Monthly Archives: September 2007

PHPMyGTD has a Sourceforge project page

For those interested in checking out my (alpha) GTD system, I’ve created a Sourceforge project for it. The project page is here. You can check it out and/or browse the source with SVN under the “Code” menu. At some point I’ll make a webpage for it.

You can check it out using Subversion with this command:

svn co https://phpmygtd.svn.sourceforge.net/svnroot/phpmygtd/

I need to add the database schemas to it at some point.

The database schema set-up and basic installation instructions have been added.

Watching EP Procedures

Over the last few days, thanks to some kind people in the Cardiology department, I had the opportunity to watch electrophysiology studies (EP studies). There are various guidelines for when this invasive procedure is warranted, but basically it is done when someone has an electrical problem with their heart, and it cannot be either (a) diagnosed or (b) fixed without seeing precisely what’s going on, and possibly taking action while in there.

What we do in our lab is somewhat abstracted from the human heart. We use computer models. Because human hearts are so large, we use mostly rabbit models and smaller geometries suited to whatever problem we’re studying. It’s also hard (impossible? Maybe if MRI gets a lot faster we can do it) to get good geometry from a healthy human heart, for obvious ethical reasons. Finally, the biggest advantage of computer modeling is that we can see what is going on everywhere within the tissue, at all times, down to the level of ion channel gates. We typically look at trans-membrane voltage, and at smallish reentrant circuits. Even our larger reentrant circuits are typically limited to the atria or the ventricles, but do not involve both.

In EP studies, the patient has (from what I’ve seen) 1-4 or maybe 5 catheters fed into the heart through the veins. These leads have anywhere from 2-5 bi-polar electrodes on them, capable of monitoring extracellular electrograms (as opposed to trans-membrane). Additionally, the patients have many electrodes positioned on their skin to monitor the surface ECG (or EKG for our Germanic friends). Cardiologists can glean an enormous amount of information from the surface leads alone. I’m not really any good at that, though I’m a lot better than I was three days ago. For a good overview, see the ECG Learning Center, always linked in my right sidebar on the blog. Whereas we look at reentries in smaller parts of the heart, often patients suffer from macro-reentry, such as occurs when an accessory pathway results in “V-to-A” (ventricle(s) to atri(um/a)) conduction, something that should basically never happen under normal conditions.

Once the leads are all placed using a fluoroscope (and a good imagination — you can’t see the heart on the fluoro, just the leads) the sterile scrubs and gloves come off and everything moves over to the computers. From there, it’s possible to monitor all of the leads, signals scrolling by, and to administer a wide range of pacing protocols. It’s kind of odd. It goes from a surgery to a more abstract experiment-like environment, where the main focus is the set of data on-screen.

I’ll talk more about what happens next in the next few posts.

What is Scientific Computing?

My friend Rob has just written a post about trying to describe his field. He distinguishes between the casual “so what are you studying” and true interest in your research field. The difference between the conversation-halting, “Parallel scalability for algebraic multigrid methods applied to symmetric positive definite systems that arise from computational biological problems,” and the better-thought out

Abstracting further, [the products of] my field can solve differential equations, which means that it can solve most equations produced by physics. The solutions produced by these calculators describe how the world works. When ever you see a weather forecast, you’re seeing the output of these types of these advanced calculators.

is vast. This goes along with something I discussed with Amanda the other day. It doesn’t matter what field you’re writing for – the message should never be hidden behind words. He actually gives several levels of abstraction, a useful set of responses for tailoring your response to your audience.