The First Week

Before I continue, I should mention the two weeks that transpired before my first week as a DMP Summer mentee. Approximately three weeks ago, I graduated from Rensselaer Polytechnic Institute, with a Bachelors in Computer Science. I had specialized specifically in Computational Biology, with interests of going on to graduate school for Computational Biology or for Bioinformatics. When I had applied to DMP this past February, I had done so with the desperate knowledge that I may not even get into the graduate schools I had applied to, and therefore I craved the experience that DMP would give me. I heard about the program my freshman year itself, and when my GPA plummeted after an especially rough semester, I lacked the confidence to apply until this year, my senior year. To my absolute joy, I was accepted. To my even greater joy, I got into Graduate School (at Rensselaer), and I would be working with a professor I knew well and was being offered funding.

But even though it seemed that the plans for the summer were all for moot (it was for preparation to go to grad school, after all), I was more excited and determined to do well than ever. This, this was my chance to prove myself. To put all the knowledge I had acquired about Computational Biology to the test and produce something meaningful, wonderful, and above all, publishable. I had 10 weeks, which, I knew, was not that much. So I asked for a headstart. After crashing for a week after graduation, I e-mailed my mentor Tiffani Williams, and asked her for suggested reading. She sent me three research papers which I read, and I began to get an idea about what the research was about. Dr. Williams was into phylogeny, a research area that I have long been curious about, and have even seriously considered making it my research niche of choice in Computational Biology. By the time I met her a little more than a week later, I had read all the research papers.

Coming into Texas was interesting. I had never been to Texas in my entire life, and, in fact, never even crossed into the continental U.S. lower than Virginia (save for Nebraska). Being in Texas is a very big change, especially for a girl brought up in the northeast like myself. It was an even bigger change, considering that I went to school where snow lies perpetually on the ground for almost five months out of the year. A nice day in Albany, NY was around 65, 70 degrees farenheit. A hot day was around 80. In Texas, a hot day can be anywhere from 95 to 110 degrees farenheit, and with the humidity, it feels still more unbearingly warm. Needless to say, I spend most of my days indoors, silently praising God for the man who invented air conditioning.

The first week in College Station, TX went very quickly, but was fairly good. We got microfridges in our room and our own microwave oven, so we could buy some food. I also met with Tiffani for the first time last Tuesday. I told her how excited I was from reading the research papers, and showed her some of the ideas I had about potential research projects for the summer. Dr. Williams was very movating, and very encouraging. She seemed to like the ideas I had, and told me to run with them. We set up a meeting time to be every thursday, with additional meeting times as necessary.

By the time we met on thursday, I had an idea for an algorithm. While it did not exactly match the maximum parisimony approaches she was working on, she suggested that I change my focus to the construction of starting trees, which was absolutely delightful, since I had recently discovered that it was possible to beat the neighbor-joining approach to phylogenic tree construction. This would tie into her research, since I will be studying how starting tree construction effects maximum parsimony searches. I left the meeting, absolutely elated, and on friday, set to work on what I hoped would be an improved distance metric.

My problem with current distant metrics designed to measure the evolutionary distance between two sets of taxa had two parts. First, I didn't like the fact that all bases, and thefore all mutations, were treated with equal weight. Since it was more likely for one type of nitrogenous base to mutate into another (say A to G), than to another one(say to T), I felt that in cases where the same amount of mutations were present, it was important to consider mutations that were more likely as denoting a closer evolutionary relation than those that were less likely. Second, the only evolutionary change that is considered are mutations. The effects of deletions and insertions were not considered (at least to my knowledge). For this reason, I decided to create a new metric based on the pairwise alignment scores based on two taxa. I hoped this would yield more accurate distances, and therefore, make a better starting tree than, say, one produced by neighbor joining. By friday, I had a basic algorithm for this new method down on my computer. I planned to flesh it in on monday. Last week ended on a very happy note.