O Captain! my Captain! our fearful trip is done,
The ship has weathered every rack, the prize we sought is won,
The port is near, the bells I hear, the people all exulting,
While follow eyes the steady keel, the vessel grim and daring;
But O heart! heart! heart!
O the bleeding drops of red,
Where on the deck my Captain lies,
Fallen cold and dead.
— Walt Whitman
Two years ago, I was absolutely sure of the direction I wanted my life to take: there were no valid paths open me other then graduate school. It appears this path has become overgrown with vegetation, as i can no longer seem to find it. Maybe it was the immaturity of the forest of life that made this path so easy to maintain.
I am reminded of a time when I was much younger; all I wanted was to be a paleontologist. I quickly discovered that the dreams of a child are often fleeting, as my they quickly turned towards becoming an electrical engineer; to follow in the footsteps of my grandfather. Eventually this dream also slipped into an abyss as I discovered a fascination for computers.
I am still mesmerized by computers, and have a strong desire to do something in the general field of computer science, but am no longer sure that dream involves graduate school at all. I think I need some time for a little self discovery; time to discover more closely who i am, and what I want to do with my life and career.
In case it is not yet obvious, I am talking about getting a job. I am hoping a few years in the workforce of my chosen trade will help me decide if I want to work in research, or if I will be content with a lifetime of software development. Maybe the death of my previous path will allow me to forge a better one, as I proceed into the future.
Computer Science is no more about computers than astronomy is about telescopes.
— E.W. Dijkstra
The summer REU has ended and it was,
overall, a very rewarding experience. I do not think I was really
prepared for the overwhelming amount of work that goes into research,
but I did learn a lot about computer science
in general. The project I was participating in was entitled, Dynamics of Knowledge Creation in Open Biomedical Ontologies.
The goal of this project was to examine how knowledge grows over
time, and what intrinsic qualities in a social network leads to maximal growth in a technical network.
First, a little bit of background. An ontology is a set of concepts within a domain and these concepts must be representable in a machine parseable form. Think of an ontology like a dictionary; ontologies contain a set of terms which define a domain, and a set of relations mapping terms to other terms, and terms to other domains. My part of this involved parsing these ontologies and placing them into a database so that we can build knowledge graphs, and look at how they change over time.
Most of the communities in Open Biomedical Ontologies communicate by either mailing lists, SourceForge's bug tracker, or both. Notre Dame provided us with an API to access most of the data required, but some of it was not provided; like the mailing list data. I built a webcrawler to place this information into a database.
Once I had all of the required data, I needed a tool to calculate some graph metrics on it; such as centrality, density, and clustering coefficient. I built a gdf parser to parse Guess graph information, and output the data in the form of csv files.
In essence, I spent most of the summer
building tools to download empirical data. I plan to compare this data to a
simulation designed by Dr. Yilmaz. Once we are confident in the accuracy of this simulation, we can begin to examine how
changing structural elements of the social network affect the
technical network, and which characteristics maximize innovation.
All in all this project has been fascinating. It quickly turned into a multidisciplinary project involving sociology, graph theory, and computer science. A friend of mine once sent me that E.W. Dijkstra quote. He mentioned that Computer Scientists are often wanted for their ability to manipulate massive quantities of data in a variety of fields. I am now convinced he is right.
