It took a phone call to Antec to find what I needed, and even knowing what’s on the page, I can’t find it with Google, so here it is:

Hopefully that’ll save someone else the trouble I went through.

ADDENDUM: The commentor is correct. It has been moved. If you call Antec and find the new location please post it here.

This year I finally started keeping track of lessons learned, not on a per-incident basis, but in the form of ‘principles to live by’ — things I’ve noticed forming a pattern over time. I’ll preface this list by saying that these principles apply to me specifically — I won’t say that they’re appropriate for everyone. However, they might give you something to think about in terms of your own best practices. None of this is original either, but out of all of the advice I’ve read, these things have really worked for me. Without further ado:

Brock’s Principles to Live By Based on Personal Experience

• Don’t exercise until done with work for the day
• Don’t drink alcohol until done with work for the day – yes that includes irish cream in the coffee and a beer if you go out to lunch with people and they’re having beers.
• Exercise regularly, both strength and aerobic
• Get enough sleep
• Limit caffeine consumption to the equivalent of 2-3 cups of coffee per day, and none after lunch
• Eat enough fiber
• Plan your day
• Don’t plan to do any work while watching an infant/toddler
• Plan to clean/tidy/play while watching an infant/toddler
• Limit work hours – work expands to fill the allotted time
• Batch
• Emphasize the positive, deemphasize the negative
• Don’t complain
• Know your goals
• Say No
• Don’t buy it if you can rent it, unless you’re going to use it regularly
• Don’t keep it if you’re not going to use it regularly or unless it’s very hard to get. Give it away or sell it.
• Give people the benefit of the doubt
• Clean environment – clean mind
• Keep an accountability partner
• Where possible, never leave any preparation to the day of an event — things always seem to pop up that prevent last-minute prep
• Avoid instant messaging. It makes it too easy for conversations to drag on. Use email for asynchronous and phone for synchronous conversation.
• Act professional in business, and give the best you can at the fairest price you can. It will pay itself back quickly and repeatedly.
• Wait for the upgrade. You don’t have the time or money to be an early adopter anymore.
• Pack lighter. You can almost always buy something you need there.

Much of this learning has been done through and inspired by the “Think Try Learn” / Edison philosophy/platform, now at v1.0. I’ve learned some other, more specific things through that site, including how to really increase my strength and musculature quickly, and how true the “what gets measured gets managed” mantra is.

What have you learned this year? Do you have any “principles to live by”?

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.

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.

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.

How do you budget your spending?

Apparently my way of doing it is strange –here’s what I do. I know my annual salary, and I know my paycheck amounts (after taxes), and all of the other relevant income numbers. I also know my recurring expenses — the mortgage, food, utilities, day care, and so on. (I break those into needs and wants as well, but it’s not really important for this post.) For the sake of simplicity, you can assume that I include my savings, Roth IRA contributions, etc, in the tally of recurring ‘expenses’.

When I subtract my recurring expenses from my income, I get my discretionary income. I have it in annual, monthly, weekly, and per-paycheck increments.

How do I budget that part out? Apparently the normal way to do that is to plan how much to spend on this and that, and then try to stick with it. Track expenses in each category meticulously, make sure everything adds up. That’s too much overhead, and I’ll never stick to it. Instead, I say to myself, “Self, you’ve got $200 to spend and you’ve got to make it last a week. If you run out before then, you’re out of luck.” The relevant numbers, then, are how much time I have left in my budget period, and how much money I have to cover it. I trust myself to look at my wallet and, based on those numbers, decide whether I can afford to go out to eat tonight, or order that book or electronic gizmo.

That worked when I spent most of my money in person. However, these days I spend most of my discretionary funds online, via a credit card. I’m not keen to use something like Mint.com (imagine if someone hacked Mint.com — they’d have all of your login information for all of your accounts — a single point of failure), and I don’t think it would let me do what I need to do anyway. One option is to have an amount of cash equal to my weekly budget, and set any aside that I’ve spent online. Then I could take it back out and supplement it from my bank account when my budget rolled over. That’s what I did for a while.

A second option is to keep a little notebook and tally expenses. I think that’s actually a great option, but I don’t like carrying a notebook and pen with me. I would prefer not to carry anything extra.

However, I am always carrying my Android phone. As such, I decided to write a little program for it that tracks my monthly and weekly budgets, and allows me to subtract from them by spending an arbitrary amount. On the weekly and monthly budget reset dates it resets and optionally rolls over any remaining amounts or amounts over-budget (as negative amounts).

So far it doesn’t seem to be a very popular app. It was suggested to me that that was because nobody budgets this way. Is it so strange? How do you budget?