Phyloinformatics Hackathon at the National Evolutionary Synthesis Center
Mix together a couple of dozen computer programmers with a common set of goals, lots of coffee, and stir for a week. That's the recipe for the Phyloinformatics Hackathon being held this week at the National Evolutionary Synthesis Center (NESCent). The word "hackathon" may sound sinister to some people, but in fact these hackers are not breaking into any bank accounts. They have converged on Durham for five days to collaboratively write software that will be used every day by thousands of scientists around the world.
"This is a very unique way of doing things," says Kathleen Smith, the director of NESCent. "It's unlike any other scientific meeting in that the goal is to actually create new software tools as a group, face to face, in real time."
Phylogenetics is the study of the evolutionary relationships between organisms and their genes. The field is fundamental to many areas of basic biological research, and has applications from tracking the progress of disease epidemics to figuring out how best to conserve endangered populations. Techniques from phylogenetics even have been used to study the relationships among human languages and among medieval manuscripts.
Researchers rely on a bewildering array of phylogenetic methods for various specialized tasks. Solving complex problems often relies putting these individual methods together in complex ways. "The flowchart can get very complicated very fast", says Amy Zanne, a postdoctoral researcher at NESCent whose research combines morphological, physiological and ecological data with phylogenetic methods. "Glue software is needed to make these tools speak the same language".
Leading programmers from as far away as Japan and New Zealand have come to NESCent to build the missing pieces of glue software. Participants include developers of specific phylogenetic software packages, on the one hand, and experts in designing glue software toolkits such as BioPerl and BioJava. "The participants are learning a lot from each other," says computational biologist Arlin Stoltzfus of the National Institute of Standards and Technology. "The phylogeneticists know what the cutting edge phylogenetic methods are and what users need, while the toolkit developers have lots of experience working with standards that allow different software packages to communicate".
"The face-to-face interaction allows for a very fast software development cycle", says Jason Stajich, a postdoctoral researcher at the University of California Berkeley, "you can pose a problem and someone with the solution is sitting in the same room".
In addition to the programmers, a number of biologists are lending their expertise to the hackathon. "The biologists keep us honest by making sure that the code that we produce solves real problems that they care about", says Hilmar Lapp of NESCent, who organized the meeting.
The software produced will be freely available, under what is referred to as an open-source license, and it is being documented as it is being produced. "It is impressive to see this group at work, and to see how dedicated they are to making tools that are useful to, and easily used by, the larger research community", says Todd Vision, the Associate Director of Informatics at NESCent. He adds, "the participants are also identifying areas for future work, and I expect that this meeting will launch some new collaborations".
The first Phyloinformatics Hackathon is taking at place at NESCent in Durham, NC from December 11-15, 2006. NESCent (rhymes with "crescent") is an NSF funded center designed to promote synthetic research in evolutionary biology. It is a collaboration between Duke, the University of North Carolina at Chapel Hill, and North Carolina State University. More information about NESCent is available at www.nescent.org.
For more information about the hackathon, contact Todd Vision, Associate Director for Informatics at NESCent, (919) 668-4596, [email protected], Hilmar Lapp, Assistant Director for Informatics at NESCent, (919) 668-5288, [email protected], or Kristin Jenkins, Education and Outreach Program Manger, (919) 668-4544, [email protected].
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