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. Kocabasÿ, 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. Kocabasÿ, 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	{{nRXN}}	{{nMET}}	{{nGENE}}

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

Basic user

If you want to use the model for your own model simulations, you can use any software that accepts SBML L3V1 FBCv3 formatted model files. This includes any of the following:

MATLAB-based

• RAVEN Toolbox v2.10.3 or later (recommended, see Installation instructions)
• COBRA Toolbox

Python-based

• cobrapy

Please see the installation instructions for each software package.

Developer

MATLAB-based

If you want to contribute to the development of Human-GEM, or otherwise want to run any of the provided MATLAB functions, then the following software is required:

• RAVEN Toolbox v2.10.3 or later (recommended, see Installation instructions)

Python-based

You can also contribution to the development of Human-GEM via python (e.g. cobrapy), even if you would not be able to run any of the model-specific MATLAB functions. To curate the model, you can still edit Human-GEM.yml, genes.tsv, metabolites.tsv and reactions.tsv, all located in the model/ folder.

Recommended solver

• When performing simulations with Human-GEM, you are encouraged to use Gurobi Optimizer.

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.

The model development is based on the yml file (to facilitate tracking of model changes), so that this is the only model format available on non-main branches (such as develop). See also the location of annotation information.

Usage

Loading/saving the model in MATLAB

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

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

By default, additional annotation information and external identifiers for Human-GEM reactions, metabolites, and genes are not kept in the yml file, but rather provided as tsv files in the model/ directory (reactions.tsv, metabolites.tsv, and genes.tsv, respectively). The annotateGEM function can add those annotations in MATLAB, while direct import/export of this annotation data is done through 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 🐛	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 🐛 🖋