Flux Balance Analysis Python Packages

biosimulators-cobrapy

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

cellmetpro

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

biosimulators-cbmpy

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

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!

miom

Mixed Integer Optimization for Metabolism

biosimulations-bigg

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

pymcadre

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

contrabass

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

pipegem

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

pymgpipe

Python implementation of mgpipe

parmmosahn

PaRMMoSaHN - Pangenome Reference-based Metabolic Modelling by Saving Homolog Networks

fastsl

Python implementation of FastSL