Bio::Blogs #3

With half the world taking its annual August hiatus, I feared the worst, but in the end I have the pleasure of bringing to you the third edition of Bio::Blogs, the favorite blog carnival of those of us who like to mix our biology with computation or vice versa

This editorial was started at a Starbucks, only fitting since I move to Seattle next week. So in honor of my new abode, this edition of Bio::Blogs is like the coffee menu at a Starbucks, with offerings from around the world and an eclectic set of flavors.

Courtesy Panos Photographics

We start with a report that required some globetrotting. All the way from Heidelberg, none other than Pedro has a report on the recently held Science Foo camp (held at the Googleplex). If there was ever such a thing as living vicariously, I did that through this (and other) reports. It would be wonderful to find out more about the discussions around the communication of science, data and web infrastructure, and the discussion on open science. One topic that seemed to be missing was the need for tools to accurately predict drug interactions with biological systems.   I wonder if that ever came up?

From Berkeley, Chris Patil has a short article on advanced sequencing technology. I must admit this is the first time I have ever read anything about mitochondrial DNA arrays. In keeping with the theme of the Ouroboros blog, Chris talks about the implications for aging and age-related diseases. I suspect that in time there will be a number of researchers looking for age-related (and other) markers in mitochondrial DNA.

Evolgen writes about evolution and genetics. In this months entry, RPM writes about a rather pertinent subject, the rift in the biological sciences, the rift between “wet” biologists and computational biologists. I am sure almost everyone reading this carnival has probably felt this at some point in his/her career. It is a sad state of affairs that science can build walls between disciplines, especially at a time when silos are increasingly breaking down. I suspect that to a degree, our system is to blame. Computational biology in particular is a very recent field, pulling in mathematicians, computer scientists, theoretical chemists, etc. All too often computational (and bench) scientists work too in a vacuum. The post has some wonderful insights on how limiting that is, and why these divisions hurt the field more than anything else.

We get a little French flavor courtesy of Pierre at YAKAFOKON. For those familiar with the blog’s themes, it should come as little surprise that we get this wonderful little bookmarklet allowing people to make offprint requests from their browser.

I save the best for last … Sandra Porter, from my new home of Seattle, and the next host of Bio::Blogs, has a series of fabulous posts on (to quote Tara Smith) “using a bad virus to do something good”. You can tell that Sandra is an educator. The entire series, from which I learnt a lot, is a guide through a set of experiments on HIV evolution, an demonstration of how HIV can be used to show the process of evolution.

Part I. Gives some background info on HIV, a link to a nice animation of the life cycle, and presents the problems that being investigated.

Part II. Gives instructions for performing the experiment.

Part III. The results (free from any biased interpretation).

Part IV. Sandra’s analysis along with a quick look at the protein structure to see if we can explain why the mutant viruses are positively selected and why these mutations might lead to drug-resistance.

… and this months extras

From our previous host is a post on managing structural genomics data.

Out of left field, Christine Herron writes about a favorite subject of these parts, open data standards. While there is no mention of biology, there is much to learn from such discussions.

We end with a jolt from Italy from C. Maria Keet (who I think is Dutch … it’s wonderful how our field is so truly international). She writes about the synergies between computer science and engineering, biology and medicine and a seminar series organized at her university. I like the fact that she brings a philosophical and ethical compass to the discussion as well. Thanks to Pedro for sending this my way.

Next month, Bio::Blogs will be hosted by Sandra Porter at Discovering Biology in a Digital World. I must say that her editorial is eagerly awaited.

Technorati Tags: Bio::Blogs, Blog Carnival, Computational Biology, Bioinformatics, Scifoo, HIV, Evolution, Science, Life Science, Data, Data Standards

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