nodalpoint.org

These days, new Google products and code seem to appear on a weekly basis. Take, for example, Google Gears which takes advantage of SQLite, mentioned on nodalpoint recently. They certainly don't hang about at the Googleplex in Mountain View, California. Wouldn't it be great if Google applied some of that engineering expertise and agility to science and bioinformatics? Just imagine: we could have Google Metabolic Maps, a virtual globe of the cell for scientists everywhere...

After the first interview with Joe Felsenstein, I am continuing with this small project, SciView, with an interview with Brian Golding, from the McMaster University in Hamilton, Canada. For those who don’t know, Brian is the person behind EvolDir, where many researchers find new jobs, solve problems and check the next meeting. I would like to thank him for taking the time to answer my (sometimes) dull questions.

The interview can be read at

http://blindscientist.genedrift.org/2007/05/29/sciview-scientific-interv...

If you had 100,000 DNA sequences, each 1000 nucleotides long, and you wanted to cluster them or create a phylogeny, which software would you use?

Also, what if they were amino acid sequences, rather than nucleotides?

As we near the end of the month I will be collecting posts for Bio::Blogs #11. I am posting this reminder a little sooner than usual because this month Michael Barton from Bioinformatics Zen volunteered to edit and host a separate special section dedicated to tips for computational biologists. Anyone can participate in this section as well by sending some sentences with your own tips to him by email (mail at bioinformaticszen.com). This section will be posted on his blog and the main Bio::Blogs issue will be posted here in Nodalpoint, both on the 1st of June. Submissions for Bio::Blogs#11 can be sent to bioblogs at gmail.

New version NOC-3.0 is released for Windows/Linux/Mac OSX/FreeBSD/Solaris with source code.
Downloading is available at http://noch.sourceforge.net
NOC is:
a easy and fast protein explorer for structure visulization, analysis;
a powerful tool for crystallographic mapping, modeling and refinement;
a efficient viwer for GROMACS/AMBER MD trajectories;

Musings on the Semantic Web from the Wilkinson Laboratory

I've noticed that a couple of people here describe themselves as "computer guys" working for "biologists" (just like me). I wonder if there is any one well-known like this, a computer scientist that started in a biological lab and who was successful enough in doing this to start his own group later on. Someone like a role model for computer guys that do something that "is rather desperate". If you think that a weblab is not a career-killer for bioinformatics than I would appreciate a concrete counter-example.

The Hitch-hiking novelist Douglas Noel Adams (DNA) once remarked that the World Wide Web (WWW) is the only thing whose shortened form - 'double-you double-you double-you-dot' - takes three times longer to say than what it's "short" for [1]. If he were still with us today, there is plenty of stuff at the 16^th International World Wide Web conference (WWW2007), currently underway in Banff, that would interest him. Here are some short, abbreviated notes on a couple of interesting papers at this years conference. They are relevant to bioinformatics and worth reading, whichever type of DNA you're most interested in.

Those people at Open Biomedical Ontologies (OBO) are hiring which might be of interest to job-seeking nodalpointers. The positions are based in sunny Berkeley, California. Even if you're not a job seeker, its interesting to see what this group are up to and what skills they are after. More information at www.berkeleybop.org

As the deadline for my Ph.D. thesis looms over me, I've been working recently with a certain quantity of data of the same type (basically a variant of microarray gene expression) but from different sources and/or software.