Refelections on AGBT2011

[Written Sunday, Feb 6th, while flying home to Vancouver.]

From my vantage point at 30,000 feet, I can take a good look back at this year’s Advances in Genome Biology and Technology conference.  There were certainly a few things that were worth reviewing.

The one change that impacted me the most was the surprise policy on blogging and tweeting.  Judging by the reactions of the people I spoke to, it wasn’t really on anyone’s radar until the the slide describing the policy went up – and of course when Elaine Mardis announced that the default of the conference would be opt-in, rather than opt-out.  Some of the surprise in the audience appeared to come from people who had never heard of twittering until the word appeared here, while others appeared quite enraged by the existence of a policy at all.

Not to belabour the point, but AGBT exerted a fair amount of forward thinking by having a policy at all – and I was glad that they had one – however, much of the confusion or “controversy” of the policy could have been avoided by educating the speakers on what twittering is – and what it means.   As for being a trend-setter in the science world, they could have done a better job by providing a more reasoned approach to it, however, by not being entirely draconian and banning it, they’ve already taken the first step, and realized that social media isn’t going away.  I’m certain that AGBT2012 will be a much more dynamic event, if social media becomes better integrated.  (I understand that there was even talk of a separate screen showing the tweets in real time, but that the organizing committee wasn’t quite ready for that yet.)

That aside, there were some fantastic highlights, and one that stands out for me is Pacific Bioscience’s lunchtime talk.  It was a great departure from previous years where they told big stories without a lot of specifications.  Don’t get me wrong – I still love the technology, but I think the more humble approach sits better with me.  Whereas in previous years, we weren’t given many details, the candid admission that Pac Bio isn’t going to displace all of other technology, but will rather supplement them, is a big step forward in the vision.   Furthermore, it’s also interesting to hear that single molecule sequencing isn’t going to have the same accuracy as the “ensemble” or colony sequencing devices, where base calling can average over the signals of many molecules.  Fortunately for them, they were able to demonstrate exactly why that doesn’t matter.

Pac Bio’s Eric Schadt also gave a talk that created quite a stir on the last day with some big ideas, including constant virus monitoring for effluent management stations and some very “big brother” like monitoring of DNA passing through Pac Bio’s own headquarters.  (I am a little worried about the pig and chicken DNA splattered around their kitchen, but at least they asked their employees to volunteer for the nose swabs used in some of their pet projects.)  Frankly, even if their technology is perfect, I’m not sure I buy into the “sequencing every restaurant” model.  Yes, it would drive sales of their technology, but is it really necessary to have a virus weather map in real time?  What actionable results would it give?

Unfortunately, the other hot topic of the conference was from a session I couldn’t attend myself. In the upcoming technology group, several groups were discussing work on nanopore sequencing, which appears to be showing significant progress.  While I missed those talks, I did see the talk on replacing alpha hemolysin channels with an MspA protein channel – and results presented from that talk did look very good.

Other things of interest included the usual travel delays and cancellations – once again the conference organizers managed to plan the conference for days with some of the worst storms – and as usual, they affected just about everyone.  I found myself thinking that Dallas looks better without snow – which would have seemed like a nonsensical thought if I hadn’t seen it first hand.  Fortunately, deicing delays in Dallas were the worst I had to put up with.

The conference was also notable for what wasn’t talked about as well.  I didn’t see any new methodologies presented, nor were there that many people talking about novel experiments.  People seem to be digesting a year of incremental improvements in the sequencing technology and the massive jumps in the amount of data available – which led to a lot of pipeline focused talks, as well as attempts to apply the information to influence clinical outcomes.  Those are both signs of maturity of the field, but a little disappointing from a conference called “Advances in Genome Biology and Technology”.

Another thing that has dropped off the radar was chip-seq.  Two years ago, EVERYONE was talking about it and there were tons of posters on the topic.  As a chip-seq software author, the complete lack of epigenetic posters, and the casual way in which epigenetics was mainly absent from talks, was pretty stark – and it makes me wonder if we’ve all just accepted the field the way it is, or if people have simply had enough of it and have given up.

I suppose one also has to mention the lack of bioinformatics talks as well.  I won’t say there weren’t any, as I did see a few, but in most cases, the presenters simply listed the tools they used on one slide, and moved on. The biology also took a back seat to the clinical applications, when possible.  It almost appeared as if the hierarchy of topics started with tear-jerking stories, moved through some systems biology, passed briefly over the bioinformatics, and maybe included some hardware issues.  Of course, that’s just my sampling – other opinions probably differ.

Probably the best part of the conference, for me, was the networking.  I met a people who are pioneering in bioinformatic business models or VC funding for life science, in addition to the academics and corporate scientists.  That diversity really makes me appreciate the experience of going to a conference like this.  As a fellow Canadian pointed out during the feedback session, the vendor parties also made for fantastic networking sessions and had struck a great balance between networking time and learning time.  (I should also point out that the number of twitterers I met was pretty incredible.  It was really neat to put faces to icons…)

Of course, I probably lost out on some of the free time by trying to blog all of the talks, but I’m told that my notes enabled other people to skip out on a few talks themselves and get in some beach time.  Although, despite the work that goes into the notes, I really enjoyed the process.  Without them, I wouldn’t have met as many neat people as I did.

