BIOL398-01/S10:Class Journal Week 4

Kristoffer Chin

Week 4 Assignment

Week 4 Entry

1. 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.
2. 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
3. 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.
4. 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)

Alex George

1. 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.
2. 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.
3. 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)

Ryan Willhite

1. What was the purpose of this assignment?
2. What did I learn from this assignment (head, hands, heart)?
3. What did I not understand (yet) about this assignment?