Off to ISMB 2008

Tomorrow I'll be heading off to ISMB in Toronto. I haven't attended the big show before, other than a 1 day SIG 3 years ago in Detroit, so I'm sure it will be enlightening, perhaps for the science, but also for the sheer surreality of packing thousands of normally bunkered down and repressed scientists into a small and contrived space.

I hope I can smuggle my poster tube onto the airplane without them noticing that I also have a carry-on and personal item already. But kind of hard to hide something that's almost 4 feet long... speaking of transporting posters, how cool would it be to have electronic poster boards at conferences? No more poster tubes, little sheets of paper, curled edges, or push pins - just upload your file before you get on the plane, bring a thumb drive just in case, and you're good to go. Sure, they'd be expensive, delicate, heavy, and perhaps prone to glitches, but nothing a few years of tech investment can't fix.

AMIA Summit on Translational Bioinformatics

Hundreds of clinical scientists, biologists, bioinformaticians, and policy gurus descended on the swanky Intercontinental Mark Hopkins hotel for the first AMIA-sponsored Summit on Translational Bioinformatics last week. Stanford's Atul Butte rallied impressive troops for this inaugural meeting, including the leaders of all of the National Centers for Biomedical Computation (NCBCs, 7 or so total). Since translational bioinformatics is not simply about research, but about translating research into tangible benefits (clinical diagnostics, therapeutics, and standard of care), this meant a many faceted conversation involving basic researchers, large-scale integrative projects (e.g. caBIG, the NCBCs), clinical scientists, informaticians, and government agencies. This was reflected by the structure of the meeting, which consisted of tutorials; policy, technology, and organization panels; primary paper sessions; and posters covering topics ranging from how to establish collaborative projects to ontologies and phenomics.

Given the breadth of the audience, I'm sure the highlights of the conference vary from person to person. Below are some of mine:

Eitan Rubin from Ben Gurion University, Israel (Talk highlight). "Reverse translational bioinformatics: a bioinformatics assay of age, gender and clinical biomarker." A self-proclaimed biologist, Eitan presented some intriguing work in what he called "reverse translational bioinformatics" - using clinical/medical data to make useful discoveries about biology. As an additional aim, he strove to show that existing bioinformatics tools could be applied to clinical data with little modification. To do this, he took an immense data set - thousands of variables collected for tens of thousands of individuals (part of a nutrition and lifestyle survey that was epidemiological in nature), including laboratory tests, questionnaire answers, and medication data - and essentially turned it into a microarray after binning by age. Note that this was a proxy for clinical data since no such data is currently publicly available. He then subjected this array to the same kinds of analyses one would perform on an array of molecular biological data: normalization, calculation of median values, clustering by age and variable. The results encompassed both the expected and the surprising. For example, when he clustered by age, he found distinct boundaries between somewhat intuitive ages - at 12 yrs and 16 yrs for both sexes, at 40 yrs for women and again around 49, and around 45 for men; these could point to interesting biological changes going on at these age boundaries. He also plotted the median values for variables like serum lead level vs age and found distinct patterns. At this point, he has only begun to analyze the enormous amounts of data, and more interesting patterns are sure to emerge. In the meantime, it helps drive home the potential behind open data and data (and methods!) re-use.

Yael Garten from Stanford University (talk highlight). "Pharmspresso: a text analysis tool for linking pharmacogenomic concepts." [Disclaimer: Yael and I are colleagues in the same lab and I helped to critique her presentation.] Yael's work on a semantic, scoped search engine for pharmacogenomics is worth mentioning because of its immediate and potential utility. Pharmspresso allows a user to query a corpus of documents (currently about a thousand pharmacogenomic-related articles previously curated by the PharmGKB team) for keywords, genes, drugs, and/or polymorphisms occurring in the same sentences. Based on the Textpresso ontology created for mining the C.elegans literature, Pharmspresso includes semantic support for human genes, drugs, and genetic polymorphisms and additionally improves upon more general search engines such as Google and PubMed by limiting the scope of the hits to the sentence-level and returning hits color-coded within each sentence for easy evaluation of search results. Pharmspresso has already helped the PharmGKB curators and in the future will be incorporated into an automatic curation pipeline.

Selected papers to be published in BMC Bioinformatics. At the close of the conference, the surprise announcement was made that 15 of the 27 presented papers had been selected to be published in a summer issue of BMC Bioinformatics as a joint agreement between the Open Access journal and AMIA, who would foot the bill. The papers would need to be expanded and updated for submission but the peer review process had happened for the conference and so they were already considered accepted for the journal. A couple of big conferences already do something similar - ISMB/ECCB and RECOMB - but it would be great if every major conference had some kind of arrangement like this with a journal. It seems like it would be a win-win for everyone - peer-review already taken care of, an increased audience for that issue of the journal, and a nice CV boost for the authors (and no more hard decisions between presenting at a conference vs publishing in a journal). Given the fact that this was the very first meeting for this conference, it was a very nice surprise indeed.

