nodalpoint.org

Given that the backbone of sequence analysis and as such bioinformatics is alignment, this news has the potential to shake some ground in the community: There is a new company claiming that their new BLAST is as sensitive but 10.000 times faster than the original by improving the seed searching phase. I'm very sceptical... local alignments have been worked on for decades without a lot of speed improvement while keeping accuracy. Which is why there are special hardware solutions for this problem (I wonder who is buying them).
But the company's website does not look like a joke and they're shipping demo versions... I have no clue how that could work. Suffix arrays? But that has been applied to local alignment seed search, right? Anyone out there with rumors about this company ?

Ben Good from the University of British Columbia in Vancouver has just been visiting our laboratories here in Manchester. Ben is doing some interesting web experiments in mass collaboration, inspired by the likes of BioMOBY and Connotea. If you have any time to spare, or are just curious, please join in and mass collaborate!

The 3rd Integrative Bioinformatics Workshop began yesterday at Rothamsted Research Centre in Harpenden, England. Rothamsted Research is a lovely campus reminescent of the Wellcome Trust Genome Campus just south of Cambridge. It has a long history of plant research, andwas also the workplace of the mathematician and statistician Ronald Fisher. This is a summary of the first day of the workshop (mainly discussing the keynote speech), on 4 September 2006.

A new paper by Raghava and Barton has just gone online "Quantification of the variation in percentage identity for protein sequence alignments" at BMC Bioinformatics.

Initially I was shocked .. how, in 2006, could anyone manage to publish anything original about percentage identity (PID), that simple but oft used/abused measure that is fundamental in the definition of the "twilight-zone" of sequence similarity (for infering structural similarity or relatedness by sequence alone).

Well, it turns out (and becomes obvious when you try to code it), that there is more than one way to calculate the PID of a multiple sequence alignment, and each method yields different results. Authors rarely state exactly which method they used and, not surprisingly, no matter how you chose to measure the PID the multiple alignment algorithm used also has a substantial impact.

Computer scientists often have a hard time getting used to bioinformatics people. They are trained to write readable, documented, non-spagetti-code software, trained for years, they were told about UML diagrams and some even had special courses for it, the once hyped "software engineering". We're taught that this is the most important part of computer science all the time and that losses amount to billions every year because of poorly written software.

In science, everything is different, of course. Documentation does not matter.

It's been 3 years since I made it to a meeting - that was ISMB 2003, here in Brisbane. Next week I'll be attending ComBio2006...here in Brisbane. Ah well.

The "com" in ComBio is "combined" rather than "computational" - it's a large conference for a number of Australian/New Zealand life science societies. There are 10 streams including several of interest to Nodalpointers, especially bioinformatics/systems biology, gene expression/regulation and protein structure/function. I'll do my best to blog any interesting stuff here and at my place, possibly "live" depending on the facilities.

update: the blogging is at my place and it ain't live thanks to the (non) facilities.

We just posted an overview document of our idea for a Gene Wiki at The Synaptic Leap

We encourage all folks at Nodal Point to come and add their comments. To maximize our feedback (the more the better), I have removed the login restrictions for comments for a brief period.

Thanks in advance for helping us out.
-Ginger

Bio::Blogs #3 is now live on my blog. Check it out

The October 1 edition will be hosted by Sandra Porter