I began the week with an introductory luncheon where I met my mentor, the other student I would be working with, as well as the other students in similar programs. After lunch our graduate student gave a presentation which briefed us on the overall goals of the project. We were then given a lot of reading to do. I spent most of my first week reading, going to luncheons, and atteding meetings. All of the computer science and engineering students were given a seminar on research methods the first week, it explained how research was executed and the fact that things don't always go as planned. Every Thursday there is a Brain Networks Lab group meeting, since the research we are doing is a part of their project we go to the meetings so we understand the role that our work will eventually play.
This week was a lot busier than last week. We started the week by reading the NSF proposal for our project that is currently being reviewed. We were then given the assignment of finding the user manual for Mfinder on the internet and figuring out how to use it. Our grad student explained that being able to find your own resources is an important part of research. This week our research plan was due, on this paper we had to explain our project as well as give an outline of our tasks with the dates we hope to complete eash task. On Thursday one of the grauate students in our department defended his thesis. Perry and I were able to listen to it and see how thoroughly everything must be discussed, as well as hear the type of questions one would be asked. On Thursday all of the students were brought together for Cookie time where we had the oppurtunity to sit and talk about our projects. It was very interesting to hear what everyone else was doing.
This week our assignment was to make up a small network that consisted of ten nodes and run the set of tools provided by Dr. Choe. First I made up a completely random one, then I realized that there wasn't a single motif in the network so I had to go back and fit in at least one. After I had my network I had to look at all the Read Me files to figure out how to work the programs. Figuring out the correct way to enter the data took awhile, but once I figured that out it was easy. This task was supposed to be completed by Thursday before our weekly meeting. Thursday morning I woke up to an email saying that I needed to have a ten minute presentation ready about the work I had done. So I spent Thursday morning putting together a presentation that I had to give in front of a group of grad students and professors. It was an intersting experience to actually have to talk in during the meeting instead of just listen.We also had a seminar on how to use the library for research.
One of the tasks we were given was to find other visualization tools to present the C elegans neuronal network. Perry, a grad student and I found a tool called Walrus on the Caida website. It takes an input file and displays the network in 3-D. Perry and I each wrote a program, he wrote one that took the adjancency matrix and found a spanning tree while I wrote a program that would take the new adjancency matrix as input and produce a file that fit the input standards of Walrus. This week we also had two seminars on applying to grad school and the things on which your application is judged.
This week we looked into how to label the nodes in the representation the Walrus gave us, once we figures this out we looked to see whether or not the picture had placed the nodes in an anatomically correct order. It was strange because the picture looked as though it was the shape of a worm. It was long, skinny, and tapered off at the ends. But once we looked at it more closely we realized that it was just a coincidence. I then generated a random network with about the same number of nodes and connections as the C elegan and it did not come up as the same shape. We also had our monthly luncheon where the head of the engineering department gave a talk and we had a seminar about getting money for grad school.
This week I moved on to analyzing the higher order connectivity matrices of the C elegans neuronal network. I ran a program called Mfinder on the adjancency matrices up to the sixth power. When I got up to the higher powers it took Mfinder a long time to run so I wasn't able to come to any conclusions this week. This week's seminar was about the different types of research going on at Texas A&M, it was intersting to hear about all of the different projects that are going on. The professors who were there talked about their own research and the research of the other professors who couldn't make it. One of the professors at A&M is the creator of C++, I thought that was really cool.
This week I found another visulization tool on Boston University's webpage called visANT. It turned out to be a very useful tool because it was created to analyze and visualize biological networks. I worked with this program all week. First I had to figure out what it was actually capable of doing, next I put in the data for the C Elegan network. The feature I found to be the most useful was its ability to find motifs then single out just the neurons involved in that particular motif. This week's seminar was on how to write a technical paper. Hopefully the information will come be useful when I write my paper.
After this week I only have two left, but this week and the next are the only ones where I can really get much done. I have to prepare a poster for next Friday and I have to take the last week to write a paper. The realization that the summer's almost over has sunk in. I had a meeting with my mentor this week about pulling eveything together, I've realized that I have quite a bit of data but I'm not sure what it all means. So now I have to do the analysis part, which is a lot harder than it sounds. So I spent all week trying to figure out how everything relates.
This week was really stressful, on Friday we had a poster presentation session with the engineering REU. Nobody realized that our summer was coming to an end so fast.Dr. Choe and I spent a lot of time this week trying to take the data I had gathered this summer and the analysis I had done to draw some conclusions that we could put on my poster. It was really tough to sit down with everything and try to link them together in a logical manner. I didn't think I would have enough information to fill up the poster but when it came down to it we realized that I had way too much information and the poster was too small for all of it. So after a couple of very stressfull days I got everything to fit on the poster and the presentation went very well. Everyone had two judges and overall I did pretty good on the evaluation. It was an interesting week because I finally got to see what the other people had been working on all summer. This week was kind of like a closing week for everything, since all of the DMP students were grouped in with the engineering REU and there's ended the following Wednesday. To see pictures of the poster session Go here
The only task I had this week was to write a technical paper, it wasn't as easy as I thought it was going to be and it took a lot more time than I had planned. We were given a template to follow and filled it in with our own information. After preparing the poster it was easy to know what kind of information to put into the paper, but it was hard to get away from the type of writing I'm used to. Techincal writing is so dry and concise compared to writing for an english class. But my mentor helped me through this.