The Bioinformatics Buzz

by Bruce Stewart

The hallways and confererence rooms are buzzing with activity here in San Diego at the O'Reilly Bioinformatics Technology Conference.

Tim O'Reilly introduced the morning keynotes, and gave a short introduction explaining why O'Reilly & Associates has been involved in bioinformatics. Tim explained that it was continuing O'Reilly's tradition of bringing news from the future and following the alpha geeks, and he noted the strong ties to open source software that exist in the bioinformatics community.

Following Francis Ouellette's keynote on genomic annotation, one of the heros of genomics was recognized, as Jim Kent was awarded the Ben Franklin award. Kent, who practically singlehandedly beat the commercial effort to decode the human genome, followed the award with a timely keynote on the state of genomics aptly titled, "The Genes, the Whole Genes, and Nothing But the Genes".

After starting out with a slide that made an amusing comparison between himself and Richard Stallman, who bears a resemblance to the shaggy Kent ("He's 'Free as in Freedom', I'm 'Free as in Free Lunch'), Kent went on to detail the different methods that are currently in use genomics. Kent colncluded that neither computational or traditional "wet" biological research methods were enough on their own, and a combination of both types of research were necessary to be able to make serious progress in identifying genes.

Besides Kent's keynote, some of the sessions generating the most interest here were Doug Tidwell's "XSLT for Bioinformatics" tutorial, and Nat Goodman's "BioPerl: Reality vs. Myth". In an informal survey taken by Tim O'Reilly this morning, Perl emerged as the language of choice by this crowd, and Goodman's overflowing session confirms that.