Beta Science

Antarctica Part 2 - Getting to Mount Erebus

2010-11-27T16:03:00.000-08:00

After arriving in Antarctica, many days were spent preparing for the 2 weeks we would spend out in the field on Mount Erebus. Basically, science gear all had to be listed, boxed, and weighed before departure. Additionally, gear had to be separated into two shipments: 1) for the gear going with us to Fang Camp, 2) the gear we would need once we got to Lower Erebus Hut.

I spent quite a bit of my downtime drinking tea and writing in my journal while looking out at the sea ice and pressure ridges from the lounge area. I also got out for a couple of walks along the pressure ridges, which was very scenic and refreshing.

What made the walks even more interesting were the Weddell seals that had chewed their way through the ice and were lounging on the sea ice near the marked trail.

After spending nearly a week at Scott Base preparing, we got confirmation that we would be heading to the field the next morning. After a few last minute changes, it was determined that we would it take 2 helicopter trips to get the 6 of us and our gear up the mountain to Fang camp. Fang camp is about two thirds of the way up the mountain and is used as a stop for a couple of days to get used to the altitude. Flying directly to Lower Erebus Hut isn't done much anymore since the altitude is 12000 ft, which feels more like 16000 ft since it is so far from the equator, and altitude sickness is a real concern. In fact, most of us took Diomox to help adapt to the altitude sickness along with drinking at least 4 liters of water per day.

It was my first helicopter ride and it was simply amazing.

Once we landed, everyone helped unload and start to get gear put into our tents. A few helicopter trips later and we were on our own on the side of Mount Erebus.

Antarctica Part 1 - Getting to the ice.

2010-11-24T20:45:00.000-08:00

After about 20 hours of traveling I arrived in ChristChurch, New Zealand. It was early morning, and I didn't really now where I was going so I walked from the airport to Antarctica New Zealand. I tried on all of my clothing that they provided including enough to have 6 layers on top, 4 layers on bottom, 2 pairs of boots, and lots of other accessories. I met with the rest of the research team who are based out of University of Waikato:
Craig Cary, PI
Ian McDonald, PI
Craig Herbold, Post-doc
Chelsea Vickers, Master's student

That night we all attended the 2010 New Zealand Research Honours Dinner. This was the beginning of a crash course in NZ culture. Considering that I would be spending most of my time with these people in close courters with out running water, it seemed fitting to start the trip with everyone all dressed up.

After spending a day getting little things done in Christchurch, our flight for Antartica left the next morning. For our flight we had to be wearing (or at least carrying) all of our ECW (Extreme Cold Weather) gear. We were given a short intro video on Antartica, then we went through security, and boarded a bus. A short bus ride took us out onto the tarmac and we picked up a bagged lunch as we boarded our plane.

Seating was first come first serve so I grabbed one of the business class seats and settled in for the 5 hour flight. Almost everyone on board are scientists so there was lots of interesting projects being discussed on the flight. For example, the person beside me worked for NASA and was studying the soil and microbes in the McMurdo Dry Valleys, because these regions are thought to be very similar to Mars.

Interestingly, the cock pit was open and you could go up at anytime to chat with the pilots and to check out their view. The visibility was perfect and the views were fantastic as we started to approach Antarctica.

As we got closer to Ross Island, Mount Erebus was clearly visible and it was unimaginable that I would be living on top of it for 2 weeks.

After landing on the ice runway, it was a short drive through the American McMurdo Station (max. ~1100 people) and into the smaller, cozier, New Zealand Scott Base (max. 86 people). At last I had arrived!

Heading to Antarctica!

2010-11-05T16:57:00.000-07:00

On Nov. 8th I will depart from sunny California and with a quick one day stop in Christchurch, New Zealand I will be in Antarctica. Now this isn't just a trip to Antarctica, this is the trip to Antarctica. Please allow me to gloat a little bit. After arriving at Scott Base on Ross Island I will begin a 5 day field training course to make sure I survive the expedition I will be taking on. After training, 8 of us will be flown halfway up Mount Erebus where we will acclimatise to the altitude by living in unheated tents for a couple of days. Then we will travel to the top of Mount Erebus to reach the "Lower Erebus Hut" at an altitude of 12,000 ft. We will stay there for 2 weeks doing daily trips to "fields"/fumeroles where the snow has melted away due to hot volcanic gases (did I forget to mention that the Mount Erebus is a active volcano?). The main goal is to collect soil samples and environmental data to examine the microbes living in this extreme environment. At the research station there is a small heated hut for meal times and work, but sleep will still be in the same cold tents with 24 hour sunshine. Dehydrated food and -20 to -40 C temperatures will ensure I lose some weight, but that is an added bonus.

To say that I am excited is an under-statement. Sure it will be hard to be away from my family for a month and the altitude sickness will make me feel like crap, but the chance to go on such a crazy expedition ruled out any chance of me turning it down.
How many scientists, especially those that do bioinformatics, gets a chance to do field work like this!?

Review of Open Science Summit 2010, #OSS2010

2010-07-31T10:11:00.000-07:00

I have been attending Open Science Summit 2010 at Berkeley, CA and although not quite finished yet I feel like I can give an overall review of what I thought of the conference. You can check out my individual comments during the conference on Twitter.

I would like to state that in general I am grateful and respect the work that Joseph Jackson and the organizing committee conducted to make this open science conference a reality. It is a tremendous amount of effort and the following is only meant as a constructive criticism for possible open science summit conferences in the future.

