SysBioChalmers/yeast-GEM


The consensus GEM for Saccharomyces cerevisiae

http://sysbiochalmers.github.io/yeast-GEM/

License: CC-BY-4.0

Language: MATLAB

Keywords: genome-scale-models, systems-biology, yeast


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:

Taxonomy Template Model Reactions Metabolites Genes
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.

Installation

Required Software - User:

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).

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

Project Statistics

Sourcerank 7
Repository Size 26.2 MB
Stars 24
Forks 19
Watchers 15
Open issues 20
Dependencies 0
Contributors 4
Tags 6
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Top Contributors See all

Benjamín Sánchez hongzhonglu The Gitter Badger feiranl

Recent Tags See all

v8.0.1 April 16, 2018
v8.0.0 March 30, 2018
v7.8.3 February 28, 2018
v7.8.2 January 30, 2018
v7.8.1 January 25, 2018
v7.8.0 January 18, 2018

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