Copenhagenomics 2011, in review

It’s early Saturday morning in Copenhagen and Copenhagenomics 2011 is done.  I was going to say that the sun has set on it, but the city is far enough north that the sun really doesn’t do much more than sink a bit below the horizon at night.  That said, the bright summer sunshine has me up early – and ready to write out a few thoughts about the conference.

[Yes, for what it’s worth, I was invited to blog the conference so I may not be completely impartial in my evaluation, but I think my comments also reflect the general consensus of the other attendees I spoke to as well.  Dissenters are welcome to comment below.]

First, I have to say that I think it was an unqualified success.  Any comments I might have can’t possibly amount to more than suggestions for the next year.  The conference successfully brought together a lot of European bioinformaticians and biologists and provided a forum in which some great science could be shown off.

The choice of venue was inspired and the execution was flawless, despite a few last minute cancellations.  These things happen, and the conference rolled on without a pause.  Even the food was good (I didn’t even hear Sverker, a vegetarian Swede, complain much on that count) and the weather cooperated, clearing up after the first morning.

As well, the conference organizers’ enlightened blogging and twittering policy was nothing short of brilliant, as it provided ways for people to engage in the conversation without being here first hand.  Of course, notes and tweets can only give you so much of the flavour – so those who did attend had the benefits of the networking sessions and the friendly discussions over coffee and meals.  The online presence of the conference seemed disproportionately high for such a young venue and the chat on the #CPHx hashtag was lively.  I was impressed.

With all that said, there were things that could be suggested for next year.  Personally, I would have liked to have seen a poster session as part of the conference.  It would have been a great opportunity to showcase next-gen and bioinformatics work from across europe.  I know that the science must be there, hiding in the woodwork somewhere, but it didn’t have the opportunity to shine as brightly as it might have.  It also would have served to bring out more graduate students, who made up a small proportion of the attendees (as far as I could tell). Next year, I imagine that this conference will be an ideal place for European companies and labs to do some recruiting of young scientists – and encouraging more graduate students to attend by submitting posters and abstracts would be a great way to facilitate that.

Another element that seemed slightly off for me was the vendors.  They certainly had a presence and were able to make their presence noticed, but the booths at the back of the room might not have been the best way for companies to showcase their contributions.  That said, I suspect that copenhagenomics will have already outgrown this particular venue by the next year anyhow and that it won’t be a concern moving forward.

While I’m on the subject of vendors, what happened to European companies like Oxford Nanopore, or the usual editor or two from Nature?  Were some UK attendees scared off by the name of the conference?  I’m just putting it out there – it’s entirely possible that I simply failed to bump into their reps.

In any case, the main focus of the conference, the science, was excellent.  There were a few fantastic highlights for me.  Dr. John Quackenbush‘s talk challenged everyone to seriously re-consider how we make sense of our data – and more importantly, the biology it represents.  Dr. Elizabeth Murchison‘s talk on transmissible cancers was excellent as well and became a topic of much conversation.  Heck, three of my fellow twitter-ers were there and each one did a great job with their respective talks. (@rforsberg, @dgmacarthur and @bioinfo)

In summary, I think the conference came off about as smoothly as any I’ve seen before – and better than most.  If I were given the opportunity, this would be a conference I’d pick to come back to again. Congratulations to the organizers and the speakers!

A few notes on Ubuntu 11.04

Right off the bat, I have to say that I’ve been using 11.04 on one of my computers since one of the earliest alpha releases, so I’ve had the opportunity to watch it mature.  It’s something I often do – pick one computer, and use it to test out the new versions of ubuntu, upgrading the packages daily to follow along with the progress of the development. It’s usually a rewarding process, and I enjoy fixing bugs and learning how the operating system components fit together.

This was one of the few times that it was a disappointment for me.

Normally, I’ll start the process a month after the newest release, spending about two months using highly unstable versions, which then improve over time so that nearly all of the bugs are gone about a month before the official release.  This time, the release has come and gone, and my computer still doesn’t feel particularly useful.

Unlike the majority of Ubuntu users, I’m not using the default Ubuntu with Gnome window manager (or is it unity, now?), but rather KDE + Compiz.  Unfortunately, while the KDE version of Ubuntu (Kubuntu) doesn’t appear to get nearly as much attentention from the devs, it usually does march in lockstep, giving reasonable releases that come together at the last minute.  Unusually, compiz just never did come back together for me.  Perhaps it has to do with the upgrades to the xorg packages, but something is just not right when using compiz.

The symptoms are frequent restarts and crashes of the windowing system, in which the CPU usage of compiz soars to 100% and fails to respond to anything short of a the “killl -9” command.  Unfortunately, that makes compiz totally unuseable.  Ironically, it seems to happen only when closing windows, which seems like a strange place for a bug.

The workaround, if it’s actually a work around, is to completely disable compiz, which means switching back to the default KDE window manager.  Fortunately, it’s stable, so at least I can use the computer.  Unfortunately, I find Compiz to be a significant boost to my productivity, with the rotating cube desktop, the scale plugin, etc.  All of those things really make the experience on the computer, so turning all of them off it just unapealing.

In any case, for now, I’ll be staying with 10.10 on my laptops and production computers until compiz is fixed, with the possibility of jumpping straight to 11.10 as soon as that begins if I see compiz gets a bit more of the attention it deserves.

Your milage may vary, but 11.04 isn’t likely to make an appearance on my main computers anytime soon.