Repositories list

• cobratoolbox

  Public
  The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

  tutorialmetabolomicsreconstruction+ 12

  tutorialmetabolomicsreconstructiontranscriptomicscobrametabolic-modelsstrain-engineeringmetabolic-reconstructionconstraint-based-modelingmicrobiome-analysis+ 5

  MATLAB

  •

  Other

  •336336 forks•282282 stars•6161 issues•55 pull requests•Updated Apr 24, 2026Apr 24, 2026

• reconstructor

  Public
  Open source tool for biochemical network reconstruction

  Java

  •

  GNU General Public License v3.0

  •22 forks•33 stars•00 issues•00 pull requests•Updated Apr 24, 2026Apr 24, 2026

• COBRA.tutorials

  Public
  Repository of tutorials for The COBRA Toolbox

  tutorialsreconstructionsystemsbiology+ 4

  tutorialsreconstructionsystemsbiologycobrametabolic-modelsconstraint-based-modelingcobratoolbox

  MATLAB

  •6161 forks•2525 stars•33 issues•11 pull request•Updated Apr 20, 2026Apr 20, 2026

• cobrapy

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

  pythonfluxbioinformatics+ 13

  pythonfluxbioinformaticsmodelingsystems-biologycomputational-biologybiochemistrymetabolismcobrametabolic-models+ 6

  Python

  •

  GNU General Public License v2.0

  •234234 forks•559559 stars•7979 issues•1919 pull requests•Updated Apr 8, 2026Apr 8, 2026

• swiglpk

  Public
  Simple swig bindings for the GNU Linear Programming Kit

  pythonoptimizationsymbolic+ 2

  pythonoptimizationsymbolicscientific-computingmodeling-language

  Python

  •

  GNU General Public License v3.0

  •1010 forks•3030 stars•22 issues•22 pull requests•Updated Apr 2, 2026Apr 2, 2026

• cobrapy-website

  Public
  HTML

  •

  GNU Lesser General Public License v3.0

  •77 forks•11 star•00 issues•11 pull request•Updated Mar 26, 2026Mar 26, 2026

• optlang

  Public
  optlang - sympy based mathematical programming language

  Python

  •

  Apache License 2.0

  •5252 forks•268268 stars•3131 issues•11 pull request•Updated Mar 23, 2026Mar 23, 2026

• Medusa

  Public
  Analysis of ensembles of metabolic network reconstructions

  Python

  •

  MIT License

  •99 forks•2121 stars•2828 issues•2121 pull requests•Updated Feb 9, 2026Feb 9, 2026

• COBRA.binary

  Public
  Linux, Windows and Mac binaries maintained by the constraint-based reconstruction and analysis community

  MATLAB

  •77 forks•11 star•11 issue•00 pull requests•Updated Feb 8, 2026Feb 8, 2026

• sphinx_cobra_theme

  Public
  HTML

  •

  MIT License

  •44 forks•00 stars•00 issues•00 pull requests•Updated Dec 1, 2025Dec 1, 2025

• COBRA.papers

  Public
  Repository for scripts related to reproducing the results of an individual publication

  MATLAB

  •1616 forks•1010 stars•11 issue•00 pull requests•Updated Nov 14, 2025Nov 14, 2025

• escher

  Public
  JavaScript

  •

  Other

  •00 forks•11 star•22 issues•00 pull requests•Updated Oct 27, 2025Oct 27, 2025

• memote

  Public
  memote – the genome-scale metabolic model test suite

  unit-testingstandardizationcobra+ 3

  unit-testingstandardizationcobrametabolic-modelssbmlmetabolic-reconstruction

  HTML

  •

  Apache License 2.0

  •3333 forks•146146 stars•133133 issues•22 pull requests•Updated Aug 14, 2025Aug 14, 2025

• jeweler

  Public
  Test and grade genome-scale metabolic models (GEMs).

  gemnextflowcobra+ 5

  gemnextflowcobrasbmlsbml-modelnf-coregsmmmemote

  Nextflow

  •

  Apache License 2.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Aug 14, 2025Aug 14, 2025

