Canada gets Google StreetView

Google launched their StreetView program in major Canadian cities today. Of course I don't live there right now, but I did check out my old stomping grounds in Vancouver, BC.


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Also, they happened to do Chester, NS which is where I usually spend most of my summer vacations.



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Storable.pm

Most of my programming is what I like to call "biologically driven"; that is the main end result is not the development of the program itself, but rather the data that comes out of the program. Many times this involves writing a script to input data, do something to that data, and then output it back to a file which is in turn read into another script....ad infinitum.

The classic tab-delimited file is usually my typical choice for the intermediate format, but reading and writing (although simple) these gets repetitive and more complicated for more complex data structures. I finally looked into alternatives (something I clearly should have done awhile ago) and came across Storable.

Basically, it allows you to save/open any perl data structure to/from a file.
It is very easy to use:

use Storable;

#Reference to any data structure
$data_ref;

store($data_ref, 'my_storage_file');

#later in same or different script
$new_data_ref = retrieve('my_storage_file');

Check it out if you have never used it before.

Gene ontology tool suggestions

I have used a few GO tools in the past, but after looking at the massive list of tools on the gene ontology page I'm hoping someone can give me a good suggestion for my problem.

Basically, I have several lists of GO terms (~4-15 terms per list) and I would like to see if at a "higher" branch they share a common molecular function. Ideally, a tool that could be run from the command line and outputs significance scores would be great, but a GUI tool would also work since I have about 70 lists that I would need to run.

Note, that this is slightly different than the usual over-representation analysis which usually takes a list of genes as input. In my problem I am starting with GO terms.

Any suggestions would really be welcome!

Syncing Mendeley and CiteULike

I have been using CiteULike for quite awhile (after switching from Connotea), but more recently started using Mendeley. Overall, I am really impressed! Mendeley is a relatively new software project (still in beta), and I am surprised by how well it works. It has some crucial features that seperate it from other bookmarking tools such as: ability to sync bookmarks and pdf files back and forth from multiple personal computers and their online server, the ability to organize pdf files locally by title, author, journal, etc., has a citation plugin for Word (so you can stop paying for EndNote), and that the client software is available for Linux! Mendeley has been working so well that I was afraid I might end up abandoning CiteULike, since I most likely won't bookmark something twice.

However, yesterday it was announced that bookmarks from CiteULike can be accessed from within Mendeley. Note that this isn't just the simple ability to import the bookmarks, but that the bookmarks are kept synced and in their own CiteULike folder within Mendeley. Although the syncronization is currently only one way, from CiteULike to Mendeley, further integration of the two tools is suppossedly in the works.

This seems like a great colloboration since CiteULike tends to focus more on the social networking aspect, while Mendeley focuses more on providing a presonal reference manager.

It is nice to see companies colloborating instead of competing.

Automatically downloading emails in Thunderbird when using IMAP

Lots of applications have an "offline" feature that allow you to access data (email, calendar, documents, etc) when you don't have an internet connection. These are great, but I can never remember to click the "offline" mode. Bandwidth and storage are never usually concerns, so I would just prefer if applications did this by default (or at least had the option). Google Calendar is about the only program that I use daily that does this without me needing to click on update/offline.

For those who use Thunderbird as their email client and use IMAP instead of POP, you can set it to have all of your emails stored locally by default without clicking the offline mode. The trick is a couple of settings in the advanced config editor (Options->Advanced->Config Editor):

1. mail.server.default.autosync_offline_stores to true (you might have to create this value if it doesn't already exist. Right Click->New->Boolean)
2. use_status_for_biff to false
   

More information is here.

Hello California!

Well UC Davis to be more precise. I accepted a postdoctoral fellowship from Jonathan Eisen to be a part of the iSEEM project working on metagenomics. I have only been here for a few days, and first impressions seem great. First, the research field is exactly what I was most interested in; second, my previous PhD research is definitely of relevance; and third, I feel like I have lots to learn from the people around me.

Considering my previous Blog tag line/description is inaccurate:

"A PhD student's point of view on bioinformatics, evolution, and microbial diversity; with an interest in cutting edge computer tools that make them all a bit easier."

I decided to radically change it to:

"A post-doc's point of view on bioinformatics, evolution, and microbial diversity; with an interest in cutting edge computer tools that make them all a bit easier."

Jonathan's opinion on open-access publishing is quite similar to my own, so in addition to blogging about microbial evolution, expect to see more posts about my views on academic publishing.

Goodbye Vancouver!

The past 4 months have been a whirlwind. On April 16th I successfully defended my PhD thesis, after some minor revisions submitted it on April 18th, and left the country on April 29th. I wouldn't recommend such a tight time line especially if you happen to have a 5 month old baby as well!

My thesis will eventually be accessible (open-access of course) through SFU's library, but for those who are just dying to read it now, can access it here (+ appendix).

I feel obligated to give some type of advice to future PhD students. Unfortunately, I don't have any huge insight, but I would recommend not worrying too much during your graduate studies. Many times, I thought the whole thing would unravel and I would never finish, especially during years 2-3, but all of a sudden things started to fall in place. Every grad student I have ever talked to has always agreed that productivity increases greatly in the last year or two and so you can't worry about how long it took to do X in time Y. I hope I am not giving the impression that doing a PhD is easy, because it is not. It is hard, and different from all other schooling. If you think of an undergrad degree as sprinting, then a PhD is more like a marathon. I was great at sprinting, but learning to be a good marathon runner was a completely new set of skills.

In between all of the moving steps (I don't want to see another cardboard box for quite awhile), I had lots of time to reflect on my past 4.5 years in Vancouver, BC. Although there were some challenging times, I will greatly miss Vancouver and the people that I met during my time there. The first years of my marriage, living far away from family, the completion of my PhD, and becoming a Dad all happened in Vancouver and I will cherish the multitude of memories that accompany each of these milestones.

To end this post, I think I will list a few flashes of memories that are ingrained in my head from the past several years (in no particular order):

• Driving across Canada and seeing the Rockies from a distance for the first time.





• Looking out my first downtown apartment window for the first time.





• Standing on top of the "Chief".




• Snorkeling in the ocean with my wife along the "sunshine coast".



• Houseboating on a quiet lake in Vancouver Island surrounded by the most beautiful scenery.




• White water rafting near Squamish.




• Walking the sea wall countless times, and every time still being impressed by it




• The various camping adventures including a jump into a cold lake to escape a never ending swarm of flies.
• Standing at the peak of Whistler for the first time.
• The various conferences that included travel to destinations such as Maui, Vienna, Cambridge, UK, and California.
  
• The birth of my son, Gavin.
• The happiness of reading a short letter stating that I had completed all requirements for my PhD.