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https://github.com/sysbiochalmers/yeast-gem

The consensus GEM for Saccharomyces cerevisiae
https://github.com/sysbiochalmers/yeast-gem

biology consensus genome-scale-models hacktoberfest matlab metabolic-models python reconstruction saccharomyces-cerevisiae standard-gem systems-biology yeast

Last synced: about 10 hours ago
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The consensus GEM for Saccharomyces cerevisiae

Host: GitHub
URL: https://github.com/sysbiochalmers/yeast-gem
Owner: SysBioChalmers
License: cc-by-4.0
Created: 2016-02-29T08:58:07.000Z (almost 9 years ago)
Default Branch: main
Last Pushed: 2024-11-25T00:00:12.000Z (28 days ago)
Last Synced: 2024-12-15T17:11:41.702Z (7 days ago)
Topics: biology, consensus, genome-scale-models, hacktoberfest, matlab, metabolic-models, python, reconstruction, saccharomyces-cerevisiae, standard-gem, systems-biology, yeast
Language: MATLAB
Homepage: http://sysbiochalmers.github.io/yeast-GEM/
Size: 74.4 MB
Stars: 97
Watchers: 18
Forks: 46
Open Issues: 28
Metadata Files:
- Readme: README.md
- Changelog: history.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: .github/CODE_OF_CONDUCT.md

Awesome Lists containing this project

README

        # yeast-GEM: The consensus genome-scale metabolic model of _Saccharomyces cerevisiae_

[![Current release](https://img.shields.io/github/release/SysBioChalmers/yeast-GEM/all.svg)](https://github.com/SysBioChalmers/yeast-GEM/releases/)

[![GitHub Discussions](https://img.shields.io/github/discussions/sysbiochalmers/yeast-gem)](https://github.com/SysBioChalmers/yeast-GEM/discussions)

[![Memote report](https://github.com/SysBioChalmers/yeast-GEM/actions/workflows/memote-release.yml/badge.svg)](https://sysbiochalmers.github.io/yeast-GEM/release_report.html)

[![DOI](https://zenodo.org/badge/52777598.svg)](https://zenodo.org/badge/latestdoi/52777598)

# Description

This repository contains the current consensus genome-scale metabolic model of _Saccharomyces cerevisiae_. It is the continuation of the legacy project [yeastnet](https://sourceforge.net/projects/yeast/). For the latest release please [click here](https://github.com/SysBioChalmers/yeast-GEM/releases).

# 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](https://doi.org/10.1038/s44320-024-00060-7)

* For pre-yeast9 versions:

  > 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](https://doi.org/10.1038/s41467-019-11581-3)

* Additionally, all yeast-GEM releases are archived in [Zenodo](https://zenodo.org/badge/latestdoi/52777598), 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](https://zenodo.org/search?page=1&size=20&q=conceptrecid:%221494182%22&sort=-publication_date&all_versions=True).

  

# Keywords

**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](http://doi.org/10.1038/nbt1492)  

**Omic source:** genomics; metabolomics  

**Taxonomic name:** _Saccharomyces cerevisiae_  

**Taxonomy ID:** [taxonomy:559292](https://identifiers.org/taxonomy:559292)  

**Genome ID:** [insdc.gca:GCA_000146045.2](https://identifiers.org/insdc.gca:GCA_000146045.2)  

**Metabolic system:** general metabolism  

**Strain:** S288C  

**Condition:** aerobic, glucose-limited, defined media  

## Model overview

| Taxonomy | Latest update | Version | Reactions | Metabolites | Genes |

|:-------|:--------------|:------|:------|:----------|:-----|

| _Saccharomyces cerevisiae_ | 23-Nov-2024 | 9.0.2 | 4131 | 2806 | 1161 |

### Gene essentiality prediction

- Accuracy: 0.903

- True non-essential genes: 950

- True essential genes: 65

- False non-essential genes: 95

- False essential genes: 14

### Growth prediction

- Correlation coefficient R²: 0.880

![Growth curve](data/testResults/growth.png)

# Installation & usage

## Obtain model

You can obtained the model by any of the following methods:

1. If you have a Git client installed on your computer, you can clone the [`main`](https://github.com/SysBioChalmers/yeast-GEM) branch of the yeast-GEM repository.

2. You can directly download [the latest release](https://github.com/SysBioChalmers/yeast-GEM/releases) as a ZIP file.

3. If you want to contribute to the development of yeast-GEM (see [below](#below)), it is best to [fork](https://github.com/SysBioChalmers/yeast-GEM/fork) the yeast-GEM repository to your own Github account.

## Required software

### Basic user

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

  * [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.8.3 or later (recommended)  

  * [COBRA Toolbox](https://github.com/opencobra/cobratoolbox)

* Python-based

  * [cobrapy](https://github.com/opencobra/cobrapy)  

Please see the installation instructions for each software package.

### Developer

* MATLAB-based  

  If you want to contribute to the development of yeast-GEM, or otherwise want to run any of the [provided](https://github.com/SysBioChalmers/yeast-GEM/tree/main/code) MATLAB functions, then the following software is required:

  * [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN) version 2.8.3 or later

* 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](https://github.com/SysBioChalmers/yeast-GEM/tree/main/code) Python functions, you may create an environment with all requirements:

  ```bash

  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](https://git-lfs.github.com/), as `results.db` (the database that stores all memote results) is tracked with git lfs.

## Model usage

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

* In Matlab:

  ```matlab

  cd ./code

  model = loadYeastModel(); % loading

  saveYeastModel(model);    % saving

  ```

  * If RAVEN is not installed, you can also use COBRA-native functions (`readCbModel`, `writeCbModel`), but these model-files cannot be committed back to the GitHub repository.

* In Python:  

Before opening Python, the following command should (once) be run in the yeast-GEM root folder:  

  ```bash

  touch .env # create a .env file for locating the root

  ```

  Afterwards, the model can be loaded in Python with:

  ```python

  import code.io as io

  model = io.read_yeast_model() # loading

  io.write_yeast_model(model)   # saving

  ```

### Online visualization

You can interactively navigate model components and visualize 3D representations of all compartments and subsystems of yeast-GEM at [Metabolic Atlas](https://metabolicatlas.org/explore?selected=Yeast-GEM). Learn more [about Metabolic Atlas](https://www.metabolicatlas.org/about).

# Contributing

Contributions are always welcome! Please read the [contributions guideline](https://github.com/SysBioChalmers/yeast-GEM/blob/main/.github/CONTRIBUTING.md) to get started.

## Contributors

Code contributors are reported automatically by GitHub under [Contributors](https://github.com/SysBioChalmers/yeast-GEM/graphs/contributors), while other contributions come in as [Issues](https://github.com/SysBioChalmers/yeast-GEM/issues).