Flux Balance Analysis Python Packages

biosimulators-cobrapy

COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

pipegem

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

biosimulators-cbmpy

CBMPy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

miom

Constraint-based modeling of metabolism using Mixed Integer Optimization

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!

cellmetpro

Analyse cellular metabolic states of cells from scRNA-seq data using FBA and Genome-scale Metabolic Models

pymcadre

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

biosimulations-bigg

Command-line program and scheduled GitHub action for publishing the BiGG model repository to BioSimulations

contrabass

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

pymgpipe

Python implementation of mgpipe

fastsl

Python implementation of FastSL

parmmosahn

Species-agnostic pipeline that builds a pangenome-reference metabolic model and rapidly derives consistent, gap-filled strain-specific genome-scale models from bacterial genomes.