Saturday, July 01, 2006

Bio::Blogs # 1

An editorial of sorts

Welcome to the first edition of Bio::Blogs, a blog carnival covering all subjects related to bioinformatics and computational biology. The main objectives of Bio::Blogs are, in my opinion, to help nit together the bioinformatics blogging community and to showcase some interesting posts on these subjects to other communities. Hopefully it will serve as incentive for other people in the area to start their own blogs and to join in the conversation.

I get to host this edition and I decided to format it more or less like a journal with three sections:1) Conference reports; 2) Primers and reviews; 3) Blog articles. I think this reflects also my opinion on what could be a future role of these carnivals, to serve as a path for certification of scientific content parallel to the current scientific journals.

Given that there were so few submissions I added some links myself. Hopefully in the next editions we can get some more publicity and participation :). Talking about future editions, the second edition of Bio::Blogs will be hosted by Neil and we have now a full month to make something up in our blogs and submit the link to bioblogs{at}gmail{dot}com.

Conference Reports
I selected a blog post from Alf describing what was discussed in a recent conference dedicated to Data Webs. There is a lot of information about potential ways to deal with the increase of data submitted all over the web in many different formats. I remember seeing the advert for this conference and I was intrigued to see Philip Bourne, the editor-in-chief of PLoS Computational Biology, among the speakers. I see know that he is involved in publishing tools under development in PLoS.

Primers & Reviews
Stew from Flags and Lollipops sent in this link to a review on the use of bioinformatics to hunt for disease related genes. He highlights a series of tools and methods that can be used to prioritize candidate genes for experimental validation.

Neil, the next host of Bio::Blogs spent some time with the BioPerl package called Bio::Graphics. He dedicated a blog entry to explain how to create graphics for your results with this package. He gives examples on how to make graphic representations of sequences mapped with blast hits and phosphorylation sites.

Chris, a usual around Nodalpoint, nominated a post in Evolgen:
Evolgen has an interesting post about the relative importance (and interest in) cis and trans acting genetic variation in evo-devo. A lot of (computational) energy has thus far been expended in finding regulatory motifs close to genes (ie, within promoter regions), and conserved elements in non-coding sequences. Rather predictably, cis-acting variants have received the lion's share of attention, probably because they present a more tractable problem. The post deals with work from the evo-devo and comparative genomics fields, but these problems have also been attacked from within-species variation perspectives, particularly the genetics of gene expression. But that's next month's post...

Blog articles
I get to link to my last post. I present some very preliminary results on the influence of protein age on the likelihood of protein-protein interactions. Have fun pointing out all the likely flaws in reasoning and hopefully useful ways to build on it.

To wrap things up here is an announcement by Pierre of a possibly useful applet implementing a Genetic Programming Algorithm. If you ever wanted to play around with genetic programming you can have a go with his applet.

That is it for this month. It is a short Bio::Blogs but I hope you find some of these things useful. Don’t forget to submit the links for the next edition before the end of July. Neil will take up the editorial role for #2 in his blog. If you know of a nice symbol that we might use for Bio::Blogs sent it in as well.