A Python framework for structural systems biology

Python package to study microbial communities using metabolic modeling.

StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

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

Python package for building and analyzing models using ModelSEED

Constraint-based modeling of metabolism using Mixed Integer Optimization

Reaction Inclusion by Parsimony and Transcript Distribution

Multivariate thermodynamics-based metabolic flux analysis in Python.

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

Data and tools necessary to construct iJL1678b-ME, a genome-scale model of E. coli K-12 MG1655 metabolism and expression

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

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

Adjusting for false discoveries in constraint- and sampling-based differential metabolic flux analysis

Multi-scale model of Metabolism In Cellular Systems

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

ECMproject is a standalone python program, which enumerates Elementary Conversion Modes (ECMs) of metabolic models.

Bioinformatics project analyzing cancer metabolism using computational modeling and analysis. The project was awarded the GIDI-UP: Summer Research Award and includes data, models, and scripts.

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

FBAhv: FBA analysis of host-virus metabolic model (read related publication at: https://www.life-science-alliance.org/content/4/1/e202000869)