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@CompMetEng Computational Metabolic Engineering @ Chalmers

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    Repositories list

    12 repositories

    • RAVEN

      Public
      RAVEN Toolbox for MATLAB, version 3+
      systems-biologymetabolic-modelsmetabolic-reconstruction
      systems-biologymetabolic-modelsmetabolic-reconstructionconstraint-based-modelingmetabolic-engineeringgap-fillinghuman-metabolismgenome-scale-models
      MATLAB
      •
      Other
      •0•1•0•1•Updated Oct 23, 2026Oct 23, 2026

    • GECKO

      Public
      GECKO Toolbox for MATLAB, version 4+
      matlabsystems-biologytoolbox
      matlabsystems-biologytoolboxdata-integrationproteomicskineticsenzyme-constraints
      MATLAB
      •
      MIT License
      •0•2•4•0•Updated Oct 23, 2026Oct 23, 2026

    • geckopy

      Public
      GECKO Toolbox for Python
      Python
      •
      Other
      •2•3•0•1•Updated Oct 23, 2026Oct 23, 2026

    • haecon-GEM

      Public
      Genome-scale model of Haemonchus contortus
      genome-scale-modelsnematodestandard-gem
      genome-scale-modelsnematodestandard-gem
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Oct 23, 2026Oct 23, 2026

    • raven-gecko-parity

      Public
      Keeps the MATLAB and Python implementations of RAVEN and GECKO honest about their differences: parity ledgers plus cross-implementation behaviour scenarios.
      Python
      •
      MIT License
      •0•0•20•0•Updated Oct 23, 2026Oct 23, 2026

    • raven-toolbox

      Public
      Python port of the RAVEN Toolbox, built on cobrapy
      Python
      •
      GNU General Public License v3.0
      •1•9•0•1•Updated Oct 23, 2026Oct 23, 2026

    • raven-docs

      Public
      Documentation for RAVEN (MATLAB and Python)
      Python
      •0•1•2•0•Updated Oct 22, 2026Oct 22, 2026

    • ecModels

      Public
      Python
      •
      Creative Commons Attribution 4.0 International
      •0•0•0•0•Updated Oct 21, 2026Oct 21, 2026

    • gecko-docs

      Public
      Protocol for GECKO (both MATLAB and Python)
      Python
      •0•1•0•0•Updated Oct 20, 2026Oct 20, 2026

    • study_overflow

      Public
      Supplementary code and results from doi:10.1101/2020.02.20.957662
      proteomicsmetabolismyeast
      proteomicsmetabolismyeastgenome-scale-models
      Python
      •
      Other
      •0•1•0•1•Updated Oct 18, 2026Oct 18, 2026

    • toolbox-assets

      Public
      0•0•0•0•Updated Oct 18, 2026Oct 18, 2026

    • SuppOrth

      Public
      Pipeline to create support for orthologues prediction
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 15, 2026Oct 15, 2026
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