Thursday, May 17, 2012

Sorry for Leaping Over 2011

I try to have at least one blog post a year, but I blinked and 2011 flew by without one :) I wasn't snoozing. It was an EPIC year. Here are the highlights:

  • I defended by dissertation and got my second doctorate, a PhD in Biomedical Informatics.
  • I became a dad!
  • I joined the workforce as research assistant professor at Vanderbilt

I am blessed and very thankful. I'm not complaining, but if I could ask for one thing, it would be to have more time for more applied geekery. I miss coding and server tinkering. I don't do it as much as before. Although, one can argue that raising a son and trying to keep his sponge brain adequately stimulated so he can learn to be a capable autonomous human is sort of like programming.

I am (a little bit) more active on Flickr, Tumblr, and Twitter. I do have a github account that I mostly use for private repositories. I hereby publicly pledge to write and share code there.

Thursday, October 14, 2010

My AwESOmE! Brother

Last night I opened my birthday gift from my brother. It was as if he packaged a vivid memory in high-def into a box that started playing the moment I saw what was inside it. Here's the memory:

Circa 1982 when I was 5 years old my parents gave me my first watch (that I can now remember). It was a Casio digital watch. I clearly remember the features it had: stop watch (with laps), timer, an alarm setting for every day of the week, a date alarm (that I had set to my parents' anniversary), multiple alarm jingles. The alarms jingles were such a part of my sonic memory that years later when I first heard Vivaldi's Spring movement, I remember thinking that that was the Thursday alarm (and not that the Thursday alarm was Vivaldi's Spring movement!). I even remember the two note sequences going higher in pitch that accompanied every transition using the "mode" button. The last mode (Timer) had a single high note. If you pressed "mode" one more time it would loop back to clock mode and all the notes would be played in reverse order from high to low pitch. Here's me with my first watch. My mom emailed me this picture this summer when I forgot their anniversary asking me if I remember the date I had programmed into this watch (see above).

First Watch

When the Casio Databank came out (circa 1984) I was over my first watch and lusting after the Casio Databank that had a built-in calculator and (in later models) the ability to store phone numbers. I asked my parents to get me one, but they said that my watch was perfectly fine and that I can get a Databank once the old watch stopped working. After what seemed like eternity, the old watch did in fact stop working and I got my first Databank! I was actually an honest child, and did not do anything to hasten the watch's demise. I subsequently had multiple iterations of the Databank until middle school. The last one was a slick ultra-thin one with touch keys.

Here is what my brother sent me. Thank you so much for a very unexpected trip to a beautiful childhood memory. I love you, man.

Casio Databank

On a somewhat related note, there's an essay by Corey Doctorow in this month's issue of Maker's magazine about why we romanticize and like to collect old pieces of technology (hint: not because they were better made then than now). I will post a link to it once it's available online. Update: Here is the link.

The standard explanation for the attractiveness of older technology is simply that They Made It Better In The Old Days. But this isn't necessarily or even usually true.

Friday, September 3, 2010

Web of Trust

Web of Trust

I am who you believe I am.

Ever since I (somewhat) learned how the GnuPG web of trust and private/public key crypto and key management systems work, I've been fascinated with this topic. I wish more people use them for their email and online identity management.

This week I set up an Ubuntu desktop at work. GnuPG integrates very well with Linux; however, there are also tools that work well with Windows such as gpg4win. Try installing gpg4win without Kleopatra. The Gnu Privacy Assistant (GPA) works well enough for me.

If you are interested in this subject here are some links. Corey Doctorow (of Boing Boing) romanticized key signing parties for me in Little Brother.

Friday, July 16, 2010

Wednesday, May 27, 2009

A novel information retrieval model for high-throughput molecular medicine modalities

Finally this paper in Cancer Informatics is indexed by PubMed. This paper describes the early "model formulation" phase of my PhD work. As I approach the end, and obtain more shareable results, I will include more Biomedical Informatics resources on this website.

