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Fate of Bioinformatics Explored at the Second O'Reilly Bioinformatics Technology Conference

February 19, 2003

Sebastopol, CA--In his keynote address at the 2003 O'Reilly Bioinformatics Technology Conference, Lincoln Stein predicted that the term "bioinformatics" will be obsolete by 2012. Stein's assertion created quite a stir among the 683 biologists, computer scientists, software engineers, mathematicians--all bioinformaticians to varying degrees--who attended the conference in San Diego earlier this month. What could his prediction portend for the technical direction their careers are taking?

Stein's presentation was just one of many thought-and debate-provoking sessions held during the four-day conference. Stephen Wolfram, well-known in scientific circles for his Mathematica software and his recently released tome, "A New Kind of Science," delved into his book's issues and their ramifications for bioinformatics in his keynote presentation, which spilled over to an extensive question-and-answer session following his formal talk. Just prior to his keynote talk, Jim Kent was presented with the Benjamin Franklin Award for promoting freedom and openness in the field of bioinformatics by J.W. Bizarro, president of Bioinformatics.Org. Kent developed the "GigAssembler," a 10,000-line program that he wrote in a month and then used to assemble the public human genome fragments, helping to keep the data in the public domain and unrestricted by commercial patents.

Representatives from Sun Microsystems and the Blueprint Initiative, part of the Samuel Lunenfeld Research Institute at Mount Sinai Hospital in Toronto, chose the O'Reilly Bioinformatics Technology Conference to announce that the Initiative had acquired more than $5 million in Sun hardware, software, and storage to support the standard-setting BIND (Biomolecular Interaction Network Database). BIND is a growing repository of data on how the proteins that make up all life interact and control cellular life, and will benefit researchers in proteomics--the study of protein interactions.

Designed to bridge gaps between communities, sessions at the second O'Reilly Bioinformatics Technology Conference appealed to academic and industry audiences, wet lab denizens, and "chip heads" alike, exploring topics such as interaction networks, web services, grid computation, visualization, genomics, algorithms, pipelining and automation of data, and building open source applications. Other speakers at the conference included experts such as Alvis Brazma, Microarray Informatics Group Leader, European Bioinformatics Institute; James Gosling, co-inventor of Java, and VP and Fellow, Sun Microsystems; Francis Ouellette, Director, University of British Columbia Bioinformatics Centre; Steven Brenner, Assistant Professor and leader of a computational genomics research group at the University of California, Berkeley; Damian Conway, Research Fellow, Monash University; Nat Goodman, Senior Research Scientist at the Institute for Systems Biology and an Affiliate Professor of Bioinformatics at the Arctic Region Supercomputing Center at the University of Alaska; Chris Dagdigian, founding partner of BioTeam Inc.; and Bill Day, Staff Engineer and Technology Evangelist at Sun Microsystems.

Other notable conference events included tracks planned by Bioinformatics.Org and I3C (including the LSID specification), and a GMOD (Generic Model Organism Database) meeting, which was open to developers and curators of model organism system databases. Apple's Rendezvous Lounge was stocked with a stunning assortment of its most advanced hardware and software offerings for perusal by conference-goers.

"We're already starting to work on next year's program," notes Lorrie LeJeune, O'Reilly bioinformatics editor and conference program chair, confirming the success of the 2003 O'Reilly Bioinformatics Technology Conference despite the challenging economy and its toll on the meeting and conferences industry. "We'll be taking Lincoln Stein's keynote advice to heart and looking toward the biology of 2012 as well as the bioinformatics of 2004."

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