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.
Zhang, C. et al. Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community. Molecular Systems Biology (2024) doi:10.1038/s44320-024-00060-7
Lu, H. et al. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications 10, 3586 (2019). doi:10.1038/s41467-019-11581-3
Additionally, all yeast-GEM releases are archived in Zenodo, for you to cite the specific version of yeast-GEM that you used in your study, to ensure reproducibility. You should always cite the original publication + the specific version, for instance:
The yeast consensus genome-scale model [Lu et al. 2019], version 8.3.4 [Sánchez et al. 2019], was used.
Find the citation details for your specific version here.
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
Taxonomic name: Saccharomyces cerevisiae
Taxonomy ID: taxonomy:559292
Genome ID: insdc.gca:GCA_000146045.2
Metabolic system: general metabolism
Strain: S288C
Condition: aerobic, glucose-limited, defined media
Taxonomy | Latest update | Version | Reactions | Metabolites | Genes |
---|---|---|---|---|---|
Saccharomyces cerevisiae | 14-Aug-2024 | 9.0.1 | 4130 | 2805 | 1162 |
You can obtained the model by any of the following methods:
main
branch of the yeast-GEM repository.If you want to use the model for your own model simulations, you can use any software that accepts SBML L3V1 FBCv3 formatted model files. This includes any of the following:
MATLAB-based
Python-based
Please see the installation instructions for each software package.
MATLAB-based
If you want to contribute to the development of yeast-GEM, or otherwise want to run any of the provided MATLAB functions, then the following software is required:
Python-based
Contribution via python (cobrapy) is not yet functional. In essence, if you can retain the same format of the model files, you can still contribute to the development of yeast-GEM. However, you cannot use the MATLAB functions.
If you want to use any of the provided Python functions, you may create an environment with all requirements:
pip install -r code/requirements/requirements.txt # install all dependencies
touch .env # create a .env file for locating the root
If you want to locally run memote run
or memote report history
, you should also install git lfs, as results.db
(the database that stores all memote results) is tracked with git lfs.
Make sure to load/save the model with the corresponding wrapper functions:
cd ./code
model = loadYeastModel(); % loading
saveYeastModel(model); % saving
readCbModel
, writeCbModel
), but these model-files cannot be committed back to the GitHub repository.touch .env # create a .env file for locating the root
Afterwards, the model can be loaded in Python with:
import code.io as io
model = io.read_yeast_model() # loading
io.write_yeast_model(model) # saving
You can interactively navigate model components and visualize 3D representations of all compartments and subsystems of yeast-GEM at Metabolic Atlas. Learn more about Metabolic Atlas.
Contributions are always welcome! Please read the contributions guideline to get started.
Code contributors are reported automatically by GitHub under Contributors, while other contributions come in as Issues.