Category Archives: Linux

Linux

First CardioSolv Simulation Manager Demo

Today I’m really excited to finally show you something that’s been in the works, both in implementation and in the planning stages, for a long time. The CardioSolv Simulation Manager.

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.

Continue reading →

Quoted in another article on CardioSolv

The whole article is here.

The HPC service lets the small, five-employee company do the heavy lifting that would otherwise cost a fortune. “With what we could purchase out of pocket, we’d have to bootstrap very slowly, or look for VC [venture capital] funding,” said Dr. Brock Tice, the vice president of operations at Cardiosolv, a privately funded medical research firm. Instead, Tice uses a new HPC on-demand service from Penguin Computing called Penguin on Demand.

…

While Cardiosolv has its own small cluster on the premises for calculations, Tice estimates the resources he rents from Penguin would probably cost $500,000 to build, and other cloud options weren’t suitable.

“We can’t use [Amazon’s Elastic Compute Cloud] EC2, since there’s a lot of latency between the nodes,” he said.

Story on CardioSolv in The Register today

Here’s my two bits from the story:

Brock Tice is one of those scientists. As vp of operations at the Baltimore, Maryland-based CardioSolv, he works to model, yes, the heart – simulating its mechanical and electrical activity. And though he can run some simulations on Amazon’s cloud – or on individual local machines – more complex models require HPC. “We’re [sic] tried on Amazon and it just doesn’t scale,” he tells The Reg. “We can run on single EC2 instances, but if we need to scale up to a dog or human heart, it’s just impossible.

“The connections between Amazon’s machines are Gigabit Ethernet and they’re shared. If you fire up 10 machines and you want to run them like a cluster, some might be in the same rack, and others might be halfway across the data center, five or six switches away.”

You can find the full story here.

JustSit 0.2.2 is Out

Just uploaded, you can download the APK here. I think I’m going to release this one on the Android Market as well.

I fixed an outstanding screen rotation bug, made it so that vibrate mode applies to both the bell and the ringtone, and upgraded to the Android 1.5 (Cupcake) API.

Back to Windows

After many years of using and promoting Linux, and more recently the Mac, I’m giving up the fight and going back to using Windows. Perhaps ‘back’ is the wrong word, since I’ll be switching to Vista. I’ve gotten tired of not having the device drivers I need, having to research every accessory I buy to see whether it will work on the Mac or in Linux, futzing for hours with arcane commands and configuration files just to get my webcam to take a picture.

I’m also sick of missing out on current events, like the Conficker worm, which somehow made the top story on Google News last night. Top story! I was feeling really left out. Once I have windows installed on my Mac Pro, though, I should be able to join the Conficker party in no time.

Sure, it’ll be difficult to do my work, since it relies largely on UNIX-based software, but hey, that’s what Cygwin is for, right? And PuTTY. Got any recommended software for me? It’s been a while since I was a full-time Windows user. A Quicksilver replacement would be particularly welcome. And send me a copy of Conficker if you have it — thanks.