cobrapy

Python package to study microbial communities using metabolic modeling.

A Python framework for structural systems biology

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)

Python package for building and analyzing models using ModelSEED

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

Reaction Inclusion by Parsimony and Transcript Distribution

Constraint-based modeling of metabolism using Mixed Integer Optimization

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

Machine learning pipeline for genome-scale metabolic engineering and intervention ranking in E. coli using COBRApy and FBA.

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

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

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

diversity-based enumeration of optimal context-specific metabolic networks using the cobrapy library

A Mars-optimal prokaryotic genome assembled from verified Earth genes: no genome survives bare Mars, but three non-living additions flip the verdict

iPfal17 genome-scale metabolic reconstruction; lipid metabolism curation

COBRApy JSON reconstruction of CHOmpact — a reduced metabolic model of CHO cells with IgG product quality outputs (Jiménez del Val et al. 2023).