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https://github.com/sysbiochalmers/gecko
Toolbox for including enzyme constraints on a genome-scale model.
https://github.com/sysbiochalmers/gecko
data-integration enzyme-constraints kinetics matlab proteomics systems-biology toolbox
Last synced: 6 days ago
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Toolbox for including enzyme constraints on a genome-scale model.
- Host: GitHub
- URL: https://github.com/sysbiochalmers/gecko
- Owner: SysBioChalmers
- License: mit
- Created: 2016-06-15T09:48:01.000Z (over 8 years ago)
- Default Branch: main
- Last Pushed: 2024-10-19T23:11:16.000Z (18 days ago)
- Last Synced: 2024-10-25T04:25:01.309Z (13 days ago)
- Topics: data-integration, enzyme-constraints, kinetics, matlab, proteomics, systems-biology, toolbox
- Language: MATLAB
- Homepage: http://sysbiochalmers.github.io/GECKO/
- Size: 105 MB
- Stars: 67
- Watchers: 11
- Forks: 50
- Open Issues: 13
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Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE.md
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
[](https://GitHub.com/SysBioChalmers/GECKO/releases/)
[](https://github.com/SysBioChalmers/GECKO/discussions)
[](https://doi.org/10.5281/zenodo.7699818)
[](https://se.mathworks.com/matlabcentral/fileexchange/125960-gecko-toolbox)
## About GECKO 3
The **GECKO** toolbox enhances a **G**enome-scale model to account for **E**nzyme **C**onstraints, using **K**inetics and **O**mics. The resulting enzyme-constrained model (**ecModel**) can be used to perform simulations where enzyme allocation is either drawn from a total protein pool, or constrained by measured protein levels from proteomics data.
💡 In the [`GECKO/tutorials`](https://github.com/SysBioChalmers/GECKO/tree/main/tutorials) folder there are examples of how GECKO can be applied to GEMs, in either of its _full_ or _light_ forms. Each `protocol.m` contains instructions on how to reconstruct and analyze an ecModel, demonstrating how different fuctions in GECKO can be used. These two scripts complement the [Nature Protocols](https://doi.org/10.1038/s41596-023-00931-7) paper ([**PDF**](https://drive.google.com/file/d/1_AGz6GmQPOyshfUZ6K-L2myzU43rQ6tu/view)).
### Significant changes since protocol publication
- GECKO **3.2.0**: all protein usage reactions draw from the protein pool, even if they are constrained by proteomics data. This affects **Step 58** in the protocol, changing behaviour of `constrainEnzConcs` and making `updateProtPool` obsolete, `tutorials/full_ecModel/protocol.m` is updated to reflect this change. See [#357](https://github.com/SysBioChalmers/GECKO/issues/375) for more details.
_**Note:** Regarding code and model compatibility with earlier GECKO versions, see [Previous versions: GECKO 1 and 2](https://github.com/SysBioChalmers/GECKO/wiki/Previous-versions:-GECKO-1-and-2)_.
## Cite us
If you have used GECKO in your work, please cite:
> Chen Y, Gustafsson J, Tafur Rangel A, Anton M, Domenzain I, Kittikunapong C, Li F, Yuan L, Nielsen J & Kerkhoven EJ. Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0. *Nature Protocols* **19**, 629-667 (2024). doi:[10.1038/s41596-023-00931-7](https://doi.org/10.1038/s41596-023-00931-7).
## Documentation
**Installation instructions** and other information is available in the **[Wiki](https://github.com/SysBioChalmers/GECKO/wiki)**. The source code documentation is also available
[online](http://sysbiochalmers.github.io/GECKO/doc/). Use [GitHub Discussions](https://github.com/SysBioChalmers/GECKO/discussions) for support, to ask questions or leave comments.
## Contributing
Contributions are always welcome! Please read the [contributing guidelines](https://github.com/SysBioChalmers/GECKO/blob/main/.github/CONTRIBUTING.md) to get started.