Notes from the Biomass

One of the fruitful application of blogs in the life sciences is to provide realtime coverage of conferences. Summaries and reviews of scientific meetings have been a traditional part of the scientific journals such as the Trends-series by Elsevier. However, they usually appear several months after the closing of the conference and often do not provide insights beyond the abstracts book, as they rather attempt to make everyone happy rather than focussing on the highlights.

Blogs can emphasize outstanding presentations immediately, and allow for a more independent view of the conference, even if it is biased by the personal preferences of their authors. Smaller workshops, which might produce interesting outcomes from panel discussions usually lack media coverage and could use blogs (or wikis) to disseminate results. The matter is not completely free of complications - some meetings are "closed meetings" and implement strong limitations on the media coverage. Bloggers need to be aware of that, even though most would not identify themselves with The Media. However, most organizations running scientific conferences would probably appreciate "live" coverage.

Some conferences were already covered by bloggers: nodalpoint's Greg Tyrelle featured the ISMB 2005, for instance. Free Association, the blog of the editors of Nature Genetics is currently providing coverage of the Third Seattle Symposium in Biostatistics: Statistical Genetics and Genomics . I will participate in a proteomics workshop next week and will cover the meeting to some extent here.

It would be helpful if we would create a repository (some blog or wiki) that would provide links to ongoing coverage of conferences by bloggers, possibly in a similar fashion to the TravelBlog.

Many German bioinformaticians usually view the yearly German Conference on Bioinformatics as a necessary evil. Who wants to listen to mediocre talks in stale run down German university lecture theatres? - the sole reason to go was networking. However, I (and many others) consider RECOMB and ISMB - the two major bioinformatics conferences - to have a similarly disappointing line up compared to smaller workshops with a high degree of invited speakers.
The way these conferences are set up currently is just not very rewarding and while there are many submissions, the number of promising submission is fairly low. If bioinformaticians have to watch their impact factors (unlike say mathematicians), submitting to a conference is not worth the hassle, even if some of the talks are published in Bioinformatics.
Luckily, this years talks - contributed and invited - were much better than in previous years and I am glad I attended. The organization was smooth (owing to the increased registration fee, some people say) and the main building of the university of Hamburg was a pleasant venue and Hamburg, is a metropolitan city worth a visit anyway. Tübingen, certainly nice but not exactly a metropolis, will host the next GCB from September 22 to 24th, 2006.

The German Bioinformatics conference that I am currently attending has a regional focus, China. Guo-Ping Zhao from the Chinese National Genome Center, Shanghai started the day with an overview of the genomics involved in the outbreak of SARS in 2003. It was amazing to see how quickly comprehensive information such as the genomic sequence on the agent was obtained and how genotyping of the SARS-strains could be matched back to most individual cases of infections. The structural biology of several SARS proteins was investigated by Rolf Hilgenfeld, who was working on Coronaviruses before. Parts of the work that he presented - the solution of the crystal structure of the main protease of the virus - was actually performed in China in a university under quarantine.
Jin Li, director of the newly founded partner institute between the Chinese Academy of Sciences and the Max-Planck-Society presented an overview of recent developments in the HapMap-project, focussing on the insights into population genetics, Using haplotype blocks, they were able to reconstruct the major migration of the human population. It will be interesting to listen to people who criticized the project early on when The Big Paper appears, which Jin Li announced.
Obviously, the people presenting ideas on normalization of microarray data had a tougher time attracting attention. However, as long as data normalization plays such a pivotal role, we have to go a long way before microarray will deliver their potential, despite their abundant use today.

Another fine day here - both in the lecture theatre and outside.

The first day of the GCB had two sessions, "RNA structures" and "Sequence Analysis". Peter Stadler himself called the first session "dominated by the RNA mafia", referring to the group around Peter Schuster that Stadler and the other speaker were part of at some point in time.
Their work is probably known to everyone in RNA folding and evolution by the Vienna RNA package . Nice work and talks but I have no real use for studying RNA folding myself. RNA folding is one of good examples where staying in a field that was pronounced dead (when everybody was doing genome sequencing) proved to be very fruitful (when small RNAs appeared).

The highlight of the second session was the biodefense presentation by Tom Slezak from the Lawrence Livermore National Laboratory. The problem posed is interesting: how to find the best DNA regions of pathogens that distinguishes pathogenic strains from their avirulent cousins. The results are monitored by PCR for rapid diagnosis but also for surveillance on air filters. I would have hoped for a little more information but some of "the customers" - federal agencies - are secretive about many details. Outside the biodefense application, it would be nice to get information on the "air metagenome".

