Metabolic Models Python Packages

cobra

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

micom

Microbial community modeling based on cobrapy.

memote

memote – the genome-scale metabolic model test suite

metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

wildkcat

Extract, Retrieve and Predict kcat values for a metabolic model

psamm

Curation and analysis of metabolic models

q2-micom

A Qiime plugin for MICOM.

microberx

MicrobeRX

efmlrs

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

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

misosoup

Minimal Supplying Community Search with constraint-based optimization methods.

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!

corda

Genome-scale model construction with CORDA

bofdat

Package to generate biomass objective function stoichiometric coefficients from experimental data

findcpcore

findCP core package

smetana

SMETANA: a tool to analyse interactions in microbial communities

findcpcli

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

gba

Growth Balance Analysis for Python

commmodelpy

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

pymgpipe

Python implementation of mgpipe

pygenprop

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

dimedbpy

Python wrapper for DIMEdbs REST API.

contrabass

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

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).