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February 11, 2002

First O'Reilly Bioinformatics Technology Conference Built Bioinformatics Bridges

Sebastopol, CA--Not even a rare snowfall in Tucson could quench the enthusiasm of the nearly 700 programmers, scientists, developers, and researchers participating in the first O'Reilly Bioinformatics Technology Conference, held January 28-31, 2002 at the Westin La Paloma Resort. "Bioinformatics is one of the next great revolutions in the computer industry," asserts O'Reilly & Associates founder and president Tim O'Reilly. "It pushes us forward on so many fronts, not just in the raw biological science. It's an area where massive computing needs, huge databases, and innovative web services are all pushed to their limit. The conference's underlying theme was the importance of collaboration, data sharing, and peer review, and the role of open source software in keeping openness a key part of this new science."

While other bioinformatics conferences have focused on academic papers and project results, an exceptionally receptive audience in Tucson illustrated the thirst for knowledge of programming solutions to biological science issues. "Bioinformatics is about combining the collective wits of programmers and scientists to create tools that will allow us to find our way through the enormous amounts of biological data," says co-chair Lorrie LeJeune. "Yes, we have drafted a map of the human genome. We can see that there are 'streets,' but we don't yet know what planet we're on, much less the city we're in. Biological data has maddening subtleties, complexities and redundancies--with better tools, we can perform better analyses, which in turn will yield more accurate conclusions. It's these conclusions that will ultimately determine such things as treatments for diseases and drug therapies. We planned this conference to help bioinformaticians 'read the maps' because bioinformatics not only has amazing potential, it's already changing our lives."

Notes conference co-chair Nathan Torkington, "Conferences are all about the flow of information. Not only were bioinformatics software developers giving information to the audience, but there was a tremendous amount of communication between the leaders of different groups." Wet lab researchers and programmers alike came together for discussion and discovery. Every one of the six keynote addresses were packed; a second session had to be added to Peter Schattner's wildly popular "Perl & Bioperl" tutorial.

Participants heard from pioneers and up-and-coming innovators James Ostell, Ewan Birney, Terry Gaasterland and Christopher Hogue. In his closing keynote, Leroy Hood discussed how the Human Genome Project has led to several paradigm changes in systems biology, and predictive and preventive medicine. In his keynote, O'Reilly author Lincoln Stein addressed the benefits of moving towards a cooperative, formal Web services model for bioinformatics data providers to reduce the fragmentation of bioinformatics protocols, technologies and standards. In a separate session, Stein described the Distributed Sequence Annotation System (DAS), an open source protocol and tool set for exchanging annotations on genomic sequences. DAS allows a single machine to gather information from multiple, geographically separated annotation databases, collate the information, and display it to the user in a single integrated view.

James Tisdall, conference tutorial leader and author of "Beginning Perl for Bioinformatics," comments: "I think the most important result of the conference is an enhanced dialogue between biologists and programmers. Important open source infrastructure was not only presented, but was also developed in the great 'hack-a-thon' that resulted in a solid advance in the inter-operability of the major open source biology projects. My only regret was that there were so many interesting talks that I couldn't get to. But the most satisfying thing to me was the high level of interest on the part of newcomers to the bioinformatics field who were in attendance. This enthusiasm is bound to be translated into some good science in the months and years ahead."

The hackathon Tisdall refers to was the conference's unofficial kick-off, led by Ewan Birney, Ensembl project leader at the European Bioinformatics Institute. Three days of high-tech biohacking was fueled by the eye-popping hardware provided by Apple, and low-tech person-to-person interaction. Explains Torkington, "In much the same way as the invention of the web browser changed the way people accessed information on the net, this project promises to change the way bioinformaticians access sequence data on the net. Our vision is to create a single client library that knows how to fetch sequences from a variety of sources, removing the need for the end user to know *where* everything is kept to focus on what they want to do with the information."

While project design (bioperl, biojava, and biopython representatives settling on the infrastructure's essential features and support languages) was the goal for Tucson, the proof-of-concept implementations were nearly completed as well. Several new technologies are being developed as part of the hackathon work: BioFetch, a simple web-based protocol for fetching sequence information, and BioSQL, a standard interface to sequence information in a relational database. Progress continues via email, and later this month the twenty-odd developers will reunite in Cape Town, South Africa--headquarters of co-sponsor Electric Genetics-where the client library project is expected to be completed. The results of the hackathon will be free and available to all. Birney will continue his public dialogue on bioinformatics and open source by presenting a keynote address at O'Reilly's Open Source Convention in San Diego this summer.

Other highlights of the conference include:

  • Bioinformatics.Org ran a specialized track within the conference, and also revealed its first-ever Benjamin Franklin Award winner: Michael Eisen of the Lawrence Berkeley National Laboratory. Following the award presentation for promoting freedom and openness in bioinformatics, Eisen delivered a laureate talk on the Public Library of Science project.

  • Members of the Gene Ontology Consortium met at the end of the O'Reilly Bioinformatics Technology Conference to provide demonstrations and discussions of current annotation efforts of consortium members and future development plans by users of GO.

  • Sponsors and exhibitors packed the exhibit hall for two days during the conference, showcasing both the latest products and services, as well as the efforts of bioinformatics community organizations.

  • Attendees warmed to O'Reilly's "green" commitment, appreciating the recycled materials used to create the pen, writing tablet, t-shirt, and messenger-style bag for the conference.

Concludes Tim O'Reilly, "The essence of what we do at O'Reilly conferences is bring together a core group of the key developers for a given technology and people who want to learn from them. But we also try to frame the conference so that the attendees learn not just about specific tools or techniques but big picture ideas." More bridges will no doubt be crossed by the time the next O'Reilly Bioinformatics Technology Conference rolls around in early 2003.

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O'Reilly Media spreads the knowledge of innovators through its books, online services, magazines, and conferences. Since 1978, O'Reilly Media has been a chronicler and catalyst of cutting-edge development, homing in on the technology trends that really matter and spurring their adoption by amplifying "faint signals" from the alpha geeks who are creating the future. An active participant in the technology community, the company has a long history of advocacy, meme-making, and evangelism.

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