Having been to the AGBT conferences for a few years, now I’ve had the opportunity to watch the conference evolve as well.  In the beginning, there were tons of slides on the sequencing technologies being presented – from the structures of the fluorophores to animations of the sequencing process, which have all dried up. All of the companies are now competing and struggling with similar chemistry issues, and of course, this information is now top secret.  But, it does mean that the devices have gone from being applied chemistry to being “black boxes”, of which the researcher is just expected to pick the one that fits best to the experiment they have planned.  In a way, that completely validates the Complete Genomics business model, in which I expressed so much skepticism when I first met them at past AGBT conferences.

And speaking of Complete Genomics, a last point would have to be the much re-tweeted announcement of 60 publicly available genomes from Complete Genomics.  It was clearly a signal that Complete Genomic’s model is working, and that they have nothing to hide – I know we already have people downloading them and I’m looking forward to seeing the data when I get back to work on Monday.  Whatever skepticism I may have had about what they can do is clearly being dissipated – and they definitely have my respect for going out of their way to engage the community. (It’s noteworthy that they’re the only company that actively makes an effort to talk to bloggers and twitterers, even though 8am breakfast meetings with shy and sleepy bioinformaticians can’t be all that exciting.)

I’m sure there were other things that would be worth mentioning, and several of the talks above are worthy of entire discussion sessions, but I think I’d like to wrap this up neatly.

With the rapid advances of the past years giving way to small but constant improvements in sequencing technology (mostly via chemistry improvements), this conference will likely find themselves re-evaluating the focus of their sessions in the near future.  I certainly don’t think that the advances will dry up any time soon, but I’m not sure that they’ll be able to bring in the same crowds in the future.  With the increasingly “black box” technology platforms and the lack of new methods being presented, I’ll be very curious to see where the conference goes in future years – and of course, how they adapt to the pressures of social media.

8 thoughts on “Refelections on AGBT2011

  1. Pingback: Tweets that mention Refelections on AGBT2011 | --

  2. I benefited from your twittering last year, when I was unable to attend AGBT. I did not expect how much I would still appreciate reading your perspective this year, when I did attend. Just sorry I did not get the opportunity to convert your icon to a face, and thank you personally at the meeting. Still, the electronic mode is available, so, thank you for sharing your view of AGBT.

    • Hi Naomi,

      Thank you very much for the comment – that’s very high praise indeed! I am always happy to meet the people who’ve enjoyed my notes Hopefully we’ll have another opportunity in the future.

  3. I was glad we had the opportunity to meet in person, albeit briefly. Hopefully next year’s meeting will provide more time for discussion.

    I’m not sure if this is feasible, but we could attempt to coordinate our activities for next year’s meeting. I believe there were a few sessions not covered by anyone (Tweeting or blogging) and if the purpose is to disseminate information, those outside the meeting might appreciate fuller coverage. For myself, I really liked your approach of simultaneous blogging/tweeting. And although I don’t currently blog outside the activities of my 2 year old, for next’s years meeting I may try to expand.

    • Hi David,

      Unfortunately, I probably won’t be at next year’s AGBT – I’m hoping to finish my degree before this fall and I don’t know where I’ll be by next February. However, I’m happy to pass along the mantle – and I’d certainly read any blogging you do next year! (If not, I’ll be following the tweeters!)

      Either way, it was good to have the opportunity to meet, even briefly – and I hope we bump into each other at another conference.

  4. Just wanted to chip and say that your blog was again incredibly useful. Its an invaluable resource both during and after the conference. I know I’ve found myself going back to it to remind myself of who gave a particular talk or what the gist of it was. I think I speak for the silent majority when I cry out in despair at your statement that you “probably won’t be at next year’s AGBT”. That’s a real loss to the conference in my opinion. Maybe we should suggest an “official blogger” role be advertised by the conference organizers to make sure this resource continues. As suggested above, it might be best if it were shared between 2 or 3 so that concurrent sessions would be covered. I think a reasonable honorarium from the conference would be a really good investment for the conference and a good incentive for dedicated bloggers like yourself to continue the good work. The preferred bloggers each year could be selected democratically by voting through twitter or something. Just a thought. Good luck writing up!

    • Hi Obi,

      Thanks for the comment – that’s high praise indeed! I’d be thrilled to officially blog a conference, but I suspect that AGBT’s organizing committee is a long way from being ready for that yet. They still don’t seem to have quite worked through twittering yet. But hey, if the conference calls to asks me to go, I don’t think I’d turn them down. You learn a LOT in a short time at AGBT, no matter how you slice it.

      On further reflection, I suppose that would be a good way to start a science journalism career… (=

  5. Pingback: Wrapping up AGBT | SNP Genotyping

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