For the past two summers (before my junior and senior years) I spent a lot of time in lab at the University of Houston in the Department of Biology and Biochemistry in the lab of Dr. George Fox. Most of what I worked with had to do with DNA related things and I found it really cool to be seeing in front of me, on a computer screen, nearly 3.5 million DNA positions. As I looked at a mind-numbing amount of data, I learned the different ways to separate the positions in order to find where mutations occurred. In this process I came to love Linux, and well…the same cannot be said about Windows. I learned new tools like awk and picked up bits of programming languages such as Python.
The first summer I worked mostly with the bacteria DNA. I knew what the species was and by using the different indicators on each DNA position, I tried to separate the normal from the abnormal. Of course, it’s almost impossible to go through several million positions one-by-one, so I wrote scripts in awk in so that it would go through the data for me. And often times, I got to upload my scripts and data and run them on blazing fast supercomputers. For a geek, that is exciting. From the several million, the lists of interesting, potentially mutated positions came down to a few thousand, and these had to be examined properly.
The next summer, I worked with something even cooler. This time I just had DNA, but had no idea which species it came from. What made it even better is that this DNA was found on space shuttles (in space). I learned how to use various software in order to figure out which areas of the DNA were continuous. Then I wrote a script in Python in order to compare it to a huge repository of DNA information available on the National Center of Biotechnology Information (NCBI)’s website. Unfortunately it seems that the strand that I was working on was a mix of several different organisms and so it was difficult to match it up to any of the organisms in the database. Around this time, it was getting to be the end of my time there (I think I was there for about 5 weeks this last summer, because before that I had Boys State and HAS, and after that I went on a road trip, temple camp, and then school started).
So after I left, they were working on getting new samples from space. Luckily, because of the way I wrote my script, they will be using the same script in order to go through the new samples as well, and so this should save a considerable amount of time. And currently there is a paper in the works on this, and I’m going to be acknowledged in it for my part :).
During this time, I normally took a ride with a CS professor…because I really didn’t want to get a parking pass. So one day, he took me to his lab and made me an experiment subject. Apparently, I’m not a very good one -_-.