openCOBRA

All

36 repositories

COBRA.papers
Public
Repository for scripts related to reproducing the results of an individual publication
MATLAB
•16•9•1•0•Updated Nov 14, 2025Nov 14, 2025
cobratoolbox
Public
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
tutorial metabolomics reconstruction transcriptomics cobra metabolic-models strain-engineering metabolic-reconstruction constraint-based-modeling microbiome-analysis
MATLAB
•
Other
•333•270•58•2•Updated Nov 12, 2025Nov 12, 2025
reconstructor
Public
Open source tool for biochemical network reconstruction
Java
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GNU General Public License v3.0
•2•1•0•0•Updated Nov 10, 2025Nov 10, 2025
COBRA.tutorials
Public
Repository of tutorials for The COBRA Toolbox
tutorials reconstruction systemsbiology cobra metabolic-models constraint-based-modeling cobratoolbox
MATLAB
•57•23•3•0•Updated Nov 7, 2025Nov 7, 2025
sphinx_cobra_theme
Public
HTML
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MIT License
•4•0•0•0•Updated Nov 6, 2025Nov 6, 2025
swiglpk
Public
Simple swig bindings for the GNU Linear Programming Kit
python optimization symbolic scientific-computing modeling-language
Python
•
GNU General Public License v3.0
•10•29•2•2•Updated Nov 1, 2025Nov 1, 2025
cobrapy
Public
COBRApy is a package for constraint-based modeling of metabolic networks.
python flux bioinformatics modeling systems-biology computational-biology biochemistry metabolism cobra metabolic-models
Python
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GNU General Public License v2.0
•230•523•79•19•Updated Oct 29, 2025Oct 29, 2025
escher
Public
JavaScript
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Other
•0•0•2•0•Updated Oct 27, 2025Oct 27, 2025
Medusa
Public
Analysis of ensembles of metabolic network reconstructions
Python
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MIT License
•9•21•28•23•Updated Sep 26, 2025Sep 26, 2025
memote
Public
memote – the genome-scale metabolic model test suite
unit-testing standardization cobra metabolic-models sbml metabolic-reconstruction
HTML
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Apache License 2.0
•30•143•133•2•Updated Aug 14, 2025Aug 14, 2025
jeweler
Public
Test and grade genome-scale metabolic models (GEMs).
gem nextflow cobra sbml sbml-model nf-core gsmm memote
Nextflow
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Apache License 2.0
•0•1•0•0•Updated Aug 14, 2025Aug 14, 2025
optlang
Public
optlang - sympy based mathematical programming language
Python
•
Apache License 2.0
•52•265•31•1•Updated Jan 8, 2025Jan 8, 2025
MASSef
Public
Mathematica
•1•0•16•0•Updated Nov 9, 2024Nov 9, 2024
COBRA.models
Public
Set of models used for testing COBRA code in continuous integration environments
Julia
•3•0•0•1•Updated Nov 7, 2024Nov 7, 2024
MATLAB.devTools
Public
MATLAB Development Tools
MATLAB
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GNU General Public License v3.0
•35•28•2•0•Updated Sep 27, 2024Sep 27, 2024
cobrapy-website
Public
HTML
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GNU Lesser General Public License v3.0
•7•1•0•1•Updated Aug 22, 2024Aug 22, 2024
cobrapy-scope
Public
Evaluation of a user survey from 2020 on what scope of methods is desirable in COBRApy.
HTML
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Apache License 2.0
•0•0•0•0•Updated May 19, 2024May 19, 2024
memote-docker
Public
Easily use the memote command line interface from a docker container.
docker-container cobra sbml sbml-model memote memote-command
Shell
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Apache License 2.0
•2•3•0•2•Updated Nov 21, 2023Nov 21, 2023
cookiecutter-memote
Public
A cookiecuttter template for memote model repositories
Python
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MIT License
•4•2•3•0•Updated Sep 18, 2023Sep 18, 2023
COBRA.jl
Public
High-level, high-performance, constraint-based reconstruction and analysis in Julia
analysis high-performance julia cobra large-scale high-level constraint-based-modeling huge-scale
Julia
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Other
•32•62•7•0•Updated Apr 26, 2023Apr 26, 2023
ctf
Public
Chemical table files for constraint-based modelling
GNU General Public License v3.0
•3•3•1•0•Updated Feb 18, 2023Feb 18, 2023
driven
Public
Data-Driven Constraint-based analysis
Python
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Apache License 2.0
•10•12•6•2•Updated Nov 4, 2022Nov 4, 2022
COBRA.binary
Public
Linux, Windows and Mac binaries maintained by the constraint-based reconstruction and analysis community
MATLAB
•7•1•1•0•Updated Sep 1, 2022Sep 1, 2022
cookiecutter-python-package
Public
Extensive cookiecutter template for openCOBRA Python packages.
Python
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Apache License 2.0
•0•2•0•0•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.
serialization sqlalchemy orm cobra pydantic
Python
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Apache License 2.0
•0•3•0•0•Updated Oct 6, 2021Oct 6, 2021
opencobra.github.io
Public
Official openCOBRA website
CSS
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MIT License
•3•0•0•0•Updated Jun 22, 2021Jun 22, 2021
artenolis
Public
Automated Reproducibility and Testing Environment for Licensed Software
automation continuous-integration computational-biology test-driven-development software-quality cobra artenolis
Java
•2•0•0•0•Updated Jun 15, 2021Jun 15, 2021
kb_memote
Public
Python
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MIT License
•2•1•0•0•Updated Dec 3, 2019Dec 3, 2019
COBRA.java
Public
Constraint-based reconstruction and analysis via Java
1•0•0•0•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
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Apache License 2.0
•3•0•1•0•Updated Jan 7, 2019Jan 7, 2019