Notes from the biomass

After ten years in research, I finally make it to Boston next Tuesday.  I’ll attend the Recomb Satellite meeting, which comprises the 5th Annual RECOMB Satellite on Regulatory Genomics, the 4th Annual RECOMB Satellite on Systems Biology, and the 3rd Annual DREAM reverse engineering challenges and will be covering the events via FriendFeed.

This will be a little exploratory, most talks are scheduled for 15 minutes, including questions. Being RECOMB related, I expect math-heavy talks, so let’s see how to get this across. and that the accompanying publications in Genome Research and Molecular Systems Biology are accessible. Those in the Journal of Computational Biology are already online to give you a taste. Correction: None of the papers presented will be available publicly for some time, if I read the conference site correctly.

I’ll stay past the meetings to work with collaborators. Anyone up to pay Old Ironsides a visit on Sunday afternoon?

[Picture by cheeseroc, cc by attribution]

I appreciate my short legs most on long flights. In a about an hour, I’ll put them to good use, first to leave this wretched coffee shop at LHR Terminal 4 and then board the airliner bound for Singapore, where I’ll be contributing to a computational biology course in the upcoming week.

The return jet lag will hopefully be cushioned by a couple of days on that pine forested beach called Mecklenburg. And then there’s Nature’s Science Blogging conference, on August 30th to conclude a very enjoyable month.

The 20. Genetics Congress just started in Berlin. Its one of the biggest conferences in the field and was a regular topic in the canteen of the Max Planck Institute for Molecular Genetics, my place of work, even during the European football championship.

Martin Fenner will cover the conference today and tomorrow and from Monday on, I will have the pleasure to follow up. I’ll use the blog of the Nature Network group Berlin. We (the Berlin group) have organized several activities around the meeting, including open dinners with outstanding scientists over the course of the next week (thanks to Nature for the support). If you happen to be in Berlin, come and see us.

In August, there will be an EMBO world course on Computational Biology that I co-organize with a number of colleagues, who also taught at the event in Mexico last year. Our course, entitled “From genomes to cells and systems” is intended for PhD students and PostDoc and is aimed to provide basic skills in computational biology with a particular focus on the treatment of data from next generation sequencing technologies. This year’s focus is on the application to the study of human disease and less on metagenomics.

The application deadline is April 1st, 2008, there’s more information at the EMBO website of the course.

[Skyline of Singapore by * etoile(License)]

GCB 2007, Germany’s annual bioinformatics conference ran from Wednesday until yesterday. This year it met in a conference hotel in Potsdam and saw 180 participants, mostly researchers located in Germany.
People from institutes in Potsdam and our department at the MPI for Molecular Genetics were organizing the conference, and which ran very smoothly both in terms of the program and the organization. My favourite key note by Yitzhak Pilpel, who is studying general mechanisms of the cell, such as translation one a cellular scale by mixed bioinformatics-experimental approaches, is my most noteworthy discovery. Contributions to the conference are aimed to come from PhD students and younger Postdocs rather than initial presentations of ground breaking research. What surprised me most this year was the high quality of the presentations. It would be nice if all talks at major conferences where as thoroughly prepared as those of the average student at this year’s GCB.

Still, it occasionally receives loathing for not comparing to focused workshops or international conferences, mostly from people who don’t seem to enjoy networking and expect presentations to be unique entertainment. You can hear similar criticism from the same people on the ISMB. While I was disappointed by the conference in earlier years, too, the previous GCB I attended, 2005 in Hamburg, was already a conference worth going to. GCB 2008 will take place in the Museum of Hygiene in Dresden, which appears to be a much more interesting place than what it sounds like and I hope that I’ll find the time to go.

Sounds like the malaise is in other places at the moment.