Pros

Bringing together a very intelligent diverse group of speakers. Good mix of policy makers, developers, traditional scientists, biotech, young and old, etc.
Great use of technology. Providing a live video stream of conferences is an idea that I wish more conferences implemented. Also, using backchan.nl is a nice additional add-on that couples well with the live video stream.
Willingness to try to adapt (as much as possible) to conference attendees comments via twitter, back channel, etc.

Cons

No scheduled breaks. Breaks are needed for numerous practical reasons: people need bathroom breaks, time to get some fresh air, and time for talks to get back on schedule. Even more importantly, it allows people to mingle. People travel to conferences so that they can get a chance to connect with people face to face (otherwise they would just watch the online feed).
No time for Q & A. Questions immediately after speakers not only is informative, but gives a temporary "mind break" for the audience. It also gives time for IT to get the next presentation queued. Note: this did tend to improve as the conference proceeded.
Too many speakers. Having 25 speakers in a single day (without parallel sessions) is just too much information for people to take in and sit through.

Additional lessons learned

A no slide presentation is not a guarantee that it will be a good one.
Videos do not always make a presentation better.
Having 2 or more speakers from the same organization or having the exact same opinion is not really beneficial.

Comments from FriendFeed

Use Mendeley to list your publications on your personal homepage

2010-05-04T15:12:00.000-07:00

I was updating/creating my personal website a little while ago and was looking for a good method to keep my "Publications" page updated without having to edit it manually.
At first I played around with using Exhibit. This was kind of fun and allowed my publications to be sorted in all kinds of ways and exported in lots of formats.However, this method seemed like overkill (might be more useful if I had hundreds of publications....maybe one day but not today), and required that I update a .bib file every time I had to add a publication.

Then I noticed that my Mendeley profile has a nicely formatted page of my publications. Unfortunately, Mendeley doesn't yet provide html code to embed this on your own page, there is a slight workaround.

In your Mendeley software client create a new collection and name it "Publications" (you can rename this later if need be).
Add your publications to this new collection. Note!! The publications need to be added from oldest to newest one at a time. This is because Mendeley orders the publications by the date they were added to the collection (and not by pub. date).
Right-click->Edit Settings, then under "Collection Access" choose "Public - visible to everyone". Then click "Apply and Sync".
Go to the settings again for the collection and follow the web link to the collection online.
In the upper right click on "Embed on other websites". You can customize the size and the color if you want. Then copy the html code to your website, blog, etc.
That's it! When you have a publication to add just add it to your new "publications" collection, sync, and now your personal page is updated as well.

The default settings will result in your publications looking like this:

Publications is a group in Biological Sciences on Mendeley.

For my personal website I changed the color and made it a bit larger so it looks like this.

An interview with the creator of BioTorrents

2010-04-14T12:17:00.000-07:00

Who better to interview the creator of BioTorrents than the creator himself? :)

Interviewer: So Morgan, your article entitled “BioTorrents: A File Sharing Service for Scientific Data” was published today in PLoS One. BioTorrents uses the popular peer-to-peer file sharing protocol, BitTorrent, to allow scientists to rapidly share their results, datasets, and software. Where did this idea come from?

Morgan: Well about 6 months ago I was downloading some genome files from NCBI's FTP site and was watching the download speed hover between 50-100Kb/s and I said to myself (much like this interview) I wish could download these with BitTorrent. I have used BitTorrent for downloading other non-scientific data (lets not discuss what they may be) and I know it is a much faster and more reliable way for getting large files. A few minutes later I posted to Twitter asking if anyone had thought about setting up a BitTorrent tracker for scientific data and the response was over-whelming (well only 1 response, but I could feel it had a larger impact). About a week later, I brought up the idea again over coffee with some members of my lab and more importantly my post-doc supervisor Dr. Jonathan Eisen. He thought it was a good idea and well worth pursuing, which was all I needed to push aside all my other "real" research and focus on this much more "fun" project.

Interviewer: Thanks for that long-winded response. Maybe you could comment more briefly on the benefits of using BioTorrents/BitTorrent for sharing scientific data.

Morgan: I think it is explained fairly well in the manuscript and in my previous blog post, but to reiterate the major benefits are:
1) Faster, more reliable, and better controlled downloading of data that scales well for very large files.
2) Instant "publishing" of data, results, and software.
3) Very easy for anyone to share their data. No dedicated web server needed.

Interviewer: Who should consider sharing data on BioTorrents?

Morgan: Everyone that has something to share. Large institutions can benefit from reduced bandwidth requirements, while individual users can benefit from the simplicity of sharing with BitTorrent technology. Personally, I really like the idea of open data and the idea of sharing results before publication. How many times has someone done an all vs all blast of microbial genomes? In theory this can be done once, and that person can be recognized (referenced, co-authored, etc.) when other researchers use that data.

Interviewer: Are there any challenges/limitations to using BitTorrent with scientific data?

Morgan: BitTorrent excels at transferring very large popular datasets. Therefore, if only one person is "seeding" a file and only one person is downloading the file most of the advantage to using BitTorrent is lost. However, even in this worst case scenario, the transfer speed would be roughly equivalent to using traditional file transfer methods such as FTP/HTTP and BitTorrent still provides the benefit of error checking and ease of data transfer control (pause, resume, etc.). Another possible problem is that some institutions often try to limit BitTorrent traffic since it is often considered illegal non-work related network traffic. However, I would encourage users at these institutions to explain to their network administrator that many times BitTorrent traffic is legitimate and shouldn't be blocked.

