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@SysBioChalmers

Systems and Synthetic Biology at Chalmers University of Technology

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  1. Human-GEM Human-GEM Public

    The generic genome-scale metabolic model of Homo sapiens

    MATLAB 172 65

  2. yeast-GEM yeast-GEM Public

    The consensus GEM for Saccharomyces cerevisiae

    MATLAB 134 51

  3. RAVEN RAVEN Public

    The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

    MATLAB 131 62

  4. GECKO GECKO Public

    Toolbox for including enzyme constraints on a genome-scale model.

    MATLAB 92 55

  5. DLKcat DLKcat Public

    Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction

    Python 202 67

Repositories

Showing 10 of 114 repositories
  • 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.

    SysBioChalmers/raven-gecko-parity's past year of commit activity
    Python 0 MIT 0 3 0 Updated Sep 13, 2026
  • GECKO Public

    Toolbox for including enzyme constraints on a genome-scale model.

    SysBioChalmers/GECKO's past year of commit activity
    MATLAB 92 MIT 55 16 2 Updated Sep 12, 2026
  • RAVEN Public

    The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.

    SysBioChalmers/RAVEN's past year of commit activity
    MATLAB 131 62 9 (1 issue needs help) 1 Updated Sep 12, 2026
  • raven-toolbox Public

    Python port of the RAVEN Toolbox, built on cobrapy

    SysBioChalmers/raven-toolbox's past year of commit activity
    Python 6 MIT 1 0 0 Updated Sep 12, 2026
  • geckopy Public

    GECKO Toolbox for Python

    SysBioChalmers/geckopy's past year of commit activity
    Python 1 1 0 0 Updated Sep 12, 2026
  • Human-GEM Public

    The generic genome-scale metabolic model of Homo sapiens

    SysBioChalmers/Human-GEM's past year of commit activity
    MATLAB 172 CC-BY-4.0 65 94 13 Updated Sep 12, 2026
  • papla-GEM Public

    Genome-scale metabolic model of Papiliotrema laurentii

    SysBioChalmers/papla-GEM's past year of commit activity
    MATLAB 0 CC-BY-4.0 0 1 1 Updated Sep 8, 2026
  • yeast-GEM Public

    The consensus GEM for Saccharomyces cerevisiae

    SysBioChalmers/yeast-GEM's past year of commit activity
    MATLAB 134 CC-BY-4.0 51 23 (5 issues need help) 0 Updated Sep 6, 2026
  • haecon-GEM Public

    Genome-scale model of Haemonchus contortus

    SysBioChalmers/haecon-GEM's past year of commit activity
    Jupyter Notebook 0 CC-BY-4.0 0 0 0 Updated Aug 31, 2026
  • sysbio.se Public

    The sysbio.se source code

    SysBioChalmers/sysbio.se's past year of commit activity
    CSS 0 MIT 2 1 0 Updated Aug 27, 2026
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