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!

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?

IslandViewer

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!

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.

Microbial Genomics Conference (Last Update)

I promised in a previous post to add more details about the Microbial Genomics conference in Lake Arrowhead. However, my wife went into pre-term labour, and is now on bed rest so I am a little short on time. I did give a conference review at a recent lab meeting so I thought I would post that as a quick substitute.

Microbial Genomics 2008 Conference Review

View SlideShare presentation or Upload your own. (tags: conference review)

Review of Arrowhead Conference

I was hoping to write this during the conference, but every talk I went to was really interesting and I ended up not using that time for blogging. However, there is at least one talk that I wanted to mention before I forgot to much.

I thought the most interesting talk was from Kim Lewis, who describes "persistor cells" as those bacteria that lay dormant in a population. These persistors are resistant to antibiotics because they are essentially shut down and passivly allow antibiotics to simply wash over them as opposed to normal bacteria cells that actively block or pump out antibiotics. Lewis also showed that late samples taken from cystic fibrosis patients had high levels of persistor cells. Kim then discussed unculturable bacteria (of which 99% of bacteria are) and suggested that when plated on media that these are actually dormant and not dead. To support this Kim showed that by innoculating an unculturable sample with E.coli caused growth of an unculturable strain around the E.coli spot. He later found a mutant that did not cause the effect and identified the key gene to be a sideophore. Lewis ends with this little tidbit, "Dormancy is the default mode of bacterial life". I find this really interesting because it suggests that most bacteria depend on a few bacteria to signal when their surrondings are optimal for growth.

There are a couple of more talks that I hope to blog about in the next day or two.