Human-GEM: The generic genome-scale metabolic model of Homo sapiens

Brief Model Description

This repository contains the latest version of Human-GEM, a human genome-scale metabolic model.

Citation

J. L. Robinson, P. Kocabasÿ, H. Wang, P.-E. Cholley, et al. An atlas of human metabolism. Sci. Signal. 13, eaaz1482 (2020). doi:10.1126/scisignal.aaz1482

Model Keywords

Utilisation: predictive simulation, multi-omics integrative analysis, model template
Field: metabolic-network reconstruction
Type of Model: reconstruction, curated
Model Source: HPA, HMR2, iHsa, iHepatocytes2322, Recon3D
Omic Source: genomics, proteomics
Taxonomy: Homo sapiens
Metabolic System: general metabolism
Condition: generic metabolism

Model Overview

Taxonomy	Template Model	Reactions	Metabolites	Genes
Homo sapiens	HMR2, Recon3D, iHsa	13417	10138	3625

Administration

This repository is administered by Jonathan Robinson (@JonathanRob) and Hao Wang (@Hao-Chalmers), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.

User Guide

Detailed instructions on the installation and use of the Human-GEM model and repository can be found in the Human-GEM user guide.

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

Model Files

The model is available as .xml, .xlsx, .txt, .yml, and .mat in the modelFiles/ directory. Note that only the .yml version is available on branches other than master (e.g., devel), to facilitate tracking of model changes.

Usage

Loading/saving the model

HumanGEM.mat (Recommended if on master branch)

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

HumanGEM.yml (Recommended if on devel or other branches)

• Load using the importHumanYaml.m function (in code/io/)
• Save using the writeHumanYaml.m function (in code/io/)

HumanGEM.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 Human-GEM content.
• The Human-GEM user guide provides detailed instructions and examples for using the Human-GEM model and repository.

Metabolic Maps

A collection of manually curated 2D metabolic maps associated with Human-GEM are stored in the Human-maps repository. These maps can be downloaded from the repository or explored interactively using Metabolic Atlas.

Contributing

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

Contributors

• Jonathan L. Robinson, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory (SciLifeLab), Chalmers University of Technology, Gothenburg Sweden
• Pÿnar Kocabaÿ, Chalmers University of Technology, Gothenburg Sweden
• Pierre-Etienne Cholley, Chalmers University of Technology, Gothenburg Sweden
• Avlant Nilsson, Chalmers University of Technology, Gothenburg Sweden
• Hao Wang, Chalmers University of Technology, Gothenburg Sweden