Metabolic Models Python Packages

cobra

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

micom

Python package to study microbial communities using metabolic modeling.

memote

memote – the genome-scale metabolic model test suite

metage2metabo

Automatic reconstruction of draft metabolic networks with Pathway Tools and graph-based metabolic analysis

wildkcat

Extract, Retrieve and Predict kcat values for a metabolic model

microberx

MicrobeRX

autopacmen-paulocracy

The AutoPACMEN package

psamm

Curation and analysis of metabolic models

commmodelpy

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

corda

Genome-scale model construction with CORDA

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!

bofdat

Generate biomass objective function stoichiometric coefficients for genome-scale models from experimental data

efmlrs

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

q2-micom

A Qiime plugin for MICOM.

pipegem

Processing and integrating data with genome-scale metabolic models (GEM)

findcpcore

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

misosoup

No description available

smetana

SMETANA: a tool to analyse interactions in microbial communities

findcpcli

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

contrabass

Constraint-based model vulnerabilities analysis

gba

Growth Balance Analysis for Python

dimedbpy

Python wrapper for DIMEdbs REST API.

pymgpipe

Python implementation of mgpipe

pygenprop

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