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

Join the chat at https://gitter.im/SysBioChalmers/Human-GEM GitHub version DOI All Contributors

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

Installation Instructions

% 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)

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
Anne Niknejad

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Avlant
Avlant

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BenjamΓ­n SΓ‘nchez
BenjamΓ­n SΓ‘nchez

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Christoff1993
Christoff1993

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Christoff1993
Christoff1993

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Daniel Weindl
Daniel Weindl

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Devlin Moyer
Devlin Moyer

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Eduard Kerkhoven
Eduard Kerkhoven

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Hao Wang
Hao Wang

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Jiahao Luo
Jiahao Luo

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Jonathan Robinson
Jonathan Robinson

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Jorge Ferreira
Jorge Ferreira
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Jose L. Cadavid
Jose L. Cadavid

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Juliette
Juliette

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Justin Reimertz
Justin Reimertz

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Marco Pagni
Marco Pagni

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Mihail Anton
Mihail Anton

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Pierre-Etienne Cholley
Pierre-Etienne Cholley
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Pierre-Etienne Cholley
Pierre-Etienne Cholley
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PkiwiBird
PkiwiBird

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Pranas Grigaitis
Pranas Grigaitis

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Pınar Kocabaş
Pınar Kocabaş

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Rasool Saghaleyni
Rasool Saghaleyni

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Sarah Cherkaoui
Sarah Cherkaoui

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Simonas MarciΕ‘auskas
Simonas MarciΕ‘auskas

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TunahanCakir
TunahanCakir

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Xuhang Li
Xuhang Li

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feiranl
feiranl

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johan-gson
johan-gson

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manas-kohli
manas-kohli

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smoretti
smoretti

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stairs
stairs

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