I scaled up the rabbit heart a bit and flattened the base. It prints much more nicely now.

This is a model I have seen on my computer screen over and over since 2002. Now I can print it and hold it in my hand! Look for me at HRS next week if you want one.

Here’s a video of it printing:

Thunderbird to the rescue!

I use Mozilla Thunderbird for my email for mostly the same reason I still use FireFox to browse the web: there’s a plugin for almost anything I want to do. Also, in Linux it’s easy to use a CUPS-PDF virtual printer to print to PDF. Combining this with the attachment extractor Thunderbird plugin allows me to dump all of the attachments and emails to files on my hard drive in just a few clicks.

I have ‘Invoices’ and ‘Receipts’ email folders that need to be dumped, so I just go into each folder, select all messages, print them using CUPS-PDF, and then right-click and tell AttachmentExtractor to dump any attachments as well. Done, in about 5 minutes. Trying to do this manually would take countless hours, meaning in reality that I would just never do it, and if my taxes were audited, it would be a total nightmare.

Hopefully if you have this same problem google + this post will help you out. Enjoy!

The article is entitled Models of cardiac cell [sic].

Kudos to Drs. Fenton and Cherry for the excellent article, it looks like it was quite a lot of work to put together!

Following some instructions here and using the patch provided here (from this thread), I was finally able to get it working.

Here’s the resulting package.

python-qwt5-qt4_510dfsg-1ubuntu1_amd64

Steps to build:

Create some directory where you want to build this. Change to that directory. Then…

sudo apt-get build-dep python-qwt5-qt4

(installs dependencies for building)


sudo apt-get source python-qwt5-qt4


This should download the package source. Download the patch from the comment I linked to above, then change into the directory and patch the files. You may have to change the directory ownership so that your user can write to it (sudo chown -R yourusername .)


patch -p0 < ~/Inbox/pyqwt-final.diff

(of course your patch may be located in a different location)

Per the GPLv2, here's the patched source I used to build the .deb file (note -- I think you can just download this instead of patching it yourself).

brocks_patched_pywqt5_src.tar.bz2

Once it's patched, rebuild it with:

sudo dpkg-buildpackage -rfakeroot -uc -b


Go get a cup of coffee or whatever, it's a fairly involved build. When it's done, in the directory above you should find your .deb packages. A simple:

sudo dpkg -i python-qwt5-qt4_5.1.0.dfsg-2_amd64.deb

(replace the filename with whatever yours is, of course)

will install it for you. Hope this is helpful for someone, as I wasted a few hours trying to install this all from source and so on.

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.

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.

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.

One thing that is asked a lot of people graduating from anything is what they plan to do next. I have been waiting for some time to be able to answer that question, and now I can.

The lab of which I have been a member since late fall of 2002, the Trayanova lab is one of (if not the) the leading groups in the world when it comes to cardiac electrophysiology and mechanics research. I would guess that the lab as a whole has probably run an order of magnitude more simulations, at a minimum, than the next closest group. A lot of my time and effort as a graduate student went into improvement of the tools used for generating and running models, and I have nearly seven years of experience setting up, running, and analyzing simulations.

The lab does very interesting things, and cutting-edge research. Almost every new study is accompanied by tool and methodological development. However, there are a lot of practical applications that are never explored by the lab, because they don’t necessarily constitute scientific discovery of the kind valued in academia.

It takes a long time to train people to use simulation software developed in an academic research environment. It is extremely powerful, and has far more options available than any one user will ever use. This is acceptable for graduate students that will be spending years in the lab, and will often be digging in the guts of the code and adding their own features. It’s not acceptable for, say, industrial or academic wet-lab researchers that just want to run some simulations and figure something out.

That’s where CardioSolv comes in. CardioSolv, LLC, is a new cardiac simulation and services company. Its aim is to commercialize cardiac simulation, and make it easy for new users to rapidly produce scientifically valid and useful results. To that end, we are building a web interface that will by default handle most of the difficult choices for users, while still allowing them to specify detailed parameters if necessary.

My role in this company is Vice President of Operations. I’ll be managing the day-to-day operations of the company, interacting with customers, and guiding product development. My hope is that we can bring our technology and our discoveries out of academia, and into the drug and device development markets, with the ultimate goal of improving patients’ safety and quality of life.

Today, while doing this, I noticed that there’s an “Export comments to Data File” option in the Comments menu. “Hmm,” I thought, “I wonder how easy it would be to read this data file?” It turns out that it’s just some ASCII text with a bunch of (to me) useless information, and the highlighted comments in parseable “Contents([highlighted text here])” containers.

I wrote a quick and dirty Perl script that pulls the comments into a text file. I can then just copy and paste that file into FreeMind, and it creates all of the leaves for me. This will save me hours carpal-tunnel-syndrome-inducing mousing and frustration. The perl script, for your perusal (improvements welcome) is available here: extract_comments.pl.

Kindly Let me know if you get any use out of this, and if you find any parsing bugs. It’s in the public domain.