Diary of an Enraged Macrophage, Part 1

October 28, 2011

Yeah yeah yeah, I know, they aren’t called “enraged” anymore, they’re called Activated Macrophages.  But I concur with my Microbiology professor that “Enraged Macrophage” sounds better while being more descriptive.  But anyways, that’s not the point.

I was trying to find a catchy title related to Cell Bio, but there isn’t much in that field that lends itself to catchy AND pun-ny titles.  Although “See You In The ER” might have been ok… Alternatively, “I Ran, I Ran-GEF’ed So Far Away” is just bad, and I’ve been trying to figure out ways to use COPII, MAPK, NLS, and a handful of others with no success.  This is way off topic, though, so let me get to the purpose of this.

I need to blog more, which is something I’ve been saying almost ever since I started this damned thing.  I like blogging, and I like blogging about more interesting or relevant things than just the doldrums of my day-to-day.  It’s hard for me to find something to consistently write about, however, so my plans to be more consistent usually fall apart.  I’m hoping to change that by chronicling my Misadventures in Bioinformatics.  Hey… that’s not a bad title.  But titles aside, I think this is actually something I can accomplish.  I have to write a weekly “blog” for my Modeling in Biology class anyways, and that class is also having me put together a model of my own, complete with a Lit Review, a proposal, and, of course, a model that I have to present and defend.  How does a quarter-long class get me to write more consistently?  Well, in addition to the class I’ve (finally) begun working in the lab I’ve been trying to get into since my Freshman year, and I’m working with Metagenomic data of a very large number of Archaea; Halophilic Archaea, to be precise  (“Halophile Ever Know” might have been a decent title too.  But now I really need to stop).  And I’ve managed to find connections between the modeling project for my class and my lab work in the lab.  Both of which give me something to talk about at regular intervals, as I slog through everything.  It may or may not be interesting, but it’s at least an excuse to blog more often, and about things I actually can say something about.

So that brings me to where I am currently: trying to narrow down my modeling project while trying to relearn Unix/bash and “relearn” Perl, along with learning bioinformatics the old-fashioned way — Coffee, Google, bang head against wall, repeat until you have a vague idea of what you’re doing.  I’m not new to bioinformatics, but I’m extremely new to genomic data from multiple genomes, database management, protein family annotation, and constructing phylogenies from phylogenomic data.  And like all good bioinformatics projects, I’ve been sent out into the wild with nothing more than a pat on the back, some vague info, and a dark spot on the horizon that I’m supposed to walk towards.  Oh, and Google.  But Google pre-Google maps, because it can’t tell me what that dark spot on the horizon is.

So what’s there to look forward to? Well, data and info, for one.  And the excitement of finally (and hopefully soon) figuring out how to do everything I need to do efficiently.  I say that because the people in my lab basically created a lot of the methods that we and many other labs are using to do research of this sort, and they pull their hair out constantly.  They still have issues with everything they use, but they’ve at least found ways to make the head-bashing minimal and more efficient.  But what I’m really, really, really, REALLY excited about is the potential for my modeling project and my lab work to overlap and (hopefully) turn into my own actual research project, complete with experiments, data, and maybe even publication.

So yeah, what is my modeling project?  I’m trying to look into and model the interactions between microbes and humans that might cause tumor formation and cancer.  While I might be working on the genomics of haloarchaea, the major research focus of my lab is in microbe-host interactions.  But hey, what’s that?  An article from 2010 describes finding Halophilic Archaea in human intestines?  Some of the species found in the study are some of the species who’s genomes we’re studying?  Even if there really isn’t anything there, it’s a start.  It’s something I can keep an eye on.  And it’s something I can blog about.

Woot!

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