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

Genome-scale model for Danio rerio
https://github.com/sysbiochalmers/zebrafish-gem

standard-gem

Last synced: 19 days ago
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Genome-scale model for Danio rerio

• Host: GitHub
• URL: https://github.com/sysbiochalmers/zebrafish-gem
• Owner: SysBioChalmers
• License: cc-by-4.0
• Created: 2020-11-24T10:28:09.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2023-12-10T15:37:11.000Z (about 1 year ago)
• Last Synced: 2024-06-07T11:46:59.224Z (7 months ago)
• Topics: standard-gem
• Language: MATLAB
• Homepage:
• Size: 19.4 MB
• Stars: 4
• Watchers: 2
• 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

        

# Zebrafish-GEM: The generic genome-scale metabolic model of _Danio rerio_

[![GitHub version](https://badge.fury.io/gh/sysbiochalmers%2FZebrafish-GEM.svg)](https://badge.fury.io/gh/sysbiochalmers%2FZebrafish-GEM)

#### Brief Model Description

This repository contains the latest version of Zebrafish-GEM, a zebrafish 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:** _Danio rerio_  

**Taxonomy ID:** [7955](https://identifiers.org/taxonomy:7955)  

**Genome ID:** [GCA_000002035.4](https://identifiers.org/insdc.gca:GCA_000002035.4)  

**Metabolic System:** general metabolism  

**Tissue:**  

**Bioreactor:**    

**Cell type:**  

**Cell line:**  

**Condition:** generic metabolism

### Model Overview

|Taxonomy | Template Model | Reactions | Metabolites| Genes |

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

|_Danio rerio_ |   Human-GEM |  12910  | 8347 | 2714 |

## 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/Zebrafish-GEM/tree/main) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Zebrafish-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

`Zebrafish-GEM.mat` (Recommended if on `main` branch)

* Load and save using the built-in MATLAB `load()` and `save()` functions.

`Zebrafish-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 Zebrafish-GEM content.

### Contributing

Contributions are always welcome! Please read the [contributing guidelines](.github/CONTRIBUTING.md) to get started.