Interviewer: Why publish in PLoS One?

Morgan: I have been a big fan of the PLoS One journal and ever since I blogged about it last year "Is PLOS One the future of scientific publishing?", I have been wanting to submit a paper there. Also, considering that BioTorrents is aimed at improving open access to data in all fields of science, PLoS One seemed like the most obvious journal choice for our manuscript.

Langille, M., & Eisen, J. (2010). BioTorrents: A File Sharing Service for Scientific Data PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010071

Please don't use Clustal for tree construction!

2010-03-02T14:33:00.001-08:00

Image via Wikipedia

There are reams of books, articles, and websites about the correct way to build a phylogenetic tree. My post is not to argue about what is the best method, but rather point out that most people do not consider Clustal (e.g. ClustalX or ClustalW) to be an optimal solution in almost any circumstance. Countless times I have asked people how they built their particular tree and they give me the vague "Clustal" answer. Of course this answer is fine if this is the first tree you ever constructed, but beware you will be labelled as a phylogenetic newbie.

Clustal is technically a multiple alignment algorithm, but it also includes methods for tree construction in the same interface. Most of these methods are not really considered "good" tree building methods. If you do use Clustal, at least specify what tree building method you used (ie. "Clustal with neighbor joining"). Most people don't use Clustal even for multiple alignment anymore, because Muscle has been shown to be at least as accurate as Clustal and is much faster.

For tree construction, most people would agree that a Maximum Likelihood or Bayesian method would almost always be a better solution; PhyML and Mr. Bayes seem to be the most popular implementations for these methods. Advanced users might also want to look into using Beast.

I usually interact with most of these programs through a command line interface, so I don't have an expansive knowledge of the best graphical tool. However, I did come across, "Robust Phylogenetic Analysis For The Non-Specialist" which does a good job allowing easy interaction between various methods for multiple sequence alignment, tree construction, and tree viewing.

Whatever you use to build trees, just make sure it isn't Clustal!

Using Aspera instead of FTP to download from NCBI

2010-02-24T14:11:00.000-08:00

If you often download large amounts of data from NCBI using their FTP site you might be interested in knowing that NCBI has recently started using the commercial software Aspera to improve download transfer speeds. This was announced in their August newsletter and at first was only for the Short Read Archive (SRA). However, I recently found out that they are now making all of their data available.

How to use it (web browser)

Download and install the Aspera browser plugin software.
Browse the Aspera NCBI archives.
Click on the file or folder you want to download and choose a place to save it.
The Aspera download manager should (see below) open and show the download progression.

How to use it (command line)

The browser plugin also includes the command line program: ascp (In linux this is at: ~/.aspera/connect/bin)
There are many options but the standard method is:

ascp -QT -i ../etc/asperaweb_id_dsa.putty anonftp@ftp-private.ncbi.nlm.nih.gov:/source_directory /destination_directory/

e.g.:
ascp -QT -i ../etc/asperaweb_id_dsa.putty anonftp@ftp-private.ncbi.nlm.nih.gov:/genomes/Bacteria/all.faa.tar.gz ~/

Critique

Windows machine with Firefox worked with no problems and download speeds at my institution were much faster than with FTP (~0.5 - 4.0Mbps vs 50-300kbps)

Browser plugin with Firefox on Linux would not work! Plugin seemed to be loaded properly, but Aspera download manager would not start. Update: This was due to me trying to install the plugin as root and causing a permission error. The plugin is installed in your home directory and must not be installed as root.

Download with command line in Linux was unreliable. This was a huge disappointment as this was the primary method I was hoping to use. Files would start to download correctly with very fast transfer speeds (1-4Mbps), but connection would drop with error: "Session Stop (Error: Connection lost in midst of data session)". Unfortunately, there is no way to resume the download so each time I had to start over. On about the 8th try it downloaded the file (6889MB) correctly. Update: see below

Personal Opinion
Although I was excited to see NCBI trying to improve data transfer speeds I was not very impressed with the Aspera solution. Hopefully, it will become more reliable in the future.
Of course, my personal solution would be for NCBI to embrace BitTorrent technology and make use of BioTorrents, but I will save that discussion for another day.

Update:
All ascp options are shown below (by typing ascp without arguments). However, I can't find any further documentation on these options. As noted in the comments below, -k2 is supposed to resume a download, but this didn't work for me when I tested it.

usage: ascp [-{ATdpqv}] [-{Q|QQ}] ...
[-l rate-limit[K|M|G|P(%)]] [-m minlimit[K|M|G|P(%)]]
[-M mgmt-port] [-u user-string] [-i private-key-file.ppk]
[-w{f|r} [-K probe-rate]] [-k {0|1|2|3}] [-Z datagram-size]
[-X rexmsg-size] [-g read-block-size[K|M]] [-G write-block-size[K|M]]
[-L log-dir] [-R remote-log-dir] [-S remote-cmd] [-e pre-post-cmd]
[-O udp-port] [-P ssh-port] [-C node-id:num-nodes]
[-o Option1=value1[,Option2=value2...] ]
[-E exclude-pattern1 -E exclude-pattern2...]
[-U priority] [-f config-file.conf] [-W token string]
[[user@]host1:]file1 ... [[user@]host2:]file2

