11 results found Sort:

opencobra
cobrapy opencobra
218
474
gpl-2.0
37
COBRApy is a package for constraint-based modeling of metabolic networks.
flux sbml cobra python modeling metabolism sbml-model cell-design biochemistry bioinformatics sbml-simulation systems-biology metabolic-models metabolic-network strain-engineering computational-biology
Created 2012-11-02
2,741 commits to devel branch, last one 23 days ago
opencobra
cobratoolbox opencobra
319
254
other
33
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
cobra tutorial gap-filling metabolomics cobra-toolbox reconstruction transcriptomics human-metabolism metabolic-models strain-engineering microbiome-analysis metabolic-engineering omics-data-integration metabolic-reconstruction constraint-based-modeling
Created 2012-11-02
9,302 commits to master branch, last one about a month ago
franciscozorrilla
metaGEM franciscozorrilla
42
208
mit
5
: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
mags snakemake metabolism microbiome metagenomics bioinformatics gut-microbiome systems-biology metabolic-models microbial-ecology metabolic-modeling computational-biology flux-balance-analysis genome-scale-metabolic-model metagenome-assembled-genomes
Created 2018-06-14
669 commits to master branch, last one 4 months ago
jotech
gapseq jotech
32
164
gpl-3.0
10
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
r cobra curation gap-filling metabolic-models metabolic-pathways metabolic-reconstruction
Created 2017-11-01
1,460 commits to master branch, last one 16 days ago
opencobra
memote opencobra
28
129
apache-2.0
20
memote – the genome-scale metabolic model test suite
sbml cobra unit-testing standardization metabolic-models metabolic-reconstruction
Created 2016-05-13
893 commits to develop branch, last one 11 months ago
SysBioChalmers
RAVEN SysBioChalmers
54
104
other
13
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
sysbio gap-filling systems-biology human-metabolism metabolic-models genome-scale-models metabolic-engineering metabolic-reconstruction constraint-based-modeling
Created 2016-04-05
1,973 commits to main branch, last one 6 hours ago
SysBioChalmers
yeast-GEM SysBioChalmers
46
97
cc-by-4.0
18
The consensus GEM for Saccharomyces cerevisiae
yeast matlab python biology consensus standard-gem hacktoberfest reconstruction systems-biology metabolic-models genome-scale-models saccharomyces-cerevisiae
Created 2016-02-29
1,013 commits to main branch, last one 28 days ago
micom-dev
micom micom-dev
18
94
apache-2.0
5
Python package to study microbial communities using metabolic modeling.
flux cobra python cobrapy modeling community microbiome microbiota biochemistry hacktoberfest systems-biology metabolic-models
Created 2017-02-14
813 commits to main branch, last one 10 days ago
johon-lituobang
MM johon-lituobang
15
61
unknown
9
Infer metabolic directions from moment differences of mass-weighted intensity distributions
moment moments annotations mass-spectra metabolomics mass-spectrum metabolic-models mass-spectrometry metabolic-network metabolic-networks metabolic-pathways metabolic-engineering mass-spectrometry-data metabolic-flux-analysis
Created 2023-11-25
23 commits to main branch, last one 10 months ago
AuReMe
metage2metabo AuReMe
7
54
lgpl-3.0
6
From annotated genomes to metabolic screening in large scale microbiotas
bioinformatics metabolic-models bioinformatics-pipeline
Created 2019-03-14
562 commits to main branch, last one 4 months ago
cnapy-org
CNApy cnapy-org
7
47
apache-2.0
3
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, ...
fba fva sbml cobra bioinformatics systems-biology flux-variability metabolic-models metabolic-networks computational-biology flux-balance-analysis metabolic-engineering constraint-programming stoichiometric-modeling metabolic-reconstruction constraint-based-analysis constraint-based-modeling constraint-based-reconstruction
Created 2019-11-15
777 commits to master branch, last one 24 days ago