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20 Hackers + 1 Whiteboard + 1 Windowless Room = Open Bio Database Access: Jan 31, 2002

This article has been updated from a previous version to clarify the organizational support and sponsorship for the event.  

 

TUCSON, Ariz., Jan. 29 - Part I of the first-ever biohackathon wrapped up this afternoon with a new specification for accessing biological sequence databases across multiple languages and platforms.

 

The specification, Open Bio Database Access, will give bioinformatics developers a library of modules to ensure seamless access to sequence databases. The spec is being incorporated into the four primary open source bioinformatics projects, BioPerl, BioPython, BioJava, and BioRuby.

 

Organized and sponsored by Electric Genetics and O'Reilly and Associates, along with the help of other commercial sponsors, the biohackathon kicked off the O'Reilly Bioinformatics Technology Conference taking place here through Thursday. But while most early arrivals for the conference spent the weekend hiking in the nearby Santa Catalina mountains or basking in the Arizona sun, the 20 biohackathon participants spent three full days coding diligently under the fluorescent lights of a stuffy hotel conference room.

 

But the consensus was that it was all worth it.

 

"This is a brilliant example of how well open source works," said Antoine Van Gelder, chief bioinformatics programmer at Electric Genetics. "The level of productivity here has eclipsed anything I've seen in my life."

 

Other participants agreed that the results of the event far exceeded their expectations and that there was a surprising level of agreement among programmers, many of whom met face-to-face for the first time after months or even years of communicating electronically.

 

"It's good to be able to just shout at people instead of waiting for them to wake up and answer their e-mail," joked Ewan Birney of the European Bioinformatics Institute, who served as technical leader of the event.

 

Participants made the most of their rare opportunity to work together, share ideas, and engage in the occasional debate. A whiteboard set up Saturday morning was soon filled with a "magic matrix" of projects and modules. Developers set to work with a degree of concentration and cooperation not typically available to them, checking off their assigned boxes on the whiteboard as they completed each component.

 

"It was great to not have to worry about work or school and just have time to focus," noted Andrew Dalke of Dalke Scientific Software.

 

By the end of the event, over three-quarters of the boxes had been checked off, about twice as many as expected. The rest of the work, as well as a full performance test, will be completed at the second part of the biohackathon, scheduled to take place in CapeTown, South Africa, February 24-March 1.

 

Birney said the OBDA standard should benefit system administrators, database operators, and application developers who currently have to draw from several in-house or third-party tools to access sequence data reliably from multiple sources.

 

"We have 12 different systems for this problem at the Sanger Center," Birney noted. Once the library is fully tested, it is expected that developers will have ready-made modules on hand that should greatly simplify the process.

 

Birney added that a usable OBDA specification should be available by Spring.

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