Thoughtful A/V setup. This is simply a logistical highlight. We've all sat through our share of technical difficulties, but this conference (at least in the main room) was astonishingly free of them. A large part of this was due to the presence of dedicated A/V staff who knew just when to dim and raise the lights, cue mood music, and put up the "transition screen" - a screen blank except for the AMIA logo. This screen went up whenever a presenter's slides were NOT up, and prevented those awkward moments when the audience could see the desktop of the presenter's laptop or the view of the Powerpoint application. It was also nice not to have to see the blue or black screens when video input was changed. All in all, it imparted a much-appreciated professional touch to the conference which other meetings would do well to emulate.

In summary, there were some informative panels on various policies and the NCBCs, interesting research, and nice extras that made this first Summit on Translational Bioinformatics a big success!

Going forward on the PSB proposal

After finding out more information about conference logistics, it looks like we have enough momentum to start writing the proposal. Most of the discussion is taking place on Science in the Open, so let's just keep it there, at least until I get the draft of the proposal up. If you are interested in contributing to the proposal, please email me so I can set up editing permissions in the draft document!

An additional feeler for PSB

In an earlier post, I mentioned the possibility of submitting a proposal to PSB for a session on Open Science. Since then, I've gotten some informal feedback that the organizing committee is interested in the idea, but needs more information. The advice I received was to submit a regular session proposal detailing what kind of papers are expected and the people who would potentially participate. Essentially, the topic needs to be able to attract enough substantial, scientific papers for the committee to be convinced of its merit. Part of the process will involve soliciting paper submissions from specific people known to be working in the field.

On Cameron Neylon's blog, the point was made that PSB is an expensive conference to attend, and for this reason it could be a non-optimal choice for an Open Science meeting. However, if there are no strong objections to having multiple meetings on Open Science in the next year or two (if there are, then that is definitely worth discussing!), then we have nothing to lose (and probably some to gain) from submitting a proposal to (and if all goes well, hosting a session at) PSB. As Pedro Beltrao points out, it doesn't hurt to gain more exposure, even if it ends up being just a short tutorial. Also, I've been seeing a lot of Open Science activity in the US and Europe, but have yet to catch wind of it elsewhere; PSB, being located in the Pacific, draws a lot of attendees from Asia and Oceania, and it would be interesting to see what efforts and issues regarding Open Science are happening there.

So my big questions are these:

1. What should be the focus of this session on Open Science? (first, frame it as a traditional PSB session, then perhaps as a "creative" session)
2. What kind of substantial/technical/research papers can be written about Open Science?
3. Who are the major players in the field? Who would the session chair invite to submit a paper?
4. Who is willing to help write/organize the actual proposal and session?

But my most important question is this: Is anyone involved in the field interested in chairing this session?

Being a novice grad student who has very little experience with Open Science (this blog is it so far, and it only started a week ago!), I feel that such a session would be much more effective with a more senior Open Science advocate as chair. One of the duties of the session chair is to give a tutorial on the subject, another reason why someone with more experience would be better suited to this role.

Again, the deadline for session proposals is Feb 8th, so if it is going to happen, it will have to happen pretty fast. The community has already shown that bigger things (a grant proposal) can be accomplished in less time (a week), so I am not worried about getting it done if a consensus is reached.

If you have any answers or suggestions for the above 4 questions or about the session in general, and especially if you are interested in chairing, please respond to this post or email me!

* Edit: I originally mixed up Cameron's blog (Science in the Open) with JC Bradley's blog (UsefulChemistry), and have corrected it. Apologies to both!

Open Science at PSB 2009?

I attended a seminar today where we came up with a list of ideas for sessions for the 2009 meeting of the Pacific Symposium on Biocomputing (PSB). This group of people organized a session at PSB 2008 called "Multi-scale modeling", so many of the ideas were related to computational modeling. But since I am interested in Open Science, I asked whether there would be interest in having an Open Science session at PSB.

PSB is a pretty prestigious conference that prides itself on covering only the "hot topics" in biology and biocomputing. Combine that with their locale (Hawaii), and you can imagine it is fairly difficult to get accepted. But even though a session on Open Science would differ from their traditional sessions (less primary research papers, more tutorials / descriptions of experiences / discussion), I think it would be great to talk about Open Science there, since A) PSB is prestigious, B) attendees are probably pretty forward-thinking, C) by Jan 2009, we will be ready to have some really productive discussion, and D) did I mention Hawaii?

The deadline for submitting a session proposal is Feb 8th, which is in only a couple weeks. If there is support for this, I will try to carry it through. Here is the call for papers, which includes guidelines for what makes a good session, and responsibilities of a session chair. I'm not sure that I would be the best choice for a session chair since I have not participated in an open science endeavors yet and the session chair is required to give a 1 hr tutorial on the session topic, so if anyone is interested in being the session chair, please let me know! Ideas for what kind of papers could be solicited would also be appreciated.