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@@ -8,6 +8,18 @@ If you are using RAVEN in any scientific work, please cite: [R. Agren, et. al,
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Please report any technical issues and bugs [here](https://github.com/SysBioChalmers/RAVEN/issues). For other issues, please contact [Eduard Kerkhoven](https://github.com/edkerk).
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-----
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## Overview
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[Releases](#releases)
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[Installation](#installation)
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[Tutorials](#tutorials)
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[Hidden Markov Models for KEGG reconstruction](#hidden-markov-models-for-kegg-reconstruction)
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-----
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## Releases
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RAVEN can be installed via cloning the GitHub repository as per below or by downloading and extracting one of the a zipped [release](https://github.com/SysBioChalmers/RAVEN/releases). Please note that the releases do not always represent the most up to date version.
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```
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* Alternatively, download the latest [release](https://github.com/SysBioChalmers/RAVEN/releases) of RAVEN Toolbox as a ZIP file, and extracted to your favourite directory.
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Once extracted, ensure that all other software dependencies (e.g. libSBML, Gurobi) are installed (see above for [list](#dependencies), below for [instructions](#libSBML). Then, open MATLAB and run the following command:
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Once extracted, ensure that all other software dependencies (e.g. libSBML, Gurobi) are installed (see above for [list](#dependencies), below for [instructions](#libsbml). Then, open MATLAB and run the following command:
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```matlab
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cd('[location]/RAVEN/installation'))
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checkInstallation
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#### Mosek
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1. Download from the link [above](#dependencies) and install Mosek to your favourite location.
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2. Make sure you obtained a [license](https://www.mosek.com/products/academic-licenses/) following [instructions] (https://docs.mosek.com/8.0/install/installation.html#setting-up-the-license).
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2. Make sure you obtained a [license](https://www.mosek.com/products/academic-licenses/) following [instructions](https://docs.mosek.com/8.0/install/installation.html#setting-up-the-license).
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3. To install Mosek in MATLAB, follow [instructions](https://docs.mosek.com/8.0/toolbox/installation.html#id1). Note: the documentation mentions version 8, but RAVEN only works with version 7 of Mosek.
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4. Make sure that MATLAB remembers the Mosek installation for next time, by running the following command:
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| Dataset | KEGG version | Phylogeny |
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|:-------:|:------------:|:---------:|
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|[eukaryota](http://biomet-toolbox.org/tools/downloadable/files/euk100_kegg82.zip)|58.1|eukaryota
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|[prokaryota](http://biomet-toolbox.org/tools/downloadable/files/euk100_kegg82.zip)|58.1|eukaryota
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|[prokaryota](http://biomet-toolbox.org/tools/downloadable/files/euk100_kegg82.zip)|58.1|eukaryota
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## Links
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For more systems biology related software and recently published genome-scale models from the Systems and Synthetic Biology group at Chalmers University of Technology, please visit the [Github page](https://github.com/SysBioChalmers). For more information and publications by the Systems and Synthetic Biology please visit [SysBio](www.sysbio.se).

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