Category Archives: Tech

Tech

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.

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.

Budgeting and Spending Cash

(Disclosure — this post is about budgeting and mentions my Android app for doing the same, so take that as you will.)

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?

SpendingCash Posted to the Android Market

SpendingCash 0.3

SpendingCash 0.3


I posted my first for-pay app to the Android Market yesterday. It’s something I wrote because I couldn’t find anything like it. It’s very simple, and the point of it is to simply track one’s spending within weekly and monthly budgets.

I have tracked, using a spreadsheet, my disposable income for at least five years. I used to take out my weekly budget in cash every week, but now I work at home and so most of my spending is online via credit cards. I wanted something that would let me track how much of my budget I had left and tell me how long I had to stretch that money.

My first thought was to produce some sort of thin, credit-card-sized device that would do it, but I realized that would be too time consuming and expensive. Instead, I wrote this simple Android app. After all, I pretty much have my phone with me at all times, so I’d never be far from entering my expenditures.

I hope that there are people out there that have a similar need and are willing to pay $1 to have that need met. The first 24 hours have not been promising, but in the end I have an app that I like, and I guess if people eventually try it and decide they like it as well, it’ll be a little extra spending cash for me.

I made a simple site for the app: SpendingCash

Would this sort of thing interest you? Why or why not? Do you think it’s worth $1?