nodalpoint.org

Happy Christmas from the myGrid team, who are pleased to announce the release of version 1.5.0 of the Open Source Taverna bioinformatics workflow toolkit [1]. This is now available for download on the Sourceforge site and includes some substantial changes to version 1.4.

Dear Santa, all I want for Christmas* is a better version of Connotea, please can you sort out it's duplicated redundant links? In my book this particular bug is “buggotea” number one. Here is the problem... [update: buggotea is partially fixed, see comments from Ian Mulvany below]

All I want for Christmas is a book about the semantic web, written by people who are actually building and using it, rather than “visionaries” who don't have to. Maybe this year I'll be lucky...

The Top Bioinformatics Challenges according to Chris Burge at MIT and his colleagues are as follows...

Update: I totally forgot about Postgenomic's conference section when I originally wrote this post. So I've added a paragraph at with additional information on this great resource.

Welcome to the sixth edition of Bio::Blogs, or for python enthusiasts: from bio.blogs import *. This edition is the 'conference edition', brought to you from the semi-conductor capital of the world, Hsin Chu.

Finally after three weeks of recovery, I give you my write up of the Noalpoint European Tour. I had a great time in The Netherlands at Advances in Microarray Technology, visiting the Sanger Center in Cambridge and I also had the opportunity to catch up with Alf Eaton and Euan from postgenomic over a few pints in London.

This forum post is just to see how others in the field of bioinformatics think about an issue that in my opinion is rather important. By "software fit for publication" I mean software that is rushed out just for the paper then not actively mantained, mantained poorly, or down right abandoned.

At least in the field of microarrays I've seen a couple examples of such software. Most falls under the "poorly mantained" category, for example CNAG (Copy Number Analyzer for GeneChip) that despite having an interesting DNA copy number estimation algorithm, from the software point of view it is terrible (hint: when a list of references is empty the program should output an error, not crash horribly). I won't even get started on CARAT", an algorithm that has been published without a working implementation...

Walking in a Webby Wonderland

Have you recently built a bioinformatics web application useful to the wider community that you'd like to tell the world about? Are you also looking to score brownie points for a rigourously peer-reviewed publication that stands a reasonable chance of being well cited? If that's you, then you have one month from today (December 1st) to sort your code out, and get your abstract in, for the fifth annual Nucleic Acids Research (NAR) Web Server issue published by Oxford University Press (OUP) in 2007. All articles in this issue are published under an open access model.