From fa75b3c65368201c157a558aad161624f82ec673 Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Tue, 23 Jan 2024 09:01:02 +0200 Subject: [PATCH] chore: update doi --- README.md | 12 ++++++------ tutorials/full_ecModel/protocol.m | 2 +- tutorials/light_ecModel/protocol.m | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 18cf4853..77aab20e 100644 --- a/README.md +++ b/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. diff --git a/tutorials/full_ecModel/protocol.m b/tutorials/full_ecModel/protocol.m index c1b17eca..19805f4a 100644 --- a/tutorials/full_ecModel/protocol.m +++ b/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 diff --git a/tutorials/light_ecModel/protocol.m b/tutorials/light_ecModel/protocol.m index f6467131..bccc053b 100644 --- a/tutorials/light_ecModel/protocol.m +++ b/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