More tomorrow.

Today, the GCB, Germanys most important bioinformatics conference opens in Hamburg. The venue, the university of Hamburg, has a strange touch to it - this was the location of my very first "conference". Not on saving the world from bugs using computers but on fantasy role playing games - back in 1989. Well, I won't get to sleep on some floor this round and with WLAN set up, expect some posts on the conference later.

Back in Germany and with a couple of days passed, the meeting can be called on of the best ones I attended so far. In short, the quality of the talks (and many posters) was high, the organization smooth and the location very inspiring anyway.
The abstracts books lists about 250 participants from all over the world, not surprisingly, US based scientists were in the majority. Talks were usually well attended with no parallel sessions. A strict time limit was enforced for the individual contributions (10 or 30 minutes) but there was no time set for the next speaker, allowing flexibility for questions. All nights, we concluded after 10pm, thereafter one could mingle with the participants at the one bar. The venue enhances the interaction - all activities focussed in a single lecture theater, the dining hall and the bar, all very close by each other, and speaking to anybody was easy this way.

And the science?
This was a meetings for experimental microbiologists with relatively little immunology (phew) and no bioinformatics, which was to be expected from the speakers list. It would not be fair to report details from a closed meeting, even if the CSH press policies does not list blogging in particular. Greg uttered some concerns on closed meetings; I do think that such meetings foster co-operations and mutual trust rather than providing only some cheap thrill of exclusivity. Several speakers provided insights into current work that I felt glad to see early and presented openly - not all work was in the process of submission.
The next CSH meeting on Microbial Pathogenesis and Host Response will be from September 15th to September 18th, 2007. However, there are many other meetings held at Cold Spring Harbor in other fields that might be more interesting to bioinformaticians. Venue and organization can definitely be recommended.

Taking a stroll down to the beach, Lincoln Stein walked past us right outside the Max-Delbrueck-Laboratory, where bacterial genetics was invented. Instead of making a smart remark (such as a foot fall) or flickring him, I was just thinking: "Hey, new haircut!"

Damn you, Stew, damn you!

Common lore has it that 10% of the people actively listen to and understand your presentation, 20% don't get it and 70% are thinking about sex. This might have been true in the 80s but I am convinced that the 70% in the audiences in this millenium think about whether to get out their laptop when the Sigmas start their Slow Waltz and the gene names receive superscripts in cyrillic.
Flipping the lid of your laptop open is certainly as socially outlawed as publicly approaching your old lady/heartthrob/manifestation of a Leonardo DiCaprio in indecent manners. The main reason why we do see laptops in audiences is probably because they are easier to access - and more tempting.

On this conference, nobody uses their laptop during talks but the focus is easily noticable - as soon as the light goes on to allow for questions, many people in the back rows reach for their portable computers.
Bioinformatics conferences were different: There were always people with note books, such as the director of the Center for Intelligent Intelligence whose halo of white hair radiated "Before your contribution to the entropic death of the universe by uttering abbreviations has come to end, little fellow on the stage, I will have commanded my minions to solve the mysteries of cancer using Markov Ball-and-Chains". Or the geek grad student, showing of his vintage installation of HolyBSD on his extra-heavy notebook with a crack, inviting you to watch the recompilation of the kernel and his Dungeon & Dragons character sheet. Or the pundit in the second row who downloaded and browsed the papers of the speaker during the talk to poke him with questions about material that was not presented.
I don't know what to make of it - is it better to "work" in the back row than to let your mind wander aimlessly?

[N.B. No, I did not write this in the lecture theater]

Obviously, there will be as many answers to questions as there are scientists (plus one). However, if you focus on the scientific quality of the talks, I always got the impression that the questions and the reactions of the audience are a supreme measure, particular if I do not understand the specifics of the presentation to the T. If you get heated debates, clever questions and interaction between the speaker and the audience, I feel in a good place.
If you get the pundits talking about papers they read by chance or if you get deafening silence after every talk, finally relieved by the chair of the session, chances are I am wasting my time.
Just re-discovered the positive feeling here...

Maybe, I'll even see a creationist!
Well, starting Wednesday this week, I will attend a conference in Cold Spring Harbor (not a likely hideout for those, if I think about it). It'll be my first non-bioinformatics conference in a long while though.