Lu2019 - Genome scale metabolic model for Saccharomyces cerevisiae - yeastGEM8.5.0

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Model Identifier
BIOMD0000001063
Short description
yeast-GEM: The consensus genome-scale metabolic model of Saccharomyces cerevisiae. Further curations of this model will be tracked in the GitHub repository:https://github.com/SysBioChalmers/yeast-GEM For you use yeast-GEM, please cite the yeast8 paper: Lu, H. et al. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications 10, 3586 (2019). https://doi.org/10.1038/s41467-019-11581-3. FROG analysis was performed with the yeastGEM_rich_medium.mat, which is with rich medium setup.
Format
SBML (L3V1)
Related Publication
  • A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism.
  • Lu H, Li F, Sánchez BJ, Zhu Z, Li G, Domenzain I, Marcišauskas S, Anton M, Lappa D, Lieven C, Beber ME, Sonnenschein N, Kerkhoven EJ, Nielsen J
  • Nature communications , 8/ 2019 , Volume 10 , Issue 1 , pages: 3586 , PubMed ID: 31395883
  • Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96, Gothenburg, Sweden.
  • Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 and an associated ecosystem of models that represent a comprehensive computational resource for performing simulations of the metabolism of Saccharomyces cerevisiae--an important model organism and widely used cell-factory. Yeast8 tracks community development with version control, setting a standard for how GEMs can be continuously updated in a simple and reproducible way. We use Yeast8 to develop the derived models panYeast8 and coreYeast8, which in turn enable the reconstruction of GEMs for 1,011 different yeast strains. Through integration with enzyme constraints (ecYeast8) and protein 3D structures (proYeast8DB), Yeast8 further facilitates the exploration of yeast metabolism at a multi-scale level, enabling prediction of how single nucleotide variations translate to phenotypic traits.
Contributors
Submitter of the first revision: feiran
Submitter of this revision: Mikal Daou
Modellers: feiran, Mikal Daou

Metadata information


Curation status
Non-curated

Modelling approach(es)

Tags

Connected external resources

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Model files

yeast-GEM.xml SBML L3V1 annotated representation Genome scale metabolic model YeastGEM 8.5.0 for Saccharomyces cerevisiae 11.53 MB Preview | Download

Additional files

Description_miniFROG_yeastGEM.xlsx miniFROG description for YeastGEM in rich medium setup 24.77 KB Preview | Download
FROG_Report_YeastGEM_rich_medium.zip FROG report for YeastGEM in rich medium setup 43.18 KB Preview | Download
Yeast_GEM_rich.mat Genome scale metabolic model YeastGEM 8.5.0 for Saccharomyces cerevisiae in rich medium setup 681.01 KB Preview | Download
yeast-GEM.omex Frog report with annotated model 399.93 KB Preview | Download

  • Model originally submitted by : feiran
  • Submitted: Apr 28, 2022 3:33:50 PM
  • Last Modified: Aug 12, 2022 1:44:18 PM
Revisions
  • Version: 3 public model Download this version
    • Submitted on: Aug 12, 2022 1:44:18 PM
    • Submitted by: Mikal Daou
    • With comment: Automatically added model identifier BIOMD0000001063
  • Version: 2 public model Download this version
    • Submitted on: Aug 12, 2022 1:26:37 PM
    • Submitted by: Mikal Daou
    • With comment: added annotations
  • Version: 1 public model Download this version
    • Submitted on: Apr 28, 2022 3:33:50 PM
    • Submitted by: feiran
    • With comment: Import of Lu2019 - Genome scale metabolic model for Saccharomyces cerevisiae - yeastGEM8.5.0

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Curator's comment:
(added: 12 Aug 2022, 13:33:03, updated: 12 Aug 2022, 13:34:15)
This model is curated using FROG standards. We used FBA and FROG Matlab toolbox to curate the model. FROG Report , miniFROG Report