-A: report version; -Q: adapt rate; -T: no encryption
-d: make destination directory; -p: preserve file timestamp
-q: no progress meter; -v: verbose; -L-: log to stderr
-o: SkipSpecialFiles=yes,RemoveAfterTransfer=yes,RemoveEmptyDirectories=yes,
PreCalculateJobSize={yes|no},Overwrite={always|never|diff|older},
FileManifest={none|text},FileManifestPath=filepath,
FileCrypt={encrypt|decrypt},RetryTimeout=secs

HTTP Fallback only options:
[-y 0/1] 1 = Allow HTTP fallback (default = 0)
[-j 0/1] 1 = Encode all HTTP transfers as JPEG files
[-Y filename] HTTPS key file name
[-I filename] HTTPS certificate file name
[-t port number] HTTP fallback server port #
[-x ]]

Update 2:
After spending an afternoon with Aspera Support, I have some answers to my connection and resume issues when using ascp. The problem has to do with me not using the -l option to properly limit the speed at which ascp sends data. I thought this limit would only be relevant if 1) I wanted to not use all of my available bandwidth or 2) my computer hardware could not handle the bandwidth of the file transfer. Surprisingly, the recent for my disconnects was because NCBI was trying to send more data than my bandwidth allowed and thus causing my connection to drop. I would have thought that ascp would look after these type of bandwidth differences considering that all other data transfer protocols that I know of can control their rate of data flow. If this is the case, it would suggest that my connection may be broken if for some reason my available bandwidth drops (which would happen often due to network fluctuations at a large institution) even if I set the limit appropriately. Hopefully, Aspera can make their data transfer method a little more robust in the future. I don't think I will be replacing ftp with ascp in my download scripts quite yet.

Update 3:
Michelle from Aspera finally let me know that -Q is default option I should be using to allow adaptive control. Now, I am trying to get a entire directory to download, but I am still having connection issues. Here is a screenshot of my terminal showing that the directory resume is not working and I am losing my connection:

Filtering Blast hits by coverage using BioPerl

2010-01-30T22:46:00.000-08:00

A couple of days ago I wrote about how I had to throw away a ton of data because I ran out of disk space for a large Blast analysis. One of the reasons I ran out of room was because I opted to use the XML output format over the simpler tabular output. The XML format provides much more information about each hit including the lengths of query and subject genes, which allows easy retrieval of the coverage in BioPerl using the "frac_aligned_query()" and "frac_aligned_hit()" functions. For example:

my $searchio = Bio::SearchIO->new(
-format => 'blastxml',
-file => $blast_file
);
while ( my $result = $searchio->next_result() ) {

#process the Bio::Search::Hit::GenericHit
while ( my $hit = $result->next_hit ) {

my $evalue = $hit->significance();
my $identity = $hit->frac_identical();

######Get amount of coverage for query and hit #######
my $query_coverage = $hit->frac_aligned_query();
my $hit_coverage = $hit->frac_aligned_hit();

###Filter based on evalue and coverage
if ( ( $query_coverage > $coverage_cutoff )
&& ( $hit_coverage > $coverage_cutoff )
&& ( $evalue < $evalue_cutoff ) ) { ##do something ##}

This is fairly simple, but if you have to use the tabular output of Blast (due to say file size limitations) the lengths of the genes are not included in the Blast output. Therefore, you have to retrieve these manually somehow and then either calculate coverage yourself (remembering to tile the HSPs for each hit) or tell BioPerl about the gene lengths so you can call the same functions. This isn't obvious or documented in BioPerl, so I had to hack away until I found out the solution. See comments for explanation.

my $searchio = Bio::SearchIO->new(
-format => 'blasttable',
-file => $blast_file
);

while ( my $result = $searchio->next_result() ) {
my $query_id = $result->query_name();

#get the length of the query sequence
#Note: you need to write this function yourself since the length is not in the blast output file.
my $query_len = get_gene_length($query_id);

#################
#This sets the query length for each hit by directly manipulating
#the objects hash (instead of through a function)
foreach my $hit(@{$result->{_hits}}){
$hit->{-query_len}=$query_len;
}
#################

#process the Bio::Search::Hit::GenericHit
while ( my $hit = $result->next_hit ) {
my $hit_id = $hit->name();
my $hit_len = get_gene_length($hit_id);

###Setting the hit length is much easier!!
$hit->length($hit_len);
#################

my $evalue = $hit->significance();
my $identity = $hit->frac_identical();
my $query_coverage = $hit->frac_aligned_query();
my $hit_coverage = $hit->frac_aligned_hit();

if ( ( $query_coverage > $coverage_cutoff )
&& ( $hit_coverage > $coverage_cutoff )
&& ( $evalue < $evalue_cutoff ) ) { ##do something ##}

Note that if you don't tell BioPerl the lengths your script will die with a "divide by zero" error.

Large BLAST runs and output formats

2010-01-28T10:42:00.000-08:00

I have used BLAST in many different forms and on many scales, from single gene analysis to large "all vs all" comparisons. This is a short story of how I decided to delete 164GB of Blast output.

I will save my reasoning for doing such a large Blast for another post. For now, all you have to know is that I am doing an "all vs all" Blast for 2,178,194 proteins. That is (2,178,194)^2 = 24,744,529,101,636 comparisons. Sure quite a few, but nothing that a large compute cluster can't handle (go big or go home is usually my motto).

