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Bio::Blogs: Bio::Blogs logoWelcome to the 10th edition of the Bio::Blogs, the monthly roundup of bioinformatic related blog journal. This months edition is brought to you from the CRG, Barcelona. I am here for two weeks to work under less than ideal conditions :). As before a PDF version can be found here for anyone preferring to read this offline.

Before kicking off with the submissions I wanted to mention two interesting discussions that went on this month around the science related blogs. One was triggered by a post by Nick Matzke in The Panda's Thumb regarding a paper published in PNAS. Nick Matzke was very critical of the paper and proceeded to point out in 2 other blog posts what he considered to be significant flaws in the analysis. I don't want to go into the science part here but instead note the amount of discussion generated around this one paper. One thing that came up was if we should use blogs for this purpose since the authors might not be aware of what is going on and therefore will not have an equal chance of responding (as Carl Zimmer noted in an excellent post).
I think we should use blogs for commenting on papers, for the same reason it is important to participate in journal clubs. It is useful to have other people point out possible flaws or interpretations that we might have missed. There are technical difficulties in aggregating information regarding a paper across different blogs and other medium but this is something that should be possible to solve (see Postgenomic or Techmeme).

The other interesting discussion that went on recently was the Wiley/Batts story. Very briefly for those that missed it, Shelley Batts blogged about a paper (published by Wiley) using part of the paper figures to support her main points. She then received an email from an assistant editor of the journal to take down the copyrighted material or potentially face legal consequences. Many people voiced their support for Shelley via their blogs or emails, mostly agreeing that the journal would only gain from this publicity and that this should be considered fair use. About the time when Boing Boing and Slashdot gave coverage to the issue, Shelley received an email from an the director of publications at the Society of Chemical Industry (that are responsible for that particular journal) apologizing for the incident.
My take on this is that it was an honest mistake and that this shows that mostly everyone is just trying to adapt to the changes to online publishing.

Both of these events illustrate the growth of science blogging. If Shelley Batts and Nick Matzke had blogged those same posts one or two years ago none of that discussion that fallowed would have happened. There is another common theme to both these stories. Everything happened at an amazing speed (a couple of days). This is one of great things about blog discussions. There can be a global conversation among like minded people at an incredible pace. The downside of this is that things can get easily out of control. If bloggers are not critical and do not take the time to read about what they are writing the echo chamber can really distort the news as it relays from blogger to blogger.

Getting back to our corner of the bioinformatics related blogs lets start with some announcements.

Announcements
Roland Krause announced in his blog that he and others are organizing a computational biology conference in Cancun: "From genomes to cells & ecosystems". It is a 7 day workshop on computational methods with particular focus on metagenomics.

(via Pierre from Yokofakun) The Human Frontier Science Program started the HFSP journal that aims to publish "high quality, innovative interdisciplinary basic research at the frontier of biology over a wide range of organizational levels (from the molecular level to population biology) using principles strategies or technologies from the more quantitative disciplines (e.g. physics, chemistry, mathematics, engineering, or informatics)".

Paraschopra pointed out in his blog to a website dedicated to sharing lab related videos (LabAction.com).

Finally, Jean-Claude Bradley announced in Useful Chemistry that the first paper coming out of their open science efforts is being written in the lab wiki. At this moment an abstract and a part of the introduction are already written. It will be interesting to see how this progresses. Eventually there will be some discussions with the publishers regarding this issue. A wiki or blog posts should not be considered prior publication but there are no clear polices on the part of the publishers on the matter.

News and Views
Keith Robison discussed in his blog post "(Still)Birth of a Neologism?" the origins and evolution of science jargon. In reaction to a review article in MSB he ponders what leads to the acceptance or not of a new term and necessity of new jargon.

GrrlScientist sent in a link to a blog post regarding a recent Science paper about the genetics of dog size. This paper describes the importance of the IGF1 locus in explaining dog size variability.

From my own blog I can highlight a post about gene expression changes in response to unforeseeable events. This blog post discusses a paper published in MSB where the authors tracked gene expression profiles of different population of S. cerevisiae responding to to perturbation that these cells should not have seen during their evolutionary history.

Conference Reports
Jonathan Eisen attended a NIH workshop were the human microbiome project was discussed. The objective of the meeting was to access the need to sequence the microbes in or on us. He describes the meeting in two blog posts.

Konrad Förstner sent in a link to his report on a conference organized by Alen press - Emerging Trends in Scholarly Publishing. See also the reports by Richard Akerman and by Chris Surridge.

Blog Articles
We start off this section with a post submitted by Deepak where he discusses the interests of Google and Microsoft in healthcare. I would personally prefer that these companies would have a stronger interest in biosciences. Things like data sharing, management and visualization. There is probably not such a strong incentive to the development of these tools as there is for search and advertisement.

Data visualization is precisely the subject that Euan Adie covered in a recent post at Nascent. Data visualization has a long history and it is extremely important since it constrains the way we contact information. In this post Euan Adie calls out for new ideas to represent genomics and proteomics data on the web.

Next up are two great posts by Neil Saunders. The first is a short example of the power of current open source tools to work your way from data file to image and statistics output all using command line interfaces. As Neil says, we can all thank a "disparate group of enthusiasts around the world share the belief that software should be free, shared and available to all". The second post is a very useful tip on how to get all the protein structure information for a domain family. The tutorial is based on the kinase domain but the code provided can be used for any domain family with available markov model.

We end up this months edition with a blog post sent in by Michael Barton. He continues his series on improving productivity and organization. This time is discusses the use of a wiki as a lab book.

Thanks to everyone that participated by sending in links. If it is ok with everyone the next edition will likely stay here at Nodalpoint.
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