SciPy '07: General Report

Last week, SciPy 2007 came to Caltech. Unfortunately, I wasn't able to attend many of the talks because I was busy with lab work and other deadlines, and because SciPy was held immediately upstairs from my lab I could just duck out to go back to work. However, I did attend a few of the talks and found all of them interesting -- and I heard that I seriously missed out on one or two. Hopefully other people will blog about those.

The talks I am qualified to comment on are the two other biology-based ones that I could attend. One was on pygr, given by Chris Lee, and the other was on Galaxy, given by James Taylor. Together with my talk on Cartwheel, I think they illustrated three entertainingly diverse approaches to bioinformatics and biology. Chris focused on addressing query paradigms (pygr implements a graphic database) as well as data size issues in alignment and annotation of large sequences. James talked a lot about building workflow interfaces to packages, thereby presenting a possible solution to many of the current problems in bioinformatics such as formatting, reproducibility, and software interaction. And I talked about how Cartwheel provided biologists with one specific way to answer one specific kind of problem, and did so in about as simple a manner as you can imagine. I already have plans for cross-fertilization...

Hopefully we can attract other bio talks to SciPy next year!

I also gave a rather low-key tutorial on "idiomatic Python", which went OK but was, well, low-key. I attended two birds-of-a-feather, one on testing (organized by fperez) and one on biology (organized by me). I'll write more about those later.

The BoFs and the after-talk interactions really convinced me that SciPy is a very useful conference for meeting other people who have similar problems to you (perhaps in slightly different fields). While I feel the talks are widely scattered by topic, ultimately a lot of the issues -- data handling, interfaces, visualization, parallelization -- are shared by everyone, and because we all use Python we can actually use each other's technology! Very cool stuff. Next year I'd suggest having more mixers and shorter presentations, so that we can get more of a sense of what's going on out there, but that's all I would suggest.


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