This repository contains the latest version of Human-GEM, a human genome-scale metabolic model. We encourage contributions.
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
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
| Taxonomy | Template Model | Reactions | Metabolites | Genes |
|---|---|---|---|---|
| Homo sapiens | HMR2, Recon3D, iHsa | 13078 | 8370 | 3625 |
This repository is administered by Jonathan Robinson (@JonathanRob) and Hao Wang (@Hao-Chalmers), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.
Contributions are always welcome! Please read the Contributing guidelines before start.
Detailed instructions on the installation and use of the Human-GEM model and repository can be found in the Human-GEM user guide.
- A functional MATLAB installation (MATLAB 7.3 and higher).
- The RAVEN toolbox.
- The COBRA toolbox (not necessary for most functionality).
- The libSBML MATLAB API (version 5.13.0 is recommended).
- Gurobi Optimizer for any simulations.
- Clone the main branch of this repository, or download the latest release.
- Add the directory to your MATLAB path (instructions here).
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.
Human-GEM.mat (Recommended if on main branch)
- Load and save using the built-in MATLAB
load()andsave()functions.
Human-GEM.yml (Recommended if on develop or other branches)
- Load using the
importYaml.mfunction (incode/io/) - Save using the
exportYaml.mfunction (incode/io/)
Human-GEM.xml (SBML format)
- Load using the
importModel.mfunction (from RAVEN Toolbox) - Save using the
exportModel.mfunction (from RAVEN Toolbox)
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.
- 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.
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.
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