Welcome to the 11th edition of Bio::Blogs, a monthly round-up of bioinformatics related blog posts (with some additional -omics and open science flavors). The PDF version for this month can be found here for offline reading. For the curious, the previous PDFs for Bio::Blogs #8,#9 and #10 have been downloaded 50, 83 and 100 times respectively. This edition has two special sections. The first one is dedicated to tips and tricks for bioinformatics and it is hosted separately in Bioinformatics Zen. Thanks to Michael Barton for having the idea and for organizing it. The second section is dedicated to personalized medicine, mostly because there were many posts about it during this last month. Both of these have separate PDF versions. The one on personalized medicine can be downloaded here. The PDF for the tips and trips section is available from Bioinformatics Zen (it looks awesome).
Personalized medicine
As Konrad announced in his blog, James Watson genome was sequenced and delivered to him recently. According to Technology Review It took 2 months and $2 million to sequence. According to the 454 press release it was done for less than $1 million. In any case it is an amazing improvement on the 13 years and $2.7 billion that took to sequence the first genome assembly.
This was the kick-off for a series of celebrity genomes announcements that are meant to defuse public distrust towards the idea of having their genome sequenced (also known as marketing campaign). According to the Nature news article Craig Venter will have his genome analysis published soon in PLoS Biology and has even a book about it to come out in October.
What is a personal genome good for ? In a four part series Blaine Bettinger discusses issues relating to the personal genome: 1) The Archon X PRIZE for Genomics; 2)The International HapMap Project; 3)The Ethical Issues and 4)The Impact.
A personal genome should inform us of our own genetic predisposition towards certain diseases and help us make more informed decisions regarding treatment. For this we have to first make an association between individual genetic variation and disease. In two posts suicyte, blogs about recently published genome-wide association studies.
In the middle of the up-coming hype it is worth remembering that genome sequencing is not the only way towards a more personalized medicine. To exemplify this, I commented recently on a paper showing how microbial gut population can directly change the mouse metabolism and how metabolic profiling can be used to study microbial-host interactions.
That is it for this section. How does this affect bioinformatics at all ? Understanding how genome variation might be linked to disease in any causal way will require at lot of data integration from variety of sources (genome sequencing, metabolic profiling, gene expression analysis, protein-protein interaction mapping, protein structure,etc) and new methods of analysis.
Conference Reports
This past month Jonathan Badger went to the conference of the American Society for Microbiology. In three blog posts he covered the main highlights of the conference (adaptive landscapes,predation of bacteria, new species of Bacillus,biodiversity of metal-reducing bacteria, etc).
Alf attended the XTech 2007 conference and wrote up some notes about the event. Not a lot of bio, but interesting tech ideas.
Blog Articles
Even in the best conditions we all experience difficulties in accessing published papers sometimes. Sandra Porter set out to find out the best ways to find freely available research manuscripts. Have a look at her progress in parts (I,II,III,IV).
In a more tech related post, Neil talked about moving from the desktop to the web. He gives examples of web apps and ways to organize them that might convince you to move more of your tasks online.
Benjamin Good blogged about ontology evaluation. Is it possible to evaluate the quality of an ontology classification analyzing its instances ?
Finally, a post by Pierre showing how he created a visual navigation for the social network interactions taken from Nature Network.
That is all for this month. Next month will be the 12th edition marking the 1st anniversary of Bio::Blogs. Ideas for celebration are welcomed :). If nothing else comes up, it will be hosted here again. If someone is interested in hosting or editing maybe it would be a good time to change editors to have a change of style/content.
