Computer Science Internship: Part 1

I thought that I would take a minute to post about my summer plans since I begin my summer job tomorrow at the Oregon Health Sciences University. I will be working in the same lab in which I spent the past three summers conducting protein research, but I am beginning a new computer science project in the lab for the first time this year, which should be really exciting!

It turns out that computers make life in a protein chemistry lab a lot easier. In fact, without computers, proteomics would not be nearly the field that it is. The experimental research that I performed in the lab for the past few years generates literally hundreds of thousands of files per experiment. Searching and analyzing a large enough experiment to determine which proteins are present and any modifications to their usual structures can take twelve hours or more. Even opening a folder containing the data from a single experiment can take several minutes since the computer has to load hundreds of thousands of files.

Efficient storage, analysis, and presentation of these huge amounts of data are fundamental to a successful experiment, and fortunately modern computers give scientists the ability to do all of this. But somebody has to write programs to sort and analyze the data, and that’s what I will be learning to do this summer.

I have to say that the University of Puget Sound prepared me very well for this internship. In fact, taking computer science this last semester is what inspired me to think about working on the computer side of protein research. My Intro to Computer Science class really sparked my interest in programming. I’m finding out, too, that it really prepared me to program “real” applications. My mentor passed on a couple of books about the programming language I’ll be using this summer, and while the language is different, I learned all of the programming concepts that I’ll need in my Intro to Computer Science class! It’s quite a testament to the quality of Puget Sounds’ Computer Science department that its introductory class gives students enough background for them to teach themselves a new programming language. I can only imagine how much more I will learn after taking upper-division classes.

Of course, the internship hasn’t started yet: while I’m confident that I understand most of the programming techniques involved, I’ve never worked with huge sets of data before, nor have I written as much code as I will need to this summer. This internship will certainly push my programming skills, and I’ll come back to my computer science classes with a lot of hands-on experience. Also, the language I’m working with, Python, is a great one to know. Google uses it to prototype most of their online applications, and it’s used extensively in the science world for its efficiency and readability.

I’ll continue to update this blog about my science internship and about everything else I’m doing this summer. I’m sure that I’ll be doing more protein chemistry research in the lab for the project I worked on last summer. My Chemistry Analysis and Equilibrium class was definitely helpful for keeping my lab and chemistry skills in practice. I’m also working on a musical score this summer, so that should keep me busy the rest of the time. While I have most of the songs “written” (meaning that I can play them at the piano), I have yet to write anything but a few notes down on paper, so hopefully I’ll make some headway this summer. While I really enjoy the creative side of music composition, the necessary transference of notes to paper is always far more tedious than I anticipate. It’s amazing how much new music you can improvise when you’re procrastinating on actually writing down the notes!

That’s all for now. I’m writing this blog post outside and the sun has finally come out, a rarity even in June here in Portland, Oregon. Time to get off the computer and laze away the rest of the afternoon in the sun.

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