yeast-GEM: The consensus genome-scale metabolic model of Saccharomyces cerevisiae
- Brief Model Description:
This repository contains the current consensus genome-scale metabolic model of Saccharomyces cerevisiae. It is the continuation of the legacy project yeast.sf.net. For the latest release please click here.
- Model KeyWords:
GEM Category: Species; Utilisation: maximising growth; Field: metabolic-network reconstruction; Type of Model: curated, reconstruction; Model Source: Yeast 7.6; Taxonomy: Saccharomyces cerevisiae; Metabolic System: General Metabolism; Bioreactor
Last update: 2018-04-12
|Saccharomyces cerevisiae||Yeast 7.6||3496||2224||922|
This repository is administered by Benjamín J. Sánchez (@BenjaSanchez), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.
Required Software - User:
- A functional Matlab installation (MATLAB 7.3 or higher)
- The COBRA toolbox for MATLAB.
Required Software - Contributor:
Dependencies - Recommended Software:
- libSBML MATLAB API (version 5.15.0 is recommended).
- For simulations, Gurobi Optimizer for MATLAB (version 6.5.2 is recommended).
- Just want to use the model? Clone it from
masterin the Github repo, or just download the latest release.
- Wish to also contribute? Fork it to your Github account, and create a new branch from
missingFields: Folder with functions for adding missing fields to the model.
addGeneNames.m: Adds the field
geneNamesby extracting the data from KEGG.
getConfidenceScores.m: Assigns confidence scores based in a basic automatic criteria.
getMissingFields.m: Retrieves missing information (
subSystems) from KEGG & Swissprot. It uses
changeRules.mfor properly reading the gene-reaction rules, and
deleteRepeated.mfor reading the databases. The latter 4 functions are adapted versions of functions from the GECKO toolbox.
modelCuration: Folder with curation functions.
addiSce926changes.m: Updates the model to include curation from the iSce926 model.
calculateContent.m: Calculates the protein and carb fraction in the biomass pseudo-rxn.
changeBiomass.m: Rescales the biomass composition for varying protein content in anaerobic case. Also changes GAM and NGAM.
checkMetBalance.m: Shows rxns that consume/produce a given metabolite in the model.
makeFormulasCompliant.m: Fixes the compliance problems of some metabolite formulas.
modelCorrections.m: Corrects various issues in yeast7 (biomass composition, proton balance, Ox.Pho., GAM and NGAM).
takeOutFromFormula.m: Takes away from formula each of the elements specified.
metabolite_manual_curation.tsvand updates the model with it.
otherChanges: Folder with other types of changes.
anaerobicModel.m: Transforms the model to anaerobic conditions.
clusterBiomass.m: Separates the biomass in 5 main components: protein, carbohydrate, lipid, RNA and DNA.
convertYmn2FBC2.m: Converts yeast7 from COBRA-compatible SBML2 to FBC v2, thereby adding the missing annotation data, which could not be retained with the older COBRA versions.
getNewIndex.m: Finds the highest index available in either metabolites or rxns, and then adds one to it, for creating any new species.
dependencies.txt: Tracks SBML versions and levels used for saving the model.
boundaryMets.txt: Contains a list of all boundary metabolites in model, listing the id and name.
increaseVersion.m: Updates the version of the model in
version.txtand as metaid in the
.xmlfile. Saves the model as
saveYeastModel.m: Saves yeast model as a
.txtfile, and updates
loadYeastModel.m: Loads the yeast model from the
iSce926curatedGeneRules.tsv: Manually curated gene rules added to the model based on the iSce926 model.
iSce926newGenes.tsv: New genes added to the model based on the iSce926 model.
metabolite_manual_curation.tsv: All manually curated data added to metabolites.
SGDgeneNames.tsv: Short gene names for each gene ID.
kegg.tsv: KEGG data for S. cerevisiae.
swissprot.tsv: SWISSPROT data for S. cerevisiae.
- Eduard J. Kerkhoven (@edkerk), Chalmers University of Technology, Gothenburg Sweden
- Feiran Li (@feiranl), Chalmers University of Technology, Gothenburg Sweden
- Hongzhong Lu (@hongzhonglu), Chalmers University of Technology, Gothenburg Sweden
- Simonas Marcišauskas (@simas232), Chalmers University of Technology, Gothenburg Sweden
- Benjamín J. Sánchez (@BenjaSanchez), Chalmers University of Technology, Gothenburg Sweden