nodalpoint.org

Welcome to the 12th edition of Bio::Blogs, a monthly blog journal covering bioinformatic related blog posts. This month officially marks 1 full year that Bio::Blogs has been running (we skipped a month along the way). In the last couple of months Bio::Blogs has been sticking around Nodalpoint but I was hoping that other people could now give it a try at hosting this in their blogs. Also, maybe we could find a different (and easier) way of voting for blog posts to include. I was wondering if we could somehow get feeds like the stared Google reader items or link blogs or social bookmarking feeds from several different people together to come up with an automatic selection from the individual filtering done by everyone.

The PDF version of this month is a bit late so I might update this post once I get around to doing it or I might just skip it this month (depending on time availability).

The value of our attention information

There were a series of announcements this month that I think can be connected together to talk about attention information. First, two open access journals hit milestones: PLoS ONE published it's 500th peer-reviewed paper in less than 6 months (or around 83 papers per month and probably rising); and BMC Bioinformatics received 105 manuscripts for evaluation in one single month. Just out curiosity a quick check reveals that BMC Bioinformatics published around 55 articles in June. I will not even try to count how many papers are published per month by all of BMC.
On another front, Nature continues to roll out interesting services. Nature Precedings hopes to create a forum for communication and discussion of early findings. An overly concerned blogger writes: "nature opens slush pile to the world". Nature also released a service called Scintilla, a recommendation engine for science papers, blog posts and news. It is Nature's first steps into using attention data to help us navigate the flood of online science related activity.

So the connection between these announcements is straightforward. If you are like me you have way too much to read online right now. We continue to have more science related activities online, from open electronic lab books, science blogs, conference videos and reports, published early findings, peer-reviewed specialized and high-impact findings, to reviews and books. The more we have available the more we need tools to filter content in way that we might get detailed information close to our area of interest and just the high-impact or digested important bits the further way from our personal interests. This means we need quick ways of accessing impact.

We know that the journal impact factor is actually a very poor measure of impact for individual papers but right now there is little more that we can use (citations take too long to accumulate). Scintilla and related recommendation engines (i think SciLink has a similar product) are interesting initiatives in this direction. They aim to capture our attention information and learn from it, what a person with these interest might also like. Google and many other web companies are making fortunes with this. In the long run, maybe science publishers should be making money not so much on the publishing process but out of related activities such as helping scientists navigate the information. Think personalized advertisement: Publisher service: "you are reading a lot about this protocol, here is a paper that might also be useful and here is a contact of an expert .. by the way maybe you would be interested in buying this reagent/machine, here is a list of sellers."

News and Views
Ian York, an assistant professor of immunology and virology at Michigan State University has a very nice new science blog. He blogged about and open-source code, released my Microsoft, for analysis of antiviral immunity (http://atom.research.microsoft.com/bio/). This was followed by a post about a paper published in the Journal of Virology were Kotturi and colleagues make use of epitope prediction software to enrich the peptides library they used to screen for true epitopes.

This month also saw the publication of several papers related to the Encode project. Roland Krause, talked about one particular publication (Gerstein et al. 2007) that asks the question: "What is a gene, post-ENCODE?".

From The Seven Stones blog comes a post about comparative genomics: "E. coli counts in base 117". In a PNAS paper, Wright and colleagues detail their study of very regular spacing found between phylogenetically conserved gene pairs in the genome.

Blog Articles
We start off this month's blog articles with some more organizational tips from Michael Barton. This time it is a review of alternatives to PubMed for searching scientific content.

Deepak sent in a link to a discussion about pharmacovigilance (wikipedia: "the pharmacological science relating to the detection, assessment, understanding and prevention of adverse effects, particularly long term and short term side effect of medicines"). In particular he talks about the increase in complexity of data and tools required to deal with post-marketing issues.

Next up is a post by Keith Robison on next-generation sequencing tools that are hitting the market. We continue on the trend of low cost sequencing and it is good to keep thinking of ways to explore DNA sequencing. For bioinformatics this of course means yet more data to analyze.

Even if you are not into bioinformatics you have probably heard about the Gene Ontology project. GO aims to provide a "controlled vocabulary to describe gene and gene product attributes in any organism". In a 3 part series suicyte discusses some of the potential shortcomings of GO (part I, II, III).

Getting know a bit more technical (warning, code starts here) we have a blog post from Egon Willighagen on how to use a Firefox addon called Operator to combine microformats embeded in websites to actions in other applications. In this case Egon is trying to get chemical information published in blog posts to open directly in Bioclipse.

We end up this month with some more code from Pierre Lindenbaum to play around with the XML output of PUBMED. In the first post he shows us how to query Pubmed to get affiliation and email information. I hope few spammers find this out :). In the second post, the same code is used to map research topics onto the different countries using ManyEyes.

That is it for this month. Thanks to everyone that contributed with links. Anyone interested in editing/hosting future editions send in a mail to bioblogs at gmail. Ideas on how to automatize the voting for entries using RSS feeds from stared items or link blogs etc are very welcomed.