Merge pull request #362 from SysBioChalmers/chore/update-doi

chore: update-doi

README.md

@@ -4,24 +4,24 @@
 [![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.

tutorials/full_ecModel/protocol.m

@@ -1,4 +1,4 @@
-% 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.
 %
 % The function of this script is to demonstrate the reconstruction and
 % analysis of a *full* ecModel. As example, it here uses the yeast-GEM

tutorials/light_ecModel/protocol.m

@@ -1,4 +1,4 @@
-% 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.
 %
 % The function of this script is to demonstrate the reconstruction and
 % analysis of a *full* ecModel. As example, it here uses the yeast-GEM