Group: Bioinformatics

Well, I just gave my talk on phylogenomic and functional predictions and am going to try and catch up with blogging.

Earlier today, on Hacker News, I found a link to an announcement for

Time for a rant. I spend a lot of time fussing with records from sources such as GenBank and DiGIR providers, trying to extract strings that might be identifiers, with a view to linking sequences to specimens (and thus to localities), sequences to publications, publications to GUIDs, etc.

An anonymous reader writes "Google has revealed a new project aimed at the scientific community. Called Palimpsest, the site research.google.com will play host to 'terabytes of open-source scientific datasets'. It was originally previewed for scientists last August .

Note to self: how many biological databases provide their release notes as an RSS feed? One of my database mining scripts failed today; on reading the SwissProt What’s New page, I discovered why:

There has been a large increase in the number of people and organisations interested in extracting or capturing chemical information from the public domain.

How will Britain's new supercomputer affect researchers?

Some of you may have picked up from - e.g. the Open Grid Forum - that Microsoft (Tony Hey, Lee Dirks, Savas Parastatidis) have been collaborating with Carl Lagoze (Cornell) and Herbert van de Sompel (LANL) on bringing together Chemistry and OAI-ORE - the next generation of interoperable repository software.

Bioinformaticians like tabular data; plain ASCII text delimited by tabs, commas or whatever. In the past, I’ve written an awful lot of scripts that begin something like this:

Have you ever wanted a simple program to calculate the RMSD between two protein structures? Well, if you’re clever, you might figure out how to do it in PyMOL or VMD, but sometimes you just want to do it from the command line.