I'm honored to announce that Richard Neher and I have won the Open Science Prize for our work on nextstrain.org. This has been a really fun journey. The initial idea stemmed from a workshop at the Kavli Institute in Santa Barbara in summer 2014, where there were lots of discussions between me, Richard, Michael Lässig, Marta Łuksza and Colin Russell about flu forecasting. This inspired me to start on a prototype pipeline that would download flu data, build trees and do a simple D3 visualization. I put this up on GitHub and wasn't doing much with it until Richard picked it up and used it for a project on "local branching index". We joined forces at this point and ended up with the first version of nextflu in February 2015. We've been been working steadily to improve flu functionality since then. The next major innovation came in summer 2015, when Nick Loman contacted us about getting Ebola phylogenies shared from his on-the-ground work. We stood up a pipeline heavily borrowed from flu in June 2015 and continued updating the site as new data came in from Nick, Josh Quick, Matt Cotten, Ian Goodfellow and others. Since then, we've been trying to stay on top of Zika virus, with an initial version going up in Feb 2016 with all of the 17 available Zika genomes. Nick Loman (again), Oli Pybus and Kristian Andersen have been great at sharing sequences for this. With Alli Black in the lab, we also got involved in the actual sequencing work in Brazil and in the USVI.
So, it seems fitting that almost exactly two years after initial launch of nextflu in Feb 2015, that we're launching a completely revamped nextstrain.org site. We've been engaged in this refactor for almost 9 months now and it's finally out the door. We have a bunch of new features (like a zoomable map showing transmissions, multiple tree layouts, root-to-tip plots, multiselect filters, and sharable visualization state via the URL). All this was made possible by a lot of clever and dedicated work by Colin Megill and also James Hadfield. Check out the new site. We hope you find it interesting / useful.