Daily Life
After the work day, I made my way to the buses. Of four trips, I managed to make my way directly to my destination twice. Once I caught the bus on the wrong side of the road and traveled to the opposite end of town. Another time, I was at the right bus stop, but boarded the wrong bus. When the bus turned off the road, I realized my mistake. Of the other two times, on one return trip, I (incorrectly) thought I had missed the last bus of the day and called a taxi. It pays to print those maps and schedules!
The laptop I ordered arrived on Tuesday! And my phone charger stopped working. My daughter used Skype to call me to be sure I was awake until I was able to buy an alarm clock. On one of my bus trips, I had learned that the charger I needed was no longer being made, and was unavailable in local stores and from my internet provider. Luckily, I found one for sale on the internet. I should have the use of my phone back in a few days!
Research
During week 2, we familiarized ourselves with another mapping process. This was better suited for proteins as multiple dimensions could be addressed. We experimented with changes in the number of flexible and rigid bonds of a protein.
Some of the results I obtained during week 1 seemed unexpected, therefore, a fresh copy of BasicPRMStrategy (the file that housed the parameters we were evaluating) was obtained to repeat the summary experiments. This was compared to the copy used for the final results and some undesired differences were noted. These were likely due to changes made during testing that were inadvertently left in the file after the test was completed, and were then copied into the next test.
The clean copy was tested to determine why there was an increase in edges. It was found that the increase was due to a correct change in a parameter and should have been expected. The residual changes did have a slight, but negligible effect on the results and the original summary results are acceptable.
We familiarized ourselves with a mapping process for proteins. This is better suited for proteins as multiple dimensions can be addressed. We experimented with changes in the number of flexible and rigid bonds of a protein. We presented our findings to Dr. Tapia and the graduate students on Thursday. On Thursday we also attended a brown bag lunch discussion on Graduate Student Life with computer science graduate students as guests. They spoke of the various paths that brought them to their studies. Each of these students were enjoying their program and spoke of the benefits of graduate and/or post doctoral studies.
At the weekly group meeting, we discussed the Project Proposal paper. John (one of the graduate students working for Dr. Tapia on this project) summarized it as 'We're applying the probabilistic road map to immune proteins. We're trying to get multiple folding proteins and discover why some bind and some don't.'
On Friday we were invited to an STMC meeting with a presentation given by Jeremy Edwards, UNM Modeling Core Director, on Progress towards the spatiotemporal modeling of cell signaling: the ErbB and IgE receptor pathways. I also submitted my DREU website for approval, the committee indicated a reply on it's acceptance or need for improvement early next week.
Next Week
For week 3, additional experiments on parameter variations will be done, and I will review the paper 'A Machine Learning Approach for Feature-Sensitive Motion Planning (M. Morales, L. Tapia, R. Pearce, S. Rodriguez, N. Amato). At the end of the week, I will submit a weekly report on the work done and I will continue to revise and add weekly journal entries to my website.