Diary of an Enraged Macrophage, Part 2

November 6, 2011

I’ve been running blast for ~73-74 hours (Daylight Savings Time kinda messes that up), and so far I have a 1.1 Gb table of output… and it’s not done.

On the bright side, I wrote a successful and useful Perl script after having not coded in Perl in 5 months.  And it was my first ever serious experience in Perl.  Oh, and I remember how to use bash now! Google and the O’Reilly Pocket Reference I picked up have helped considerably.  That and the Grad Students who know the small tricks that make life easy.

Things I’ve noticed:
1) Bioinformatics is all about Open Source software and things that people can use without much experience, if any.  But every piece of software I’ve had to use has extremely obfuscated User Guides, Tutorials, and Instructions.
2) There’s no rhyme or reason for anything as far as software or scripting language choice.  I could write everything in Python… except no one in the lab knows Python.  But even our Postdoc, who is a CS/Bioinformatics person exclusively, doesn’t know Perl and uses Google to figure out things he hasn’t seen before.  He’s never actually learned Perl, and neither has anyone else in the lab. Hell, I could use Javascript (if I knew it), because we don’t use any of the scripting language to work between software/applications.
3) I prefer this type of work to most things I’ve ever done.  Yeah, I’m being thrown out into the wild without knowing where I’m going, but that’s what I like (I think).  It actually feels like MY project, not someone else’s that I’m doing the grunt work for.  That’s refreshing, and very cool.

As far as the project… The BLAST I’m running right now is not actually going to be a part of that project (for the moment, anyways).  The project I’m working on has switched from Protein Family ID to building a Phylogenetic Tree with our Genomes after comparing them to references.  From there protein families might come back in.  But I’m waiting on that data anyways, so until then…

I’m having a BLAST.  Oh yeah, I went there.

If you’re interested in what I’m doing, you can go to archaea.ucdavis.edu (if it’s working).  It has a pretty general overview of the work, and even though it’s being run by the lab that my lab is collaborating with, it’s kinda cool to see it all visualized and whatnot.

 

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