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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) reconstructionyeast-GEM
The consensus GEM for Saccharomyces cerevisiaeHuman-GEM
The generic genome-scale metabolic model of Homo sapiensGECKO
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.Yarrowia_lipolytica_W29-GEM
Genome-scale model of Yarrowia lipolytica.OrthOmics
Collection of scripts for gene age sorting and multi-omics data mining and analysisecFactory
A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolismMuscleATPProductionSimulation
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 RFruitfly-GEM
Genome scale model for Drosophila melanogasterMouse-GEM
Genome-scale model for Mus musculusSingleCellModeling
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-GEMsybil-SBML
SBML (Systems Biology Markup Language) integration in sybilZebrafish-GEM
Genome-scale model for Danio rerioMulti_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 toolboxBrainMetabolismModeling
Modeling of the energy metabolism of the brainproYeast8-GEM
Mutation mapping analysis using CLUMPS and hotspot method with aid of protein 3D structures for the metabolic gene from yeast GEMMLEssential
A computational toolbox to predict essential genes using machine learning based on sequence and evolution-based informationKiwi
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 norvegicusWorm-GEM
Genome-scale model for Caenorhabditis elegansLactobacillus_reuteri_MM41A_GEM
bacterial-exclusion-prediction
Estimating the anti-bacterial property of surfaces based on SEM imagesDSAVE-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 conditionsHuman-GEM-guide
Guide for Human-GEMFALCONET
The FALCONET R package enables to build and visualise metabolic maps of GEM automatically with aid of cellDesigner 4.4 and R platformPenicillium-GEMs
CODY
overflow
Supplementary code and results from doi:10.1101/2020.02.20.957662EnzymeConstrained_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 studentsEPO_GFP
Transcriptome analysis of EPO- and GFP-producing HEK293 Cell-linessybil-glpkAPI
R Interface to C API of GLPKEnzymeConstrainedSmallYeast
Enzyme constrained model of intermediary metabolism in S. cerevisiaerhto-GEM
Genome-scale metabolic model of Rhodotorula toruloidesYeast_kapp
mitoYeast-GEM
yeast-GEM with an expansion of the mitochondrial compartmentsreproduce
Assesing the quality and reproducibility of absolute proteomic dataChildrenGutMicrobialGEMs
58 GEMs for gut bacterial species from microbiota of healthy and malnourished children.Kluyveromyces_marxianus-GEM
The consensus GEM for Kluyveromyces marxianusworkshops
A collection of Sysbio workshops.Human-maps
Human1 metabolic mapscplexAPI
R Interface to C API of IBM ILOG CPLEXYeast-maps
Metabolic maps for the Yeast-8.3 GEMCofactorYeast
Integration of cofactors with proteome-constrained model of Saccharomyces cerevisiaesybil-gurobiAPI
Gurobi support for sybilYarrowia_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 generationYeast-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".Love Open Source and this site? Check out how you can help us