Reflections on ASHG 2010

As conferences go, the American Society of Human Genetics (ASHG) annual meeting is a pretty big deal. Anyone who’s anyone in human genetics is there, and if you want to be someone you better be there, too. And it’s big — this year’s meeting saw more than 6,000 attendees spread throughout a gigantic convention center that spanned four square blocks in the heart of Washington, D.C. Academics, publishers, clinicians, policy wonks, and industry reps staked out their territory among an endless sea of posters, eye-popping demo booths, and cavernous session halls. The international meeting for bioinformatics that I’ve gone to the past seemed quaint by comparison.

At bioinformatics conferences, the common theme is computational methods, applied to a wide variety of topics. At a conference like ASHG, the common theme is human genetics, probed and interpreted with a variety of methods. But even the topic is breathtakingly broad. Sessions covered complex disease, non-coding RNAs, methylation, ethical/social/legal/education issues surrounding genomic research and genetic testing, mouse models, high-throughput sequencing, population and evolutionary genetics, pharmacogenetics, cilia, computational methods, and Mendelian disorders, to name just a few.

I made my first visit to ASHG this year as part of a small contingent from 23andMe*, a direct-to-consumer genomics company. Although I missed a good portion of the conference due to my schedule, some of my colleagues took notes on sessions that I missed, and ample coverage of many of the sessions could be had by following the Twitter hashtag #ashg2010. The following summaries and reflections represent a composite of tweets, other people’s notes, and my personal notes and impressions.
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Little trouble on the Big Island: thoughts on organizing a workshop and tourist notes


View from the lobby at the Fairmont Orchid hotel

As some of you know, I helped organize a workshop on Open Science at this year’s Pacific Symposium on Bicomputing. I was grateful to have as my co-chair a certain Cameron Neylon, who has spent far longer pondering the issues we were going to discuss and has organized some similar meetings in the past. Cameron took on most of the meat work of the workshop for this reason – writing the introduction for the proceedings, giving the introduction to the session, moderating the panel discussion, and presenting the highlights to the rest of the conference. As for me, I tried my best to be useful!

Others have summarized the workshop nicely so I won’t be doing that here. (If you’re interested in viewing any of the slides or talks, you can access a full list of them from the workshop’s media page.) Instead, I’ll just reflect a bit on what it was like to organize a workshop for the first time, and how I found the Big Island of Hawai’i (hint: it’s a very unique place).

Hurry up and wait

Organizing something starting from almost a year ahead of time was an interesting exercise, marked by short bursts of furious activity followed by long stretches of inactivity. For most of the year, I wondered if I was supposed to be doing anything! But the reality is often that there simply isn’t anything to do until certain times, and then you have to get a lot of things done quickly. For us, we had about 5 flurry points: getting the proposal submitted, taking care of administrative stuff after the proposal was accepted, evaluating and responding to talk proposals, preparing the introduction for the proceedings, and running the actual workshop.

It’s all about the Benjamins

One very important task that didn’t quite fit the mold of hurry up and wait was fundraising. We started looking into this in the spring after our proposal was accepted, and didn’t really stop looking until early fall. One challenge was the nature of the workshop itself, which didn’t fit very neatly into existing categories. Most funding organizations have specific topic areas in which they will fund projects, but these tend to be domain-based, e.g. cancer or infectious disease. Others will fund individuals – minority scientists, for example – working in specific areas of research. We felt it might be difficult to obtain funding from the traditional granting agencies so we tried several companies and organizations associated with companies. Even with connections at some of them, our proposals didn’t get any consideration.

Our only successful proposal was to the Burroughs Wellcome Fund, which, ironically, is more of a traditional granting agency. I sent essentially identical proposals to two different topic areas, one of which was rejected twice – the program officer deleted it the first time thinking it was a conference invitation, and then formally rejected it the second time after I wrote again to inquire about it. (This was actually a problem I never really came up with a good solution for. What do you put as the subject line in an email so that it doesn’t sound like spam?) The other was the one that ended up getting funded. Nothing distinguished it from the other requests except where we sent it, and even here, I had to inquire more than once to make sure someone saw it.