I usually use the tabular output format for Blast (-m 8). However, one of the nice functions in BioPerl allows you to calculate the coverage of all hsps with respect to the query or subject sequence. BioPerl handles the tiling of the hsps which is annoying to have to code yourself. I often use this coverage metric to filter Blast hits downstream in my pipeline. So here comes the annoying thing. The tabular output of Blast does not include the start or end positions (or length) of the sequences in the Blast comparison. Therefore, to calculate coverage you need to go back to the original sequence and retrieve the length of the sequence. I know this is not a hard thing to do, but I am a lazy programmer and I like fewer steps whenever possible. Therefore, I decided to try out the Blast XML format (-m 7). A few test runs showed that the files were much larger (5X), but this format includes all information about the Blast run including the sequence coordinates. Therefore, I decided not to worry about space issues and launched my jobs. Bad decision.

Well 3 days later, I find out my quota is 300GB and since I already had 150GB from another experiment the blast output put me over. I can't easily tell which jobs completed normally, so I am faced with the decision to either write a script to figure out which jobs completed normally, or scrap all the data and re-run it the right way. I have opted to delete my 164GB of blast output and re-run it using the tabular format and I might even gzip the data on the fly to ensure this doesn't happen again.

Of course this isn't rocket science, but I thought I would tell my tale in case others are in similar circumstances.

MCE Remote Stops Working

2010-01-21T21:22:00.000-08:00

Quick post in case it happens to me again. My MCE IR remote stopped working suddenly and after some Googling I found out that I needed to change the batteries. The weird part is that it also required the remote to be "reset". One way is to short the battery terminals, but that didn't work for me so I found another solution.

Take the batteries out of the remote.
Hold the power button down and then press every other button on the remote once.
Replace the batteries.
Pray to the Microsoft gods.

Hopefully this helps someone else.

BioTorrents - a file sharing resource for scientists

2009-10-21T12:07:00.000-07:00

Let me ask you a question. If you just wrote a new computer program or produced a large dataset, and you wanted to openly share it with the research community, how would you do that?

Image via Wikipedia

My answer to that question is BioTorrents!

This has been a side project that I have been working on lately and considering this is the first international Open Access Week I thought I should finally announce it.

BioTorrents is a website that allows open access sharing of scientific data. It uses the popular BitTorrent peer-to-peer file sharing technology to allow rapid file transferring.

So what is the advantage of using BioTorrents?

Faster file transfer

Have you tried to download the entire RefSeq or GEO datasets from NCBI recently? How about all the metagenomic data from CAMERA? Datasets continue to increase in size and downloading speed can be improved by allowing multiple computers/institutions to share their bandwidth.

More reliable file transfer

BitTorrent technology has file checking built-in, so that you don't have to worry about corrupt downloads.

Decentralization of the data ensures that if one server is disabled, that the data is still available from another user.

A central repository for software and datasets

Rapid and open sharing of scientific findings continues to push for changes in traditional publication methods and has resulted in an increase in the use of pre-print archives, blogs, etc. However, sharing just datasets and software without a manuscript as an index is not as easy. BioTorrents allows anyone to share their data without a restriction on size (since the files are not actually hosted or transferred by BioTorrents).

Titles and descriptions of all data on BioTorrents can be browsed by category or searched for keywords (tag cloud coming soon).

As long as there is at least one user sharing the data it will always be available on BioTorrents. Those pieces of software or datasets that are not popular and not hosted by a user will quietly die (removed from Biotorrents after 2 weeks).

I am continuing to update BioTorrents, so if you have any suggestions or comments please let me know.

Other Tags:Website Hosting, Inventory Software

Canada gets Google StreetView

2009-10-07T09:55:00.000-07:00

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.

View Larger Map

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

View Larger Map

Storable.pm

2009-08-02T14:37:00.000-07:00

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

2009-07-15T11:57:00.000-07:00

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

2009-06-03T12:20:00.000-07:00

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

2009-05-20T10:33:00.000-07:00

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):

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)
use_status_for_biff to false

More information is here.

Hello California!

2009-05-13T13:42:00.001-07:00

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!

2009-04-30T21:33:00.000-07:00

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?

2009-03-31T14:06:00.000-07:00

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:

Importance of research is determined by a very small number of reviewers and usually a single editor has the final decision
Significance or novelty of research is very subjective and can vary widely between reviewers
Significance can change over time as future experiments confirm or depend on the results of the current research (including negative results)
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

2009-03-10T10:31:00.000-07:00

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

2009-02-19T11:38:00.000-08:00

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

2009-02-03T12:38:00.000-08:00

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".

Pseudomonas and Langille in the media

2009-01-27T11:15:00.000-08:00

Ok, this is some serious self-promotion, but scientists (well PhD students anyway) don't get a chance to brag about their research being in the media very often. Plus, it is my blog, so why not?!

The actual science:
The research in question surrounded the sequencing of the Liverpool Epidemic Strain of Pseudomonas aeruginosa that was causing increased virulence in cystic fibrosis patients. One of the interesting things in the paper is that we identified several genes related to virulence (using STM) and that several of these genes were within genomic island and prophage regions. Of course virulence factors have been found within these types of regions before, but to have actual in-vivo (chronic rat lung infection model) experimental evidence that these genes are involved in virulence in an epidemic strain, really makes this research notable. The research was published in Genome Research and is open access.

The media coverage:
Lancet Infectious Diseases (sorry not OA).

Vancouver Sun

Ok, now for the fun stuff:
SFU News - Notice those sleepy eyes? That is what having a 2 month old will do to you!

The story even made some news on a non-English site:
http://news.sina.com.hk/cgi-bin/nw/show.cgi/32/1/1/962395/1.html
Automatic translation results in me being referred to as "blue Gull", SFU as "West gate Philippines Sand University", and UBC as "Inferior poem University".
http://tinyurl.com/68ge47

Looking for a bioinformatics expert?

