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laduplessis committed Feb 4, 2017
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58 changes: 55 additions & 3 deletions README.md
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# Taming the BEAST
# Taming the BEAST website

To be completed later. This site is based on Trevor Bedford's lab website ([http://bedford.io](http://bedford.io))
Taming the BEAST is a platform for collating a comprehensive and cohesive set of BEAST 2 tutorials in one location, providing researchers the resources necessary to learn how to perform analyses in BEAST 2. This GitHub repository stores the source code for the Taming the BEAST website. The site is based on Trevor Bedford's lab website ([http://bedford.io](http://bedford.io)).

## Build site

To build the website locally, clone the repo with:

```
git clone https://github.com/Taming-the-BEAST/blotter.git
```

Then install necessary Ruby dependencies by running `bundle install` from within the `blotter` directory. After this, the site can be be built with:

```
bundle exec jekyll build
```

To view the site, run `bundle exec jekyll serve` and point a browser to `http://localhost:4000/`. More information on Jekyll can be found [here](http://jekyllrb.com/).

To include the tutorials, preprocessing scripts are necessary to clone tutorial repos and update Jekyll metadata. This can be accomplished with:

```
ruby _scripts/update-and-preprocess.rb
```

Then `bundle exec jekyll build` works as normal.

See [Building a local copy of the site](https://taming-the-beast.github.io/contribute/Building-a-local-copy-of-the-site/) for more information.


## License
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**The MIT License (MIT)**

Copyright (c) 2013-2016 Trevor Bedford
Copyright (c) 2016-2017 Louis du Plessis, 2013-2016 Trevor Bedford

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.


## TODOs

### Website source
- Add RSS/Atom feed for updated tutorials
- Add link for RSS/Atom feeds
- Add BEAST version to tutorial layout page
- Clean up repository and remove unnecessary files


### Website contents
- Write a proper style guide for tutorials (current style guide is just a markdown syntax cheatsheet)
- Rewrite documentation on adding tutorials (mentioning style to be followed)
- Add documentation for converting between Markdown and Latex
- Need new news posts (funding for future, new style guide etc.)
- About page should be rewritten to make sure it is concurrent with the paper.


### Tutorials
- Update Latex and layout for all latex tutorials (should use auto-generated latex from markdown tutorial)
- Fix Structured coalescent tutorial (estimate gamma shape)
- Fix Structured birth-death tutorial (estimate gamma shape)
- Add FBD tutorial (need precooked runs and xml)
- Structured coalescent tutorial markdown
- FBD tutorial markdown
83 changes: 66 additions & 17 deletions about/index.html
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<head>
<meta charset="utf-8"/>
<title>About Taming the BEAST</title>
<title>Taming the BEAST / about</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">

<!-- RSS feed -->
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<!-- Google Analytics -->
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');

ga('create', 'UA-26244371-2', 'laduplessis.github.io/Taming_the_BEAST_blotter');
ga('send', 'pageview');
ga('create', 'UA-86786826-1', 'auto');
ga('send', 'pageview');

</script>

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<a href="/tutorials/">tutorials</a></li>

<li class="active">
<li>

<a href="/about/">about</a></li>
<a href="/contribute/">contribute</a></li>
</ul>
</div>

</div>
</nav>
</div>

<!--div class="headerspacer"></div-->

<div class="container">

<div class="row">
<div class="col-md-10">
<div class="bigtitle">
<div class="col-md-2">
</div>
<div class="col-md-8">
<div class="title">
About Taming the BEAST
</div>
</div>
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<div class="post">
<p>Phylogenetics and phylodynamics are central topics in modern biology. Phylogenetic inferences reconstruct the evolutionary relationships between organisms, whereas phylodynamic inferences reveal the dynamics that lead to the observed relationships. These two fields have many practical applications in disciplines such as epidemiology, developmental biology, paleontology, ecology and even linguistics. However phylogenetics and phylodynamics are complex and fast-evolving fields. As such, inference tools are not easily accessible to researchers who are not from a computational background.</p>

<p>BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.</p>
<p><a href="http://beast2.org">BEAST 2</a> is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results. A core aspect of the BEAST 2 design philosophy is to allow researchers to extend the core program without the involvement of the BEAST 2 developers. New methods are implemented as standalone packages that are developed and maintained separately of BEAST 2 itself. </p>

<p>BEAST 2 is a complex program and with the resources available on the internet it is challenging to learn BEAST without the help of an expert.
Workshops, summer schools and lectures can only reach a handful of the people interested in performing BEAST analyses.
The <strong>Taming the BEAST</strong> website will provide a platform that collects all tutorials for <a href="%22http://beast2.org%22">BEAST 2</a> (and perhaps BEAST 1 as well) in one central repository.
In this way a set of well-curated and up-to-date tutorials will be available for the community at large. </p>
<p>BEAST 2 is a complex program and it is challenging to learn BEAST without the help of an expert.
Workshops, summer schools and lectures are a great resource, but can only reach a handful of the people interested in performing BEAST analyses.
<strong>Taming the BEAST</strong> is a platform for collecting a comprehensive set of BEAST 2 tutorials in one location.
By providing a set of well-curated and up-to-date tutorials Taming the BEAST aims to fill this gap and provide researchers with the resources necessary to learn how to perform analyses in BEAST 2!</p>

<p>In keeping with the BEAST 2 design it is possible for anyone to extend or correct the set of tutorials on the website. Thus, Taming the BEAST relies on the community to curate tutorials and raise issues to ensure that all of the tutorials are up-to-date. Furthermore, it is possible for developers to upload tutorials to newly implemented packages. Finally, we also encourage anyone else with useful BEAST 2 teaching materials to upload them. Find out how you can <a href="/contribute">contribute</a>!</p>

</div>
</div>
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</div>

<div class="footerspacer"></div>

<div class="footer">
<div class="container">
<div class="col-md-6 reduced-gutter">
<div class="bigspacer"></div>
<ul class="list-inline">
<li class="footernav">
<i class="fa"></i> <a class="foot" href="/about/">about</a>
</li>
<li class="footernav">
<i class="fa"></i> <a class="foot" href="/workshops/">workshops</a>
</li>
<li class="footernav">
<i class="fa"></i> <a class="foot" href="/contact/">contact</a>
</li>
<li class="footernav">
<i class="fa"></i> <a class="foot" href="/license/">license</a>
</li>
</ul>
<div class="spacer"></div>
</div>

<div class="col-md-5 text-right">
<div class="bigspacer"></div>
<ul class="list-inline">
<li class="footernav">
<i class="fa"></i>powered by <a class="foot" href="http://pages.github.com">GitHub</a> and <a class="foot" href="http://www.jekyllrb.com">Jekyll</a>
</li>
</ul>
<div class="spacer"></div>
</div>

<div class="col-md-1 reduced-gutter">
<div class="spacer"></div>
<div class="title text-gray">
<a class="foot" href="http://www.github.com/taming-the-beast"><i class="fa fa-github fa-fw"></i></a>
</div>
<div class="spacer"></div>
</div>
</div>
</div>

<div id="footer"><span style="display:none">foo</span></div>
<!--div id="footer"><span style="display:none">foo</span></div-->

</body>
</html>
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10 changes: 3 additions & 7 deletions all-posts.json
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{
"posts" : [

"/news/Website-demo/",
"/news/Welcome-to-Waiheke!/",

"/news/Markdown-tutorials/",
"/news/Engelberg-lecture-slides/",

"/news/Adding-a-new-tutorial/",

"/news/Distributed-vs-Central/",

"/news/Style/"
"/news/Welcome-BEAST-tamers!/"

]
}
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