README.md

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. We encourage contributions.

Cite us:

If you use Human1 in your research, please cite:

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

Starting from Human-GEM v1.5.0, all the releases are also archived in Zenodo from which specific version can be cited if used.

If you use Mouse1, Rat1, Zebrafish1, Fruitfly1, or Worm1 in your research, please cite:

H. Wang, J. L. Robinson, P. Kocabas, 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: 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	12971	8455	2887

Contributing

Contributions are always welcome! Read more about the project's philosophy in our wiki or have a look at the Contributing guidelines before starting.

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 main branch of this repository, or download the latest release.
• Add the directory to your MATLAB path either by using the lines below or manually (instructions here).

% Replace "/my/path/" with the actual path to the Human-GEM folder
cd /my/path/Human-GEM/code
% This will add the relevant paths to the path variable in MATLAB
HumanGEMInstaller.install
% It is also possible to remove Human-GEM from the MATLAB path using
HumanGEMInstaller.uninstall

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 main (e.g., develop), to facilitate tracking of model changes.

Usage

Loading/saving the model

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

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

Human-GEM.yml (Recommended if on develop or other branches)

• Load using the importYaml.m function (in code/io/)
• Save using the exportYaml.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)

Reaction, Metabolite, and Gene Annotations

Additional annotation information and external identifiers for Human-GEM reactions, metabolites, and genes are provided as tsv files in the model/ directory (reactions.tsv, metabolites.tsv, and genes.tsv, respectively).

To import/export this annotation data to/from MATLAB, use the importTsvFile and exportTsvFile functions, respectively.

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.

Contributors

Anne Niknejad 🐛 🖋 🔬	Avlant 🐛 🖋	Benjamín Sánchez 💬	Christoff1993 🐛	Christoff1993 🐛	Daniel Weindl 🐛	Devlin Moyer 🐛 🖋 🔬 👀	Eduard Kerkhoven 🐛 💻 💬 👀
Hao Wang 🐛 💻 🔣 📖 🤔 🚇 🚧 📦 📆 💬 🔬 👀 ⚠️ 📢	Jiahao Luo 🐛 🖋	Jonathan Robinson 🐛 💻 🔣 📖 🤔 🚇 🚧 📦 📆 💬 🔬 👀 ✅ 📢	Jorge Ferreira 🐛	Jose L. Cadavid 🐛 🔬	Juliette 🐛 🖋	Justin Reimertz 🐛 🖋 👀	Marco Pagni 🐛 🔬
Mihail Anton 🐛 💻 🤔 🚇 👀 ⚠️ 📢	Pierre-Etienne Cholley 🐛 💻 🖋 🔬 👀	Pierre-Etienne Cholley 🐛	PkiwiBird 🐛 🔬 💻	Pranas Grigaitis 🐛 🖋 💻 🔬	Pınar Kocabaş 🐛 🔬 👀	Rasool Saghaleyni 🤔 🔬	Sarah Cherkaoui 🐛 🖋 💻 🔬
Simonas Marcišauskas 💬	TunahanCakir 🐛	Xuhang Li 🐛	feiranl 🐛 💻 🔣 📖 🤔 🚇 🚧 📦 📆 🔬 👀	johan-gson 🐛 🖋 🔬	manas-kohli 🐛	smoretti 🐛 🔬	stairs 🐛 🖋