BIOL398-01/S10:Class Journal Week 6

KP Ramirez

1. The purpose of the assignment this week was to begin working on our experiments that we had begun last week. I started by downloading the raw data visit from my subjects and using the biology workbench and the clustdist tools to generate unrooted trees. This was followed by graphing the T-Cell decline from the raw data excel graphs. After this time was spent to see the similarities between our new paper and how it related to our study.
2. What I learned from this week just more of getting comfortable with Biology workbench as well as analyzing data in different ways.
3. For the most part I understand everything so far, i'm just trying to make sure that the connections between papers are clear

KP Ramirez 2:37 February 28 2010

Individual week 6

Salomon Garcia

1. The purpose of this assignment was to continue working on what we as a group had began working on and to further elaborate on our work in order to complete our presentation that will be presented on Tuesday.
2. One of the most important things that I've learned while working on this assignment was to interpret the data that was in front of me and to better understand Biology Workbench and how a great of a tool it is if used correctly.
3. Overall based on how to use the tools for this class and similar things I understand. The only thing that I'm a bit confused about is some of the data presented in the article that we found for our presentation, but my partner has cleared up some of the questions that I had in regards to them. I had these questions because the article had a lot of data and statistical analysis that at times was hard to decipher.

(Salomon Garcia Valencia 22:28, 28 February 2010 (EST))

Alex George

1. This week we continued working on our HIV Evolution projects. We used Biology Workbench to run our various analysis tests and drew conclusions from our results.
2. I further learned how to use Biology Workbench. In addition, I learned the difficulties of coming up with related tests to determine our hypothesis. I knew what kind of information I wanted to get, but it took a little longer to figure out which test to run in order to obtain the information I wanted.
3. As we were preparing our presentation, I didn't understand if the same rules for Journal Club applied to our presentations. Should we not have one word titles?

J'aime Moehlman

1. The purpose of this assignment was to work on the experiment questions we designed from the Markham article last week. We also worked on putting this information together in a powerpoint presentation in order to share our data/discoveries with the rest of the class. This process also helped us become more comfortable with the Biology Workbench in determining whether or not our hypothesis was correct.
2. What I learned this week was how to analyze the data we needed from the Biology Workbench, I also learned how to recover from discovering that our hypothesis may not be accurate and how to work through that in our research project. I learned that sometimes a research project doesn't necessarily go the way that you want it to go, but that this is okay; and that it helps you discover other questions that you have based on the original hypothesis made.
3. This week really helped me understand how to use the Biology workbench as well as how to tie in a related article we chose from ISI. It also really cleared up any confusion I had regarding the Markham article and how to create a research project.

J'aime C. Moehlman 21:48, 28 February 2010 (EST)

Week 6 Assignment

Week 6 Assignment Page

Kristoffer Chin

1. The purpose of this assignment was to utilize the tools we have learned from last week using the Biology Workbench and to create a presentation on questions we would ask using Markham's HIV data.
2. I learned how to efficiently use the Biology workbench better. I also had a better understanding of working with a partner on a presentation. I gained a better understanding on the use of the S, theta, and min and max distance from the ClustalW. I also learned how to work better with my partner for the lab.
3. I think all of my questiosn that I have been asking for the past 2 weeks were answered with working on this presentation.

--Kristoffer T. Chin 01:55, 1 March 2010 (EST)

Kristoffer Chin: Week 6

BIOL398-01/S10:Week 6

Michael Piña

1. What was the purpose of this assignment?
   • The purpose of this assignment was to answer the question we has regarding the paper on our own (with some guidance, of course). Also, to organize a Powerpoint presentation in the manner of a professional.
2. What did I learn from this assignment (head, hands, heart)?
   • With my head I learned that there is a lot of missing data in the Markham article. I had to focus on the data so that I could interpret it to answer my question. This was not so easy because for the data I was looking at (dS-dN values) there wasn't really any explanation as to how they got them; Dr. Dahlquist explained to me that they authors likely converted the value in to a log scale so it would be more consistent with the other data.
   • With my hands we were required to perform the exercises from last week again so I got more practice using the Biology Workbench tools so I feel more comfortable with them now.
   • I enjoy working with a partner and we were actually available to meet multiple times outside of class which is a rarity but something that I find very beneficial.
3. What did I not understand (yet) about this assignment?
   • The additional article that we found has a lot of data. Although I think my partner and I came to a conclusion about it, I will talk to Dr. Dahlquist about it to make sure.

