The O’Reilly Bioinformatics Technology conference concluded today in Tucson, and everyone is walking away happy.
The final day started out with a keynote from James Ostell, from the National Center for Biotechnology Information (NCBI), on the role of NCBI in the genome era. Ostell jokingly referred to the creation of the NCBI by an act of Congress in 1988 by pointing out that, unlike other bioinformatics research instituitons, “if we don’t do our job, we’re breaking the law.” Ostell went on to discuss the history of the NCBI and some of the principles they use to organize and prioritize their efforts. He used the Entrez retrieval system, a retrieval system for searching several linked databases, as an example of the kind of infrastructure work the NCBI is involved in.
Extra chairs were rushed in to seat the overflow audience attracted to Lincoln Stein’s talk on the Distributed Sequence Annotation System (DAS). Lincoln wowed the audience with his clear explanation of this potentially revolutionary technology. DAS is based on a client/server model that uses a common language for describing genome annotation information. The power of DAS lies in its ability to create a standard user interface to easily compare different group’s genome data, as well as to compare genomic annotations. The basic idea is that a DAS client queries a reference server that is identified for a genome, and then different annotation servers can be added to the client’s interface to make comparisons. The technology behind DAS is all open source and industry-standard, based on XML and traditional Web servers.
Perhaps commenting on Ewan Birney’s earlier remarks about how he has become unhappy with XML due to it’s high amount of overhead, Lincoln quipped “XML is the worst possible solution, except for all the other solutions.” While it is clear the overhead associated with XML can be problematic with some of the huge datasets used in bioinformatics, it seems to be working like a champ in DAS.
Finally, Dr. Leroy Hood delivered the closing keynote on his specialty, systems biology. Hood touched on many of the topics I discussed with him in a previous interview, explaining why biology has come to be considered an informational science. Hood commented that one of the fascinating aspects of biology is that it has at its core a digital language, which is ultimately knowable. Hood acknowledged the dramatic paradigm changes that the Human Genome Project has brought to biology, and he stressed that even more important than understanding the specific genome data will be the challenge of learning the mechanisms of the regulating networks that specify the behavior of the genomes.
It’s impossible to be everywhere at once at a conference, and the only complaint I heard was the difficulty in choosing which sessions to attend, because there were so many interesting options. One area I have neglected in my coverage is the Bioinformatics.Org track, which featured talks by the director, Jeff W. Bizarro, and contributing members of this open source bioinformatics organization. I did get a few minutes to talk with one of those members today, Warren DeLano, whose open source molecular visulaization program, PyMOL, is getting rave reviews here. DeLano has big plans to help create an open source environment for drug discovery research, and I’m sure we’ll be hearing more from him.
As the conference winds down, plans are already underway for next year’s Bioinformatics Technology conference. Plan for it to be sometime in the first quarter of 2003. Details will be published on the O’Reilly Conferences Web site as soon as they are available. And if you’re interested in the speaker notes and slide presentations from this year’s conference, keep checking the Bioinformatics Technology Conference page. They will be posted there soon.