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112 repositories

raven-toolbox
Public
Python port of the RAVEN Toolbox, built on cobrapy
Python
•
MIT License
•1•4•0•5•Updated Jul 21, 2026Jul 21, 2026
Human-GEM
Public
The generic genome-scale metabolic model of Homo sapiens
human-metabolism genome-scale-models standard-gem
human-metabolism genome-scale-models standard-gem
MATLAB
•
Creative Commons Attribution 4.0 International
•64•171•92•16•Updated Jul 19, 2026Jul 19, 2026
RAVEN
Public
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
systems-biology metabolic-models metabolic-reconstruction
systems-biology metabolic-models metabolic-reconstruction constraint-based-modeling metabolic-engineering gap-filling human-metabolism genome-scale-models sysbio
MATLAB
•
Other
•61•131•10•1•Updated Jul 18, 2026Jul 18, 2026
Human-GEM-guide
Public
Guide for Human-GEM
MIT License
•0•1•0•1•Updated Jul 18, 2026Jul 18, 2026
geckopy
Public
GECKO Toolbox for Python
Python
•
Other
•0•1•0•0•Updated Jul 16, 2026Jul 16, 2026
Yarrowia_lipolytica_W29-GEM
Public
Genome-scale model of Yarrowia lipolytica.
systems-biology stoichiometric-reactions metabolic-models
systems-biology stoichiometric-reactions metabolic-models metabolic-network metabolic-reconstruction constraint-based-modeling metabolic-engineering omics-data-integration yarrowia-lipolytica genome-scale-models
MATLAB
•
Creative Commons Attribution 4.0 International
•9•12•14•0•Updated Jul 8, 2026Jul 8, 2026
GECKO
Public
Toolbox for including enzyme constraints on a genome-scale model.
matlab systems-biology toolbox
matlab systems-biology toolbox data-integration proteomics kinetics enzyme-constraints
MATLAB
•
MIT License
•54•91•14•2•Updated Jul 7, 2026Jul 7, 2026
raven-data
Public
0•0•0•0•Updated Jul 1, 2026Jul 1, 2026
yeast-GEM
Public
The consensus GEM for Saccharomyces cerevisiae
python biology matlab
python biology matlab systems-biology consensus reconstruction hacktoberfest yeast metabolic-models genome-scale-models
MATLAB
•
Creative Commons Attribution 4.0 International
•51•129•29•2•Updated Jul 1, 2026Jul 1, 2026
panAsp-GEM
Public
Jupyter Notebook
•
Creative Commons Attribution 4.0 International
•0•0•0•0•Updated Jun 30, 2026Jun 30, 2026
sysbio.se
Public
The sysbio.se source code
CSS
•
MIT License
•2•0•1•0•Updated Jun 18, 2026Jun 18, 2026
MESBcourse
Public
MESB course
HTML
•0•2•0•0•Updated Jun 16, 2026Jun 16, 2026
sce-crabtree-neg-study
Public
To see the results:
MATLAB
•
MIT License
•0•0•0•0•Updated Apr 24, 2026Apr 24, 2026
overflow
Public
Supplementary code and results from doi:10.1101/2020.02.20.957662
proteomics metabolism yeast
proteomics metabolism yeast genome-scale-models
MATLAB
•
Other
•0•1•0•0•Updated Mar 15, 2026Mar 15, 2026
Ecoli-GEM
Public
Genome-scale metabolic model for Escherichia coli
systems-biology genome-scale-models standard-gem
systems-biology genome-scale-models standard-gem
HTML
•
Creative Commons Attribution 4.0 International
•1•3•5•2•Updated Feb 19, 2026Feb 19, 2026
DiversifyCodons
Public
R Shiny App for diversification of codons. We strive to create diverse DNA strings that translate to the same protein sequence.
R
•
MIT License
•0•0•0•0•Updated Jan 27, 2026Jan 27, 2026
sint-GEM
