Saturday, November 29, 2008

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)

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!

Friday, November 28, 2008

Sorry Connotea, it's not you, it's me.

I used to really like Connotea and the idea of being able to easily bookmark and share journal articles was what drove me to encourage many people in my lab to start using it. I truly believed it would evolve into a tool that would be essential for researchers and would be a major improvement to existing methods of tracking new papers.

Well, boy was I wrong. I haven't seen any improvements in Connotea for at least a year including a search engine that would be better replaced by Google. Even worse for the past few months Connotea website has been getting slower so that instead of looking up my papers there I just go back to searching Pubmed. Finally, for the past few days Connotea seems completelly useless so that papers I was hoping to cite for my near future thesis writing days are inaccessible.

Like any bad relationship I was hoping it would get better over time, but I have waited long enough and I'm breaking it off before I get any more committed. If the site does ever become accessible again I plan on exporting my bookmarks and taking them elsewhere. Any recommendations?

Tuesday, November 18, 2008


My most recent research has resulted in website for viewing predictions of genomic islands (GIs), large regions of horizontal gene transfer, in bacterial genomes. IslandViewer integrates three different methods of GI detection IslandPick, SIGI-HMM, and IslandPath-DIMOB. SIGI-HMM and IslandPath-DIMOB use sequence composition bias to detect GIs and were found to be the most accurate in a recent publication. IslandPick is a method I recently developed that uses comparative genomics to find GIs by identifying regions that are present in one genome but absent from several related genomes.

Predictions for all three tools are pre-computed for all sequenced bacterial genomes (those available from NCBI Microbial genomes). Also, users can submit their own newly sequenced genome for analysis and receive an email when complete (usually within a couple of hours).

Update:IslandViewer has been published in Bioinformatics!

Any feedback or comments on the design or usefulness on the website is appreciated!

Friday, November 14, 2008

My New Little Scientist

My first baby was born on Nov. 5th weighing in at 7lbs. After much debate during the pregnancy my wife and I decided to name him Gavin Nathaniel Langille. The first week was tiring of course, but I don't think I really noticed due all the excitement and the newness of it all. However, now that I am in the middle of the second week it is starting to catch up with me!

One thing about having the baby is that I am very focused on finishing my PhD and I am in serious job hunt mode. People keep asking me about what type of position I am looking for. The most likely is a post-doc in academia, but I haven't ruled out taking a job in industry. I have at least one post-doc position and one bioinformatics scientist position industry that I plan on applying by next week.

I would have to say that the biggest limitation for job hunting is location. Having a baby really is drawing me to move closer to home, Atlantic Canada, but I am still keeping a fairly wide search distance down to the Boston area.