4 Aug 2017 by Louis
The workshop organisers and participants outside of the London School of Hygiene and Tropical Medicine.


The third edition of Taming the BEAST took place last week at the London School of Hygiene and Tropical Medicine. I had a lot of fun at the workshop in London and also learned a lot. Thanks to a great bunch of participants who came out to learn about BEAST2 with us, I hope you enjoyed the workshop!

A lot of thanks goes to Stéphane Hué for organising and hosting the workshop at the London School of Hygiene and Tropical Medicine. Thanks also to Stéphane Hué, Sebastian Funk and Tanja Stadler for contributing to the cost of the workshop. Many thanks for the great talks from the invited speakers: Oliver Pybus, Alexei Drummond, Tim Vaughan, Huw Ogilvie, Tanja Stadler, Erik Volz, Nuno Faria and Nicola de Maio. All of their slides, as well as the lecture slides are available online. Thanks also to Remco Bouckaert and Walter Xie for their support all the way from New Zealand.

This was the first time the workshop was organised by a group not directly involved in developing BEAST2 packages. I think it went really well and I'm looking forward to the next edition! It was also the first time we ran the BEAST clinic - two 2-hour sessions specifically designed for participants to come to us with their own datasets and problems. I really enjoyed learning about what everyone is doing in BEAST2 and trying to help them improve analyses and get their runs mixing. Unfortunately the workshop was too short to get to everyone and solve all of the problems. I hope everyone got some pointers and got at least their most urgent issues resolved!

Before the workshop we also made a few tweaks to the website, added two new tutorials and updated several of the older tutorials:

Finally, it is now also possible to read the news feed and see tutorial updates by subscribing to the RSS feeds.

Our paper is now available in Systematic Biology!


5 May 2017 by Louis

A preliminary programme for Taming the BEAST in London is now available on the workshops page.

Just a reminder that registration is still open until 26 June and that the workshop costs only £245!

We are happy to announce that the next installment of Taming the BEAST will be in London, where it will be hosted by the London School of Hygiene & Tropical Medicine! Thanks to Stephane Hue for organising!

The workshop will take place from 24-28 July this year and will cost £245. Unlike previous workshops the fee does NOT include accommodation. It's the first time we are holding a workshop in a big city and it proved just too complicated to book a venue with accommodation, so we ask that participants arrange their own accommodation.

For more information visit the workshop's homepage.

Registration will be open until 26 June.

A preliminary programme will be posted on the workshops page soon.


The workshop organisers and participants on the beach outside the workshop venue.


It has already been more than two weeks since the second Taming the BEAST workshop took place on Waiheke island in New Zealand. Thanks to the group from the University of Auckland for putting up an amazing workshop in a stunning location! Thanks also to all the speakers for agreeing to take part and making the long journey to New Zealand!

The workshop was the first test of the website as a workshop tool. Although there were a few issues and misunderstandings, the website seems to be working. I'll be going over the feedback from the workshop in the next month and integrating any suggestions to the website. We also identified some issues with a few of the tutorials during the workshop and I'll also be updating them soon as well. If there are any further issues, please raise them on the Github repository of the tutorial in question. Finally, all of the lecture slides from the workshop have been uploaded and are available from the workshops page.

We are currently discussing and planning the next workshop in the series and it will be posted here as soon as the dates have been finalised!

At the Goldie estate vineyard where we had the workshop dinner.


5 Feb 2017 by Louis

The next Taming the BEAST workshop is officially about to start, on the beautiful Waiheke island, in the Hauruki Gulf of New Zealand! This time the workshop was organised by Alexei Drummond's group at the University of Auckland. The workshop program can be found here.

To prepare for the workshop we also uploaded 5 (five!) new tutorials and updated several of the older tutorials. The new tutorials are:

Thanks to Tim Vaughan, Walter Xie, Remco Bouckaert, Huw Ogilvie, David Duchêne and Simon Ho for their help preparing and checking tutorials!

I would also like to congratulate Tanja Stadler and her group for successfully writing a grant to host another Taming the BEAST workshop and to support 3 more workshops in the future! Keep checking the workshops page for updates on future workshops!

All of the lecture slides from the workshop held in Engelberg are now available for download. The slides are kept in a GitHub repository, and there is a link to the repository on the workshops page. Thanks to everyone for making their slides available! Please do not forget to attribute the authors if you use the slides anywhere!

In June this year we organised the first Taming the BEAST workshop, surrounded by the Swiss Alps, in Engelberg, Switzerland. The idea of holding a BEAST 2 workshop has been brewing for a while, motivated by the need for a Bayesian phylogenetics workshop that is focused on BEAST 2 and facilitates exchanges between developers and (both current and future) BEAST 2 users. During the workshop we realised that the materials we created and assembled for the workshop represent a very useful resource and that we could reach many more users by making them available to the community.

The 2016 workshop organisers and participants.


Originally we intended to simply release the tutorials and lecture slides in a single GitHub repository. However, after some discussions, we decided to build a Taming the BEAST website. The website provides a user-friendly front-end that collects tutorials, lecture slides and more in one location. To start, we have collected all of the tutorials from this year's workshop on the website (a couple are still missing, but they will be uploaded soon). Behind the scenes each tutorial lives in its own GitHub repository, where it's bundled along with all of the supporting data files and scripts needed to run the tutorial. We've also bundled example XML and output files with each tutorial. Although everything is available on a GitHub repository, there are also links to all of the files on the website.

All tutorials are available as PDF files from the website. We have started converting some of the tutorials to Markdown, which can be more easily displayed in a web browser. So far, three tutorials have been converted:

We hope that with time we will be able to convert all tutorials to Markdown. Don't worry if you want to print or download tutorials - PDFs of tutorials will always be available! (At present there is no PDF tutorial for the Structured birth-death model, but this will be uploaded shortly).

Since tutorials are stored on GitHub, it is easy for anyone in the community to contribute to Taming the BEAST. Because each tutorial is stored in its own repository the website is robust to changes in any single repository. We hope that the community will play an active role in curating the tutorials, either by updating or correcting existing tutorials, or by contributing new tutorials. For instance, someone who has developed a new BEAST 2 package can add a tutorial for the package to Taming the BEAST, where it will be accessible in a central location, along with other BEAST 2 tutorials, making it easier for BEAST 2 users to become familiar with the package.

We hope that the website will serve as a central repository that collects BEAST 2 teaching resources in one central location. The resources on the website are not only useful for individuals who want to learn how to use BEAST2, but also as a teaching aid, for workshops or even regular university courses.