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.

Is PLOS One the future of scientific publishing?

I just read about PLOS One's new features through their relatively new blog, EveryOne. Although the new features are not really ground breaking they do provide a much improved layout and a new "Related Content" page. These changes show that One is dedicated to improving connectivity between peer-reviewed papers and commentary from comments, blogs, etc., giving me some hope that publishing may be changing (yet still at a snails pace).

So back to the question that is asked in the title of this post, "Is PLOS One the future of scientific publishing?", I am going to have to say a tentative "Yes". I think their basis of publishing papers not on novelty, but focusing peer-review on ensuring that the methods, and conclusions drawn from the results are scientifically sound, opens many doors for how scientists publish their findings. Currently, scientists compete for a limited space in a "high-impact" journal. In the majority of cases papers are not rejected because of their methods, results, and conclusions are not valid, but due to a better paper being submitted at the same time. This competition is justified, but in this current format has various drawbacks including:

1. Importance of research is determined by a very small number of reviewers and usually a single editor has the final decision
   
2. Significance or novelty of research is very subjective and can vary widely between reviewers
3. Significance can change over time as future experiments confirm or depend on the results of the current research (including negative results)
   
4. Not making the cut (i.e. rejection) results in a large waste of time as authors have to reformat, resubmit, and respond to new reviewers comments

The separation of the evaluation for competitiveness, novelty, significance, etc. versus scientific robustness helps reduce many of these problems. The largest hurdle to overcome using this model is to move from a journal impact factor to a paper impact factor measurement. Therefore, "signficant" papers are still valued and reconizable in PLOS One and other journals that will likely follow their publishing methods.

Personally, I have never published in PLOS One and by no means do I think PLOS One in its current form is the pinnacle of publishing. However, I do appreciate that they are trying to change the way science publishing is currently conducted.

Google Calendar Available Offline

I am just starting to peek my head out of the thesis hole and noticed that Google Calendar is now available offline using Google Gears. By default it only syncs your personal calendar, but shared calendars can also be synced under the offline options.

I'm not offline that often, but it is nice to know that my calendar is always available now.

Considering Gears has been around for quite awhile now, I am surprised that it took Google this long to add the offline mode for their calendar.

HubMed Citation Manager

I just came across HubMed yesterday and I found one of their tools incredibly useful for getting references into EndNote (or other reference manager software tools). Basically, HubMed Citation Finder will take a bibliography (say from one of your favorite papers), split them up, find the citation in PubMed, and return the list of references in several citation formats such as RIS, BibTex, RDF, etc. This file is then easily imported into your reference manager's library.

It just saved me a couple of hours and would have saved me even more if I had known about it a few weeks ago.

Personal Genomics & The Burden of Knowing

Like many bioinformatists, biologists, scientists, and technologists I am very interested in personal genomics. I have kept track of the start ups that are doing personal SNPs analysis and have been eagerily waiting for sequencing costs to drop to the point were the $1000 genome is possible. I envisage everyone having their personal genome done and programs to analyse the data being so widespread that even a "My Genome Facts" Facebook application would not seem out of place.

Of course I have read lots about ethical worries about how the data could be mis-used or how the public can not handle the probabalities of having a certain disease. Personally, I have always thought these were blown a bit out of proportion and that personal genomics will in general be a good thing. More data is better right?

Well, I just read an article called "The Burden of Knowing" by Catherine Elton in the Boston Magazine and it really made me reconsider my previous thoughts. Elton starts out explaining about personal genomics and specifically about Knome, the first company to do complete personal genome sequencing. She then starts to delve into her personal choices regarding her susectibility to having the BRCA1 gene. The article is extremely well written, and unless I am becoming a complete softy, quite sobering.

A small excerpt that I really enjoyed was this:

The counselors then mentioned another option: having my ovaries taken out and my breasts removed. Here we were, talking about science's ability to look along a submicroscopic piece of DNA, searching for missing letters on a strip of a gene, and yet if science found that letters were missing—if the gene had the cancer-risk mutation—the best it could do was amputate or sterilize. These options seemed as though they should have been filed away in a medieval remedy book, somewhere between leeches and bloodletting.

So did the story change my view on personal genomics? No not completely, but I do think that getting my genome sequenced might not be as fun as I first thought. Too bad there are not many positive attributes linked to genes like "gene variant Y will allow you to live a long life despite your lack of physical exercise" or "you have an improved version of the alcohol dehydrogenase gene, so feel free to drink more beer".