I found this neat video on YouTube today when looking at some related videos to my own. This shows how an ectopic focus in the heart can develop into a spiral wave.

As the models used in our lab become larger both in resolution (more detail) and gross size (bigger pieces of tissue), the time and effort required to visualize and otherwise check results increase. With the largest model currently used in the lab (mine), one short simulation produces 2.0 GB of uncompressed data. Compression gets it down to about 500 MB or so. That still means that — just to make sure the simulation ran correctly — I have to download 500 MB of data, load my model into a viewer of some kind, and load and view the data. This is not acceptable, especially since even loading the data requires a machine with significant graphical power and a large hard drive.

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.

I’m planning on doing some more advanced videoblogging in the future, including screencasting and perhaps presentations. As such, I decided to give iMovie a try. Combined with an iSight, it’s a beautiful thing, and much easier to use than I expected.

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

Have you noticed that everything is named in CamelCase these days? Anyway…

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.

This just warms the cockles of my heart: