James and the Giant Corn Genetics: Studying the Source Code of Nature

June 27, 2008

Work, Class, and Dreams of Cake-Shakes

Filed under: Uncategorized — Tags: , , , — James @ 5:33 pm

Two years ago, I said the most fun I’d ever had while getting paid was the afternoon I spent doing sequence analysis for a seed company while listening to female fronted metal music. Well I’ve earned more money and had more fun since then, but there’s still something about working at a speed limited only by your own ability to think, while listening to a song like “Ice Queen.” I’ve been working on an computational genomics project in the lab, which means I’ve been coding and analyzing to Within Temptation and Leaves’ Eyes all week. The nice thing is that when I make a mistake with working on the computer it usually takes me a few minutes to correct it. Working in a wetlab a simple mistake could close me anywhere from an hour (I forgot to add something to a PCR reaction) to two weeks (I grew seedlings, harvested their tissue at the right age, extracted RNA, and then somehow let the RNA degrade to uselessness). So that’s the good news. The bad news is that I make a lot more mistakes working with the computer. But I’m getting better.

And a lot of the credit goes to the guy I’m working for, who has given me a project that was right on the edge of my ability and then known when to throw me a life preserver and when to let me sink or swim on my own. It means I’m producing results more slowly than I would have on a project more in my area of my experience, but I’m sitting right in the optimal part of the learning curve.

The two weeks of class before this were very instructional. We learned everything from R (A mathematical computer language that does a lot of the same stuff as matlab, only instead of costing hundreds of dollars it’s free), to machine learning algorithms (not as cool as they sound, but still plenty cool), to online annotation of genomes (it’s crowd sourcing for geneticists, but do all the geneticists in the world constitute a big enough crowd to be useful?).

What sounds like the lone surviving toad (apparently the new cat doesn’t turn his nose up at them like that old one) is singing in the pond out back. 

There was another mention of cake shakes this weekend (possibly tied to monty burgers) but I’ll have to wait and see what happens.

June 11, 2008

Graduation and Iowa City

Filed under: Recreational Travel — Tags: , , , , , — James @ 11:09 am

Lots of exciting stuff happening. Graduating. Doing the thousand mile drive for the ninth and likely final time. (Though I’ll be driving twice as far to reach California in the fall, the impossibility of doing the drive in one day, combined with ever rising price of gas makes it unlikely I’ll drive back for breaks). Carpooling out to Iowa City to celebrate a friend’s birthday.


Graduation was good. The actually ceremony took place out at the football stadium and where I sat, unable to see who was speaking over heads of hundreds of my classmates, watching the heat ripples rise from our black robes. My parents came out and I was able to at least point myself out to them during the procession in by calling on my cell phone. (Makes you wonder how people managed before every college student and their parents had a cell phone).

Visit to Iowa City:

-Almost didn’t make it as flooding was shutting down major roads out of town.
–Estimates of this fall’s harvest all already being reduced as a result of the constant rain.

-William is 22!

-Red Velvet Cake Shakes at the Hamburg Inn #2.
–Possibly the best form of food discovered by mankind to date
–The Hamburg Inn is one of the places presidential candidates always visit in the run up to the Iowa caucus. I sat under a picture from John Edwards’ visit.

-Disk Golf
–Surprisingly fun
–I’m surprisingly bad at it 😉
–Continued to play since I’ve returned home

On monday I started a two week course on bioinformatics and computational biology…will update on this over the weekend…

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