Work: Weekly Progress

Week 0
(Since the transition is part of the experience, I will begin with the shock of experiencing Texas for the first time.) While packing this week, I took some pictures near my home (see the picture of the Beaverhead river), because I knew I would shortly be missing the mountains. When I left Montana, the temperature was somewhere close to 60 degrees (F) and the humidity was practically non-existent. When I arrived in College Station, it was very hot (in the 90s) and about 30% more humid than I was used to.

Week 1
After meeting everyone in the lab, I spent some time sorting out odds and ends. Getting my accounts on the lab machines and the computer science department machines was the first big event. Then, I got the assignment of reading several papers. This would get me up to speed with the research that Guang had already done on protein folding.

Week 2
I began to run proteins through the folding program. The goal was for me to understand the results produced by the protein folding program. Much of my time was spent working with Matlab to create plots of the results and reading through the protein folding code. It was important that I understand specifically how the probabilistic roadmap (PRM) method was applied to protein folding.

Weeks 3 & 4
This week was the beginning of a two-week project involving the addition of more path analysis options to the protein folding program. These new options were designed to provide more flexible, rigorous, and stable analysis methods. At the same time, we ran the protein folding program with many different options on quite a few proteins. This helped us to validate our methods and understand the program better.

Week 5
A paper presentation on several RNA folding papers was the highlight of this week. Xinyu and I researched several papers and prepared a talk that addressed everything from an introduction covering the biochemistry of RNA to the topics of the papers. The goal of the presentation was to facilitate discussion among the research group regarding how we could apply PRM techniques to RNA folding.

At this point, our agenda every meeting became fixed. For the next five weeks it was to be roughly the same:


Week 6
After discussing our options last week, we began to consider what algorithms we needed to write. At this point we got to fill out our meeting agenda a bit by adding in the algorithms that belonged in each step.

In order to kick-start the work on the RNA folding program, we set an ambitious goal of having a running framework by Friday. My assignment was to hash out the details of the data representation of RNA and to write the algorithm that would randomly close contact pairs for some RNA sequence.

Needless to say, we did not quite meet our very ambitious goal...

(...Climb every mountain, search high and low, follow every byway, every path you know...)


Week 7
... so the construction of the framework continued on to this week. By this week, our meeting agenda had grown a bit as we continued to explore better ways of doing things:

The development of our meeting agenda over time is a reflection of the progress of our research. So, clearly we were making progress!


Week 8
Coding and debugging were the major projects for the week. We were now finally getting close to accomplishing our ambitious goal of several weeks ago. We nearly had a framework for RNA folding. We just needed to figure out a way to validate the roadmaps our program produced.

Week 9
Oh my goodness! The framework ran without bugs!!! Three cheers!

Week 10
Wowww! It was hard to believe that my ten weeks were over. But they ended in a busy rush. Writing a paper and preparing a presentation took most of the time I did not spend on improving the framework.

Comment on the picture at the right.
I kept telling everyone that the sky is more blue in Montana than in Texas. Here is my proof.



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For comments or questions, email bkirk@cs.tamu.edu.