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It's Alive

So Wired News has picked up on Marshall Bedoe’s genuinely interesting work on applying Bioinformatics to
network protocol analysis. (I’m actually quoted in the article!) I saw Marshall talk
at Toorcon, and it’s some fantastic work. As I told him — you actually found a protocol more complex than SMB, and it is
us… 🙂 Seriously though, I’ve been talking about the “Medical Ghetto” for
code for quite some time. Here’s a few packages I’ve been raving about
that really nobody ends up using:

  • Large Graph Layout: Graphs — collections of interconnections — are actually alot of fun to play with. Graphviz is generally considered the standard tool for graph layout (in the sense that you just describe what links to what, and it puts everything together in some visually meaningful way) but it doesn’t scale past a few thousand links. What if you’ve got more to work with — say, a network the size of the Internet? Enter LGL, from some brilliant guys over at the University of Texas. Since protein interrelationships are extraordinarily complex, tools to visualize them are necessarily scalable. Of course, the tool is easily generic enough to visualize all sorts of non-biologically derived data…
  • PRAAT. Ostensibly a tool
    for analyzing human speech through a large number of algorithms, this absurdly
    portable, scriptable, and object oriented program is probably the most complete
    toolkit for deep audio analysis you can get — and it’s quite free. I was
    working on a project some time ago to swap melodies between two female
    vocalists, using the PSOLA manipulation interface. Certainly not what they
    had in mind at the Institute of Phonetic Sciences, but it worked pretty well.

  • Volsuite. People keep
    asking me what I used to create the scenes from the Angel project, my on-again-off-again attempt to do something neat and artistic. (Pretty pictures are cool, and as we saw with Phentropy, occasionally really useful at imparting
    useful information). Volsuite is a fast, full color, portable, open source volumetric renderer of three dimensional data, normally used for scientific and medical data but noticably applicable to so much more…

So that’s what I think is cool. Please mail me if you have any other thoughts 🙂 And yes, I miss Sweetcode…

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