Metabolic Models Python Packages

cobra

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

memote

memote – the genome-scale metabolic model test suite

micom

Python package to study microbial communities using metabolic modeling.

metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

gba

Growth Balance Analysis for Python

wildkcat

Extract, Retrieve and Predict kcat values for a metabolic model

pipegem

Python package for integrating omics data with genome-scale metabolic models and running comparative constraint-based metabolic analysis.

psamm

Curation and analysis of metabolic models

microberx

MicrobeRX

q2-micom

A Qiime plugin for MICOM.

efmlrs

Python package and workflow for EFM calculation via (mp)lrs and efmtool

bofdat

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

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!

smetana

SMETANA: a tool to analyse interactions in microbial communities

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

findcpcore

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

corda

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

misosoup

Minimal Supplying Community Search with constraint-based optimization methods.

friend-or-foe

A collection of datasets obtained from metabolic modeling

findcpcli

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

contrabass

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

pymgpipe

Python implementation of mgpipe

dimedbpy

Python wrapper for the DIMEdb REST API.

pygenprop

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