https://github.com/sysbiochalmers/human-gem

The generic genome-scale metabolic model of Homo sapiens
https://github.com/sysbiochalmers/human-gem

genome-scale-models human-metabolism standard-gem

Last synced: 8 months ago
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The generic genome-scale metabolic model of Homo sapiens

Host: GitHub
URL: https://github.com/sysbiochalmers/human-gem
Owner: SysBioChalmers
License: cc-by-4.0
Created: 2017-10-04T09:43:30.000Z (about 8 years ago)
Default Branch: main
Last Pushed: 2024-06-24T23:14:29.000Z (over 1 year ago)
Last Synced: 2024-09-06T18:44:31.756Z (over 1 year ago)
Topics: genome-scale-models, human-metabolism, standard-gem
Language: MATLAB
Homepage: https://sysbiochalmers.github.io/Human-GEM-guide/
Size: 312 MB
Stars: 93
Watchers: 16
Forks: 40
Open Issues: 81
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md

Awesome Lists containing this project

README

          # Human-GEM: The generic genome-scale metabolic model of _Homo sapiens_

[![Join the chat at https://gitter.im/SysBioChalmers/Human-GEM](https://badges.gitter.im/SysBioChalmers/Human-GEM.svg)](https://gitter.im/SysBioChalmers/Human-GEM?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![GitHub version](https://badge.fury.io/gh/sysbiochalmers%2FHuman-GEM.svg)](https://badge.fury.io/gh/sysbiochalmers%2FHuman-GEM)

[![DOI](https://zenodo.org/badge/105752644.svg)](https://zenodo.org/badge/latestdoi/105752644)

[![All Contributors](https://img.shields.io/badge/all_contributors-32-success.svg)](#contributors)

 

### Brief Model Description

This repository contains the latest version of Human-GEM, a human genome-scale metabolic model. We encourage [contributions](#contributing).

### 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](https://doi.org/10.1126/scisignal.aaz1482)

 

Starting from Human-GEM v1.5.0, all the releases are also archived in [Zenodo](https://doi.org/10.5281/zenodo.4099692) 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](https://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](https://github.com/SysBioChalmers/Human-GEM/wiki) or have a look at the [Contributing guidelines](https://github.com/SysBioChalmers/Human-GEM/blob/main/.github/CONTRIBUTING.md) 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](https://sysbiochalmers.github.io/Human-GEM-guide/).

## Installation

### Required Software

* A functional MATLAB installation (MATLAB 7.3 and higher).

* The [RAVEN toolbox](https://github.com/SysBioChalmers/RAVEN).

* The [COBRA toolbox](https://github.com/opencobra/cobratoolbox) (not necessary for most functionality).

### Dependencies - Recommended Software

* The libSBML MATLAB API (version [5.13.0](https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/) is recommended).

* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations.

### Installation Instructions

* Clone the [main branch](https://github.com/SysBioChalmers/Human-GEM/tree/main) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Human-GEM/releases/latest).

* Add the directory to your MATLAB path either by using the lines below or manually (instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)).

```matlab

% 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](https://github.com/SysBioChalmers/RAVEN))

* Save using the `exportModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN))

## 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](https://metabolicatlas.org/) enables visualization and exploration of Human-GEM content.

- The [Human-GEM user guide](https://sysbiochalmers.github.io/Human-GEM-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](https://github.com/SysBioChalmers/Human-maps). These maps can be downloaded from the repository or explored interactively using [Metabolic Atlas](https://metabolicatlas.org/explore/map-viewer/human1).

## 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
🐛 🖋

ecosyste.ms

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https://github.com/sysbiochalmers/human-gem

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