Urban Hafner : Tag bioinformatics, everything about bioinformatics

Large-Scale Sequencing of Mammoth DNA

urban@bettong.net (Urban Hafner) — Sat, 04 Feb 2006 16:56:00 +0000

A while ago I found a link to a Science article on the sequencing of part of the mammoth genome on Stephen Rudd’s blog . The article itself is quite technical and therefore not the most interesting read ever, but it’s interesting to know how far you can get with sequencing the genome of an extinct species. After all they managed to sequence 3,000,000bp.

Also, you get to read the words metagenomics and paleogenomics. Which might either make you run away screaming or inspire you to create new ones (anyone for meta-paleo-metabolomics? Submission of better (i.e. longer and less comprehensible) ones now open)). ;-)

What's a version-control system?

urban@bettong.net (Urban Hafner) — Sat, 17 Dec 2005 10:34:00 +0000

Just found a link to Where’s the Real Bottleneck in Scientific Computing? on the BioWeka Blog. It’s basically about scientists writing software without knowing much about it. As the title of this entry suggests, when asked if they use version control you might well get the answer “What’s version control?”.

Thinking of bioinformatics, I have the feeling that we’re getting there slowly. As more people get in there that have studied bioinformatics (like me :)), and more computer scientists too, we might see them influence their biology colleagues to apply more “common” tools to their programming.

A Bioinformatics Wiki

urban@bettong.net (Urban Hafner) — Thu, 20 Oct 2005 09:53:05 +0000

Some fellow students from my faculty started a bioinformatics wiki. Even though there is some information on bioinformatics in Wikipedia, I think it is a good idea to have a specialized wiki for bioinformatics. Not only to get all the definitions, but also to get information on all the tools available.

The Genographic Project

urban@bettong.net (Urban Hafner) — Sun, 16 Oct 2005 11:52:25 +0000

The first time I heard of the Genographic Project was in the podcast of the talk by Kris Lichter on IT Conversations. It’s a cooperation of IBM and National Geographic. What they are trying is to find out how the human race migrated from Africa across the world. For that they are using genetic markers from indigenous people around the world.

But what makes it interesting is that everybody can participate. You just buy a kit from national geographic, send back your DNA and they analyze it. When the analysis is finished you can find your results on their website. Of course totally anonymous, or so they say. With the money for the kit you payed for the genetic analysis of your DNA and also support some projects to help indigenous people. Maybe that’s why the kit costs $100 (plus $26.50 shipping outside of America) or if the analyses are just that expensive.

After carefully reading the website I finally couldn’t manage to resist any longer. So I ordered the kit and I’m really looking forward to receiving it and to find out what haplogroup I am. And apart from that the project is just cool :)