Sunday, March 15, 2009

OMG Bioperl!

So, I've been doing a lot of thinking and have not had much time to actually put any of that thought into action. I have two short stories that I swear I'll sit down and write... sometime. I'm thinking spring break, which fortunately enough starts oh-so-soon (by which I mean, basically, Tuesday).

BUT, what I have been doing is programming in Perl. Specifically, bending those wanton BioPerl modules to my will. And I am (fairly ridiculously) proud of the output, so you all get to see it. I think it's pretty darn beautiful, if I do say so myself. Once I figured out how to print anything in an image, the rest of it was fairly straightforward (surprisingly, since it took me basically a full day to find a server I could run my script on and get it to print anything even close to what I wanted). The overlay at the bottom took me quite a bit of puzzling to figure out, because online there were three tutorials that described ways to do it (none of which worked, of course), and because the parts of BioPerl that our instructor even vaguely went over were all "here's how you download a sequence" and "here's how you find enzyme digest sites on that sequence" and not "here's how you output a picture".

Next quarter: Computer Analysis of Biological Images, in Java! I will learn how to deal with the data I was getting last year; all those pictures of nuclei I dreamed about. And given that my favorite parts of this quarter have been learning Perl, I think it's fitting that I'm now taking a class in Java. I'm pretty excited, but I predict that my friends will not be in that class, since they (by and large) did not enjoy Perl nearly as much as I did. Which is sad. *sigh*

1 comment:

Duff said...

Perl I have found to be lots of fun.