Systems and Synthetic Biology at Chalmers University of Technology

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102 repositories

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
•41•98•130•14•Updated Nov 6, 2024Nov 6, 2024
sysbio.se
Public
The sysbio.se source code
CSS
•
MIT License
•2•0•1•0•Updated Nov 5, 2024Nov 5, 2024
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
•
Creative Commons Attribution 4.0 International
•2•0•6•1•Updated Oct 30, 2024Oct 30, 2024
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
•
Other
•52•101•8•1•Updated Oct 29, 2024Oct 29, 2024
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
•46•95•30•2•Updated Oct 28, 2024Oct 28, 2024
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
•51•67•11•2•Updated Oct 19, 2024Oct 19, 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•5•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•3•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
•1•4•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•7•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•2•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
•54•130•4•0•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
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
•4•8•1•1•Updated Mar 14, 2023Mar 14, 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
•
MIT License
•5•32•1•0•Updated Feb 11, 2023Feb 11, 2023
Penicillium-GEMs
Public
genome-scale-models
Perl
•
Other
•1•1•1•0•Updated Jan 27, 2023Jan 27, 2023
SingleCellModeling
Public
Code for the publication "Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data"
MATLAB
•
MIT License
•1•5•0•0•Updated Dec 21, 2022Dec 21, 2022
Yeast-Species-GEMs
Public
A universal metabolic model knowledge database (pan-GEM) for current existing yeast species with genome sequence, based on which we will build the GEMs of high quality for each yeast species.
pan-metabolic-model pan-genome-annotation strain-specific-metabolic-model pathway-conservation-analysis yeast-species
Pep8
•
MIT License
•5•8•7•0•Updated Dec 7, 2022Dec 7, 2022