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.

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".

Pseudomonas and Langille in the media

Ok, this is some serious self-promotion, but scientists (well PhD students anyway) don't get a chance to brag about their research being in the media very often. Plus, it is my blog, so why not?!

The actual science:
The research in question surrounded the sequencing of the Liverpool Epidemic Strain of Pseudomonas aeruginosa that was causing increased virulence in cystic fibrosis patients. One of the interesting things in the paper is that we identified several genes related to virulence (using STM) and that several of these genes were within genomic island and prophage regions. Of course virulence factors have been found within these types of regions before, but to have actual in-vivo (chronic rat lung infection model) experimental evidence that these genes are involved in virulence in an epidemic strain, really makes this research notable. The research was published in Genome Research and is open access.

The media coverage:
Lancet Infectious Diseases (sorry not OA).

Vancouver Sun

Ok, now for the fun stuff:
SFU News - Notice those sleepy eyes? That is what having a 2 month old will do to you!

The story even made some news on a non-English site:
http://news.sina.com.hk/cgi-bin/nw/show.cgi/32/1/1/962395/1.html
Automatic translation results in me being referred to as "blue Gull", SFU as "West gate Philippines Sand University", and UBC as "Inferior poem University".
http://tinyurl.com/68ge47

Looking for a bioinformatics expert?

What I have to offer:

• A balanced background in both biology (BSc) and computer science (BCS)
• Soon to be completed PhD
  
• Extensive research experience in bioinformatics, genomics, phylogenetics/phylogenomics, evolution, and bacteria pathogenesis
• Some previous research experience in medical imaging, ontology development, and metagenomics
  
• An impressive publishing record (7 papers, 3 first authors, 2 more first authors under review)
  
• Solid computational skills including Perl programming, database design (MySQL), parallel programming, and web design (PHP & JavaScript)
• Good communication and social skills
  
• More information

What I am looking for:

• Post-doc or job (academic or industrial)
• Preferably, a position where I have some significant manager or leadership responsibilities
  
• Geographically interested in north eastern parts of North America (Ottawa down to New York), but would entertain positions elsewhere in N.A.

I didn't put any limitations on research interests, since I am open to many areas. However, anything having to due with the human microbiome project, human-bacteria interactions, or metagenomics would be of particular interest.

Please email me if you are interested or if you have suggestions on some good openings.

Airports & Interviews

Quick question: Why do people line up or huddle around an airport gate before they are called to board? The plane is not leaving until everyone has boarded, so why would you want to sit even longer in a cramped up airplane than is absolutely necessary?

I contemplated these questions and other airport mysteries (like who would pay a $38 service fee for changing Canadian to US currency) while recently sitting in airports for 7 hours and 5 hours on two separate trips.

Fortunately, both flights were worth while since one was a flight home where home made meals and warm fireplaces greeted my new family of 3 and the second was for a job that I am quite interested in at Boston. Luckily, another interview I had arranged did not require a flight so my sanity was slightly saved.

I would say that both interviews went fairly well, and overall I actually enjoyed the experience. Doing a PhD (or any large project I suppose), you tend to lose sight of the accomplishments that you have made along the way. Getting a chance to present my work to an audience that is genuinely interested (not just lab mates that have to be in attendance) does not happen that often and even though it can be a bit stressful, I usually find it rewarding.

Two thumbs up for CiteULike

After getting tired of the slowness and lack of features of Connotea I decided to try out CiteULike. My only regret is that I wish I made the switch about 6 months ago, since CiteULike seems superior to Connotea in almost every way.

In particular, I really like the built in priority list for indicating the level of importance for me to read a certain article. This is much better than my old Connotea method of using a "to_read" tag. Also, the use of tag clouds (instead of simple lists) not only for my personal tags but also for authors is a really nice feature. I was really surprised to see that you can upload a pdf of the paper being cited for storage on CiteULike. I'm not sure how much I will use this feature, but it is a nice option for those papers that you might not have easy access to all the time. Lastly, the search function is simple yet effective and the site runs smoothly without any waiting or timeouts.

The transfer of my bookmarks from Connotea to CiteULike was easy. I simply exported my bookmarks from Connotea in RIS format (which of course took about a minute of waiting) and then imported them into CiteULike. The only small hiccup is that CiteULike doesn't handle multiple words as a single tag (ie. no spaces allowed), but CiteULike did convert all of these cases using dashes instead of spaces.

Overall, I am a happy social bookmarker again and you can follow what I am reading here:
http://www.citeulike.org/user/mlangill

Firefox & Thunderbird Addons

Yesterday, I was watching someone on the bus scroll on their iPhone and I was thinking "Why doesn't my scrolling look that smooth on my laptop"? After a quick search I found the "Yet Another Smooth Scrolling" add-on for Firefox and it works perfectly!

I have tried lots of different add-ons, but the ones that I find essential are:

Firefox (in order of importance)
-Foxmarks Bookmark Synchronizer - allows backing up and syncing of bookmarks (and recently passwords) between computers
Adblock Plus - blocks all of those annoying ads
Download StatusBar - makes a smaller download status bar
Yet Another Smooth Scrolling - smooth scrolling
Greasemonkey - allows tons of different of scripts (including some nice ones for browsing Craigslist)

Thunderbird
Slideshow - allows easy viewing and resizing attached pictures
Signature Switch - a single button that quickly turns on or off your signature (and allows multiple signatures)

If you have any other essential add-ons, please let me know!