Bioinformatics Conference--Day 3

by Bruce Stewart

The halls are buzzing with activity here in Tucson and it's clear lots of good connections are being made. The
job-posting board is full, and people have come from all over the world to network with other bioinformaticists and take in the conference talks. I've seen attendees from the U.K., Brazil, Germany, Denmark, and Egypt, as well as from all over the U.S. Judging from the intensity of some of the lunch-table conversations, learning is happening outside of the conference sessions as well as in them.

Yesterday's keynotes looked at bioinformatics from a
big-picture point of view, but today's speeches drilled down to more specific aspects of the scientific side of the field. Terry Gaasterland from Rockefeller University gave a detailed talk on data integration called "Integrating Gene Expression Data and Genome Sequence Data," using genome examples from humans, mice, cattle parasites, and a pathogenic bacterium. Chris Hogue from the Samuel Lunenfeld Research Institute of Mt. Sinai Hospital gave an impressive afternoon keynote on "Saccharomyces cerevisiae: Some Assembly Required." I spoke to a group of programmers who were visibly excited by the methods Hogue described.

After Hogue's keynote I attended an interesting panel called "Open Data Open Source." Four speakers from diverse backgrounds addressed the issues associated with making bioinformatics data and software open source. All four argued in favor of open source methods, with Ewan Birney echoing his statements from Monday that making the actual data open was of paramount importance. Although a couple of the speakers strayed from the subject a bit, I was especially impressed with Steven Brenner's contribution to the panel.

Brenner is a contributor to the BioPerl project, and when he was invited to join the faculty at U.C. Berkeley he realized their standard employment contract wouldn't allow him to continue his open source work. So he worked with the campus administration to craft a contract that would. The school eventually accommodated Brenner's request, but only after much time and legal expense. Based on his experience Brenner is trying to rally an effort in the bioinformatics community to create a standard employment contract that will allow for work on open source projects. His feeling is that if a standard contract existed universities would be more willing to accept it, and each time a faculty member faced this situation they wouldn't be starting from scratch. He's championing an effort to raise awareness on this issue as well as funds from the open source bioinformatics community to pay the legal costs associated with creating such a standardized employment contract. For more information, visit the Open Bioinformatics Foundation site, where you can join the Open Source Authors Contract Working Group discussion list.

Later in the afternoon O'Reilly had an author-signing event. Not only were Perl luminaries Damian Conway, Lincoln Stein, and Nathan Torkington kept busy signing copies of their books, but our newer bioinformatics authors, Cynthia Gibas and James Tisdall were also quite popular. And, of course, many people crowded around Tim O'Reilly to get his take on bioinformatics and his signature on a book.

Tomorrow is the last day of the conference, and it promises more good keynotes and presentations. I'm especially looking forward to Lincoln Stein's presentation on his latest pet project, the Distributed Sequence Annotation System (DAS), and the closing keynote by systems biologist, Dr. Leroy Hood. Check back tomorrow for reports on both.