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June 28th
Today I finished the paper on Self Organizing Maps. The paper is ten pages and is about algorithms and applications. I found seven algorithms. Some using expectation maximization steps and others using if statements. I then searched the Internet for a simulation of Self Organizing Maps using MATLAB. I found a useful Self Organizing Map Toolkit for MATLAB it allows you to input data and then it shows a 3-dimensional representation of the data. LINK TO SELF ORGANIZING MAP PAPER
June 29th
No Entry.
June 30th
No Entry.
July 1st
Today I spoke with Professor Valova and we started to discuss the next project. The next project deals with protein sequences and conformation. The basic idea is that each protein consists of a sequence of amino acids. The secondary structure of a protein consists of alpha helixes and beta sheets. The tertiary structure of a protein consists of the three-dimensional orientation or the subunits. The quaternary structure of a protein consists of the multiple subunits. The program is to first read the primary sequence and then compare this pattern to another protein, to determine if the sequences are similar. The next part of the program deals with training the net using SOMs to understand the protein by its shape.
July 2nd
I started thinking about how I will perform the first part of the code. I decided I should use C++ and a switch statement to test the amino acid. Then with the SOM and shape of the protein use MATLAB since its more graphical. I have a few ideas on how to encode the protein sequence. Since there are four letters that represent nitrogenous bases in the genetic code I would need four different symbols. Therefore I could use binary numbers to represent each letter or I could choose symbols.
July 3rd
Today two of my friends from home (New York) came to see me. It actually worked out well because tonight the school is doing a fireworks show. It is funny though I thought the holiday was called The Fourth of July. So I showed my friends the campus and told them about this project and what my job is all about. The fireworks lasted about fifteen minutes. The whole idea behind fireworks is kind of interesting. People get so excited when they see the pretty colored lights in the sky and the cute shapes they make. My how the human race is so easily entertained.
July 4th
Happy Independence Day! Today more of my friends came to visit me. I took my friends to see my suite. They were shocked when I told them I donít have air conditioning. We went to eat because its what we do best. We went to New Bedford to watch the fireworks. On the way there I apparently made a wrong turn because we werenít in the right place. So I hopped back on the highway and made the right turn this time. So we watched the fireworks. My car alarm is extra sensitive so it went off about five times. All in all it was a very nice day.
July 5th
Today my friends and I decided to take a cultural trip. We took a tour of Boston. We went to Quincy Market, Fanueil Hall, the Aquarium, and the Cheers Bar where our New York accents were picked up very easily. From there we went to Boston Common; which was gorgeous. Then we went back to North Dartmouth.
July 6th
Today my friends and I went to Cape Cod. I was so impressed with the way the water looked. It was clean and blue and I couldnít believe I was in New England. We went to Scusset Beach where there were a lot of people. Then on the way back to the school we hit a lot of traffic.
July 7th
I woke up early today so I could say goodbye to my friends. I guess I was trying to delude myself into thinking that I didnít miss my friends and family. Well back to my project. I started to do research on how others have used neural networks particularly self- organizing maps to predict the shape of a protein.
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