Thursday, February 19, 2009

HubMed Citation Manager

I just came across HubMed yesterday and I found one of their tools incredibly useful for getting references into EndNote (or other reference manager software tools). Basically, HubMed Citation Finder will take a bibliography (say from one of your favorite papers), split them up, find the citation in PubMed, and return the list of references in several citation formats such as RIS, BibTex, RDF, etc. This file is then easily imported into your reference manager's library.

It just saved me a couple of hours and would have saved me even more if I had known about it a few weeks ago.

Tuesday, February 3, 2009

Personal Genomics & The Burden of Knowing

Like many bioinformatists, biologists, scientists, and technologists I am very interested in personal genomics. I have kept track of the start ups that are doing personal SNPs analysis and have been eagerily waiting for sequencing costs to drop to the point were the $1000 genome is possible. I envisage everyone having their personal genome done and programs to analyse the data being so widespread that even a "My Genome Facts" Facebook application would not seem out of place.

Of course I have read lots about ethical worries about how the data could be mis-used or how the public can not handle the probabalities of having a certain disease. Personally, I have always thought these were blown a bit out of proportion and that personal genomics will in general be a good thing. More data is better right?

Well, I just read an article called "The Burden of Knowing" by Catherine Elton in the Boston Magazine and it really made me reconsider my previous thoughts. Elton starts out explaining about personal genomics and specifically about Knome, the first company to do complete personal genome sequencing. She then starts to delve into her personal choices regarding her susectibility to having the BRCA1 gene. The article is extremely well written, and unless I am becoming a complete softy, quite sobering.

A small excerpt that I really enjoyed was this:
The counselors then mentioned another option: having my ovaries taken out and my breasts removed. Here we were, talking about science's ability to look along a submicroscopic piece of DNA, searching for missing letters on a strip of a gene, and yet if science found that letters were missing—if the gene had the cancer-risk mutation—the best it could do was amputate or sterilize. These options seemed as though they should have been filed away in a medieval remedy book, somewhere between leeches and bloodletting.

So did the story change my view on personal genomics? No not completely, but I do think that getting my genome sequenced might not be as fun as I first thought. Too bad there are not many positive attributes linked to genes like "gene variant Y will allow you to live a long life despite your lack of physical exercise" or "you have an improved version of the alcohol dehydrogenase gene, so feel free to drink more beer".