It’s currently non-trivial to show movies in papers, so instead we do time-lapse type things called activation maps. These show the activation times as a series of lines (‘isochrones’ or ‘isochronal lines’, meaning that all of the points on the line are activated at the same time) or bands of color representing the same thing. We can extend this to also show repolarization times, or non-sequential data such as action potential duration maps and dominant frequency maps.

Here’s a sample activation map of a wave moving across a sheet from right to left:

Activation Map Right to Left

And here’s one of a spiral (this with 20ms isochrones):

Activation Map of a Spiral Wave

To give you an idea of the correspondence between an activation map and a movie of the simulation, here’s a movie of that spiral:
Spiral Wave

There’s a lot more to this — for instance, deciding when a cell has activated or repolarized, and back-end processing. We use a program I wrote that does the analysis in parallel, making it rather quick to analyze even huge datasets, provided you have the computing power.

If you have any questions about the process I’d be happy to answer them here or on the CardioSolv post.

Running cardiac electrophysiology (and mechanics) simulations has traditionally been really complicated. It involved learning a bunch of UNIX command-line tricks, dealing with queuing systems and their associated script files, and so on. Furthermore, there are many, many options in a sophisticated cardiac simulator, and the novice user (and even the expert) can easily get lost in all of the choices.

We’ve taken years of experience setting up, running, and analyzing simulations to build a really cool (excuse my excitement) web interface that handles all of the dirty work, and guides the user through the important choices when running simulations.

The video below is my first demo. In it, I demonstrate how to create a plane wave moving across a sheet of tissue, then create a spiral wave, all from the web interface.

Note: If you’d like to view the high-definition version, I suggest you either click through to YouTube or expand the video to full-screen mode.

The post about it on the company blog is here, with contact info and all of that.

There are other ways to visualize our data. A little while ago (two years?), our programmers Rob and Umar put together an off-screen renderer for the IBVRE project. It’s based on VTK and coded in Python. It simply loads the model with views from all 6 sides, maps the data on to the surface, and then writes an image file.

I spent 12 hours Saturday resurrecting this software and tweaking it for my own needs. Now it just loads one view of my model, efficiently steps through a specified number of time steps (it did this very very inefficiently before), writing them all to image files, and then exits. I run this on the cluster with a script that joins all of the images into a movie, and then emails them to me.

I currently have the cluster email me when a job is done. I also have mail filters that forward these messages to my phone. However, I can now do better. I have integrated the rendering program with my cluster run scripts, such that the following happens. When a simulation is finished, the visualization program is run and dumps images of all of the time steps. They are then joined to make a movie, emailed to me, and emailed directly to my phone. Thus, when the simulation is finished, I not only get an email notification, but I can review the video right on my phone.

If you’re not a geeky type, this may not impress you. To me, it is the very apex of cool. Enough so that it drove me to stay at work for nearly 13 hours on a Saturday. Here’s a sample video:

Now, instead of downloading 500 MB or more to a high-powered workstation (or let it limp on my laptop) to check the outcome of a simulation, I can have a 1 to 4 MB video automatically sent to my mobile phone and watch it wherever I am.

Here it is (the subject matter is not serious) with an homage to Ze Frank:

I’ve had a couple of conversations with Dr. Rachel Karchin here at the ICM regarding Open Access scientific publishing, and PLoS specifically. Last week, she forwarded an email to me regarding PubCasts on SciVee. (Example here.)

A “PubCast” is basically the same thing as a “SlideCast“. (Have you noticed that everything is named with “Cast” at the end lately, all spawned from the term “Broadcast” and made popular by “PodCast”?) Let’s start with a SlideCast. The idea with a SlideCast is that presentations are not composed merely of speaking or merely of slides. Many people make their presentations in such a way that the slides stand on their own, but these are typically awful presentations. They’re just slide-formatted outline notes. A good presentation requires the visuals and spoken commentary. In a SlideCast, slides with their various animations and transitions are shown with an audio narration by the presenter. PubCasts go one step further and actually include video of the presenter speaking along with the slides. They also preferably include the paper. I think the video is probably not necessary, unless it’s video of the person presenting in front of the actual slides, but that requires green screening or extremely high quality video (for the slides to be readable), both not worth the hassle.

On the whole, I think PubCasts are an excellent idea. A proper scientific presentation should get the audience engaged by getting them emotionally involved, making them see why they should be interested, while a paper gives all of the gory details. In this way, you get both together. How often do you have the paper handy to follow along when watching a scientific presentation? In my experience, pretty much never. People usually present the stuff they’re working on, not the stuff they’ve published (background excepted).

Unfortunately, I don’t have any true Open Access papers yet. My paper that’s supposed to come out next month will not be Open Access, as the fee from the publisher for it was outrageous, and I couldn’t really justify it to my advisor. Nonetheless, I already have a slide deck put together for the paper, and have presented it, so in the near future I’m planning to do a SlideCast of it and post it here on the blog.

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