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	13082	8378	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 model/ directory. Note that only the .yml version is available on branches other than master (e.g., devel), to facilitate tracking of model changes.

Reaction, Metabolite, and Gene Annotations

Additional annotation information and external identifiers for Human-GEM reactions, metabolites, and genes can be found in the respective reactions.tsv, metabolites.tsv, and genes.tsv files in the model/ directory. To import/export this annotation data to/from MATLAB, use the importTsvFile and exportTsvFile functions, respectively.

Usage

Loading/saving the model

Human-GEM.mat (Recommended if on master branch)

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

Human-GEM.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/)

Human-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 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