
opencobra / cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
cobra-toolbox reconstruction tutorial metabolic-models metabolic-reconstruction metabolic-engineering gap-filling strain-engineering omics-data-integration metabolomics transcriptomics cobra constraint-based-modeling human-metabolism microbiome-analysis
Language:MATLAB 237
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
metagenomics computational-biology metabolic-models gut-microbiome snakemake metagenome-assembled-genomes mags metabolism bioinformatics flux-balance-analysis genome-scale-metabolic-model metabolic-modeling microbial-ecology microbiome systems-biology
Language:Python 165
jotech / gapseq
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
metabolic-models metabolic-reconstruction metabolic-pathways curation gap-filling cobra r
Language:R 143
opencobra / memote
memote – the genome-scale metabolic model test suite
metabolic-models metabolic-reconstruction standardization unit-testing sbml cobra
Language:HTML 122
SysBioChalmers / RAVEN
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
genome-scale-models constraint-based-modeling metabolic-reconstruction gap-filling human-metabolism metabolic-models metabolic-engineering systems-biology sysbio
Language:MATLAB 97
SysBioChalmers / yeast-GEM
The consensus GEM for Saccharomyces cerevisiae
genome-scale-models yeast systems-biology hacktoberfest saccharomyces-cerevisiae matlab biology reconstruction consensus python metabolic-models standard-gem
Language:MATLAB 87
micom-dev / micom
Python package to study microbial communities using metabolic modeling.
microbiota cobrapy modeling metabolic-models flux biochemistry systems-biology microbiome python cobra community hacktoberfest
Language:Python 78
tubanlee / MM
Infer metabolic directions from moment differences of mass-weighted intensity distributions
annotations mass-spectra mass-spectrometry mass-spectrometry-data mass-spectrum metabolic-flux-analysis metabolic-models metabolic-network metabolic-networks metabolic-pathways metabolic-engineering metabolomics moment moments
Language:R 59
cdanielmachado / smetana
SMETANA: a tool to analyse interactions in microbial communities
microbial-communities genome-scale-models metabolic-models
Language:Python 53
AuReMe / metage2metabo
From annotated genomes to metabolic screening in large scale microbiotas
bioinformatics bioinformatics-pipeline metabolic-models
Language:Jupyter Notebook 44
CNApy
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!
metabolic-models constraint-programming bioinformatics flux-balance-analysis sbml systems-biology computational-biology cobra stoichiometric-modeling constraint-based-modeling constraint-based-analysis metabolic-reconstruction constraint-based-reconstruction metabolic-networks flux-variability metabolic-engineering fba fva
Language:Python 41
zhanglab / psamm
Curation and analysis of metabolic models
python metabolic-models bioinformatics metabolic-network
Language:Python 34
SBRG / cobrame
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
cobra python metabolic-models systems-biology cobrapy gene-expression metabolism computational-biology
Language:Python 33
jclachance / BOFdat
Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data
genome-scale-models biomass-objective-function metabolic-models metabolic-flux-analysis machine-learning
Language:Jupyter Notebook 26
Gibbons-Lab / isb_course_2022
Materials and presentation for the 2022 ISB Microbiome course.
microbiome 16s-seq analysis metabolic-models microbial-ecology qiime2 sequencing systems-biology
Language:Jupyter Notebook 23
Matteopaluh / KEMET
KEGG Module Evaluation Tool
kegg kegg-modules metabolic-models metabolic-reconstruction gap-filling genome-scale-metabolic-model gem
Language:Python 22
resendislab / corda
An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al
metabolism reconstruction cobra cobrapy modeling metabolic-models flux biochemistry systems-biology genome bioinformatics metabolic-network metabolic-reconstruction
Language:Python 21
m-jahn / fluctuator
R package to Import and Modify SVG (XML) Graphic Files
r-package svg svg-images network metabolism metabolic-models omics-data
Language:R 20
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.
gut microbiome metabolic-models agora
19
MetabolicAtlas
MetabolicAtlas / MetabolicAtlas
Open source genome-scale metabolic models of human and model animals
metabolism metabolic-models metabolic-network atlas metabolic-atlas nbisweden
Language:Vue 18
opencobra / COBRA.tutorials
Repository of tutorials for The COBRA Toolbox
tutorials cobra cobratoolbox systemsbiology reconstruction metabolic-models constraint-based-modeling
Language:MATLAB 18
Gibbons-Lab / isb_course_2023
Materials and presentation for the 2023 ISB Microbiome course.
16s-seq analysis metabolic-models microbial-ecology microbiome pathogens qiime2 sequencing systems-biology hacktoberfest
Language:Jupyter Notebook 17
mauriceling / advancesyntoolkit
Toolkit for Modelling and Simulation of Gene Expressions and Metabolism
modeling-tool simulation-toolkit python3 metabolic-models metabolic-pathways systems-biology synthetic-biology computational-biology metabolic-engineering bioinformatics
Language:Python 12
sirno / misosoup
Minimal Supplying Community Search with constraint-based optimization methods.
metabolic-models microbial-communities constraint-based community
Language:Python 12
klamt-lab / autopacmen
Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method
systems-biology computational-biology metabolic-models bioinformatics
Language:HTML 11
rcolpo / pgp_reconstruction
Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models
bioinformatics community-simulations computational-biology fba flux-balance-analysis genome-scale-metabolic-model genome-scale-model metabolic-modeling metabolic-models metabolism microbial-communities
Language:Python 11
ChristianLieven / memote-m-capsulatus
Genome-scale metabolic model of Methylococcus capsulatus.
genome-scale-models systems-biology methylococcus methanotrophy c1 metabolism constraint-based-modeling metabolic-models metabolic-reconstruction
Language:HTML 10
micom-dev / q2-micom
A Qiime plugin for MICOM.
qiime2 metabolic-models 16s-seq hacktoberfest
Language:Python 10
YosefLab / compassR
An R library for conducting analyses on COMPASS data.
computational-biology metabolic-models scrna-seq compass postprocessing r umap statistical-tests
Language:R 10
Micromeda / pygenprop
A python library for programmatic usage of EBI InterPro Genome Properties.
genomics genome-properties metabolism metabolic-models pathway-analysis
Language:Python 9
modsim / FluxML
A Universal Modeling Language for Metabolic Flux Analysis
metabolic-engineering metabolic-models metabolic-network modeling-language specification-language metabolic-flux-analysis 13c-mfa
Language:C++ 9
SysBioChalmers / Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.
yarrowia-lipolytica metabolic-engineering metabolic-reconstruction systems-biology stoichiometric-reactions omics-data-integration constraint-based-modeling metabolic-models metabolic-network genome-scale-models
Language:MATLAB 8
GRONINGEN-MICROBIOME-CENTRE / MicrobeRX
MicrobeRX
cheminformatics computational-biology drug-design enzymes gut-microbiome metabolic-models metabolite metabolite-identification metabolite-prediction microbiome
Language:Python 7
SysBioChalmers / ecFactory
A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism
cell-factory enzyme-constraints metabolic-models microbes
Language:MATLAB 7
korem-lab / pymgpipe
Python implementation of mgpipe
cobra metabolic-models metabolic-reconstruction microbiome modeling systems-biology flux-balance-analysis mgpipe microbiome-modeling-toolbox
Language:JetBrains MPS 6