Great primer on the why and how of genome sequencing

I’m often asked to explain the human genome project, or sequencing in general when discussing what I do with those outside of the field.  I’d like to think I’m not bad at explaining it in lay terms, either.

On the other hand, there’s now a video that does a VERY good job of this, written by Mark J. Kiel, from the University of Michigan.  The illustrations are a great mix of simplicity and detail, that captures the essence of the process while not omitting the actual science.  It’s pretty impressive and well worth the 5 minutes it takes to watch it. You can also catch the full thing on Youtube:


Ok, you’ll never guess what I came across today!  Or, well, if you’ve read the topic, you might…  I found an (apparently) owner-less Wacom tablet.  That probably doesn’t mean much to most people, but in my experience, you don’t just find Wacom tablets lying around gathering dust… unless they’re broken of course.

So, while I was cleaning up the desk next to mine for a rotation student, I discovered it just sitting there.  I’d never seen one without a fancy engineering template taped on top, so I assumed it was either broken or missing a piece or relegated to its dust gathering status for some equally horrific disfigurement.  I cheerfully set it aside, thinking I’d just plug it in later to see why it was discarded.

Well, much to my surprise, the thing works!   If you’ve never seen a Wacom tablet before, it’s the king of mice, the grand father of touch pads, the cats pijamas.  Holy cow are they cool.  I plugged it in and started doodling with it immediately in inkscape.  Seriously, that is a nice piece of hardware.

I have the feeling that, if no one claims it, I’ll be doing some serious doodling for all of my projects – and with my plans for doing visualization work, this could be the start of some really fun images.  While I’m still feeling pumped about it, I’ll challenge myself to post something drawn with it for next week…  in 7 days I should be able to do something neat, otherwise I am clearly unworthy of such a lucky find!

Periodic table of visualization

I’m not actually impressed with this, but I’m spending a lot of time thinking about visualization these days and came across this on twitter, so I thought I’d toss this out there:

A Periodic table of Visualization

I’m kinda disappointed in the end result, but the concept is neat.  (And yes, the chemist in me is screaming about the wedging of their figure into a the periodic table: the blocks mean nothing in this table! A gross misuse of the format!) Anyhow, it’s an interesting place to start in your quest for better visualization.

Simple SNP Visualization…

Before I disappear for AGBT, I thought I’d finally get around to writing a quick post about some of the visualization work I’ve done.  In fact, this is my first shot at interactive visualization – and while I’m not necessarily thrilled with it, it is a neat first try.

The data comes from my Variation Database (which has been accepted for publication – I’ll be submitting the final revisions today), and was an attempt to make an interactive method of searching through files that can be in the hundreds of Mb long, without going insane.  The db does produce smaller summary files – which can save your mind from the pit of despair of reading a 300Mb file – but I thought there has to be a better way.

And so there is!  In the live version (for which I have yet to make an example file, but I will do that after AGBT), you can scroll forward and backwards through the “tunnel” of variants, so that it can be obvious as to which libraries variants are found in – or not.  There are some neat examples where you’ll see two polymorphisms side by side, but NEVER in the same libraries.  Neat to be able to pick out stuff like that at a glance.

If you go to the location on the web where this script resides (for now), you’ll see options for filtering on the side, but in the name of providing an explanation, I’ll just give you the static image:

Semi-circular visualization of SNVs.

Click on the image to see it in full size.

Obviously, it’s just a simple first pass – but hey, I think there’s lots of room for improvement, and likely lots of room for innovation.  If only I could find the time to do this stuff more often!

If you’re interested, I stared a wiki page for it as part of the VSRAP (here), and the code is also available from the VSRAP svn (here), and of course, all of my code is open source, so feel free to play with it, adapt it for your own, or otherwise.

And now, I have some work to do before AGBT…  see you there!  (or, if you’re not there, you can pretend you’re there by reading my notes!)  Cheers!

Ode to Expedited Delay

28 hours after my new laptop was supposed to have left china, it turns out it’s still there – and has left again! I’m not sure how many times it has to leave, but it certainly was unexpected to me to see it sit in china that long after UPS claimed it had left.

In any case, to tide you over till I have something else to write (and to keep myself from hitting refresh on the UPS screen another 1000 times) I thought I’d provide a fantastic “video” of Beethoven’s 9th symphony, 2nd movement. I often listen to classical music while working, but this visualisation is so compelling, I’ve been unable to drag myself away from it. It’s very different than most other pieces I’ve seen visualised in this manner, which is just another way that you can see Beethoven’s genius in action. If you’d like to see other videos, the same user has a whole bunch of them posted – and apparently sells them as videos for $1 each.

Actually, it’s given me a few genome visualisation ideas as well – but I’ll talk more about that soon. I need to finish the revisions for my paper first. Then I’ll talk about what I worked on over the holidays, which might be a good starting point for some future work. whee!