Systems and Synthetic Biology at Chalmers University of Technology

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104 repositories

yeast-GEM
Public
The consensus GEM for Saccharomyces cerevisiae
python biology matlab systems-biology consensus reconstruction hacktoberfest yeast metabolic-models genome-scale-models
MATLAB
•
Creative Commons Attribution 4.0 International
•51•113•31•0•Updated Sep 28, 2025Sep 28, 2025
sysbio.se
Public
The sysbio.se source code
CSS
•
MIT License
•2•0•1•0•Updated Sep 26, 2025Sep 26, 2025
GECKO
Public
Toolbox for including enzyme constraints on a genome-scale model.
systems-biology toolbox data-integration proteomics kinetics enzyme-constraints matlab
MATLAB
•
MIT License
•52•78•11•2•Updated Sep 21, 2025Sep 21, 2025
RAVEN
Public
The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.
systems-biology metabolic-models metabolic-reconstruction constraint-based-modeling metabolic-engineering gap-filling human-metabolism genome-scale-models sysbio
MATLAB
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Other
•56•113•9•1•Updated Sep 18, 2025Sep 18, 2025
overflow
Public
Supplementary code and results from doi:10.1101/2020.02.20.957662
proteomics metabolism yeast genome-scale-models
MATLAB
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Other
•0•1•0•0•Updated Sep 16, 2025Sep 16, 2025
Human-GEM
Public
The generic genome-scale metabolic model of Homo sapiens
human-metabolism genome-scale-models standard-gem
MATLAB
•
Creative Commons Attribution 4.0 International
•50•122•91•12•Updated Sep 11, 2025Sep 11, 2025
Ecoli-GEM
Public
Genome-scale metabolic model for Escherichia coli
systems-biology genome-scale-models standard-gem
HTML
•
Creative Commons Attribution 4.0 International
•0•1•3•0•Updated Sep 8, 2025Sep 8, 2025
ecFactory
Public
A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism
metabolic-models enzyme-constraints microbes cell-factory
MATLAB
•
GNU General Public License v3.0
•5•10•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 ecYeastGEM model avaiable at ecModels.
yeast constraint-based-modeling enzyme-constraints cell-factory
MATLAB
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Creative Commons Attribution 4.0 International
•2•3•6•1•Updated Feb 12, 2025Feb 12, 2025
sint-GEM
Public
Genome-scale metabolic model of Candida intermedia
metabolic-models constraint-based-modeling standard-gem yeast-species
MATLAB
•
GNU General Public License v3.0
•0•0•7•0•Updated Nov 14, 2024Nov 14, 2024
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
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
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
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
MATLAB
•
Creative Commons Attribution 4.0 International
•1•2•0•0•Updated Dec 10, 2023Dec 10, 2023
Mouse-GEM
Public
Genome-scale model for Mus musculus
standard-gem
MATLAB
•
Creative Commons Attribution 4.0 International
•5•8•0•0•Updated Dec 10, 2023Dec 10, 2023
TMEModeling
Public
Modeling of the tumor microenvironment using a diffusion model for upptake constraints.
MATLAB
•
MIT License
•0•0•0•0•Updated Dec 6, 2023Dec 6, 2023
Human-GEM-guide
Public
Guide for Human-GEM
MIT License
•0•1•0•0•Updated Nov 28, 2023Nov 28, 2023
pcSecYeast
Public
MATLAB
•
GNU General Public License v3.0
•1•5•0•0•Updated Nov 3, 2023Nov 3, 2023
KMG060-Systems-Biology-course
Public
KMG060 Systems Biology course - repo for students
systems-biology rna-seq-analysis metabolic-models flux-balance-analysis enzyme-constraints
MATLAB
•
GNU General Public License v3.0
•7•2•3•0•Updated Sep 23, 2023Sep 23, 2023
sybil
Public
Efficient Constrained Based Modelling in R
R
•
GNU General Public License v3.0
•1•6•1•0•Updated Aug 2, 2023Aug 2, 2023
sybil-SBML
Public
SBML (Systems Biology Markup Language) integration in sybil
R
•
GNU General Public License v3.0
•0•4•3•0•Updated Aug 1, 2023Aug 1, 2023
DLKcat
Public
Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction
deep-learning bayesian kinetics enzyme-constraints enzyme-turnover-number kcat
Python
•59•171•6•1•Updated Jul 4, 2023Jul 4, 2023
Human-maps
Public
Human1 metabolic maps
Creative Commons Attribution 4.0 International
•2•2•0•0•Updated Apr 8, 2023Apr 8, 2023
bacterial-exclusion-prediction
Public
Estimating the anti-bacterial property of surfaces based on SEM images
Rust
•
MIT License
•0•2•0•0•Updated Feb 21, 2023Feb 21, 2023
HGTphyloDetect
Public
HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
systems-biology phylogenetics horizontal-gene-transfer sequence-analysis evolutionary-biology high-throughput-pipeline
Python
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MIT License
•5•40•3•0•Updated Feb 11, 2023Feb 11, 2023