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

• The model:

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.

Installation

Required Software - User:

• A functional Matlab installation (MATLAB 7.3 or higher)
• The COBRA toolbox for MATLAB.

Required Software - Contributor:

• Both of the above.
• The RAVEN toolbox for MATLAB.
• A git wrapper added to the search path.

Dependencies - Recommended Software:

• libSBML MATLAB API (version 5.15.0 is recommended).
• For simulations, Gurobi Optimizer for MATLAB (version 6.5.2 is recommended).

Installation Instructions

• Just want to use the model? Clone it from master in 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 devel.

Complementary Scripts

• missingFields: Folder with functions for adding missing fields to the model.
  • addGeneNames.m: Adds the field geneNames by extracting the data from KEGG.
  • getConfidenceScores.m: Assigns confidence scores based in a basic automatic criteria.
  • getMissingFields.m: Retrieves missing information (rxnECNumbers and subSystems) from KEGG & Swissprot. It uses changeRules.m for properly reading the gene-reaction rules, and findInDB.m, getAllPath.m, findSubSystem.m & deleteRepeated.m for 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.
  • updateMetaboliteAnnotation.m: Reads metabolite_manual_curation.tsv and 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.txt and as metaid in the .xml file. Saves the model as .mat and as .xlsx
• saveYeastModel.m: Saves yeast model as a .xml, .yml and .txt file, and updates boundaryMets.txt and dependencies.txt.
• loadYeastModel.m: Loads the yeast model from the .xml file.

Complementary Data

• 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.

Contributors

• 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