Notes from the biomass

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)]

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!

Everyone is using tiling arrays these days but the quality of results is still hard to judge even for the most experienced people in the field. Designs differ in type of the oligo density, oligo length, selection algorithms and experimental procedures. On top of that, several analysis procedures claim to be superior over each other. Eight groups performed independent evaluations of tiling arrays for the human genome from the major vendors (Affymetrix, NimbleGen and Agilent) and report their findings in Genome Research, on February 7th, 2008. As the scientists had no knowledge about the PCR products that were spiked in the sample, this is an blind evaluation and thus much more powerful than the typical validations using real time PCR.

The overall results are a sobering: only 50% of the sequences selected were consistently detected at10% FDR. This is not to be taken literally as the majority of the missed samples were present in low numbers only (1.25 to 4 fold) and we do not have good data for the true fold changes in these experiments.

All three vendors supported this study and employ a good number of the authors. In that light, it is no surprise that the study does not report major quality differences between the chips. They do report that Affymetrix arrays require more repetitions to reach the same quality of the results but are of lower price (conveniently tabulated in the paper). No method performs well in the low concentration regime, although Agilent and Nimblegen arrays look a little better at it. I certainly don’t want to imply that the affiliations biased the results of this study (this is the internet after all). On the contrary, this is a very useful collaboration between chip vendors and technology leaders in academia. But read it before the next sales person in the chip business knocks on your door or you want to build trust in a particular data set.

Lars Juhl Jensen is one of the most prolific people in computational biology. A fellow scientist once said enviously: “The worst thing about him is that he is even a nice guy”. (I don’t find that particularly bad but there you go.) Lars has recently decided to post the crumbs that fall from his notebook in his blog “Buried treasure”, which you should add to your feed reader if you are but barely interested in bioinformatics.

[via Konrad]

Giving good presentations is easy. I have read all about it, practiced it many times and even won a presentation contest against half of the info elite of Berlin (n=10, once). Surprisingly, I occasionally find myself in front of an audience stuttering and apparently inept to close a single sentence appropriately. I appear to be utterly unprepared even when this is the seventh time I tell my little story about bugs and yeasts. As presenting ones work will be a regular activity of the rest of my life, I’ve been asking myself what to do about it for some time and found a little trick that has done me well often (n=3).

Listening to colleagues or seeing a scientist at conferences again and again, it seems that many people’s presentation skills vary dramatically by time, too; hence the hope that this post will reach others could put it to use.

It’s no secret: You need to start your delivery on the strong end, not only is it the first impression that your audience gets of you (or your colleagues of your new idea). Often enough, I find my grip only halfway through the slides. Even more importantly, sentences flow easily if the first three of five are on target. However, those are often the hardest and one typically starts presenting after sitting silently in an auditorium for hours or following up on the good ideas that you had while preparing the talk.

Therefore, I am trying to get a flying start whenever I can by grabbing an unsuspecting subject that doesn’t talk back too much and start an abbreviated presentation one-to-one without the slides just outside the lecture theater or seminar room. Science conferences typically have a session chair that you can finally put to use if there’s a coffee break before your talk but you can just as well coerce an interested student into receiving an advance on your presentation. You just need to reset the presentation but instead of having waited anxiously at the start of your talk, you have practised, have your head in the subject or vice versa and you will have remembered how to make audible sounds with your mouth. The transition were rather smooth and its an good way to beat the stage fright. Just keep talking.

Next: The importance of regular posts for the success of your blog.

The current issue of Nature Biotechnology contains a commentary on protein-protein interaction networks that nicely reflects the view of the informed end of the community. The only thing that I would criticize in their treatment is the lack of differentiation between the methods. Only by checking the references, you’ll notice that the lack of overlap they cite is between the now very dated data sets by Uetz and Ito. If you compare the high-confidence interactions (not the complete sets) of the 2006 studies by Krogan et al. and Gavin et al. you’ll notice that they are in good agreement, even if we are nowhere close to what we are used to from studying genomic information.

Our new paper in BMC Bioinformatics is about the only one that is not “highly accessed”. Next time we’ll take care to put “human cancer interaction” in the title.

The current issue of EMBO Reports contains a short analysis, which shows that the number of retractions of scientific publications increases dramatically. The authors give two possible explanations: Competitions amongst scientists lowers the quality of published research. It might also mean that scientists are more aware of other people’s mistakes and that “the self-correction of science is improving”.

While both alternative are plausible, my favourite suggestion is that online publications have made it feasible to retract papers and there is an incentive for the journals to show that they take care of possible misconduct. A large number of the retractions might be of heavily flawed works rather than fraud (a blogger’s assumption, I have not checked enough retractions myself). Earlier, the community would know that a particular work is not reproducible, but the retraction process was cumbersome and consumed too much time, so it was only pursued in the grossest instances.

There are so many complaints regarding position on the author list that I tend to ignore most of the conversation on the topic unless a journal actually changes something. The PLoS blog features a noteworthy idea by Michael Molla and Tim Gardner. Similar to the roll credits that appear at the end of a movie, they suggest a defined, fine grained roles. Senior author could pose as producers or director, refining their role, and obviously a story can have more than one main character. It’s definitely a step in the right direction but film posters always confuse me in that the names of the actors and the order of their faces in the poster never align. Even if the roles are better defined, the bitching for positions will surely remain.

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.