MadMode

Dan Connolly's tinkering lab notebook

A new firehose to drink from: bioinformatics

After 15 years working on web standards at W3C, the title of my new position is Biomedical Informatics Software Engineer. I know what the Software Engineer part means; I have been doing that since my first job out of school in 1990. But the Biomedical Informatics part I'll have to learn, real quick.


A couple years ago, I started prospecting for some supplemental consulting work; in From KC to MIT and back again, I wrote:

My family is here in KC but my work is at MIT and Silicon Valley and Vancouver and Edinburgh and Beijing... mostly over the Internet, supplemented by travel schedule of about one trip a month. After working remotely for 10 years, I'm interested to mix in a little more local collaboration.
Little did I know that a year later, the recession would catch up to W3C and my position at MIT would be reduced to half time and that supplemental consulting would become essential. The first gig I found was more HTML 5 work, with funding from Adobe. Then something pretty different came up: working with Science Commons, on data integration to support research on autoimmune diseases.

The bulk of the work was just decoding data from the protein databank and such and using semantic web techniques to normalize it; pretty tedious ETL stuff, except that I had to learn all about genetics and the human leukocyte antigen (HLA) while I was at it. I could just barely keep up with the presentations at the NAID bioinformatics summit.

In the last few weeks of the project I got to do a 3D visualization demo.
Image:Viz-screenshot.png

After this pilot project, we wrote a proposal for follow-on work, and it got positive technical reviews, but   somehow the funding didn't materialize.

But now I had a new keyword to use when looking for work: bioinformatics. That's how I found this new position, just a few miles from my home, in the department of biostatistics at the University of Kansas Medical center. They're putting together an informatics team to round out their qualifications for a Clinical and Translational Science Award (CTSA), and I'm excited to be part of it.