Notes from the biomass

Even amongst programmers, the semicolon has a hard time. Newer languages in the C-tree such as Python and Ruby have no use for it and mirror its unfortunate demise in the literature and journalism. Its wikipedia entry is already shorter than the ampersand’s if you need hard evidence.
I like the semicolon; when I started writing papers, I tried to squeeze at least one in every piece of work. The few that survived the review of my peers were usually removed by the editors of the journals. I almost forgot about it and was touched when I discovered it again brushing up my touch typing skills (lower row, middle finger on a German keyboard).
Now, the NYT reports the re-emergence of the written-off punctuation mark in the subway. There is hope and nothing will hold me back to inflict it on my readership. Brace for impact!

Career opportunities certainly make on of the worst topics for ones blog, please excuse a little meta-whining here. Job situations are discussed in every coffee break and at every conference dinner and I hear a lot of complaints about the career prospects for postdocs and young PIs in Germany. Many of them very much sound like Tony Hyman and Kai Simmons (not at all young researchers trying to make their mark) in the current Nature’s jobs section.

Until a couple of years ago I have disregarded the complaints from colleagues as statements that one would hear in every lab on the planet. I changed my mind in the face of the problems that many talented (as in more talented than me) friends and colleagues have with the system and compare the number of their offers from in the US vs the ones in Germany. Most of the German researchers that return to Germany (or stay) do so because of their partners and kids, not because the research situation is attractive anyway.

The German system (and likely other European systems) need an overhaul, not only for the “elite researchers” that politicians (and the authors) are concerned about but also for mundane researchers. I know, people in academia who are not in the top 10% and older than 30 should work in industry - I hear they can’t wait for people that have failed in one career path - but the lack of long term perspectives for non-tenured researchers is unlikely to increase the attractivity for the Uberscientists too. In the age of high-throughput research, it will be very important to have a number of technologists and academic specialists around that can support their family even if the 27 year old Harvard alumnus always gets the first position on the paper.

One’s happy to be a bioinformatician when the plants look better when you do not take care of them for three weeks.

Back in Berlin this morning from Cuernavaca after two weeks of travel, I try to stay awake until nightfall to minimize the jetlag. So, no science today, just an activity update. We relocated our course to Cuernavaca successfully, only two participants had to cancel. The hurricane was the third most intense ever recorded, luckily missing Cancun and other denser populated area. Cuernavaca only received plenty of rain, a little more than usual in the current rainy season.

Not that I got to see as much of Mexico as I wanted except for the ruins of Xochicalco (pic). Teaching a crowd of smart and motivated young (as in younger than me) was fun and took way into the evening hours. My personal recommendation from the course is the iTOL developed by the Bork group, which is an amazingly versatile flash front end for viewing and annotation of phylogenetic trees. It is powerful and replaces many of the odd tree viewers bioinformatics inherited from the mid-80s.More soon. Good night for now.

Our course on metagenomics, scheduled to start tomorrow in Cancun, has been postponed to Wednesday and will take place on Cuernavaca. Cancun is likely to be affected directly by hurricane Dean. Some of the participants and organizers are already in the region, let’s hope that everything works as smoothly as rescheduling the flights for me. So, for the people back home: I am still in Texas and will not even be in the area.

According to Attila Csordas over at Partial Immortalization, there’s no good laboratory web site out here. He argues that the majority were designed by the first inhabitants of the web and asks us to prove him wrong by submitting the best laboratory web site to him.

There are certainly not many stunning examples known to me, even if I would not be as bold as him. What constitutes a good lab web site to begin with - functionality, in-jokes or stunning images? Bioinformatics labs are certainly worse off picture wise than labs with a strong background on imaging and the adaptation of corporate identity templates certainly has taken its toll on creativity at many institutions. I’m curious to see the results nonetheless, so if you know a good examples, let him know.

The hypothesis behind the research of preference for heavy metal music amongst gifted teens in the UK remains obscure in this report in the Telegraph;  A comprehensive study of the last.fm profiles of researchers would be more representative and I would not be surprised if an aged matched sample would find a preference for music that some people would classify as “heavy”. After all, Dream Theater or Rush are ideal to cancel the deafening silence of an office out and with Arcade Fire et al. abound, no one should worry about the lyrics of Mastodon.

Blog carnivals: The innocent’s approach to splogging.

JoVE, a new journal featuring videos of experimental methods, went around in the scientific blogosphere quickly. The first issue is out now for some days now, take another look, there is new material and several enhancements of the site.

Over at Pimm, it was complained that the Nature news coverage mentioned the YouTubish charm of the site - I find the low key approach quite appealing. It is hard to imagine that the journal would work if it would have started with strict regulation for submission or a marketing machine. JoVE is a good example of Web2.0 at work: Use existing technologies creatively, don’t start too high, improve as you go along, don’t be pompous.

The way for JoVE to become a proper journal will be a long one still , and major publishers could offer similar services if the buzz continues and the site is picked up by the broader scientific community. Another good use for video protocols might be for the providers of reagents and scientific devices. Let’s hope that the makers of JoVE use the momentum successfully and that the good idea scales with the expected increased editorial overhead, complexity of keeping the site running and other troubles - unlike several good Web2.0 ideas.

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.