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Systems and Synthetic Biology at Chalmers University of Technology (@SysBioChalmers)

SysBioChalmers

Stars
546
Global Org. Rank 22,267 (Top 8 %)
Registered about 9 years ago
Most used languages

MATLAB
56.5 %

R
17.7 %

Python
8.1 %

HTML
6.5 %

C
3.2 %

Perl
1.6 %

Pep8 1.6 %

Rust
1.6 %

PostScript 1.6 %

Jupyter Notebook
1.6 %
Location 🇸🇪 Sweden
Country Total Rank 582
Country Ranking

MATLAB
2

Pep8 2

PostScript 11

R
34

Perl
178

Jupyter Notebook
186

Python
219

HTML
269

Rust
452

C
1,076

RAVEN

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

DLKcat

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

yeast-GEM

The consensus GEM for Saccharomyces cerevisiae

Human-GEM

The generic genome-scale metabolic model of Homo sapiens

GECKO

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

HGTphyloDetect

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.

BayesianGEM

This repository contains code and data needed to replicate the analysis carried out in the manuscript Li G, et al. 2020.

Jupyter Notebook

ecModels

A container for all enzyme constrained models created by GECKO.

Yarrowia_lipolytica_W29-GEM

Genome-scale model of Yarrowia lipolytica.

OrthOmics

Collection of scripts for gene age sorting and multi-omics data mining and analysis

ecFactory

A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism

MuscleATPProductionSimulation

Models and scripts for simulations of ATP production in muscle, the repo contains: A) A small scale enzyme constrained stoichiometric model of metabolism of the single muscle fiber B) A whole body metabolic model incorporating complex I bypass.

sybil

Efficient Constrained Based Modelling in R

Fruitfly-GEM

Genome scale model for Drosophila melanogaster

Mouse-GEM

Genome-scale model for Mus musculus

SingleCellModeling

Code for the publication "Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data"

Yeast-Species-GEMs

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.

pcSecYeast

hanpo-GEM

Draft genome-scale model of Hansenula polymorpha (Ogataea polymorpha; Pichia angusta)

SLIMEr

Collection of scripts for improving lipid constraints in yeast-GEM

sybil-SBML

SBML (Systems Biology Markup Language) integration in sybil

Zebrafish-GEM

Genome-scale model for Danio rerio

Multi_scale_evolution

Multi-scale evolution analysis of with aid of protein 3D structures for 332 different yeast species plus 11 fungal species.

YeastsModels

Container of computational models of metabolism for different yeast species.

Streptomyces_coelicolor-GEM

Genome-scale model of Streptomyces coelicolor.

Sco-GEM

The consensus GEM for Streptomyces coelicolor -

Enzyme-parameters-analysis

Global analysis of kinetic parameters in the BRENDA database, used by the GECKO toolbox

BrainMetabolismModeling

Modeling of the energy metabolism of the brain

proYeast8-GEM

Mutation mapping analysis using CLUMPS and hotspot method with aid of protein 3D structures for the metabolic gene from yeast GEM

MLEssential

A computational toolbox to predict essential genes using machine learning based on sequence and evolution-based information

Kiwi

The Kiwi python package combines gene-set analyses with biological networks to visualize the interactions between genesets that are significant in a given biological system.

Rat-GEM

Genome-scale model for Rattus norvegicus

Worm-GEM

Genome-scale model for Caenorhabditis elegans

Lactobacillus_reuteri_MM41A_GEM

bacterial-exclusion-prediction

Estimating the anti-bacterial property of surfaces based on SEM images

DSAVE-R

R Package DSAVE (Down-SAmpling based Variation Estimation). The package operates on single-cell RNA-Seq data and is useful for finding misclassified cells, comparing the outcome of clustering methods, figuring out minimum clustering sizes to get the same variation as for bulk, and comparing the technical variation across datasets. The package is compatible with Seurat.

LiverCellMetabolismSimulation

Simulation of HepG2 and Huh7 cultivations under different nutrient conditions

Human-GEM-guide

Guide for Human-GEM

FALCONET

The FALCONET R package enables to build and visualise metabolic maps of GEM automatically with aid of cellDesigner 4.4 and R platform

Penicillium-GEMs

CODY

overflow

Supplementary code and results from doi:10.1101/2020.02.20.957662

EnzymeConstrained_humanModels

Collection of scripts for enhancing humanGEM based models with kinetic and proteomics constraints and specialized simulation utilities.

SingleCellToolbox

Contains general code for handling single-cell RNA-Seq data in Matlab. Also contains some functions for bulk data some additional general functions.

KMG060-Systems-Biology-course

KMG060 Systems Biology course - repo for students

EPO_GFP

Transcriptome analysis of EPO- and GFP-producing HEK293 Cell-lines

sybil-glpkAPI

R Interface to C API of GLPK

EnzymeConstrainedSmallYeast

Enzyme constrained model of intermediary metabolism in S. cerevisiae

rhto-GEM

Genome-scale metabolic model of Rhodotorula toruloides

Yeast_kapp

mitoYeast-GEM

yeast-GEM with an expansion of the mitochondrial compartments

reproduce

Assesing the quality and reproducibility of absolute proteomic data

ChildrenGutMicrobialGEMs

58 GEMs for gut bacterial species from microbiota of healthy and malnourished children.

Kluyveromyces_marxianus-GEM

The consensus GEM for Kluyveromyces marxianus

workshops

A collection of Sysbio workshops.

Human-maps

Human1 metabolic maps

cplexAPI

R Interface to C API of IBM ILOG CPLEX

Yeast-maps

Metabolic maps for the Yeast-8.3 GEM

CofactorYeast

Integration of cofactors with proteome-constrained model of Saccharomyces cerevisiae

sybil-gurobiAPI

Gurobi support for sybil

Yarrowia_Multifactor

Data and scripts used for the RNA-seq analysis of Yarrowia lipolytica (fat-free strain and urea utilisation)

GAGome-MCED

YTKPrimerDesign

Python gui and shiny app for primer generation

Yeast-ME-GEM

GECKO2_simulations

Collection of scripts for reproduction of simulation results in "Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0".