Here’s one of the things that competes with my time for blogging: We are organizing a workshop on computational biology, which will held from August 20th through 26th 2007 in Cancun, Mexico. It’s a tour de force of bioinformatics applied to the vast amount of metagenomics data with many practical sessions. There’s so much new and interesting data in there that we aim to compile novel (as in publishable) results. There are some preliminary findings that we will explore further in the workshop and which also link the different subjects.
Cancun is a very beautiful spot from all I’ve seen and heard and provides a nice venue close to where most of the metagenomics data was sampled.
The EMBO World program is our main sponsor; Food and lodging is provided, the participant’s institutions have to arrange their travel. We encourage graduate students and Postdocs with some background in bioinformatics from all over to globe to apply.

[Picture of sunset in Cancun by 16209788@N00 (License)]

Bloggers are nothing more than users of a simple content management system. Most of the participants of re:publica, the blog conference that concluded yesterday in Berlin would probably agree. In that light, the atmosphere was very open and friendly, to the point that people on the panels complained that there was too much consensus. I prefered the in-depth discussions over random quibbles though, even if the latter would be more entertaining.

The most frustating aspect of the re:publica conference was the proximity to the institute. With too much work to do, I spend too little time at the meeting.
As far as science is concerned the hard bloggin’ scientists, a group of student through postdoc-level scientists from many disciplines hosted an entertaining and relevant “plug-in”, a workshop with little agenda, what turned out to be working nonetheless. The diversity was reflected in the 40-strong audience. The hard bloggin’ scientists were not discussed all that much; they have found a niche in adding color to the communication between scientists and the general public and are pretty well known in German blogger circles.
(more…)

Re:publica has summoned the German blogosphere to the Kalkscheune, just a couple of blocks from my office in Berlin-Mitte. With 700 attendees over three days it appears that a substantial portion came.

Does it make any sense to go to a blog meeting - wouldn’t it be better to stay at home and use the time to read? Certainly not, if I consider today. Many of the aspects of social software (and interactions of people in general) were said before but the discussions put them in a new light.

One noteworthy tidbit from the panel on blog etiquette this afternoon was the notion of blogs as a “pragmatic medium”, one that provokes direct response, uttered by Rainer Kuhlen (UNESCO chair in communications). In contrast, classical journalism as seen in newspapers are not written with the intentions for communication in the other direction. Most scientific works are published with a similar mind set: The discussion is part of manuscript, not contributed by the readers. After something has been published and passed peer review, it is true until retracted or forgotten.

The most common argument for the lack of participation in the scientific blogosphere is lack of incentives but we need to consider that we do not publish to be discussed in the first place.

Hmm. This didn’t read like a truism this morning. Let’s talk about tech instead.
A nice gadget enables everyone to comment on the presentations (or cocktail bars in the vicinity) via SMS. Not that the comments added much to the discussion for most of the time but the level of participation is what I want for any conference.

[Picture by timk75 under CC by-at license]

About time to mention Re:publica here, open for registration since the weekend.The ununconference on blogging, social media and the rest, organized by the unmissable Berlin-based bloggers Johnny Haeusler and Markus Beckedahl will take place in Berlin from April 11th - 13th 2007, halfway between my flat and the institute. Nice.
Science wise, the hard blogging scientists will host a “plug in” - not so sure what that is yet, I’ll attend anyway. If you are interested in blogging in the natural sciences, drop me a note.

Recording my first screencast for the Online EMBL PhD Symposium was an interesting experience. It pretty much felt like the very first presentation again, particular after I realized that it would not be possible to compile individual pieces in time (thank you Powerbook) and I had to take it in a single attempt. SnapZ Pro is a pretty impressive tool for recording nonetheless.

Preparing a screencast is the best presentation training available I could think of. You are not getting away with so-so this time because you have to listen to yourself. Give it a try the next time you want practice in presenting at a meeting (and remind me…).
I will talk/have talked about open issues in protein-protein interaction networks, particular shared components of complexes, to fuel the online discussion. I have tagged the relevant references in Connotea with ‘1vs‘ if you want to be prepared. Hope to see you during the next week in the IRC.