Summary

• BEAST 2 is an open source cross-platform software package for analysing genetic sequences in a Bayesian phylogenetic framework. BEAST 2 provides a growing collection of new models tailored specifically to particular data sets and/or research questions. This marked expansion of methods available in BEAST 2 has resulted in a significant increase in the complexity of the models which can be daunting (i.e. introduce errors or use inappropriate models) for new users. However, this complexity became the wellspring for Taming the BEAST workshops (https://taming-the-beast.org/workshops/) aimed at promoting interaction between BEAST 2 users and developers. Participants have the opportunity to learn from the developers while the developers gather feedback from participants regarding ease of use, platform issues, and user requirements for future software and methods development. Each workshop is an international event that places great emphasis on ensuring a collegial and collaborative atmosphere. The main objective is to provide participants with the skills and core knowledge to confidently perform and interpret inferences generated from phylogenetic and phylodynamic analyses.

• Since its inception, the Taming the BEAST workshop provides a somewhat general overview of BEAST 2, software packages, and applications. The current iteration of the Taming the BEAST workshop incorporated infectious disease transmission modelling to address the current demand for modelling transmission dynamics from molecular sequences (ex: HIV, SARS-CoV-2). BEAST 2 has been cited over 5,000 times and figured predominantly in reconstructing the evolutionary dynamics of viral pandemics of the last four decades including HIV, Influenza A virus subtype H1N1 (A/H1N1), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), Ebola virus, and more recently Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). As such, BEAST 2 is a particularly important tool for building expertise and enhancing capacity for modelling infectious diseases.

Hosts

• Jeffrey B. Joy, BC Centre for Excellence in HIV/AIDS, jjoy@bccfe.ca
• François (Frank) Cholette, Public Health Agency of Canada, francois.cholette@phac-aspc.gc.ca

Instructors

• Joëlle Barido-Sottani, Institut de Biologie de l’ENS, joelle.barido-sottani@wanadoo.fr
• Remco Bouckaert, University of Auckland, r.bouckaert@auckland.ac.nz
• Alexei Drummond, University of Auckland, a.drummond@auckland.ac.nz
• Louis du Plessis, ETH Zürich, louis.duplessis@bsse.ethz.ch
• Huw Ogilvie, Rice University, huw.a.ogilvie@rice.edu
• Jūlija Pečerska, Zürich University of Applied Sciences, julija.pecerska@zhaw.ch
• David Rasmussen, North Carolina State University, drasmus@ncsu.edu

Guest lecturers

• Caroline Colijn, Simon Fraser University, ccolijn@sfu.ca
• Michael Martin, Johns Hopkins University, mmart108@jhmi.edu
• Ailene MacPherson, Simon Fraser University, ailene_macpherson@sfu.ca
• Sungsik (Kevin) Kong, University of Wisconsin-Madison, skong32@wisc.edu

Deliverables

Participants will be equipped with the skills and core knowledge to confidently perform and interpret inference generated from phylogenetic and phylodynamic analyses. Furthermore, lectures and tutorials will be publicly available here: https://taming-the-beast.org/workshops/Taming-the-BEAST-SBT/

Schedule

Taming the BEAST workshops are one week long (5 days; https://taming-the-beast.org/workshops/Taming-the-BEAST-SBT/). This allows enough time to properly teach the principles of Bayesian evolutionary analysis by sampling trees, explore BEAST software packages, and complete the corresponding hands-on tutorials as well as provide networking opportunities. A unique feature of Taming the BEAST workshops is that there are also planned activities situated in the middle of the week and at least 1-2 group dinners to provide additional opportunities for teachers, participants, and organizers to form meaningful relationships and long-lasting collaborations. The workshop provides an extensive training opportunity for individuals at any stage of their career including post-doctoral, graduate, and undergraduate students.

Acknowledgments

This iteration of the Taming the BEAST workshop was generously supported by the Canadian Network for Modelling Infectious Diseases (CANMOD), ETH Zürich, and the Emerging & Pandemic Infections Consortium (EPIC; University of Toronto).