On Wednesday, I will be doing a practical on inferring spatiotemporal dynamics of RNA viruses from sequence data at the GenEpi workshop at the London School of Hygiene and Tropical Medicine. I put together a step-by-step guide to go along with the practical, which should be entirely self-contained. This guide is available over at GitHub. I used the 2009 H1N1 influenza pandemic as a test case, where the growth of the pandemic and its spread throughout the world can be inferred from sequence data alone. It mostly details the very basics of getting up and running with the program BEAST and its small associated ecosystem.

I found GitHub pretty ideal for these purposes. I got to write in Markdown, which makes the writing itself quite painless while still producing decent results, and it’s also easy to host all the associated files on GitHub, making for a nicely self-contained site.