VIENNA — While a quick appraisal of the throngs that descended upon the 15th annual Intelligent Systems in Molecular Biology conference showed how much bioinformatics has grown over the years, smaller snapshots pointed toward a field in flux.
The conference, held here jointly with the 6th annual European Conference on Computational Biology, drew around 1,700 delegates, according to International Society of Computational Biology officials. Attendees unofficially queried by BioInform indicated a divided discipline: old-school stalwarts trumpeting the need to keep up with biological advances, while computer scientists and bioinformaticists decrying the need for new and improved software tools.
Prior to the main conference, two days of so-called “special interest group” meetings attracted several hundred researchers who gathered to discuss new developments in bioinformatics’ many subdisciplines, from open-source software development to gene annotation, entity matching, and learning from extraction patterns in biomedical texts.
At the Bioinformatics Open Source Conference, for instance, discussions centered on data management using the myGrid platform; BioJava’s use as a graphical user interface toolkit and workbench; and Biopython’s relevance for reading, writing, and manipulating sequences.
Meantime, a special session focused on ethical and regulatory concerns around human genomic databases, organized by David Gurwitz of Tel Aviv University and Barbara Prainsack of the University of Vienna, suggested that privacy concerns and other ethical issues related to human genomic data require debate.
The session discussed how “open consent” requires a good moral reason for studying genetic code, the pros and cons of efforts to resequence the genomes of “expert volunteers,” and how “the obligation of veracity is deeply rooted in principles.”
Keynotes, Tracks Highlight Biology
Erin O’Shea from Howard Hughes Medical Institute and Harvard University kicked off the main conference with a keynote on dissecting transcriptional network structures. Later that evening, Søren Brunak of the Technical University of Denmark spoke about unraveling the mysteries of interactomes via data integration.
On day two, Michael Eisen of the University of California, Berkeley, delivered a keynote on the evolution of regulatory sequences that control gene expression, which gave more due to computational research than some of the other keynoters and was frequently cited by conference attendees.
Similarly, other talks throughout the conference stressed the biological component of bioinformatics more than the computational side of the discipline — from a paper discussing genome-wide analysis in Saccharomyces cerevisiae to one on how information on conformational dynamics can be used for a better understanding of biology at the molecular level.
While ISMB has always used biology-focused keynotes as a way to inspire computer scientists, attendees suggested that the “bio” side of bioinformatics was more pervasive at this year’s meeting than in previous years.
Waterman Passes Award Baton to Smith
On closing day, last year’s winner of the International Society of Computational Biology’s senior scientist award, Michael Waterman of the University of Southern California, presented this year’s award to his long-time friend and collaborator Temple Smith.
“You think I am going to tell you about the future of computational biology, but I did not bring my crystal ball.”
Smith, who initially earned a PhD in nuclear physics — “and soon got out of it” — said that his early impressions of biology likened its practitioners to television show investigations in which a scientist would study a single animal throughout his life. In his youth, he said, that was not for him.
“You think I am going to tell you about the future of computational biology,” he said, “but I did not bring my crystal ball.”
Smith discussed how modern-day bioinformaticists — a word he personally detests — would do well to study the classics, to learn from Darwin, for example. He added that the reams of data that seem to require sophisticated tools for mining and integration were trumped in previous times by simpler, paper-based methods, pointing to early 20th-century geneticists such as J.B.S. Haldane and R.A. Fisher as masters who could “put us all out of business.”
Prior to his talk, in an interview with BioInform, Smith noted that earlier generations of biologists even ran their own versions of Blast.
“The first [biologists]…were on hand calculators,” Smith said. “If you were in a biology lab or a molecular biology lab back in the ‘60s or ‘70s, you blew your own Blast. Did anybody even know how to do that? I can still do that.”
Smith said that over the past 10 years much has been said about computational biology “sort of being a service discipline to biology.” However, “computational biology only works if you work as a team,” he said.