Metabolic Models Python Packages

cobra

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

71K 575 234

micom

Python package to study microbial communities using metabolic modeling.

3K 133 23

memote

memote – the genome-scale metabolic model test suite

3K 148 33

metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

2K 74 6

psamm

Curation and analysis of metabolic models

1K 36 15

friend-or-foe

A collection of datasets obtained from metabolic modeling

1K 1 0

gba

Growth Balance Analysis for Python

1K 1 1

wildkcat

Extract, Retrieve and Predict kcat values for a metabolic model

991 8 0

microberx

MicrobeRX is A tool for enzymatic reaction-based metabolite prediction in the gut microbiome.

799 17 4

commmodelpy

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

754 3 0

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

631 17 8

efmlrs

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

581 6 1

q2-micom

A Qiime plugin for MICOM.

578 10 6

bofdat

Package to generate biomass objective function stoichiometric coefficients from experimental data

463 27 8

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!

451 68 18