BIOL398-01/S10:Class Journal Week 4

The purpose of this assignment is to use the bioinformatic tool of the Biology workbench with the data from the Markham HIV experiment. It allowed us to observe and analyze the diversity that they were able to find with the different subjects. The tool was able to show how the diversity of each clone actually came form a common origin. Along with visualizing the diversity, there was also a way to quantify the findings.
From the assignment, I found that there was a way to visualize diversity without needing to use a complex program that needs to be paid for. It can be accessed free online. I also learned that FASTA files can be opened up as .txt files in order to import data into the workbench. I did not know that the data from the experiment was available online which was actually very interesting because now I could see what they worked on
I am still having a hard time understanding how to calculate for the min and max difference with using the the Clustdist tool. I am unsure how the calculations are supposed to be made.
The diversity and divergence of those with the rapid progression compared to the nonprogression was clearly significant, but how was the moderate progression rate determined to be between 200 and 650 CD4 T-cells? Does something significant happen to the body is the CD4 T Cell count is above 650 or below 200?

--Kristoffer T. Chin 01:23, 13 February 2010 (EST)

Salomon Garcia

The purpose of this assignment was to learn how to use the Biology Workbench Website in order to compare and contrast genetic differences between different subjects, clones and sequences.
This assignment taught me how to use the various tools on Biology Workbench. I also learned that the distance between clones along an unrooted tree correlates to the diversity between the two.
I didn't understand the functions on the website at the beginning, but by the end of the assignment I had learned the tools fairly well. Also, I learned how to convert files from Rich Text to Plain Text making it compatible with the website.

Question: Why did you choose to categorize progressors based on cell count and not rate of cell decline? Alex J. George 17:55, 13 February 2010 (EST)

The purpose of this assignment was to learn how to use biology workbench. We used it to to work with the data from the Markham HIV experiment and we also first used it with practice data in order to figure out what the different functions were. The way it works is that is shows the diversity of different subjects and their clones. It lets us observe and analyze the data of the diversity and compare it to the other subjects.
For this assignment I learned how to use the biology workbench, I found myself frustrated with it because I didn't understand exactly what the assignment was asking for. On the website itself I didn't really understand what the diversity was so that made it very challenging. The tool itself was easy enough to work with. I also learned how to work with the different sequences found in FASTA files.
I didn't really understand what the last activity was asking us to do exactly. Also, while I understand what the term diversity means I don't understand what the numbers represented very well on the workbench.

Markham question: Is there a better way of classifying subjects as rapid- nonprogressor? The number chosen seems arbitrary; maybe a better system could involve other factors.

J'aime C. Moehlman 21:46, 13 February 2010 (EST)

The purpose of this assignment was to give us an introduction to using bioinformatic tools to analyze real data. We were also able to do some real analysis of this data.
I become more comfortable with the biology workbench, which I had never used before. Also, I learned to be patient with programs which I am just learning. I learned how to interpret an unrooted tree.
I would like the statistical significance of the values (S, theta, min and max differences) explained a bit more thoroughly in class.

Markham question: What were some of the main criticism you received from your reviewers? Of this criticism, what issues were you able to address, and were their any aspects of the study which had to be substantially modified in response to reviewer suggestions? Did you think that this criticism was fair?

Janelle N. Ruiz 04:41, 14 February 2010 (EST)

The purpose of this assignment was to use the data from the Markham experiment incorporated in Bedrock to gain experience in using a tool such as biology workbench to answer questions on the HIV evolution handout. These questions included using sequence tools and ClustW in order to make trees determining how close the sequences are to each other.

What did I learn from this assignment (head, hands, heart)? I learned a lot from this assignment including taking snap shots of my work and incorporating the images to my journal. I also learned to use biology workbench which were somewhat different from the actual handout instructions but worked out just fine since it was a pretty easy tool to use. The only thing frustrating was that there were only a limited amount of sequences to be incorporated at a time which gave me a bit extra to do. I also learned that once again, computers are not as reliable as I would want them to be and lost data and had to start over, except it wasn't too bad because a lot was saved since I had a certain session already started. That's also when I learned that the sessions can be saved automatically which is a life saver.
What did I not understand (yet) about this assignment?

Ryan N. Willhite 20:34, 14 February 2010 (EST)