Public
Genome-scale metabolic model of Sungouiella intermedia
metabolic-models constraint-based-modeling standard-gem
metabolic-models constraint-based-modeling standard-gem yeast-species
MATLAB
•
GNU General Public License v3.0
•1•1•7•0•Updated Jan 15, 2026Jan 15, 2026
OrthoBenchmark
Public
A Python- and R-based toolbox for benchmarking orthologous clustering programs
Python
•
MIT License
•1•0•0•0•Updated Dec 8, 2025Dec 8, 2025
ecFactory
Public
A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism
metabolic-models enzyme-constraints microbes
metabolic-models enzyme-constraints microbes cell-factory
MATLAB
•
GNU General Public License v3.0
•6•15•2•1•Updated Feb 12, 2025Feb 12, 2025
CellFactory-ecYeastGEM
Public
Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeas…
yeast constraint-based-modeling enzyme-constraints
yeast constraint-based-modeling enzyme-constraints cell-factory
MATLAB
•
Creative Commons Attribution 4.0 International
•3•5•6•1•Updated Feb 12, 2025Feb 12, 2025
GAGome-BCa
Public
HTML
•0•0•0•0•Updated Aug 28, 2024Aug 28, 2024
Yarrowia_Multifactor
Public
Data and scripts used for the RNA-seq analysis of Yarrowia lipolytica (fat-free strain and urea utilisation)
MATLAB
•
MIT License
•1•1•0•0•Updated Jun 24, 2024Jun 24, 2024
BrainMetabolismModeling
Public
Modeling of the energy metabolism of the brain
MATLAB
•
MIT License
•0•2•0•0•Updated Jan 14, 2024Jan 14, 2024
hanpo-GEM
Public
Draft genome-scale model of Hansenula polymorpha (Ogataea polymorpha; Pichia angusta)
MATLAB
•
Creative Commons Attribution 4.0 International
•1•6•1•0•Updated Jan 5, 2024Jan 5, 2024
GEMsforTrophicLevels
Public
HTML
•2•0•0•0•Updated Dec 19, 2023Dec 19, 2023
Worm-GEM
Public
Genome-scale model for Caenorhabditis elegans
standard-gem
standard-gem
MATLAB
•
Creative Commons Attribution 4.0 International
•1•4•0•0•Updated Dec 10, 2023Dec 10, 2023
Fruitfly-GEM
Public
Genome scale model for Drosophila melanogaster
standard-gem
standard-gem
MATLAB
•
Creative Commons Attribution 4.0 International
•3•7•1•0•Updated Dec 10, 2023Dec 10, 2023
Zebrafish-GEM
Public
Genome-scale model for Danio rerio
standard-gem
standard-gem
MATLAB
•
Creative Commons Attribution 4.0 International
•2•6•0•0•Updated Dec 10, 2023Dec 10, 2023
Rat-GEM
Public
Genome-scale model for Rattus norvegicus
standard-gem
standard-gem
MATLAB
•
Creative Commons Attribution 4.0 International
•2•2•0•0•Updated Dec 10, 2023Dec 10, 2023
Mouse-GEM
Public
Genome-scale model for Mus musculus
standard-gem
standard-gem
MATLAB
•
Creative Commons Attribution 4.0 International
•6•13•1•0•Updated Dec 10, 2023Dec 10, 2023

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Systems and Synthetic Biology at Chalmers University of Technology

All

All

112 repositories

raven-toolbox

Human-GEM

RAVEN

Human-GEM-guide

geckopy

Yarrowia_lipolytica_W29-GEM

GECKO

raven-data

yeast-GEM

panAsp-GEM

sysbio.se

MESBcourse

sce-crabtree-neg-study

overflow

Ecoli-GEM

DiversifyCodons

sint-GEM

OrthoBenchmark

ecFactory

CellFactory-ecYeastGEM

GAGome-BCa

Yarrowia_Multifactor

BrainMetabolismModeling

hanpo-GEM

GEMsforTrophicLevels

Worm-GEM

Fruitfly-GEM

Zebrafish-GEM

Rat-GEM

Mouse-GEM

All

All

Repositories list

112 repositories