I�m through the first version of my bioinformatics program for my first rotation. The results are disappointing, but you can take a look at some of them here. (You�ll need the Chime browser plug-in.) One problem lies in trying to calculate distances in three-dimensional space between a nucleotide and an amino acid that is hydrogen-bonded to it. Another problem is trying to figure out possible orientations for the amino acid that would still satisfy distance and H-bond requirements. I did some thinking on these topics yesterday, made some sketches, and then tried to do some research on 3D math on the internet. It turns out a lot of this stuff has already been worked out — a lot of it by people who do computer animation and graphics — so I don�t have the reinvent the wheel. The bad part is that it�s all horribly horribly complex. And involves vector math. Which I don�t remember. So I think I�m going to do a little more fine tuning on this algorithm, which should make it more accurate — and hopefully yield some interesting data — before moving on to other approaches that, again, will hopefully give me some really interesting results.
I’ve started work on my second rotation in Andy Ellington’s lab. It’s a bioinformatics problem, so I’ve had a crash course in Perl before I started writing any programs. But so far it’s progressing very nicely, and Andy is excited about it. I hope that before too long, I’ll be able to put the keyboard down and start doing some bench work to verify the computational work.
Previous people in the lab — mainly an undergrad who is now at Cambridge on a Marshall Scholarship — developed a database of amino acid-nucleotide interactions called “AANT”. I’ll spare you the details on how this was done, but there is a Nucleic Acids Research paper on it. Now I’m going back through the data looking for nucleotide-amino acid interactions that are at approximately the same distance and orientation as other interactions. I think ultimately Andy would like to be able to intelligently design aptamers (RNA molecules that bind other molecules) to bind proteins rather than having to screen for them, which can take months.
I taught my first two classes of the new semester today, and it went pretty well. The big thing I learned today is that you have to set the mood from the first time you walk in the door — or at least the first time you open your mouth. So I greeted everyone and asked them all their names. I made a sincere effort to learn the students names and call on them by name. They seemed to respond very well to that. They were a little bashful about coming up to the board to work problems, but they did it and seemed to take to it well.
Setting this kind of friendly, jovial classroom environment is a big step for me. I’m usually kind of quiet and reserved. I’m certainly in the habit of waiting for others to set the mood and then fitting myself into that. Of course as the instructor, it’s up to me to set the mood.
I really enjoy teaching, at least in a smaller classroom where you can interact with the students. I don’t envy the professor, having to stand before 115 blank faces and drone on for an hour about Mendel’s experiments. The part of teaching I hate the most is the grading, which the prof — lucky bastard — doesn’t have to do. I suppose there isn’t a way to have your cake and eat it, too.
Anyway, the course website is here, and you can see the website for Dr. Iyer’s lab here. He does very cool stuff with microarrays, a.k.a. gene chips. He got his PhD from Harvard and did his post-doc in the Brown Lab at Stanford, which played a big role in developing microarray technology.
I started my first rotation today. I am in Krish Roy’s lab in the biomedical engineering department. As expected, the first day was filled bureaucractic hoops (never try to get a key at UT) and many papers to read. For the time being, I am assisting with some tissue culture work. I’m not sure exactly what’s going on, so it’s overwhelming. I need to ask more questions, but that can be difficult on the first day. I don’t know how interested I am in the tissue culture work. I got put on it because that’s what the other biologist in the lab is doing, but believe it or not, I am actually more interested in the engineering side of things. That’s certainly where the cool stuff is happening — and the cool stuff is why I’m there.
I’m looking forward to getting a new laptop when I start back to school. I’ve been wanting one of the Centrino/Pentium M machines since I first read about them. Dell has one, I think it’s the Latitude D500, that looks like it wil fit my needs. I’m going with Dell because I know and none of the other major manufacturers offer the options and ability to customize that I’m looking for. I’m a very technical, nuts-and-bolts type of person when it comes to making big purchases (or even small ones sometimes).
My financial aid stuff has gone through, but with some surprises, of course. I think I should be able to borrow the maximum unsubsidized Stafford loan amount each year, but my award was less than that. I’m also concerned about how my stipend is going to affect my award. I e-mailed the financial aid folks, but I won’t hear back for a while. So it goes.
Coming Soon Commentary on EW’s review of Charlie’s Angels.
