The consensus genome-scale metabolic model of Saccharomyces cerevisiae

This repository contains the continuously updated consensus genome-scale metabolic model of Saccharomyces cerevisiae. This is a community effort, continuing the yeastnet project, and since 2018 known as yeast-GEM. The development of yeast-GEM is versioned and tracked in this GitHub repository, which enables reproducible, collaborative and open science.

Download the latest version

The latest version of yeast-GEM can be downloaded as a ZIP file, while previous versions (7.6.0 and newer) are also still available. You are typically encouraged to use the latest version, as it will have known bugs fixed and represent the latest knowledge in S. cerevisiae metabolism.

Clone or fork the repository

To enjoy the full capabilities of yeast-GEM and its tracked development on GitHub, you should not download the ZIP file, but instead clone or fork the yeast-GEM repository. If you are not familiar with git, GitHub and its terminology, you can look at this quickstart and/or this YouTube video.

Note: if you want to make contributions to yeast-GEM (see below) it is essential to clone or fork the repository.

Installation and usage instructions

Instructions on how to use the model (including load/save in MATLAB or Python) are available here, and also detailed under Installation & usage in the README.md that can be found in the yeast-GEM ZIP-file (if downloaded instead of cloned).

Feedback / help

If you have questions, require help or encounter any issue with yeast-GEM, you can have a look at the GitHub Discussions page. You can also directly report bugs or request specific assistance by opening an Issue on GitHub.

Contributing

As yeast-GEM is a community effort, contributions are always welcome! Please read the contributions guidelines to get started.

Citation

If you use yeast-GEM please cite the yeast9 paper:

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

More detailed instructions on citing specific versions are given here.