BIOL398-01/S10:Class Journal Week 4

Kristoffer Chin
Week 4 Assignment

Week 4 Entry

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

From Anton Weisstein: A CD4 count below 200 is one of the main criteria used by the Centers for Disease Control to diagnose a case of full-blown AIDS. To the best of my knowledge, this is the point below which a host is often unable to fight off typical opportunistic infectious such as PCP pneumonia, toxoplasmosis, etc. The choice of 650 between moderate and non-progressors was somewhat arbitrary. However, we did our best to base the cut-off on a empirical division in the data.

Salomon Garcia

 * 1) The purpose of this assignment was to learn how to use the program Biology Workbench which will be an essential tool as we progress in the rest of this course, and it's a very useful tool to have.
 * 2) This assignment helped me to familiarize with Biology Workbench since it's my first time ever using it, the exercise helped alot.
 * 3) I somewhat understand the purpose of using Biology Workbench but the only thing that I don't understand is why do we have to use the FATSA format when putting the info into the box.

Question: What was the reasoning behind, when you decided to categorize the 15 subjects into the 3 different categories.

Angela Garibaldi
Week 4 Assignment

Week 4 Entry

Angela A. Garibaldi 22:46, 14 February 2010 (EST)
 * 1) The purpose of this assignment was to get used to using the BenchWorks program as an introduction to programs that are utilized in creating phylogenetic trees from actual sequence data. This was also a great introduction to the basics of the entire process of collecting the sequence data, converting the data into a visual and numerical format for statistical analysis, and then completing actual statistical analysis.
 * 2) I learned how to navigate Benchworks and most of all I learned how difficult it can be to do even simple statistical analysis without a demonstration or classmates to ask. This approach can take significantly longer but I definitely learned it much more in depth as I struggled to figure it out.
 * 3) I don't completely understand the maximum and minimum numbers. I understood how to get the correct numbers but I don't understand what the actual numbers represent specifically. I also don't understand the finer implications of Theta or the depth of the equation we used to calculate it.
 * 4) Question(s) for Markham:What is the most difficult aspect about recruiting HIV positive subjects? Why did the study only sample subjects every 6 months? Would it have been easier or more difficult to have subjects come in even 4 times a year to keep them in a routine and provide more time points for statistical strength? In retrospect, are there any other tests either statistical or molecular that you would conduct to strengthen the paper against any criticisms?

Alex George
Question: Why did you choose to categorize progressors based on cell count and not rate of cell decline?
 * 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.

Alex J. George 17:55, 13 February 2010 (EST)

From Anton Weisstein: Good question! We actually considered a classification system based on slope, but eventually decided that the actual CD4 count was likelier to impact a patient's immunological status than the rate of decline. For example, consider Subjects 6 and 13. Both have nearly equal rates of CD4 decline over the study period, yet Subject 13's counts are consistently higher than Subject 6's, indicating better immune function. Alex is right, though, that a more sophisticated analysis should incorporate both counts and rates. Alex J. George Week 4

J'aime Moehlman
Week 4 Assignment J&#39;aime C. Moehlman 21:46, 13 February 2010 (EST)
 * 1) 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.
 * 2) 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.
 * 3) 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.

From Anton Weisstein: See the previous two answers [to questions from Kris and Alex]. ANY classification scheme is arbitrary to a certain extent, so we did our best to choose a system that reflected the issues we cared most about (a patient's immunological function). I would push back just a little and ask J'aime what specific factors s/he would like to include, and how to incorporate those factors without making equally arbitrary divisions. But there's no question that it's important to check whether another, equally reasonable classification scheme would give substantially different results, so the point is well taken.

KP Ramirez

 * 1) The purpose of this assignment was to get involved using the biology Benchworks and the Markham Paper. This allowed us to create our own unrooted phylogenetic trees using the sequence data from the actual experiment. This process was the first one we have done to take actual findings from experiments and allow us to make other observation as to how the experiments were run.
 * 2) This allowed me to start using Benchworks. Much like the first time I ever used the program mappfinder I found out just how much this program allows users to be able to do. However, just like mappFinder we must realize that this software occasionaly has bugs and you need to work with it to accommodate. This included downloading on the Fasta format and using TextEdit or other simple txt software.
 * 3) Unfortunately this assignment was particularly difficult for me at first. I knew that this weekend would be extremely difficult as I would be out of town so i tried to finish everything by friday. This involved coming into office hours which were helpful, however, i still could not finish. I had issues loading the matrices into excel because of the limitations of the Mac TexEdit software. Unfortunately my largest difficulties were the instructions, however, as I learned last semester in cases like this its best to edit them on your own.


