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chore: update-doi #362

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Jan 24, 2024
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12 changes: 6 additions & 6 deletions README.md
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[![GitHub Discussions](https://img.shields.io/github/discussions-search?query=repo%3Asysbiochalmers%2Fgecko&label=GitHub%20Discussions)](https://github.com/SysBioChalmers/GECKO/discussions)
[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.7699818.svg)](https://doi.org/10.5281/zenodo.7699818)

## About GECKO 3
## About GECKO 3.0

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 [protocols paper](#citation).

_**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. 2024 Jan 18:1-39. 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.

## Citation

- The GECKO 3 publication is in press at Nature Protocols. Once published, citation information will appear here.

## Contributing

Contributions are always welcome! Please read the [contributing guidelines](https://github.com/SysBioChalmers/GECKO/blob/main/.github/CONTRIBUTING.md) to get started.
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% This file accompanies the GECKO3 Nature Protocols paper (DOI TO BE ADDED).
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% This file accompanies the GECKO3 Nature Protocols paper (DOI TO BE ADDED).
% This file accompanies the GECKO 3 Nature Protocols paper https://doi.org/10.1038/s41596-023-00931-7.
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% The function of this script is to demonstrate the reconstruction and
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