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Systems and Synthetic Biology at Chalmers University of Technology · GitHub

Systems and Synthetic Biology at Chalmers University of Technology

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Human-GEM Human-GEM Public

The generic genome-scale metabolic model of Homo sapiens

MATLAB 171 64
yeast-GEM yeast-GEM Public

The consensus GEM for Saccharomyces cerevisiae

MATLAB 132 51
RAVEN RAVEN Public

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

MATLAB 131 62
GECKO GECKO Public

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

MATLAB 91 55
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 200 69

Repositories

Type Language Sort

raven-toolbox Public
Python port of the RAVEN Toolbox, built on cobrapy

SysBioChalmers/raven-toolbox's past year of commit activity

Python 5 MIT 1 0 1 Updated Aug 29, 2026
yeast-GEM Public
The consensus GEM for Saccharomyces cerevisiae

SysBioChalmers/yeast-GEM's past year of commit activity

MATLAB 132 CC-BY-4.0 51 27 (6 issues need help) 2 Updated Aug 29, 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 13 (1 issue needs help) 1 Updated Aug 29, 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.

SysBioChalmers/raven-gecko-parity's past year of commit activity

Python 0 MIT 0 4 0 Updated Aug 29, 2026
GECKO Public
Toolbox for including enzyme constraints on a genome-scale model.

SysBioChalmers/GECKO's past year of commit activity

MATLAB 91 MIT 55 19 4 Updated Aug 28, 2026
geckopy Public
GECKO Toolbox for Python

SysBioChalmers/geckopy's past year of commit activity

Python 1 1 0 0 Updated Aug 27, 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
Human-GEM Public
The generic genome-scale metabolic model of Homo sapiens

SysBioChalmers/Human-GEM's past year of commit activity

MATLAB 171 CC-BY-4.0 64 94 17 Updated Aug 19, 2026
Human-GEM-guide Public
Guide for Human-GEM

SysBioChalmers/Human-GEM-guide's past year of commit activity

1 MIT 0 0 1 Updated Jul 18, 2026
Yarrowia_lipolytica_W29-GEM Public
Genome-scale model of Yarrowia lipolytica.

SysBioChalmers/Yarrowia_lipolytica_W29-GEM's past year of commit activity

MATLAB 12 CC-BY-4.0 9 14 0 Updated Jul 8, 2026

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