2009-01-21T11:42:00.000-08:00

What I have to offer:

A balanced background in both biology (BSc) and computer science (BCS)
Soon to be completed PhD
Extensive research experience in bioinformatics, genomics, phylogenetics/phylogenomics, evolution, and bacteria pathogenesis
Some previous research experience in medical imaging, ontology development, and metagenomics
An impressive publishing record (7 papers, 3 first authors, 2 more first authors under review)
Solid computational skills including Perl programming, database design (MySQL), parallel programming, and web design (PHP & JavaScript)
Good communication and social skills
More information

What I am looking for:

Post-doc or job (academic or industrial)
Preferably, a position where I have some significant manager or leadership responsibilities
Geographically interested in north eastern parts of North America (Ottawa down to New York), but would entertain positions elsewhere in N.A.

I didn't put any limitations on research interests, since I am open to many areas. However, anything having to due with the human microbiome project, human-bacteria interactions, or metagenomics would be of particular interest.

Please email me if you are interested or if you have suggestions on some good openings.

Airports & Interviews

2009-01-07T18:17:00.001-08:00

Quick question: Why do people line up or huddle around an airport gate before they are called to board? The plane is not leaving until everyone has boarded, so why would you want to sit even longer in a cramped up airplane than is absolutely necessary?

I contemplated these questions and other airport mysteries (like who would pay a $38 service fee for changing Canadian to US currency) while recently sitting in airports for 7 hours and 5 hours on two separate trips.

Fortunately, both flights were worth while since one was a flight home where home made meals and warm fireplaces greeted my new family of 3 and the second was for a job that I am quite interested in at Boston. Luckily, another interview I had arranged did not require a flight so my sanity was slightly saved.

I would say that both interviews went fairly well, and overall I actually enjoyed the experience. Doing a PhD (or any large project I suppose), you tend to lose sight of the accomplishments that you have made along the way. Getting a chance to present my work to an audience that is genuinely interested (not just lab mates that have to be in attendance) does not happen that often and even though it can be a bit stressful, I usually find it rewarding.

Two thumbs up for CiteULike

2008-12-03T13:20:00.000-08:00

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

2008-11-29T13:31:00.000-08:00

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.

2008-11-28T16:45:00.000-08:00

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

2008-11-18T20:22:00.000-08:00

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

2008-11-14T21:55:00.000-08:00

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)

2008-10-01T10:52:00.000-07:00

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

2008-09-21T17:11:00.000-07:00

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

2008-09-17T15:13:00.001-07:00

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:

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.
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.
Better science. I find at smaller conferences the talks have been hand selected and tend to have a better line up of speakers
Location, location, location. Smaller conferences tend to have their meetings at nicer locations.
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

2008-08-19T14:32:00.000-07:00

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

2008-08-14T11:32:00.000-07:00

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

2008-03-20T11:34:00.001-07:00

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

2008-03-20T10:37:00.000-07:00

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

2008-02-18T10:36:00.000-08:00

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

2008-01-21T11:37:00.001-08:00

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.

Fecal Transplant

2007-11-14T11:40:00.000-08:00

I couldn't pass up blogging about this recent news article that discusses how transplanting feces to patients with C. difficile can cure their illness. I think it is a great example of how important and natural a balanced microfauna is to human health. I think in a short time we will start to see "probiotic" (I really hate that word) medical treatments on the rise.

Least Publishable Unit (LPU)

2007-10-03T14:50:00.000-07:00

I have been recently thinking about the Least Publishable Unit (LPU) theory in academia. Considering that I am now a month into my fourth year of my PhD and I have just submitted my first, first author research paper on my thesis work I am starting to panic slightly. I do have a previous first author research paper from undergrad research, 3 other non-first author papers, a submitted first author book chapter, and a Nature Microbial Reviews paper soon to be submitted. However, I would like to have another couple of first author papers in the next year and a half, so that I can graduate with a decent PhD career under my belt.

From my previous experience, the life sciences tend to publish more content less often, whereas computer scientists tend to publish very often with smaller amounts of research. Bioinformatics has overlap in both of these fields thus allowing different publishing rates depending on your research topic. For instance, if you are developing new tools, you would probably be publishing at a greater rate then if you are using bioinformatics to find some new biological interesting result (although this is certainly not always the case).

I would like to think that I have been focusing more on biology and thus my publishing has been slightly behind. However, I now have the skills and knowledge that I could quickly crank out a couple of useful tools that would probably be publishable (I feel like this would be somehow selling out, but maybe not).
Also, if I did go this route does it depend on how much effort was involved or rather how useful the tool would really be?

Recently, I wrote a script that would use gene synteny to make improved ortholog detection in two genomes. It is not overly complicated and uses previously developed tools (genome alignment and local alignment tools), but I think it is incredibly useful and improves upon the basic reciprocal best blast hit approach that is primarily in use. Although, my research is not focused on ortholog prediction and the tool was made so that I would not have to manually annotate 5500 bacteria genes (as part of a bacteria genome project); I have to wonder, "is it publishable?". I guess the only way to find out is by submission.

Hogue Strikes Back

2007-09-18T09:07:00.000-07:00

Just when I thought the BIND debate was finished Chris Hogue responds to a previous attack with "The other side of staying out of BIND" published recently in Nature Biotechnology.