 * Question: Why were the subjects catagorized based on the Tcell decline, additionally, if you could do the experiment over again would you stick to the injection drug users, or branch out into other samples such as transfusions.

KP Ramirez 8:06 February 14 2010

Individual week 4

Michael Piña

 * 1) What was the purpose of this assignment?
 * 2) *The purpose of this assignment was to get us looking at articles with a more critical eye. I think that many times (especially as an undergraduate student), it becomes easy to think that if a scholarly article makes it into a prestigious journal it is solid in its conclusions. This assignment forced us to look at the data ourselves and come up with our own conclusions which may not necessarily agree with the authors'.
 * 3) What did I learn from this assignment (hands, head, heart)?
 * 4) *With my hands, I got to familiarize myself with the Biology Workbench which is new to me. I found that the GUI is very lacking but the tools seem powerful and very useful for automating tedious tasks.
 * 5) *With my head, I learned that it is sometimes necessary to take scholarly articles with a grain of salt, which you sometimes take for granted when a professor says "Here, read this."
 * 6) *With my heart I learned that I can't always just jump into a computer program and know exactly how to use it; I need to take a moment to read the directions.
 * 7) What did I not understand (yet) about this assignment?
 * 8) *I know more or less what the statistic calculations mean, but I'm not entirely sure.

Question: What were the reasons for the inconsistencies in collecting the data (i.e. some subjects only have a few data points)? Do you think that these inconsistencies disrupted your conclusions significantly?

Janelle N. Ruiz

 * 1) 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.
 * 2) 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.
 * 3) 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)

From Anton Weisstein: Gosh, that was 12 years ago, so I don't recall all of the criticisms! One criticism I do recall asked whether the presence of multiple identical viral samples from the same patient might be due to duplicate amplification of a single viral particle, rather than due to separate amplification of identical viral particles. Although cloning is not my specialty, I understood this to be a reasonable question, and one which we discussed on p. 12569 (second half of 1st full paragraph). Based on the # of input copies of viral DNA, we didn't have to redo any portions of the study in response to this criticism. Janelle N. Ruiz Assignment 4

Bobak Seddighzadeh

 * 1) The purpose of this lab was to teach us how to sequence HIV data and how to interpret it using programs that actual scientists use.
 * 2) The first part of the experiment taught us to be familiar with pub med and pulling up relevant data. The we became familiar with Gen Bank. After we learned how to access information we learned how to apply it to Biology Workbench. Lastly we learned how to interpret unrooted trees and how to quantify the information from the trees.
 * 3) I am not sure as to why I was consistently the only person of all my classmates that struggled with biology workbench. For some reason day after day it would not operate well for me even when I created new accounts and started over twice. I tried different computers. I tried safari and mozilla. I tried it at different days and different times. Fortunately, I was able to use Kris Chin's account which began to work for me. I also had difficulty calculated the max and min.

Amanda Wavrin

 * Amanda N. Wavrin Week 4
 * Week 4 Assignment Page
 * 1) What was the purpose of this assignment? The purpose of this assignment was to familiarize us with GenBank and Biology Workbench.
 * 2) What did I learn from this assignment (head, hands, heart)? From this assignment I learned how to use the Biology Workbench website. I learned how to analyze HIV sequence data using multiple sequence alignments, unrooted trees, and distance matrices. I also learned how to better deal with my computer frustrations. Throughout this assignment I had many computer issues to work with.
 * 3) What did I not understand (yet) about this assignment? I really struggled with activity 2, part 2 of this assignment. I was not sure how to find S or theta.

Ryan Willhite

 * 1) What was the purpose of this assignment?
 * 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.
 * 1) 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.
 * 2) What did I not understand (yet) about this assignment?
 * I still do not fully understand the second part to activity 2, part 2. I also need work on how to do screen shots.

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

Week 4 Assignment

Ryan N. Willhite Week 4