Tuesday, June 5, 2012

The #Phylotastic hackathon, akin to scientific fashion week

This week I'm attending the Phylotastic! Hackathon at the National Evolutionary Synthesis Center (NESCent) in Durham, NC. I've never participated in a hackathon before, and I wasn't quite sure what to expect.

Luckily, a lot of other people were feeling the same way.

Essentially, it boils down to this: a group of people with diverse backgrounds, piled into a room for 5 days with the goal to PRODUCE. In many ways it reminds me of fashion week.

Twice a year, for spring/summer and fall/winter seasons, the fashion industry descends on some of the world's major cities to view the latest collections from designers. Its a frenzy of models, editors, designers and buyers, all gathered in one place to see months of work culminate on the runway. Everything is already in place and in motion. Design teams are laden with assembling the big picture, making sure the clothes fit the models and shows go off without a hitch. Sure, there are last-minute glitches and unforeseen obstacles. But you make do with what's on hand and keep werkin' the catwalk even if your shoe falls off.

At NESCent, we're using computers and keystrokes instead of fabric and footwear. Phylotastic aims to produce a set of open-source web tools that researchers can use to manipulate, trim, and label phylogenetic trees. But the main point is that we're not building anything new. The Phylogenetics community already has a stockpile of scientific tools and software--however, these aren't condensed into one place and might not be easy to use or coordinate with each other. At the Phylotastic hackathon, we're going on a mad rush to leverage existing tools, making them interoperable and accessible via databases and public APIs. Throughout the week we're focusing on three distinct goals:

  1. Extracting Subtrees from Megatrees. The Tree of Life is gargantuan. But most people don't need to see the whole tree, they're only interested in a small set of species. One Phylotastic tool will enable users to type in their list of species, and receive a tree showing evolutionary relationships among those taxa.                                                                 
  2. Matching and resolving taxonomic names. Taxonomy is an old and established discipline, and over the years a lot of redundancy has cropped up. Sometimes one species has two different names (synonyms) that need to be merged and corrected. A second Phylotastic tool will allow users to type in a list of names, and have old names "fixed" after comparisons with a name resolution database.                                                                 
  3. Integrating metadata and comparative data. Looking at a tree with species names is just the tip of the iceberg. Sure, this gives you information about the evolutionary relationships between species, but you might not know much other information. What if you wanted to interpret the tree while thinking about body size or species' habitats? A third Phylotastic tool will mine online databases (sites like the Encyclopedia of Life, or the GenBank sequence repository) and attach additional information onto species names. You might want to add pictures to tree tips or know when there is a published Genome sequence for the species in your tree.
So, yesterday the hackathon began! We started the morning with a slew of introductory talks. We asked, what are the goals for this week--what is possible and not possible? We discussed different ways in which researchers might want to use Phylotastic tools. I presented a case study for metagenomics (you can view my slides here on slideshare). Then in the afternoon we had a technology "boot camp", getting a rundown of all the tech-speak and programming acronyms like NeXML, SADI, and iPlant TNRS. Finally, we spent the rest of the afternoon brainstorming task groups, assigning hackathon projects, and then finishing up with planning and coordination for Tuesday.

By evening, we were all exhausted. It was definitely time for beer. We finished the night at Fullsteam Brewery (all ~30 of us), a great stop for locally brewed pints and spirited discussion.

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