Bioinformatics Zen

This is the February edition of Bio::Blogs, an aggregation of bioinformatics posts from the past month. This issue has a particular focus on Open Notebook Science - researchers sharing their work as they produce it.

For this edition, with the help of Cameron Neylon, Jean-Claude Bradley, and Pedro Beltrao, I’ve tried to write a short essay on open science as well as the open notebook variety. I’ve posted this on my research website.

Cameron Neylon’s proposal for an ONS Network has received comments from the reviewers, and I think this is great for moving ONS to formal acceptance by the wider community. Shirley Wu and friends have burst onto the scene with multiple blog posts on ONS, and the rapid development of an ONS session proposal for the Pacific Symposium on Biocomputing, and again is something that will gain ONS recognition. As to why openness is important for research, Cameron has a further post comparing two scenarios of open and closed science.

The biggest event in the calendar this January was the Science Blogging Conference in North Carolina, where there was a session on publicly available scientific data. Jean Claude Bradley co-chaired the event and provides links to the videos on his blog. Deepak also discussed some of his SB08 thoughts. Frank Gibson has stated his intention to post the data from his PhD online, conforming to MIAPE standards. The topic of standards and their role in a culture of data sharing was discussed by Deepak, where the web should move from a simple repository of data, to a platform that enables easy sharing of interconnected datasets. This is parallel to Duncan’s point about the explosion of databases in bioinformatics. Finally, an important issue in sharing your data prior to publication, there was a large debate your research being scooped. There is a round up of this on A Blog around the Clock, and gets a further mention on One Big Lab.

So that’s the open science part done, but there were plenty of other things going on in the bioinformatics blog community. Neil Saunders mentioned the Gene Wiki project, the aim to give every human gene a page on Wikipedia, some kind of online encyclopedia. He also gave an interesting perspective on the history of nodalpoint.org, the original bioinformatics blog. Researcherid.com, a site to give every researcher a unique id, received attention from Pierre, Neil, and Deepak. A recent paper on the uncertainty in aligning sequences took the interest of Blind.Scientist, Thirst for Science, and Computational Biology News. SNPs are hot at Open Helix and the Spittoon. Gopubmed.org is even hotter at Medical 2.0, Konrad’s Konsiderations, Peanut Butter, What You’re Doing, and BBGM. Pawel Szczesny became a Freelance Scientist, and posted a novel method for visualising repeats in sequences. Stew showed how to increase MySQL speed, and Biocurious had a biohumorous article about the anatomy of a seminar. Last, but not least Perfect Storm compared Ruby with the new programming language Scala.

That’s it, I’ve done my civic duty for the year. I’m going home to sit my room with a tin foil hat on, rolling 3d6.