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opencobra
cobra

COBRApy is a package for constraint-based modeling of metabolic networks.

62K 560 234
micom-dev
micom

Microbial community modeling based on cobrapy.

4K 127 23
opencobra
memote

memote – the genome-scale metabolic model test suite

4K 146 33
aureme
metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

2K 71 7
h-escoffier
wildkcat

Extract, Retrieve and Predict kcat values for a metabolic model

2K 6 0
zhanglab
psamm

Curation and analysis of metabolic models

1K 36 15
micom-dev
q2-micom

A Qiime plugin for MICOM.

863 10 6
GRONINGEN-MICROBIOME-CENTRE
microberx

MicrobeRX

807 17 4
cdiener
corda

Genome-scale model construction with CORDA

626 25 8
BeeAnka
efmlrs

Extracts EFMs from result file of mplrs and decompresses EFMs from efmtool and mplrs results that have been compressed with EFMlrs

607 6 1
klamt-lab
autopacmen-paulocracy

Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method. Also check out its spiritual successor, COBRA-k: https://github.com/klamt-lab/COBRA-k

571 17 8
jclachance
bofdat

Package to generate biomass objective function stoichiometric coefficients from experimental data

552 27 8
cnapy-org
cnapy

An integrated visual environment for metabolic modeling 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!

542 65 18
sirno
misosoup

Minimal Supplying Community Search with constraint-based optimization methods.

532 16 1
findCP
findcpcore

findCP core package

520 1 0
cdanielmachado
smetana

SMETANA: a tool to analyse interactions in microbial communities

449 70 14
findCP
findcpcli

findCP CLI package - find ChokePoint reactions in genome-scale metabolic models

357 3 0
charlesrocabert
gba

Growth Balance Analysis for Python

314 1 1
ARB-Lab
commmodelpy

Create stoichiometric metabolic network models of single-species or multi-species communities

262 3 0
Micromeda
pygenprop

A python library for programmatic usage of EBI InterPro Genome Properties.

238 9 5
korem-lab
pymgpipe

Python implementation of mgpipe

229 7 1
openCONTRABASS
contrabass

Constraint-based model vulnerabilities analysis - Python analysis tool http://contrabass.unizar.es

191 3 1
AberystwythSystemsBiology
dimedbpy

Python wrapper for DIMEdbs REST API.

156 5 0
qwerty239qwe
pipegem

This is a package for visualizing and analyzing multiple metabolic models. It also allow users to integrate omic data, metabolic tasks, and medium data with genome-scale metabolic models (GEMs).

142 0 2
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