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PhD position in Statistical Protein Structure Prediction, Copenhagen, Denmark

One of the major unsolved problems in bioinformatics is the protein folding problem: given an amino acid sequence, predict the overall three-dimensional structure of the corresponding protein. It has been known since the seminal work of Christian B. Anfinsen in the early seventies that the sequence of a protein encodes its structure, but the exact […]

Your Genome, Yourself?

We have Palaeolithic emotions, medieval institutions and God-like technologies. E.O. Wilson   Whole genome sequencing will soon be cheap enough to be widely affordable. We are nearing the time when omics data may be retained for patients on a wide basis. These may include full exome, haplotype, full genome sequencing, tissue level transcriptomic data, microbiome […]

Music Monday: I’ll see you in my dreams

Because.. Django reinhardt.  

The Right to Read

Since this is Open Access Week, I thought I’d do the Open-Access / CC thing and share someone else’s work. In this case, a highly topical short story written by Richard Stallman.  The author also has a constantly updated page with comments on the restrictions placed today on sharing reading materials. As you will see, […]

The 2014 International Biocuration Conference

Hi all, I’m happy to say that the 2014 International Biocuration Conference is off to a good start. I have attended this excellent meeting twice before, and this year I am honored to be on the organizing committee. There was a lot of work behind the scenes, and we have agreed on five session topics.  […]

For Ada Lovelace Day: Florence Nightingale

Note: a repost of a 2010 post I published for Ada Lovelace day. Unfortunately, I am too busy these days to write a new one. “Ada Lovelace Day is celebrated today to “…raise the profile of women in science, technology, engineering and maths.” So without further ado: She is a ‘ministering angel’ without any exaggeration […]

Why not use the Journal Impact Factor: a Seven Point Primer

After a series of tweets and a couple of Facebook posts about the problems of the Journal Impact Factor (JIF), I was approached by a colleague who asked me: “so why are you obsessed with this”?  My answer was that it irks me that I have to use the JIF next to my publications in […]

Quit smoking, more bacteria will like you

As an ex-smoker I can attest to this: quitting is  hard.  It can also make you fat. I gained quite a few kilos when I quit, and those took a long time to lose. Happily, these days I am spending money on running marathons rather than on cigarettes. Weight gain after smoking cessation is fairly […]

Postdoctoral Position in Computational Bioengineering (Rice University)

The Kavraki group at Rice University is looking to hire an enthusiastic postdoctoral researcher to enhance their research efforts in computational structural biology, drug design, and computational bioengineering. The group has significant expertise in the development of methods for motion planning for complex systems in robotics. Their Open Motion Planning Library (OMPL, http://ompl.kavrakilab.org) is now […]

Announcement: WikiProject Computational Biology Competition

WikiProject Computational Biology/ISCB competition announcement 2013 The International Society for Computational Biology (ISCB) announces an international competition to improve the coverage on Wikipedia of any aspect of computational biology. A key component of the ISCB’s mission to further the scientific understanding of living systems through computation is to communicate this knowledge to the public at […]

The Bio* projects: a history in graphs

Yesterday I received an email from Kristjan Liiva, a student at  RWTH Aachen University Germany. Kristjan has developed a really cool dashboard to analyze and visualize the development of collaborative OSS projects by mining their mailing lists and software repositories.  (If the link doesn’t work, try again later; the project is heavily under development). The […]

Are you using this blog for teaching, studies or writing?

Dear readers (Yeah, I’m talking to both of you!) If you are a school teacher, college professor or any kind of other educator, trainer or science writer, and if you have ever used this blog in your line of work, please let me know. Also, if you are a student and used this blog as […]

OK, you saw it here first

  (For those who don’t get it.)

The Second Critical Assessment of protein Function Annotations

Announcing CAFA 2: The Second Critical Assessment of protein Function Annotations Friends and Colleagues, We are pleased to announce the Second Critical Assessment of protein Function Annotation (CAFA) challenge. In CAFA 2, we would like to evaluate the performance of protein function prediction tools/methods (in old and new scenarios) and also expand the challenge to […]

Music Monday: Sequester Blues

  The sequester is hitting science funding in the US pretty hard. Francis Collins, the director of the NIH,  is lobbying any way he can to get the NIH off the hook. In 2013, there will be 700 fewer grants awarded than in 2012.  4.7% cuts across the board to grant renewals.   So, here’s […]