I'm a bioinformatics programmer/manager, currently interested in computational proteomics. My recent work has focused on making protein identification and quantification approachable to researcher-physicians who might not otherwise have access to or understanding of these powerful technologies.

I believe that, to be successful, bioinformatics software must possess three qualities in combination:

  • ‡ Statistically-sound Algorithms
  • ‡ Facile User Interfaces
  • ‡ Performance

Good algorithms are useless if their results cannot be interepreted. Similarly, an easy interface that produces results not believable by researchers may be worse than no interface at all.

My areas of interest:

  • ‡ Algorithms for protein quantification; in particular, providing statistical confidence metrics on resulting abundance values.
  • ‡ Distributed processing of terabyte-scale data sets; particular interest in so-called "embarassingly parallel" problems, which, inspite (or perhaps because) of this term still lack much necessary tooling. Support systems for "dataflow" computation.
Sub interests:
  • ‡ Distributed file systems: AFS, Lustre, etc.
  • ‡ Domain specific languages: in particular, implementing proteomics workflows using Groovy, Scala or similar.
  • ‡ Clean, approachable user interfaces, particularly layered user interfaces that provide beginners guidance and support but don't get in the way of more advanced users.

For examples of the things I've actually done, see projects.

For things I wish I had time to work on, see ideas. Maybe you'd like to help or hire me?
 

Someone asked me once what motivates me; here's how I answered:

I am motivated by the sublime saline smell of sea, by waves, by crisp mountain air, by slanted sun. I am motivated by the calm just after a hard sail, after the anchor is cleated home, after the wind slackens and the motion steadies but doesn't stop.

I am motivated by the knowing, wordless smile of tested friendship, by comfortable silence, by bare skin, by beauty. Surprising, intelligent conversation motivates me, as does music that is played with as much enjoyment as it is heard. I am motivated to give pleasure in whatever form appropriate to those I care about: in food, in wine, in laughter, in soft touch, in slow sex. I am motivated to entertain as my mother entertained, around a table full of food and fool of heart.

I find motivation in the time between when I finish the run (or the climb) and when my breath returns. After breath returns, the whole body hum of accomplishment motivates me to overcome the pain that accomplishment requires. I find motivation in extreme effort that garners extreme reward.

But most of all, I am intensely, unswervingly, obligatorily motivated to better the world; I feel I must leave the world, in at least some small way, better than how I found it. I'm motivated in this by the almost obscenely privileged life I've lived, by the opportunities I've been given, by those who have given them me, and by an irreligious, inexplicable morality.