Prototyping

I haven’t been blogging much about my capstone (thesis) project very much, so I’m not entirely sure where to start. But basically, I am exploring some different ways of providing biologists with deeper understanding and more control over the software they use. The project I am currently working on is a tool that will let a biologist step through the sequence alignment process (sequence alignment is one of the most common activities in computational biology) and watch what the computer is doing.

This will hopefully help them a) learn how the algorithm works, b) make better choices about how they tweak its the parameters, c) identify more possible uses for the algorithm, d) identify areas where they need the algorithm to work better or different, and e) provide a lens through which they might someday modify the algorithm themselves.

I am going to be showing prototypes to biologists over the next week or so, and let me tell you: prototyping has been a challenge. I’ve built an extensive paper prototype that uses transparencies and wet-erase markers, and it works… but it’s darn slow, and I’m not confident it will be terribly useful for the biologists I’m going to be talking to.

So, as a second try I’ve been trying to implement the prototype in Flash. Unfortunately, the computer scientist in me keeps pushing to make it “actually work” and that is making things quite a challenge. However, I’ve got a pretty good start, and maybe by next week I’ll have something working. You can see the first few steps here.

It’s not terribly impressive, but there’s a good deal of foundational work happening under the hood. I am hoping things keep rolling along.