https://github.com/sysbiochalmers/mouse-gem
Genome-scale model for Mus musculus
https://github.com/sysbiochalmers/mouse-gem
standard-gem
Last synced: 10 months ago
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Genome-scale model for Mus musculus
- Host: GitHub
- URL: https://github.com/sysbiochalmers/mouse-gem
- Owner: SysBioChalmers
- License: cc-by-4.0
- Created: 2019-12-20T12:57:43.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2023-12-10T15:22:29.000Z (over 2 years ago)
- Last Synced: 2025-07-29T06:56:27.248Z (11 months ago)
- Topics: standard-gem
- Language: MATLAB
- Homepage:
- Size: 124 MB
- Stars: 8
- Watchers: 1
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
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README
# Mouse-GEM: The generic genome-scale metabolic model of _Mus musculus_
[](https://badge.fury.io/gh/sysbiochalmers%2FMouse-GEM)
#### Brief Model Description
This repository contains the latest version of Mouse-GEM, a mouse genome-scale metabolic model.
#### Citation
> H. Wang, J. L. Robinson, P. Kocabaş, J. Gustafsson, M. Anton, P.-E. Cholley, et al. Genome-scale metabolic network reconstruction of model animals as a platform for translational research. _PNAS_ 118, e2102344118 (2021). [doi.org/10.1073/pnas.2102344118](https://doi.org/10.1073/pnas.2102344118)
#### Model Keywords
**Utilisation:** multi-omics integrative analysis, predictive simulation
**Field:** metabolic-network reconstruction
**Type of Model:** reconstruction, curated
**Model source:** [Human-GEM](https://doi.org/10.1126/scisignal.aaz1482)
**Omic source:** genomics; metabolomics
**Taxonomic name:** _Mus musculus_
**Taxonomy ID:** [10090](https://identifiers.org/taxonomy:10090)
**Genome ID:** [GCA_000001635.8](https://identifiers.org/insdc.gca:GCA_000001635.8)
**Metabolic System:** general metabolism
**Tissue:**
**Bioreactor:**
**Cell type:**
**Cell line:**
**Condition:** generic metabolism
### Model Overview
|Taxonomy | Template Model | Reactions | Metabolites| Genes |
| ------------- |:-------------:|:-------------:|:-------------:|:-----:|
|_Mus musculus_ | Human-GEM | 13020 | 8373 | 2959 |
## Installation
### Required Software
* A functional MATLAB installation (MATLAB 7.3 and higher).
* The [RAVEN toolbox](https://github.com/SysBioChalmers/RAVEN).
* The [COBRA toolbox](https://github.com/opencobra/cobratoolbox) (not necessary for most functionality).
### Dependencies - Recommended Software
* The libSBML MATLAB API (version [5.13.0](https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/) is recommended).
* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations.
### Installation Instructions
* Clone the [main branch](https://github.com/SysBioChalmers/Mouse-GEM/tree/main) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Mouse-GEM/releases/latest).
* Add the directory to your MATLAB path (instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)).
## Usage
#### Loading/saving the model
`Mouse-GEM.mat` (Recommended if on `main` branch)
* Load and save using the built-in MATLAB `load()` and `save()` functions.
`Mouse-GEM.xml` (SBML format)
* Load using the `importModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN))
* Save using the `exportModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN))
## Websites
- [Metabolic Atlas](https://metabolicatlas.org/) enables visualization and exploration of Mouse-GEM content.
### Contributing
Contributions are always welcome! Please read the [contributing guidelines](.github/CONTRIBUTING.md) to get started.