Personally, I think both sides have a point. Busa's being that we can't fund multi million projects without reasonable returns, and Hogue's that long term funding of databases, such as BIND, is needed.

No matter what side of the debate you fall on you have to appreciate the academic mud slinging from both parties.

Is this my equivalent of reading tabloids about OJ or Paris?

Odd Ball Science

2007-09-10T13:39:00.000-07:00

My summer was a busy one that included traveling to Germany, Austria, and England (not bad for my first trip to Europe), plus a trip home to New Brunswick/Nova Scotia. My blog took the greatest hit as I tried to keep up with my research and manuscript writing, but I hope to get back to regular blogging again.

I was one of the thousands at ISMB 2007 in Vienna, Austria and I was presenting a poster on research that I hope to submit to Bioinformatics in the next week or so. Basically, I study genomic islands (large regions of horizontal gene transfer) in bacteria including their identification, their evolutionary origins and their relationship with virulence.

During one of the poster sessions I entered a nice discussion with someone about my research. After about 30 minutes of explaining my methods, background details, future plans, etc. I asked the standard question, "What do you study and is it related to my research in anyway?" and his chipper response was "Oh, no I don't study anything like this. I just like going around to these posters on oddball topics." Now I can take suggestions, criticism, or even indifference, but "odd ball" made it feel like my research was irrelevant; leaving me to puzzle his comment for the next couple of days.

Anyway, after a visit with the bacterial annotation group at Sanger Centre, where people knew what genomic islands were and actually took some interest in my research I was worrying much less about my "odd ball " research.

Open Source Conferences

2007-07-16T12:02:00.000-07:00

Last Thursday I found out via Jonathan Eisen's blog that there was a live stream of the Metagenomics 2007 conference. I tuned in over the next couple of days and got a chance to listen to some great presentations. Although, I didn't have any questions I had a couple of offers from people I knew attending that were willing to ask for me. How cool is that?!

I hope that more conferences start webcasting proceedings and/or making the recorded presentations freely available on the internet.

Regardless, there are a few things that are necessary to make a good webcast:
1) All presenters AND questioners must use microphones (this is a good idea regardless of webcasting)
2) High resolution video so that details of the presentation slides can be seen (this is usually a major problem)
3) A nice cross platform streaming media (no windows streaming media)
4) Good encoding so that the majority of internet users have enough bandwidth

How do you find science papers to read?

2007-06-05T14:05:00.000-07:00

I use a variety of methods to keep me updated on new papers that may be of interest to me, but I am always on the look out for a new tool or method that makes this job easier. Currently, I use the following methods (in order of relevance):

TOC email alert of certain journals (Nature, PLOS, EMBO, etc)
Pubcrawler
myNCBI updates
Papers mentioned in blogs
RSS feed of Connotea groups or similar users

Of course I still have to filter through tons of papers to find ones that I want to read and I often end up missing papers that are not caught by any of these methods. Ideally, it would be great if I had a tool that recorded what I read, and figured out what new articles I would probably be interested in (giving more weight to recently read papers). I think the information from the papers I have bookmarked and tagged in Connotea would be a great starting place for such a tool.

I wonder if anyone else has some tips or tricks that help them filter through the journal haystack?

Google Street View

2007-05-31T11:21:00.000-07:00

Every once in awhile I see a new computer application that makes me sit back and think "Wow!" (and no this isn't an advertisement for Vista). Google added a new feature to their Google Maps project called Street View. Basically, this lets you view panorama pictures at street level of any place in certain cities; currently restricted to San Francisco, Las Vegas, Denver, Miami, and New York.

The cool thing is that you can actually "walk" along the street, look around 360 degrees, and zoom in/out. I'm not sure how the privacy issues will work out for Google since you can clearly view people and license plates, but I can't wait until they expand to other cities (and countries).

Also, Google put out a nice (but kind of quirky) tutorial on YouTube.

Creation Museum

2007-05-28T12:02:00.000-07:00

Today is the grand opening for the Creation Museum located just outside Cincinnati, Kentucky. I read about it in a Globe and Mail news article and couldn't help myself from blogging about it.

I am still shocked whenever I hear the statistic that ~45% of Americans believe in Creationism. However, I really wonder if it is fully explained to the people being polled that this means that our planet is ~6000 years old, humans co-existed with dinosaurs, and that millions of species have gone extinct in that amount of time. Have all of these people really took the time to think about what their beliefs are and what science implications are rejected by them by their choice? If so, I would feel much better about the situation.

However, I do worry about the gap between the public and science increasing over time. How do we keep the general public up to date with technology and science when the speed that they are increasing at is so rapid? Does anyone else see this as a potential problem?

Climate Change Myths

2007-05-17T14:50:00.000-07:00

The recent surge of climate change in the media has not really interested me. Basically, I am a bit skeptical that the political interest will last long enough to really make the necessary changes, but deep down I do have some hope.

One of the big problems is getting the information to the public. I think there is a need for information between the high level one page news reports that don't provide any real science and the detailed scientific studies that most people can't and/or don't want to read.

Second, there is usually so much bias in reviews from both sides of the debate that the major facts get missed by the public. Instead, people are inundated with threats of massive storms and flooding or threats of economy collapse. Some people don't want the two major oppositions they just want some basic facts. I think this is similar to the Evolution vs Creationism debate and is one of the best points coming out of Francis Collins' book the Language of God.

A nice example of balancing the level of science and the point of views was published yesterday in the New Scientist. The article provides a "round-up of the 26 most common climate myths and misconceptions" and does so with a true effort in maintaining scientific clarity and an unbiased opinion.

