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Metabolic Models Python Packages

Python packages with the GitHub topic metabolic-models. Sorted by relevance, with stars and monthly downloads.
opencobra
cobra

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

59K 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

1K 6 0
zhanglab
psamm

Curation and analysis of metabolic models

1K 36 15
micom-dev
q2-micom

A Qiime plugin for MICOM.

928 10 6
GRONINGEN-MICROBIOME-CENTRE
microberx

MicrobeRX

818 17 4
BeeAnka
efmlrs

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

558 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

551 17 8
sirno
misosoup

Minimal Supplying Community Search with constraint-based optimization methods.

539 16 1
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!

538 65 18
cdiener
corda

Genome-scale model construction with CORDA

527 25 8
jclachance
bofdat

Package to generate biomass objective function stoichiometric coefficients from experimental data

502 27 8
findCP
findcpcore

findCP core package

452 1 0
cdanielmachado
smetana

SMETANA: a tool to analyse interactions in microbial communities

441 70 14
findCP
findcpcli

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

324 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

300 3 0
korem-lab
pymgpipe

Python implementation of mgpipe

249 7 1
Micromeda
pygenprop

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

245 9 5
AberystwythSystemsBiology
dimedbpy

Python wrapper for DIMEdbs REST API.

194 5 0
openCONTRABASS
contrabass

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

171 3 1
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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