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.