Monday, October 01, 2007

Bio::Blogs #15

Welcome to the 15th edition of the bioinformatics blog journal Bio::Blogs.

I complained a while ago that there was very little expansion of the bioinformatics blogging community but at least in the last couple of months it looks like this is changing. Although not necessary started last month here are three blogs that I only recently noticed: At the end of the day from Stephen Spiro (Spiro lab homepage), Paradoxus and Saaien Tist from Jan Aerts.

Not only are there more blogs there are many more examples of bloggers posting original ideas and research. Most people agree that being open about research should foster collaboration but so far few people have really tried to do it. It is inspiring to read trough these examples and trying to imagine how we might be doing science in the next couple of years.
This month was also marked by the many conference reports that we had available to read and by the experiments of taking real life conferences into Second Life.

Keeping this short and to the point this edition of Bio::Blogs focuses on these conference reports and on the ongoing experiments of using blogs to post about original research. I hope this nudges more people to go ahead and give blogging and open science a try.

Conference Reports

Neil Saunders was at the ComBio2007 conference and posted his notes about it in a four part series (1,2,3,4).

Allyson from Systems Biology & Bioinformatics provided a very extensive coverage of Integrative Bioinformatics 2007. Read all about it in chronological order from parts 1 to 10 (1,2,3,4,5,6,7,8,9,10).

From my blog here are two blog posts on the FEBS workshop - "The Biology of Modular Protein Domains" (1,2). This was not really about bioinformatics but I hope it will be interesting from the perspective of what data is coming that requires good integration strategies.

I'll jump know from real life to virtual talks. Those creative people at Nature keep testing out the potential of the web to improve interchange of knowledge. They kicked-off a seminar series of digital talks in the Second Nature island withind Second Life. The first talk by Philipp Holliger, entitled "New polymerases for old DNA" was about the engineering of new polymerases to amplify ancient DNA. Joanna Scott (working at Nature) has a very nice report on the talk in her blog.

Continuing on with virtual talks, in the past month there were another 3 sessions of the series SciFoo Lives On, organized by Jean-Claude Bradley and hosted also in Second Nature. JC Bradley covered the sessions on his blog: Sept 4 - Definitions in Open Science,Sept 10 - Communicating Science with Video, Sept 24 - Open Notebook Science Case Studies. Additional coverage by other bloggers can be found via the wiki page.

Blog articles

What are some of the most frustrating bottlenecks in bioinformatics research ? Where do we really spend most of our time ? Given that we work with digitized information it should in principle be mostly about the ideas. Thinking about interesting questions, crossing information and interpreting the results. At least for me this is typically not the case. What usually takes time is gathering all the necessary information in a way that can be analyzed. Three blog posts this month discuss this problem. Hari Jayaram and Neil Saunders posted about the problems they faced when attempting to do conceptually simple tasks. In response Deepak wrote a thoughtful post on how science databases should focus also on making the information easily accessible via appropriate APIs.

From online discussions to great examples of open science we start off with Jeremiah Faith's post were he describes an idea to determine the effect of sequence level mutations on transcription, translation, and noise.

Michael Barton from Bioinformatics Zen created a new blog dedicated to posting about his research on gene expression in yeast. Jump over there to read the many blog posts that he has already there, to provide feedback and maybe find common ground for collaborations.

Also this month, RPM from Evolgen re-started his attempt to publish original research on the blog. He is trying to study the evolution of a duplicated gene in Drosophila. There are two posts covering the introduction to the problem (part 1, part 2).

The last post highlighted in this month's edition is from Benjamin M Good. He has been working on a tool called Entity Describer to add semantic controlled vocabularies to Connotea and he has posted the manuscript they will try to publish on his blog and in Nature Precedings (10101/npre.2007.945.2).

This is it for this month. As usual, if anyone is interesting in serving as editor for any future edition, tell me by email.