• MASSef

  Public
  Mathematica

  •11 fork•00 stars•1616 issues•00 pull requests•Updated Nov 9, 2024Nov 9, 2024

• COBRA.models

  Public
  Set of models used for testing COBRA code in continuous integration environments

  Julia

  •33 forks•00 stars•00 issues•11 pull request•Updated Nov 7, 2024Nov 7, 2024

• MATLAB.devTools

  Public
  MATLAB Development Tools

  MATLAB

  •

  GNU General Public License v3.0

  •3535 forks•2828 stars•22 issues•00 pull requests•Updated Sep 27, 2024Sep 27, 2024

• cobrapy-scope

  Public
  Evaluation of a user survey from 2020 on what scope of methods is desirable in COBRApy.

  HTML

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 19, 2024May 19, 2024

• memote-docker

  Public
  Easily use the memote command line interface from a docker container.

  docker-containercobrasbml+ 3

  docker-containercobrasbmlsbml-modelmemotememote-command

  Shell

  •

  Apache License 2.0

  •22 forks•33 stars•00 issues•22 pull requests•Updated Nov 21, 2023Nov 21, 2023

• cookiecutter-memote

  Public
  A cookiecuttter template for memote model repositories

  Python

  •

  MIT License

  •44 forks•22 stars•33 issues•00 pull requests•Updated Sep 18, 2023Sep 18, 2023

• COBRA.jl

  Public
  High-level, high-performance, constraint-based reconstruction and analysis in Julia

  analysishigh-performancejulia+ 5

  analysishigh-performancejuliacobralarge-scalehigh-levelconstraint-based-modelinghuge-scale

  Julia

  •

  Other

  •3232 forks•6363 stars•77 issues•00 pull requests•Updated Apr 26, 2023Apr 26, 2023

• ctf

  Public
  Chemical table files for constraint-based modelling

  GNU General Public License v3.0

  •33 forks•33 stars•11 issue•00 pull requests•Updated Feb 18, 2023Feb 18, 2023

• driven

  Public
  Data-Driven Constraint-based analysis

  Python

  •

  Apache License 2.0

  •1010 forks•1212 stars•66 issues•22 pull requests•Updated Nov 4, 2022Nov 4, 2022

• cookiecutter-python-package

  Public
  Extensive cookiecutter template for openCOBRA Python packages.

  Python

  •

  Apache License 2.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jun 3, 2022Jun 3, 2022

• cobra-component-models

  Public
  Provide SQLAlchemy ORM and pydantic data models for SQL storage and serialization of COBRA components such as reactions, compounds, and compartments.

  serializationsqlalchemyorm+ 2

  serializationsqlalchemyormcobrapydantic

  Python

  •

  Apache License 2.0

  •00 forks•33 stars•00 issues•00 pull requests•Updated Oct 6, 2021Oct 6, 2021

• opencobra.github.io

  Public
  Official openCOBRA website

  CSS

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jun 22, 2021Jun 22, 2021

• artenolis

  Public
  Automated Reproducibility and Testing Environment for Licensed Software

  automationcontinuous-integrationcomputational-biology+ 4

  automationcontinuous-integrationcomputational-biologytest-driven-developmentsoftware-qualitycobraartenolis

  Java

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jun 15, 2021Jun 15, 2021

• kb_memote

  Public
  Python

  •

  MIT License

  •22 forks•11 star•00 issues•00 pull requests•Updated Dec 3, 2019Dec 3, 2019

• COBRA.java

  Public
  Constraint-based reconstruction and analysis via Java

  11 fork•00 stars•00 issues•00 pull requests•Updated Mar 28, 2019Mar 28, 2019

• memote-webservice

  Public archive
  Run memote in a microservice with a frontend that allows you to upload and test models.

  Python

  •

  Apache License 2.0

  •33 forks•00 stars•11 issue•00 pull requests•Updated Jan 7, 2019Jan 7, 2019