ISMB 2005

I have been in Detroit for a week. The two-day Alternative Splicing meeting preceding ISMB was outstanding, and really crystallized a community of people who are working on genome scale analysis of alternative splicing.

Two things that really struck me at this meeting were:

1) the importance of ontologies (and, more generally, the formal description of scientific knowledge). There were 51 posters in the section on ontologies and NLP. One title that caught my eye was "Transforming Full-Text Literature to Formalized Facts." I was trained to believe that scientific publication was the formalization of facts! I see that it's not good enough anymore. Ewan Birney articulated this clearly in his Keynote address this morning when he said that databases are Biology, "the starting point and the end point of our understanding." I heard calls at this meeting for the formal annotation of data on function analogous to the submission of sequence data. This is clearly coming. Experimental scientists who want their results to be included in emerging system-wide descriptions will have to participate, and informaticians will have to find a way to collect formal descriptions of functional data (Janet Thornton, in her keynote, refered to this as data harvesting and showed a cartooon).

2) The idea that very few people can speak "both languages" (Biology and Computing) is outdated. Being at the alternative splicing workshop really brought this home. It reminds me of being in Miami, where virtually everyone speaks both English and Spanish perfectly. It's still true that the majority of Biologists are still inadequately familiar with databases and computers, and that the majority of computer scientists don't "get" biological questions, but virtually everyone here (a large meeting with well over 1,000 people) is completely bilingual. This is a change from just five years ago and it means that we can stop worrying about translation and get on with the research.

Another very interesting point was in the keynote by Jill Mesirov on the use of Gene Sets. By using predefined sets of genes (her "knowledge base") she was able to apply rank statistics to find signficant differences between microarray data sets between which no single gene shows a significant difference. She has published on these methods (e.g. Brunet et al. 2004) but it was new to me.

The hotel (Renaissance Marriott) was nice in many ways, but had its problems. When I arrived, they could not make keys; I had to be let into my room by a valet and come back later. Once in my room, I discovered that the phone didn't work. The internet was constantly going down (which caused problems for two of the three presentations I saw that used it). Twice (2/7 days), housecleaning did not replace the coffee packets. Access to the hotel itself, and navigation among the first three floors, was absurdly indirect. This design feature is apparently related to ideas of security more evocative of the middle ages (embattled castles protected by moats) than the Renaissance (intellectual excitement derived from an open exchange of people and ideas). The architecture reflects a philosophy which ignores the fact that inaccessibility leads to marginalization. This center houses the General Motors corporate headquaters and I was led to an image of GM executives cowering like Quasimoto in his tower, in this case the Detroit Dark Ages Center, while life goes on below them (and without them).