What have I been up to?

As a new prof, I've been too busy to blog much. What am I doing?

Apart from all the normal academic crud (meeting with people, answering e-mail, doing paperwork, etc.) and parenting & home ownership stuff, I've been teaching my Intro to Database-Backed Web Programming course. This has been neither a huge failure nor a huge success, but has at least been extremely educational for me (did I mention that jQuery is awesome?). That's consumed most of my time.

However, I do have a few technical things up my sleeve. Over Thanksgiving, I've been --

  • looking over a student's work on seqdb2, a Write-Once-Read-Many database for indexing and retrieving large DNA and protein sequence collections (e.g. Solexa reads). It's somewhat specifically aimed at providing a pygr back-end to help us manage the startlingy large amount of sequence data now available.

  • starting to get into SeqFinder, an n-mer indexing and search library for doing O(n) searching for n-length oligos in gigabase-sized genomes. The basic algorithm is simple and fairly straightforward, but the devil is in the details; a collaborator is implementing it, and I'm hoping to turn it into a fairly general oligo search tool for several nefarious purposes.

  • and, of perhaps the most general interest, I'm trying to grok Pyrex sufficiently to add code coverage recording and analysis. Since pygr, seqdb2, and SeqFinder all make use of Pyrex or its fork, Cython, this is critical for me for testing. I suspect it will be quite useful to the SciPy folk as well, once I get it working nicely.

    I do have something that basically works, but it's not integrated into either Pyrex or figleaf very well yet and I need to hack on it a bit further.

    My ultimate goal is to get coverage data from Python, Pyrex/Cython, and C/C++ all in one format so that I can do a proper job of looking at statement coverage for these multi-language applications. That's still a ways off, and one of the bigger barriers is that gcov doesn't work on shared libraries. Grr.

Hopefully I can spend some more time on these things now that the term is almost over!


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