Zebrafish-GEM: The generic genome-scale metabolic model of Danio rerio

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

Model Keywords

Utilisation: multi-omics integrative analysis, predictive simulation Field: metabolic-network reconstruction
Type of Model: reconstruction, curated
Model source: Human-GEM
Omic source: genomics; metabolomics
Taxonomic name: Danio rerio
Taxonomy ID: 7955
Genome ID: 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.
• The COBRA toolbox (not necessary for most functionality).

Dependencies - Recommended Software

• The libSBML MATLAB API (version 5.13.0 is recommended).
• Gurobi Optimizer for any simulations.

Installation Instructions

• Clone the main branch of this repository, or download the latest release.
• Add the directory to your MATLAB path (instructions here).

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)
• Save using the exportModel.m function (from RAVEN Toolbox)

Websites

• Metabolic Atlas enables visualization and exploration of Zebrafish-GEM content.

Contributing

Contributions are always welcome! Please read the contributing guidelines to get started.