In the end, the money had a huge impact. Not only did it allow me to go to the workshop (!) but we were able to fund several of our participants and had some money left over to cover an emergency (which happened, of course). Having even more money would have helped, because we could have used it to support Kaitlin Thaney from Science Commons. I learned several things:

  • Fundraising is one of the most important aspects of organizing an event
  • Look for funding in as many places as possible. Leverage your network but realize that it won’t always help you get money.
  • Apply to multiple places within one organization if you can. Sometimes the same proposal will get different consideration depending on whose desk it ends up on.
  • Be persistent. If you don’t hear back within a month, contact them again. Contact them at least twice, or until you get a response. If you get any leads at all, follow up – treat every lead like it’s the only one you might get. After all, it never hurts to have too much money, but you literally can’t afford not to have any.
  • (If applicable) Being a student has its pros and cons. On the one hand, you’re an unknown (and so might go straight into the trash folder); on the other hand, you present a sympathetic case. If you can actually get someone’s attention, they will probably understand that you really need the money and that you probably don’t have many other options. So again, be persistent, and emphasize the fact that you’re a student and the reason you need funds is for other students.

Murphy’s law is alive and well

img_9749Whatever can go wrong, will go wrong. And while rarely does everything go wrong, rarely does nothing go wrong. In our case, we had several of our headlining speakers, including the keynote, drop out at the last minute for various reasons and had to scramble to find a replacement. The workshop would probably have been fine even if we hadn’t found one, but we were extremely fortunate that Phil Bourne agreed to participate on 2 days notice, as he contributed a great deal of legitimacy as well as content to the workshop.

We were very lucky that 1) Phil Bourne was free, 2) plane fares dropped very temporarily, 3) we had some funds left over, and 4) there were still affordable vacancies at the nearby Hilton, despite them hosting a conference of their own.

Speaking of things going right, we had very few technical difficulties, even with the live webcasts, so maybe Murphy was too busy relaxing on the beach to bother us during the actual workshop. ;)

Lava, lava, everywhere

Mountain goats next to the road

Mountain goats next to the road

Love the contrast

Love the contrast

Mauna Loa? or maybe Mauna Kea

Mauna Loa? or maybe Mauna Kea

Lava as far as the eye can see

Lava as far as the eye can see

Waipio valley

Waipio valley

The Big Island of Hawai’i is strange, and wonderful. Bigger than all of the other islands put together, it is still very small by continental standards, as you can go from the west to the east in about an hour and north to south in probably about 2 hours. I can imagine a 7-10 day trip would be just about the right amount of time to explore the Big Island.

Given that there are five volcanoes (two of which are still active), the landscape is extremely varied. The central west coast is covered in piles of broken up lava rocks, making it look like a giant had recently tilled the ground with a huge shovel. Mountain goats almost the same color as the rocks perch on some of these piles. Along the ocean, however, the black lava rocks mingle with pure white wave-worn coral. One charming consequence of this is that instead of using spray paint to make graffiti, people use the white coral rocks to “paint” words and pictures on the dark rocky embankments along the roads.

As you go north, the rock piles give way to green swaths and rolling hills, all gently sloping down towards the ocean. In the center of the island are the high mounts of Mauna Loa and Mauna Kea, both of which sport snowy caps. In the valleys below them are broad expanses of young lava flows, shining black and rippled. When we visited this area, we alternately drove through thick fog, then bright sunshine and gusty winds, and finally rain.

On the northeast side of the island are the tropical forests and ridges, including the well-known Waipio valley. We got here too late to hike down into the valley, so we only went in about 1/3 of the way, but with a greater than 15% grade, it was still a workout!

At the southern end is Kilauea, the most active volcano on the island. Someone told me a story about how a small town was obliterated in the last big eruption, but some of the houses were completely spared. Lucky ducks, you think? Maybe not – it turns out those people couldn’t collect any insurance because there was no damage! Doesn’t matter if your house value just dropped to negative or if you can’t live there anymore because you’re surrounded by lava – the house is fine, so thanks for calling and have a nice life!

