SEQNET

Brian Vinter pointed this press release out to me: Denmark Creates Network for Gene Sequencing.

CLC bio and several prominent Danish research institutions have established SEQNET — a national network for developing a unique software platform for the analysis of data from the next generation sequencing technologies. The platform will integrate groundbreaking bioinformatics algorithms with a user-friendly and graphical user interface.

Apparently, my good old friend Roald Forsberg is involved:

Senior Scientific Officer at CLC bio, Dr. Roald Forsberg, states, “Next generation sequencing technologies, like 454, Solexa, or SOLiD are pushing a revolution in genetic analysis. Their massive throughput has given rise to a plethora of novel applications for DNA sequencing and has dramatically increased the ambitions of existing projects. However, handling the large amounts of fragmented data presents a great bioinformatics challenge to be dealt with before researchers can get the full value of these new technologies. Since DNA sequencing is becoming omnipresent in research we believe that the answer to this challenge is a unified next generation sequencing platform. In this network, we will make such a platform come together by combining our unique capacities for producing graphical user interfaces, algorithms and high performance computing solutions with the expertise of Denmark’s foremost researchers in the field.”

We have talked about the problems involved in dealing with data from the new high-throughput sequencing technologies a couple of times over lunch, but it seems Roald is moving faster than I am here. Good for him!

I look forward to see where this is leading!

Digital Urban Living

Browsing the Danish Research Council’s homepage — searching for some info on my own grant but failing at that — I stumbled upon this press release (in Danish, sorry). A large project in digital urban living will run in Aarhus the next four years.

I haven’t heard anything about this until today. That really shows how much I’m out of the loop these days. Since I started doing “Real Science” I haven’t been keeping track of what was going on in IT and computer science in town.

Sarcasm on!

Anyway, reading the press release it looks like a lot of the “usual suspect” visions in pervasive computing: mobile phones for news browsing (local news, in this case, probably because they want a digital Aarhus and not just any old digital urban living), mobile phones finding the closes restaurants when you go out, etc.

Let’s ignore for a sec. that I can already do that with any smart phone already. I am sure there are more visions than that…

Well, one thing they mention that smart-phones cannot do is houses changing colour according to the weather. My brick house sort of changes colour between sunny days, cloudy days and rainy days, but all shades of yellow. I am sure changing between red and green is an improvement.

Sarcasm off!

Ok, the press release is a bit daft on the concrete examples, and the remaining examples are too vague to comment on. This doesn’t mean that the project is crap, though. Boiling things down to the length of a press release is bound to dumb it down a bit as well.

I look forward to hear more information about the project. Concrete examples of what they plan to do. Find out what is in it for me! How will digital living change my life? Smart phones, ubiquity of laptop computers and wireless network has changed our life, so there is certainly a potential for IT to change the way we live.

How will this project add to this? Would the money be better spent just providing free wireless Internet downtown? ;-)

The budget is DKK 43.5 million, so it is well funded, and there is a lot of collaborators in it, so it will be interesting to see where it will lead.

More links, but all in Danish, here:

23andMe explains it so much better than me

I tried to explain my main research area in a previous post, but 23andMe even uses animations! See the animations at ScienceRoll.

23andMe is one of the new personalized genomics companies that popped up late last year. Another is deCODEme at deCODE, the company we collaborate with in the PolyGene project.

I haven’t really made up my mind about these personal genomes companies yet. Not that I think there is anything unethical about them, it is the science I cannot make up my mind about. Technologically, it is cool that you can actually type a million tagSNPs for $1000 (with the current value of the dollar that is essentially for free), but how much can you really use the information for?

Tracking the genealogy can be done with some accuracy — not sure exactly how much accuracy — but the disease risk stuff I am very sceptical about. The genetic factors of life style diseases that we know about have so little relative risk that calculating it for individuals as part of some genetic profile seems a bit dodgy to me.

Knowing that a particular genetic variant increases the disease risk ever so slightly tells us about the underlying biology of the disease, and that information is important. Making medical decisions based on the type of an individual, if the relative risk is tiny fractions of the environmental risks we know about anyway, is just plain silly.

If you know that smoking increases your risk of cancer dramatically, but you don’t stop smoking, are you likely to benefit from knowing that your genes increase your risk from 1% to 1.1%?