Category Archives: Tools of the Trade

Tools of the Trade

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.

My PhD and What Comes Next

If you’ve been following my Twitter or Facebook accounts, you’ll already know that I successfully defended my doctoral dissertation this past Wednesday. I now (essentially, absent the completion of some clerical things) have my PhD from Johns Hopkins University.

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.

Extracting text highlighted with Acrobat Pro

As mentioned here and here, I typically do my reading and note-taking-on of academic papers in Acrobat Pro these days. I then typically record my comments in a FreeMind mind map. Until today I’d been creating a content summary in Acrobat, highlighting, and then dragging and dropping each comment individually into the mind map.

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.

LaTeX Word Count

I’m working on my graduate thesis in the LaTeX document mark-up format, and trying to apply Anthony Burgess’ Martini Method. Basically, set a certain desired word count and let yourself relax after you’ve achieved that word count every day. I started off pretty well with this method, but the next day my wife Amanda went into labor, and my productivity has basically been a train wreck ever since.

I’m getting back on the horse.

Anyway, it’s a little tricky to apply the Martini Method when using LaTeX — as a markup language a bit like HTML, it’s full of special words, symbols, characters and whatnot that are not actually part of what you’re writing. A simple Emacs word count will not do the trick. Much as I’d love to count all of those extra words, the point here is to produce a certain volume of output and that would miss the point. Plus, it’s dishonest. There exists a PERL script that will parse LaTeX and count the non-special words. However, someone’s gone even a step further and made a nice web interface for it, with color coding and everything. That interface is here, apparently hosted by one Einar Andreas Rødland in Norway.

So far, it’s working quite well for me. Unfortunately, it just informed me that I’m not quite to my desired word count yet. More writing!

Oh How I Love Coffee

Coffee, or Caffeine in general… ah… we’ve had a tumultuous relationship. I remember my first real taste of coffee — blended with hot cocoa on a cold Boy Scout camp-out during a Michigan winter. Then there were the several times I mistakenly thought Mountain Dew would make a good breakfast in high school. (That’s a negative, by the way. It invariably resulted in a stomach ache.)

In college, especially freshman and sophomore years, I tested the limits of both sleep deprivation and coffee consumption. It was possible to get a 20 oz cup of coffee at the cafeteria for something like $1.25, and one refill was free on the same day with the original receipt. There were days when I had 40 or 60 oz of cheap, cafeteria coffee with chicory. Something magic happened when I had consumed that much caffeine — I wrote code for my computer science classes that worked flawlessly, yet it took me hours to comprehend what I had written the next day. The mechanism underlying this increased ability seemed to be a greater “stack depth”, meaning that I could keep more things in short-term memory simultaneously. This allowed me to reliably track a greater number of programming constructs at once, requiring less checking-back of variable names and so forth.

I quit that level of consumption, cold turkey. I wasn’t doing it all of the time, and fortunately my withdrawal symptoms were limited to minor headaches and tiredness. After quitting I felt much better. The body can only take that kind of abuse for so long. I eventually went back. I love coffee, and decaf just isn’t the same. However, I’ve never reached that level of consumption again. Subsequent periods of abstinence have not yielded the same improvement in quality of life as that first time quitting, probably because I haven’t reached a level of use/abuse that negatively impacted how I felt.

Generally, I limit myself to two to three servings a day. That level has been found to be harmless, and maybe even beneficial. However, I have just over a week left in Baltimore before I go to New Orleans for Amanda’s graduation from medical school (w00t!), and I have an awful lot to do. I’m giving myself free license to however much coffee and caffeine I want, and my productivity has been skyrocketing.

I recognize that this level of consumption is not sustainable, and that if I keep it up, I’ll surely pay for it. But wow, does it ever feel awesome for now. If I experience any dramatic shifts in mental or physical state as a result of my use, I’ll tone it down a bit. But for now, I’m just enjoying it and getting a lot done.

This post brought to you by five cups of coffee.