More information about the paper:


Significant research has been devoted to predicting diagnosis, prognosis, and response to treatment using high-throughput assays. Rapid translation into clinical results hinges upon efficient access to up-to-date and high-quality molecular medicine modalities.We first explain why this goal is inadequately supported by existing databases and portals and then introduce a novel semantic indexing and information retrieval model for clinical bioinformatics. The formalism provides the means for indexing a variety of relevant objects (e.g. papers, algorithms, signatures, datasets) and includes a model of the research processes that creates and validates these objects in order to support their systematic presentation once retrieved.We test the applicability of the model by constructing proof-of-concept encodings and visual presentations of evidence and modalities in molecular profiling and prognosis of: (a) diffuse large B-cell lymphoma (DLBCL) and (b) breast cancer.

Friday, April 10, 2009

I am very inspired by Tyler's online pledge to lose 100 pounds. Visit his website and help him meet his goal. I wish I was brave enough to document my training/weight-loss goal.

Wednesday, April 8, 2009

Magnetic Movie

Magnetic Movie from Semiconductor on Vimeo.

The secret lives of invisible magnetic fields are revealed as chaotic ever-changing geometries . All action takes place around NASA's Space Sciences Laboratories, UC Berkeley, to recordings of space scientists describing their discoveries . Actual VLF audio recordings control the evolution of the fields as they delve into our inaudible surroundings, revealing recurrent ‘whistlers' produced by fleeting electrons . Are we observing a series of scientific experiments, the universe in flux, or a documentary of a fictional world?

More info here

An Animate Projects commission for Channel 4 in association with Arts Council England.

Wednesday, January 28, 2009


If I am to say one thing this month on my blog, I would praise the CakePHP Framework. I love it. The documentation leaves a lot to be desired, but for me the fun of coding in CakePHP is looking at the code and figuring out how well everything is put together and how intuitive the framework is.

Tuesday, September 16, 2008

How True, Dr. Asimov

I am now re-reading Isaac Asimov's The Gods Themselves published in 1972. The events in the book take place in 2100 AD. A maverick scientist is warning a resistant establishment about his discovery of the dangers of Inter-Universe Electron Pumping, a new found supply of abundant free and clean energy that had revolutionized humanity. He wanted it abandoned. This is his exchange with a senator in the International Congress.

"It is a mistake," [the senator] said, "to suppose that the public wants the environment protected or their lives saved and that they will be grateful to any idealist who will fight for such ends. What the public wants is their own individual comfort. We know that well enough from our experience with in the environmental crisis of the twentieth century. Once it was known that cigarettes increased the incidence of lung cancer, the obvious remedy was to stop smoking, but the desired remedy was a cigarette that did not encourage cancer. When it became clear that the internal combustion engine was polluting the atmosphere dangerously, the obvious remedy was to abandon such engines, and the desired remedy was to develop non-polluting engines."

Inter-Universe Electron Pumping is not a danger to humanity as MANBEARPIG is though :).

Wednesday, September 3, 2008

Freedom Fry — "Happy birthday to GNU"

I was introduced by my brother to Stephen Fry, an English humorist, actor, novelist and filmmaker. He presents a show on the BBC called Q.I. (Quite Interesting). Allan Davies, the "permanently installed guest", is one of the funniest comedians I've ever seen. Fry is featured in a short film that celebrates the 25th anniversary of the GNU operating system and talks about free software. Free as in "free speech", not "free beer". See link for video and more information.

Monday, September 1, 2008

Back from the Lake

This picture should sum it up. I miss it already.

My Labor Day Weekend

Thursday, August 28, 2008

Photographing the Science Museum

I took dozens of pictures at the Smithsonian National Museums (Air and Space, and Natural History) this summer when my parents were visiting. I enjoyed it so much that I nearly declared taking photographs in science museums an official hobby. I love taking my time at museums. Having a camera in my hand establishes that and gives me an excuse to linger and wander around. I came across this article about photographing the science museum (via Boing Boing) that gave me a lot of validation. I promise to put more pictures up from previous and (hopefully) future trips. Here's a link to the set.

Stone Age Stubborness