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](#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
