Inforbiomatica

Alright, it’s been a while since I’ve posted. I’ve been up to my ears in a number of things. One, a group of six of us biomedical informatics people from across the nation (David Kane, Mike McCormick, Ethan Cerami, Karl Kuhlmann, Jeff Byrd and I) finished the first draft of a paper on agile methods in biomedical software development. We’re currently shopping it around to different journals, which thus far has been about what I expected, that is, no one has any idea what to do with us. As I’ve noted before, discussion of these matters is nearly absent in our community, at least in public. Hopefully our paper finds a home, both so it was worth the effort and because so, maybe, it helps start conversation.

Speaking of conversation, I’ll be attending the BRIITE conference in San Diego this November, at which I will try and propose a breakout session on software development practices, even though it will be a bit off topic.

I have also been working with caBIG, which has been a great opportunity to get out and meet other biomedical informatics people, learn about grid technology, etc. Shortly I’ll be co-leading the caBIG Architecture Workspace Best Practices SIG, which should be fun.

In other paper news, I have been writing a paper with Sean Martin and Ted Liefeld on the impact of LSID on biomedical informatics data. Everything I know about LSIDs I learned from Sean, Bob Robbins, Ted and others during many conversations as part of the caBIG Identifiers SIG. I never knew identifiers could be such a thorny problem, I guess the true source of the thorniness is the distributed nature of the data being identified. That would make a good blog entry some day, actually.

During the latter two quarters of the 2004-2005 academic year at Northwestern, I took/sat in on several business classes at the Kellogg school. I had always harbored the prejudice that business school classes had no content, and were all about networking. However, I was happily surprised to find out that I was just being small-minded. Although I don’t think I will ever pay the big bucks/spend the big chunk of time for the MBA, being exposed to the issues discussed in those classes was an important learning experience for me.

Finally, I went to the Agile 2005 conference this year and presented an experience report on tracking progress and estimation in software projects. We’re still working on porting the tool we’ve developed for issue tracking from ColdFusion (blech) to Ruby/Rails, but when it’s ready you can check it out at http://rhythm.sourceforge.net. This year I went with my two immediate coworkers, John and Rhett, and it was a great experience to go with them, to hear about their experiences there, and reinforce what we’ve been trying to do for the last few years. I also got to catch up with a couple people from ThoughtWorks days.