So much for volcano insurance

So much for volcano insurance

Anyway, Kilauea is still doing its thing, being hot and bothered and adding land mass to the island bit by bit. In the past, I’ve heard you could walk very close to the live lava flows, but these days the viewing areas are about half a mile from them, and so during the day all you can see is a huge column of roiling steam from the lava meeting the ocean. If you hike in close to sunset and stay after nightfall (headlamps or flashlights required), however, you can see a distinct red glow, and the occasional plume of sparks. Helicopters kept buzzing around the steam column, so if you can afford it, I bet the view from the helicopter is amazing.

Awesome column

Awesome column

img_99021 img_99474
img_99551 img_99692

There was much more to see but my stay was short and busy. If I ever go back, I’ll definitely be going up to the observatory on Mauna Kea, swimming with manta rays near Kona, snorkeling at Hapuna beach, and hiking around the northeast part of the island.

Taking conference reporting to a new level

ismb2008Who would have thought a year ago that we’d see an article in a major scientific journal about and inspired by microblogging? But indeed, PLoS Computational Biology published yesterday our report on the ISMB 2008 conference:

Saunders N, Beltrão P, Jensen L, Jurczak D, Krause R, et al. (2009) Microblogging the ISMB: A New Approach to Conference Reporting. PLoS Comput Biol 5(1): e1000263. doi:10.1371/journal.pcbi.1000263

What is FriendFeed?

FriendFeed is a web service for aggregating feeds from numerous other web services and for posting links and messages. Discussions often start up around these posts as people comment on them, providing a convenient, topic-based and searchable archive of conversations. You can post to specific “rooms”, such as we’ve started doing for meetings and (un)conferences (e.g. BioBarCamp, ScienceOnline ’09, PSB 2009) and for particular topic areas (e.g. The Life Scientists, Python for Bioinformatics). Cameron Neylon has written a longer primer on FriendFeed for scientists and Pawel Szczęsny also reflects on how scientists might interact with this tool.

The effort came out of a group of bloggers and Web 2.0 enthusiasts who contributed to the ISMB 2008 room on FriendFeed – many of whom had never before met in person. ISMB 2008 in Toronto seemed to be the first time scientists used FriendFeed to capture the content and activities associated with a conference. Once it happened, it became glaringly obvious how useful and convenient it was to use FF for this purpose.

The room became a place for people to record notes on the talks, which allowed people to attend sessions without completely missing out on all the others (an annoying problem at these larger conferences with multiple sessions going on simultaneously). People could also augment the talk notes with links to relevant papers or web resources, ask and answer questions, and provide different perspectives when several people were covering the same talk. For those unable to attend the conference, the FF room provided a way to learn about what was happening and interact through online discussion.

As the conference went on, it became clear that this online room represented perhaps the most comprehensive set of conference notes any of us had ever encountered, and would not have been possible without the collaborative effort. When Roland heard that the conference organizers were looking for reporters, he made the obvious connection and galvanized a group of us to gather our collection of notes into a summary document. After an initial brainstorming session at the conference, we went back to our separate corners of the globe and worked on the project virtually through Google Docs. Neil led the effort to see the document through to fruition, communicating with the ISMB organizers and the editors at PLoS Computational Biology.

So what might this mean for the future of conference reporting? We are already behind the times a bit as blogging is already a common component of news reporting in other areas, notably politics and sports. Twitter is becoming a popular outlet for real-time citizen reporting, especially in disaster events such as the Mumbai attacks (though not without some controversy). In our case, FriendFeed seemed to offer a useful compromise between the flexibility and speed of Twitter and the organization and discussion possible on blogs, making it a good way to gather “raw data” for conference reports.

After the successful alpha demonstration of the ISMB 2008 room, I find it likely that any conference with an attendee familiar with these FriendFeed rooms will start their own. But is this always a good idea? Conference organizers might not always view microblogging in a favorable light given the private nature of many conferences in the biomedical sciences – for example, the Cold Spring Harbor meetings have an explicit policy against recording the talks or events. Given how easy (and natural) it is now to share content with others, though, each conference ideally should have an explicit policy regarding social media-based coverage. In reality I’m pretty sure that very few do, so it may be prudent to proceed with caution: check with the organizers, encourage them to set an open policy or at least have a policy, and show them examples. Hopefully, with the help of this article in PLoS, they will be easily convinced that microblogging does indeed take conference reporting to a new – and desirable – level.

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!