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Friday, December 12, 2008

new title

That's right - I'm no longer just a "graduate student," I'm now officially a "PhD Candidate."

Not that that means anything, and not that it was really worth the pain, but I guess it's some compensation for going through the adventure of comprehensive exams.

Pain, you ask? Why pain?

Well, there was the whole idea that I should learn all of the biology of cancer in 3 weeks, which I think I did a reasonably good job of doing, only to have VERY few questions on it. Instead, my committee members asked about the following topics:
  • What are common breast cancer drugs, and what are their mechanisms?
  • How does Blast work? What algorithms are used for analyzing DNA arrays?
  • What are ESTs, and how could you apply those technologies to your research?
In general, they're not bad topics, but I didn't study a single one of those, since they're utterly unrelated to my thesis.

The examiner who asked about ESTs was making a point, suggesting that I should use a Motif scanner to search my ~220Million DNA fragments (of ~36bp each) for motifs that would indicate a splice junction point, and then use the fragments on either side of the presumed break point (down to ~16-mers) and blast those against the genome. The more I think about this idea, the less I like it. I also don't have 5 years to let the job run.

Anyhow, the exam is over with. I could have answered the questions better, I could have done a better presentation, and I probably could have prepared differently, but it never would have occurred to me to study the blast algorithm, drug mechanisms and clustering techniques for arrays. Who knew?

If I had to do comps again, I probably wouldn't have done much differently. I asked my committee members for what topics they would like to discuss with me and what I needed to study, and then prepared for those questions. One committee member was very helpful in that respect, and I learned a lot preparing for the suggested questions. I think I even answered that set reasonably well. (nerves notwithstanding.)

At the end of the day, I'm just glad it's over. It's humbling to know how much you don't know.

In my presentation today, I closed with two quotes, and I thought I'd share them here. I'm sure all graduate students can immediately grasp their relevance.

“In the fields of observation chance favors only the prepared mind.”
--Louis Pasteur

“To achieve great things, two things are needed; a plan, and not quite enough time.”
--Leonard Bernstein
Edit: I suppose I shouldn't be quite so obtuse. Many of the things my committee brought up were to demonstrate that many of the issues facing 2nd generation sequencing have been tackled by other technologies in the past, and that knowing those technologies would be a good way to keep from reinventing the wheel. That part, I take as constructive criticism. I will have to read up on how array data is processed at some point, though I still don't think I'll use motif finding on 220Million+ fragments. (-;



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