https://github.com/sysbiochalmers/worm-gem
Genome-scale model for Caenorhabditis elegans
https://github.com/sysbiochalmers/worm-gem
standard-gem
Last synced: 12 months ago
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Genome-scale model for Caenorhabditis elegans
- Host: GitHub
- URL: https://github.com/sysbiochalmers/worm-gem
- Owner: SysBioChalmers
- License: cc-by-4.0
- Created: 2020-11-24T10:09:19.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2023-12-10T15:52:42.000Z (over 2 years ago)
- Last Synced: 2025-04-06T22:04:05.737Z (about 1 year ago)
- Topics: standard-gem
- Language: MATLAB
- Homepage:
- Size: 17.7 MB
- Stars: 4
- Watchers: 0
- Forks: 1
- 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
# Worm-GEM: The generic genome-scale metabolic model of _Caenorhabditis elegans_
[](https://badge.fury.io/gh/sysbiochalmers%2FWorm-GEM)
#### Description
This repository contains the latest version of Worm-GEM, a worm 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:** _Caenorhabditis elegans_
**Taxonomy ID:** [6239](https://identifiers.org/taxonomy:6239)
**Genome ID:** [GCA_000002985.3](https://identifiers.org/insdc.gca:GCA_000002985.3)
**Metabolic System:** general metabolism
**Tissue:**
**Bioreactor:**
**Cell type:**
**Cell line:**
**Condition:** generic metabolism
### Model Overview
|Taxonomy | Template Model | Reactions | Metabolites| Genes |
| ------------- |:-------------:|:-------------:|:-------------:|:-----:|
|_Caenorhabditis elegans_ | Human-GEM | 12175 | 8140 | 1732 |
## 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/Worm-GEM/tree/main) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Worm-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
`Worm-GEM.mat` (Recommended if on `main` branch)
* Load and save using the built-in MATLAB `load()` and `save()` functions.
`Worm-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 Worm-GEM content.
### Contributing
Contributions are always welcome! Please read the [contributing guidelines](.github/CONTRIBUTING.md) to get started.