Worm-GEM: The generic genome-scale metabolic model of Caenorhabditis elegans

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

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: Caenorhabditis elegans
Taxonomy ID: 6239
Genome ID: 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.
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

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

Websites

Metabolic Atlas enables visualization and exploration of Worm-GEM content.

Contributing

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