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E-Genetics Co-hosts Hackathon with O Reilly As it Readies Launch of Open Source Suite


As the co-host of an upcoming international “biohackathon,” Electric Genetics hopes to expand the open development philosophy it has relied on since its launch into its next stage of development.

Since 1997, software developers and researchers from the South African National Bioinformatics Institute and its commercial spin-off Electric Genetics have worked closely together to develop, prototype, and test the company’s stackPACK and STACKdb tools, which are free to all academic users but provided for a fee to commercial companies. Now, as Electric Genetics gears for the launch of a new suite of open source bioinformatics tools, it considers a similarly strong relationship with the bioinformatics open source community an essential part of its future success.

Part of building this relationship, said Christina Raimondo, business development director at Electric Genetics, is providing an environment where open source programmers can work together and share ideas. Thus, the aim of the hackathon, which the company is co-producing with IT publisher O’Reilly and Associates, will be to “create an atmosphere where the developers have time to focus on interoperability — melting ideas and technical expertise to produce a result larger the sum of their individual efforts,” she said.

The hackathon sponsors are covering all travel and accommodation costs for 15-20 lead developers in each of the various open-bio projects. These include language projects such as BioPerl, BioJava, and BioCorba as well as applications and tools such as ENSEMBL, the EMBOSS package, Gene Ontology, OmniGene and the NCBI Toolkit. Developers from industry are welcome as well, but must pay their own way.

Ewan Birney of the European Bioinformatics Institute is slated to head up the technical direction of the event. While the technical details are still under discussion on the hackathon mailing list (available at biohackathon), the core objective is to improve interoperability between the various established open source bioinformatics projects, he said.

“Say you want to port Ensembl to a new place. The hardest part is not the Ensembl code itself,” said Birney. Rather, there''s no infrastructure system in place to “go from the local machine set-up to a distributed Internet-wide system.”

Current open source bioinformatics tools do not offer coordinated methods of reading from flat files, for example, or for contacting GenBank via the Internet, which means prospective users must spend extra time understanding the different packages before deploying them. The hope is that better integration and standardization between the projects will lead to more widespread use and, ultimately, faster discoveries.

Birney said that while venues such as the Bioinformatics Open Source Conferences have resulted in some cross-project development, “We don''t really have good computers set up and we don''t really have time to work on code” at theose events. The hackathon, he said, will really be the first chance for the open-bio community “to get together in the same room with nothing but computers there.”

“Electric Genetics sees the open source bioinformatics projects as a critical component in the vision of a global bioinformation network,” said Tania Hide,co-founder and CEO of Electric Genetics. Fostering these projects will be even more important as the company approaches the launch of its suite of open source bioinformatics tools — a challenging prospect that involves articulating to both open source developers and commercial end-users “that we offer significant value,” Raimondo said.

While admitting that the challenges of commercializing open source software are formidable, Raimondo noted that there are inherent risks involved in any software launch. “It’s never a sure bet,” she said, but hosting the hackathon is a sure way of “keeping a finger on the pulse of the market while actively supporting open source initiatives.”

The hackathon will take place in two parts: The first will precede the O’Reilly Open Source Bioinformatics Conference in Tucson, Ariz., January 26-28, 2002, and the second will take place in Cape Town, South Africa, February 24 - March 1, 2002.

Companies interested in supporting the hackathon should contact [email protected].

— BT

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