Bioinformatics for biologists

2007-05-15T11:33:00.000-07:00

I just read the review "Bioinformatics Software for Biologists in the Genomics Era" by Kumar and Dudley. Basically, the authors outline the need for improved bioinformatics software that can be easily used by biologists. I completely agree with the authors, but by the time I was done reading the article I was somewhat annoyed. I think the overall problem I have is that they just keep reiterating that the people developing the tools need to make them more user friendly, without giving any real review of possible solutions or roadblocks that need to be overcome.
They state that:

command-line programs are bad, GUI's are good
being able to submit batch processes is good
documentation is good
clear, human readable results is good
tools that run on all operating systems is good
being able to connect multiple tools in a pipeline (with no programming required) is good

I think even the most amateur programmer is aware of these issues, so I am left wondering who the audience of the article is meant for? In addition they don't reference any of the current tools that are being developed to improve on the situation. In particular they propose:

"Within the context of the user-friendly software, we favor a solution where the existing implementations of computational methods can be incorporated “as is,” without requiring any significant effort from the developer of the program that is being incorporated. We refer to this approach as “Application Linking,” which is similar to “wrapping” (Spitznagel and Garlan, 2003). The aim of Application Linking is to allow existing user-friendly applications to seamlessly host third-party scripts and applications through its graphical interface, such that the user is abstracted from the intricate nuances of the hosted application’s non-visual execution requirements (e.g., process control, system I/O, and control files)."

Ummm.... I guess they haven't heard of Taverna and web services?

As a student who is writing one of these programs let me elaborate on what I think is the main problem. Scientific credit is based on publishing not on producing good tools. What does this mean to me as a PhD student? It means that the time spent on producing a robust web tool would be better spent on making additional tools or conducting more biological relevant based analyzes that will lead to more publishable papers. Am I proud of this? No. Especially since I have a strong interest in reducing programming redundancy, but for now it seems that I don't have much of a choice.

Directed Evolution

2007-05-10T10:33:00.000-07:00

Five days ago I was browsing one of my RSS feeds in Thunderbird that keeps me updated on what other students in the Bioinformatics Training Program are reading and bookmarking in Connotea. Usually, this is for academic purposes, but I came across a link by Ben Good about "What if the Singularity does NOT happen?"**. I took a quick glance at the article and was enticed immediately. I remember a colleague at work mentioning to me something about this book he was reading about the future of human development and technology. I messaged him on MSN and got the name of the book, "The Singularity Is Near" by Ray Kurzeil. I reserved the next copy available at my local library and two days later I am reading about a subject that I knew nothing about a week before.

Now, I should probably hold any reviews or opinions about the book until I am finished, but something in the first chapter bothered me. Kurzweil outlines in one section "The Six Epochs",

Physics and Chemistry
Biology
Brains
Technology
Merger of Technology
The Universe Wakes Up

and explains that,

"Evolution works through indirection: it creates a capability and then uses that capability to evolve the next stage."

This from the surface seems like a reasonable and interesting model, but implies that evolution has a direction. This may work for the last 3 epochs (based on technology), but has the evolution of intelligence (brains) really been inevitable?

Initially, I flat out decided "No", based on the fact that if we started another "Earth" there is no guarantee that intelligent life would evolve. This is due to the fact that evolution works by random occurrences that are selected for by the environment. However, after some more pondering (on my daily 1 hour bus commute), I thought that Kurzweil's theory may have some merit. Essentially, it is the idea that given enough time (approaching infinity) that the probability of intelligent life eventually evolving will reach 1. So instead of directed evolution, maybe we can say inevitable evolution?

I am still not entirely comfortable with this idea, but if I had wanted to increase my personal assurances I would have read a textbook!

**The singularity is an event in the near future where computers will become more intelligent then humans and will result in a drastic change in our society.

Retracting papers

2007-05-07T14:04:00.000-07:00

A correspondence article in EMBO Reports discusses how many scientific papers should be retracted. Not surprisingly it found that high impact journals had significantly more retractions compared to low-impact journals. However, they conclude that this is due to the increased readership of the high impact journals and not on the overall quality of the papers.

Open access and internet technology get a pat on the back by the authors when they summarize,

"...the positive relationship between visibility of research and post-publication scrutiny suggests that the technical and sociological progress in information dissemination—the internet, omnipresent electronic publishing and the open access initiative—inadvertently improves the self-correction of science by making scientific publications more visible and accessible".

Indeed, as I am getting ready to submit my first, first author paper, my greatest concern is not that someone will disagree with my findings, but rather that no one will.

Canadian Bioinformatics Workshop

2007-05-04T14:39:00.000-07:00

Hello Blogosphere! I told myself about a month ago that I would stop lurking around everyone else's blog and start contributing once I had a free afternoon. Well I am finally here!

A couple of days ago I was asked to be a TA for the upcoming Canadian Bioinformatics Workshop and I graciously accepted. I am really excited to get a chance to do some teaching. I have been lucky enough to obtain funding for all of my graduate career thus far, so I haven't been required to TA any courses before. It looks as if I will be leading a lecture on global genome alignment tools, which is great since I have been using one such tool called Mauve in my personal research (soon to be submitted). Luckily, I don't have to start from scratch since I get to use material from last year's presenter Mike Brudno, who is the creator of the LAGAN alignment tools. Surprisingly, he didn't include any other tools besides his own in his lecture last year. I guess it is natural to talk about what you know best. :)