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The consensus GEM for Saccharomyces cerevisiae
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README.md

yeast-GEM: The consensus genome-scale metabolic model of Saccharomyces cerevisiae

DOI GitHub version Join the chat at https://gitter.im/SysBioChalmers/yeast-GEM

  • Brief Model Description:

This repository contains the current consensus genome-scale metabolic model of Saccharomyces cerevisiae. It is the continuation of the legacy project yeastnet. For the latest release please click here.

  • Model KeyWords:

GEM Category: species; Utilisation: experimental data reconstruction, multi-omics integrative analysis, in silico strain design, model template; Field: metabolic-network reconstruction; Type of Model: reconstruction, curated; Model Source: YeastMetabolicNetwork; Omic Source: genomics, metabolomics; Taxonomy: Saccharomyces cerevisiae; Metabolic System: general metabolism; Bioreactor; Strain: S288C; Condition: aerobic, glucose-limited, defined media;

  • Last update: 2018-12-06

  • Main Model Descriptors:

Taxonomy Template Model Reactions Metabolites Genes
Saccharomyces cerevisiae Yeast 7.6 3963 2691 1139

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:

Installation Instructions

  • For users: Clone it from master in the Github repo, or just download the latest release.
  • For contributors: Fork it to your Github account, and create a new branch from devel.

Usage

Make sure to load/save the model with the corresponding wrapper functions!

  • In Matlab:
    • Loading: complementaryScripts/loadYeastModel.m
    • Saving: complementaryScripts/saveYeastModel.m
  • In Python:
    • Loading: complementaryScripts/loadYeastModel.py
    • Saving: currently unavailable

Model Files

The model is available in .xml, .txt, .yml, .mat and .xlsx (the last 2 extensions only in master). Additionally, the following 2 files are available:

  • dependencies.txt: Tracks versions of toolboxes & SBML used for saving the model.
  • boundaryMets.txt: Contains a list of all boundary metabolites in model, listing the id and name.

Complementary Scripts

  • missingFields: Folder with functions for adding missing fields to the model.
  • modelCuration: Folder with curation functions.
  • otherChanges: Folder with other types of changes.
  • 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
  • loadYeastModel.m: Loads the yeast model from the .xml file for Matlab.
  • loadYeastModel.py: Loads the yeast model from the .xml file for Python.
  • saveYeastModel.m: Saves yeast model as a .xml, .yml and .txt file, and updates boundaryMets.txt and dependencies.txt.

Complementary Data

  • databases: Yeast data from different databases (KEGG, SGD, swissprot, etc).
  • modelCuration: Data files used for performing curations to the model. Mostly lists of new rxns, mets or genes added (or fixed) in the model.
  • physiology: Data on yeast growth under different conditions, biomass composition, gene essentiality experiments, etc.

Citation

  • All yeast-GEM releases are archived in Zenodo, for you to cite the specific version of yeast-GEM that you used in your study. Find the corresponding DOI here.

  • Additionally, if you would like to cite the yeast-GEM project, you may also refer to the yeast 7 paper, and point to the new link in the text, e.g.: "The yeast consensus genome-scale model [Aung et al. 2013], which is currently being hosted at https://github.com/SysBioChalmers/yeast-GEM, [...]".

  • Finally, if you would like to cite the idea of hosting a genome-scale model in Github, you may also refer to the RAVEN 2 paper, which mentions this idea and exemplifies it on Streptomyces_coelicolor-GEM.

Contributing

Contributions are always welcome! Please read the contributions guideline to get started.

Contributors

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