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.

How journalists report scientific progress has been criticized strongly in the scientific community, certainly blogside, and has been the subject of many scientific studies itself. A recent article in PLoS Medicine reviews some efforts for reporting on new treatments and looks into reports published in HealthNewsReports.com. There is a strong “who watches the watchblogs”-reaction in me after looking into the site conducting the reviews, and I haven’t made up my minds about how much of it can practically be done by science coverage in traditional media in the first place. For bloggers in the sciences, the evaluation criteria provide standards that you might not want to follow to the T but certainly review, at least before commenting on news coverage like “the cure for cancer by sequencing animals”.

[via the Short Sharp Science]

Berlin has numerous research institutes, which are spread all over the town and beyond. Many scientists find the connectivity amongst the researchers leaving a little to be desired. Blaming the institutes, their directors or the German research organization might be convenient and fun but of little good; luckily Phil Selenko, who is setting up shop for in-cell NMR (!) at the FMP contacted me via the Nature network a while ago when he arrived, looking for support to start an informal gathering similar to what he had experienced in his PostDoc in Boston.

We’ve had our first get-together with people from the area a month ago and  there is more to come. If you are in the life sciences in Berlin and want to meet people beyond your local crew, check the Berlin group at the Nature network for activities.

[Picture under CC-license from extranoise]

The old blog layout was perfectly OK but there was no way to maintain it any longer. Here is a fresh start that still requires tweaking. May you be happy with your blog design and may your never fish for new Wordpress themes in that big sink hole. Use Kubrick. Aren’t we all using  feed readers?

As a science publication, the journal Nature is held in highest regard; to me it shines even more for its science journalism, which is the focus of a new experiment. Somewhat modest in the light many activities at NPG and probably not entirely novel in publishing, the editors have selected three publications in journals outside the usual scope and the reader gets to select one of the topics to be investigated further. I have never heard of the journals before and one of the articles even seem to be a couple of months old but they all appear to be curious little stories, discovered by people who read more than the press releases. Last week’s story covers the genome of a giant bacterium and is freely accessible from what I can see. Let’s hope that there will always be a market that supports science journalism targeted at scientists rather than just a large crowd that wants to read hear about the latest cure for cancer.

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.