Thursday, June 25, 2009

Motif Discovery [-1]

I had hoped to show a working Gibbs Sampler for a real problem (say 10 sequences of length = 1000 each). My tests show that I will need a lot of cycles to make that work. I did write a short C program to do the time-consuming parts, but have so far failed to integrate it into a Cocoa project. Probably most people wouldn't find that useful, anyway, because it's Apple-specific. I will try to brush up my C++ in the future and do the whole thing in that.

Anyway, I'm moving on. I still have some Bayes to do, and after that I'm not sure. I need to read Drew McCormack. I should go back to phylogenetics more seriously. I could tell you more about the course I taught called "Bioinformatics for Biologists," or show the material I developed for it.

By the way, if you have read and appreciated any of my posts, I'd enjoy hearing from you.

I think of that famous question: "if a tree falls in the forest, and no one is there, does it make a sound?" It is said to be a Zen koan, but I don't have a source. Maybe it is apocryphal.

It is OK if no one is listening. I view this blog as the place I store the homeowork for my self-study class in Bioinformatics. I don't like reading other people's code, and I expect you don't like reading mine. But I get a huge learning boost from programming. It has happened many times that I only really understood something after I made it work in my own code.

Besides, even if there is no single person listening in the world right now, the internet lives forever. And the signal-to-noise ratio will improve with time. Google is just the beginning.

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