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Electric Genetics Hosts Open-Bio Community for a Week of Coding in Cape Town

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Cape Town, South Africa, played host to an international team of bioinformatics developers who gathered there two weeks ago for the second half of a “biohackathon” that began in January in Tucson, Ariz.

Over the course of the event, which spanned six weeks, two continents, and both hemispheres, 20 lead developers from several open source bioinformatics projects met to improve interoperability between the various open-bio toolkits. During the first half, a system to facilitate access to sequence databases began to take shape [BioInform, 02-04-02]. By the time participants began boarding their planes at Cape Town International Airport on March 1, the new infrastructure - dubbed Open Bioinformatics Database Access - was available at http://cvs.open-bio.org.

The hackathon was the first event of its kind in bioinformatics, and one that primary sponsor and organizer Electric Genetics would gladly see more of. “It was quite a risk for us financially,” admitted Electric Genetics CEO Tania Hide. “It was well worth the investment that we made and we would make the same kind of investment again.” Indeed, the company had quite a bit to lose going in — aside from the “large chunk of cash” the tiny company had to put up and the complicated logistics of coordinating the two-part event, there was no guarantee that Electric Genetics would immediately benefit from the results. But Hide said the paybacks, while indirect, were greater than she had expected.

“Because Electric Genetics is moving toward a business model of open source software, we wanted to make sure that we gave something back to the community,” said Hide. Strengthening existing relationships among open source developers while also establishing itself as an active player in the process was a critical goal of the company — an “intangible” benefit that Hide said is key to realizing the company’s strategy.

“If I had a strict accountant on board he probably wouldn’t have gone for it, but for us it’s part of the deal,” she said.

Additional sponsors included O’Reilly and Associates, AstraZeneca, and Dalke Scientific Software.

Hide said the company did not influence open-bio’s decision to tackle cross-project interoperability, “but from a business strategy, I couldn’t have picked a better project.” Having the toolkits work together more smoothly will help the company as it begins marketing its open source tools, “because the likelihood that a company wants to plug in different applications is greater.”

The OBDA specification will see its first real-world implementation at the Sanger Institute, where it will be used to standardize sequence retrieval methods. Jason Stajich, a PhD candidate at Duke University who heads up the BioPerl project, said the hackathon participants are considering publishing a paper on OBDA and may also propose it as a formal standard “through one of the standards bodies.”

An important element of the hackathon results, according to Stajich, was a relational database schema called BioSQL that all the projects now read and write to. The schema serves as a consistent data model for all the language projects and will eventually allow users to integrate ontological data with sequence data.

Hackathon attendees were universally enthused about the productivity enabled by the rare face-to-face interaction. “It’s really surprising how much we got done,” said Stajich. One major goal from the developers’ perspective was performance testing of the six implementations of the OBDA spec, an effort that Stajich said was completed “as best we could in a number of situations.”

Next steps include more performance testing in real-world systems, improving documentation, and stabilizing the code. Stajich said that an immediate goal is getting the tools to support OBDA fully in place within BioPerl in time for the project’s upcoming 1.0 release at the end of March. While enthusiasm for future biohackathons is high, the details of when, where, and how it may happen next have yet to be worked out. Stajich said the Open Bioinformatics Foundation “has definitely pledged to provide logistical and hopefully financial support to future hackathons.” Hide said Electric Genetics would be more than happy to make Cape Town an annual destination for the open-bio community and that discussions are already underway among this year’s sponsors for next year’s event.

— BT

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