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.

Microbial Genomics

I have been at Lake Arrowhead since Sunday for the 16th International Microbial Genomes Conference and I have to admit I am quite impressed. I think this conference has solidified in my mind that large conferences can't compete with smaller conferences. Let me list the reasons why in order of importance:

1. Food - in almost all cases the larger the group of people the worse the food will be. Now you may think I am slightly joking around saying that this is the most important, but I am quite serious. There is nothing worse than having to eat some cafeteria style food and then have to sit through 2-4 hours of talks with a cramping/rumbling/starving belly. Also, I find meals are the best place to meet and have discussions with other scientists.
   
2. Meeting people. You get a chance to meet almost everyone you want to without having to hunt them down like a gazelle. I really detest pouncing on a speaker as soon as they are done a talk. It is much nicer to see them at a break or at a meal (see above) and introduce yourself and ask a question then.
3. Better science. I find at smaller conferences the talks have been hand selected and tend to have a better line up of speakers
   
4. Location, location, location. Smaller conferences tend to have their meetings at nicer locations.
5. Beer & Wine - From my experience alcohol tends to be cheaper (or free) at smaller conferences which always makes everyone happy and tends to get scientists to loosen up some.
   

Mygazines

I recently found out about Mygazines.com, a website that allows users to upload and share scanned copies of magazines. This new form of digital piracy is getting the copyrights enforcers attention. I figured the site would be fairly lame with barely readable faded copies of old obscure magazines, but after checking out the site I was quite impressed. The images are clear and the website design is as good as any new social website. Over my lunch break I checked out the September issue of Discover and read a great article about personal DNA testing (p35). Personally, I don't see that many people cancelling their subscriptions, since most people still prefer to read from real paper. However, I was curious to see if any scientific journals were on the site. I figured some of the big ones such as Nature or Science might be, but ater a quick search it seems there are not that many scientists uploading yet. Of course I have access to all the science journals I need through my university, but I wonder if scientistis that don't have access would use such a source for information?

Evaluation of genomic island predictors using a comparative genomics approach

Well after a long hiatus from blogging I thought would start again with announcing my recently accepted paper, "Evaluation of genomic island predictors using a comparative genomics approach" in BMC Bioinformatics.

Quick Summary
This research provides a comparison of several previously published tools that are used to predict genomic islands (large regions of HGT in bacteria).These tools use various methods of identifying abnormal sequence composition, such as GC percent, to predict regions of HGT. The predicitons made by these tools were compared to reference datasets of genomic islands (GIs) and non-GIs (very conserved regions) that were constructed using whole genome alignments. One of the novel and cool (well I like to think so) things about this comparative genomics method, called IslandPick, is that it automatically selects appropriate genomes for comparison given a query genome. Normally in most compartive genomics studies the user/scientist has to pick which genomes are relavant and should be used in the comparison. This works well until you have to do it for ~1000 different genomes. If you want more information on how this works read the paper!

Publishing
This was my first experience with a very tough and stubborn reviewer. This would have been published almost 6 months ago if it wasn't for one reviewer that kept insisting that our method was flawed even after we clearly defended and addressed their concerns. After much correspondence and waiting, a fresh group of reviewers accepted the research after some minor revisions. *Sigh* Makes me wonder how much of publishing is just a crapshoot?

Master of the universe

I watch quite a bit of TV and that often includes special episodes or series based on science. Quite often when I get flustered with my own research, these shows will renew my passion and interest for science and remind me of why I am working on a PhD.

I get many of the shows I miss through the internet via multiple methods including web feeds (YouTube), download sites (bit torrent) , and live streaming (p2ptv). Disclaimer: Some of these methods may be illegal based on your location or the tv show provider so check out your laws first. :)

The first show I want to highlight is Stephen Hawking: Master of the Universe. This was a nicely balanced hour long segment that included just enough science along with a history of Hawking's debilitating illness. I remember my uncle giving me Hawking's book, "A Brief History of Time" when I was very young ( I am guessing around ~12 years old). I think I may dig it out and reread it with my much more educated brain.

Science and Beer

As always, I am looking for ways to improve my publishing and would consider pretty much trying anything. As pointed out in a recent NYTimes article a study showed that drinking less beer correlates with improved publishing.

Personally, I would suggest that the amount of beer consumed is a measure of the scientist's social life and as I think most agree better science often requires less social life. Sadly, I guess I will have to try to be the exception to the rule, since I am not quite ready to part with my bottle of suds.

TrueCrypt

I have never been one to worry about security issues online. I don't clear my cache after online banking, change my passwords every few months, worry about too much information being on Facebook, or even password protect my computers.

However, I have been doing my taxes online for the past three years and I save all of my information to pdfs and text files. I called recently to change my address with the CRA (Canada Revenue Agency) and they ask a ton of verification questions before you can get them to access any of your information. At first I thought this was robust, but then I realized that every single answer could be found in my one folder "Taxes".

After a few quick Googles I found TrueCrypt. It allows you to encrypt a single file (that acts as a container) or a complete partition. If you wanted to go over the top you can even encrypt your whole OS. The default encryption protocols are the same ones used by the top US government (and I assume they know what they are doing). It even allows you to create completely hidden volumes (not that I need that).

I quickly set up a 1GB container to put all of my tax information along with a few other files that contain my passwords that I can never remember . Now, if only I would get around to setting up a good backup system.

Researcher ID

At least a couple of bloggers have already brought to my attention the press release of ResearcherID. Basically, they are going to allow a user to make a stable and persistent id that can be used to connect aspects of a researcher's profile such as personal web page, CV, publications, etc. This is especially nice for those with a common name that is not easily found using Google.

This interests me since it will allow (I think) a researcher go one step above creating various profiles (ie. usernames and logins) on various sites and enable a single accountable online profile. The only disappointment is that it is limited to "researchers" and not any person that wants to create a unique personal identifier for them self.

I think sites like Facebook, MySpace, and LinkedIn all suggest that all people want a personal profile that they can point to and say "Hey that is me!". However, people are multifaceted and can need various profiles for the different aspects of their lives. Essentially, I would like to have multiple profiles that are all connected to one online person (that is ideally a real person); one for current friends, one for past acquaintances, one for family, one for career relationships, etc. Instead of "adding" each person's Facebook, MySpace, Flickr access to mine I simply add that person (identified by a single id).

Of course this idea is not novel and has been partially attempted before (MSN Passport anyone?), but I haven't found anyone that has done it with enough flexibility and openness to really catch my attention.