nodalpoint.org

I guess we can't let the news of Francis Crick's passing go unmentioned. OK, it's mentioned.

This month's Nature Immunology contains a Commentary article, 'Bioinformatics for the bench biologist: How to find regulatory regions in genomic DNA' and an extensive accompanying tutorial that works through all the steps involved.
[subscription required, probably]

A nice article - Myths concerning Open Access. A few parts are UK-centric, but relevant to all.

If the poster of the UCSC browser course article is wondering where the post is (I suspect not, it looked like a bulk advert job to me), it was stuffing up the page formatting, so we removed it. Feel free to send it again without aberrant HTML.

Computer scientists must find this kind of report hilarious: Gene name errors can be introduced inadvertently when using Excel in bioinformatics. It turns out that Excel's automatic data type conversion changes Riken identifiers of the form nnnnnnnEnn (where n denotes a digit) into floating point values e.g. "2310009E13" is converted to "2.31E+13". Before everyone starts laughing at poor Excel users, note that this is not an Excel specific problem. The real problem is that most biological file formats do not have schemas. Update: The Register has picked up the story: Excel ate my DNA.

I previously posted about a Pubmed search plugin for Mozilla/Firefox. The author of that plugin Craig Riedl, a genetics student at the University of Toronto, sent me some email to say that he has updated the plugin. You now have a choice of either the frames-based or text Pubmed results pages. Get the new plugins here, thanks Craig!

The beginning of what looks to be an interesting series of articles on hacking the human genome has been posted on O'Reilly's MacDev Center. Some interesting quotes:

On the UC Santa Cruz Genome Browser: "I'm not sure what Edward Tufte would have to say about the design of this, but there are a lot of annotations available and you need to see all of them to evaluate any given region."

There are a lot of well-characterized bacterial genomes available, and comparison of these gets really interesting.

I've been told that comparison of archaeal genomes is also "really interesting".

Many Life Science researchers need bioinformatics tools for the desktop. But many of the common Open Source tools are difficult to install for people without much Linux/Unix knowledge. We have created a user friendly install package for the MacOSX platform. The package installs most of the common bioinformatics packages: EMBOSS, Blast, HMM etc and also installs some biological databases. Together with the packages it is possible to configure webservices e.g. Blast. Researchers will find it very useful to be able to install a user friendly GUI in top of EMBOSS (embossRUNNER).
All packages can be downloaded at www.ebioinformatics.org. Detailed instructions and HOW-TOs have being published on the latest issues of EMBnetNews (free from www.embnet.org).