Individual Week 6

Janelle N. Ruiz

1. The purpose of this week's assignment was to begin analyzing the data we acquired last week and to begin to think about the organization and flow of our presentation. We also were able to see the fruit of our work through the results we obtained.
2. What I learned from this week was how to work well with my partner (who is awesome, by the way). I also learned the results of our analysis and since we did have significant differences between our groups, this was exciting! Additionally, I learned that research is imperfect, even in bioinformatics. I was surprised by some of the issues we found with the Markham article analysis. For example, KP and I realized that there were many missing data points and also that not all of the data was presented in the original article, which surprised us.
3. I understand a lot more about the data today than I did last week, having delved into it quite a bit now.

Janelle N. Ruiz 20:48, 28 February 2010 (EST)

Janelle N. Ruiz Assignment 6

Bobak Seddighzadeh

1. Whwat was the purpose? The purpose of this assinment was to complete our research project. We are to learn how to use the scientific method to test a question and generate data using bioinformatic tools to answer our question.
2. What did you learn? I learned that working on a project with a partner takes a lot of communication. We may have disagreements on the best approach to a problem or question. It takes trust as well. Furthermore, I learned that reading more scientific articles on the topic from previous research can really give your project more insight.
3. Do you have any confusions? No I have no confusion onto how to complete this project. It was pretty straight foreward.

• Electronic Journal

1. Bobak Seddighzadeh Week 2
2. Bobak Seddighzadeh Week 3
3. Bobak Seddighzadeh Week 4
4. Bobak Seddighzadeh Week 5
5. Bobak Seddighzadeh Week 6
6. Bobak Seddighzadeh Week 7
7. Bobak Seddighzadeh Week 8
8. Bobak Seddighzadeh Week 9
9. Bobak Seddighzadeh Week 10
10. Bobak Seddighzadeh Week 11
11. Bobak Seddighzadeh Week 12
12. Bobak Seddighzadeh Week 13

• Shared Journal

1. BIOL398-01/S10:Class Journal Week 2
2. BIOL398-01/S10:Class Journal Week 3
3. BIOL398-01/S10:Class Journal Week 4
4. BIOL398-01/S10:Class Journal Week 5
5. BIOL398-01/S10:Class Journal Week 6
6. BIOL398-01/S10:Class Journal Week 7
7. BIOL398-01/S10:Class Journal Week 8
8. BIOL398-01/S10:Class Journal Week 9
9. BIOL398-01/S10:Class Journal Week 10
10. BIOL398-01/S10:Class Journal Week 11
11. BIOL398-01/S10:Class Journal Week 12
12. BIOL398-01/S10:Class Journal Week 13

• Assignments

1. BIOL398-01/S10:Week 2
2. BIOL398-01/S10:Week 3
3. BIOL398-01/S10:Week 4
4. BIOL398-01/S10:Week 5
5. BIOL398-01/S10:Week 6
6. BIOL398-01/S10:Week 7
7. BIOL398-01/S10:Week 8
8. BIOL398-01/S10:Week 9
9. BIOL398-01/S10:Week 10
10. BIOL398-01/S10:Week 11
11. BIOL398-01/S10:Week 12
12. BIOL398-01/S10:Week 13

User Pager

Amanda Wavrin

• Amanda N. Wavrin Week 6
• Week 6 Assignment Page

1. What was the purpose of this assignment? The purpose of this assignment was to complete our HIV research project with our group and to organize our results into a power point presentation.
2. What did I learn from this assignment (head, hands, heart)? From this assignment I learned how to cooperate and work with my group. I also got more practice using the biology workbench website, using the different tools available. Using biology workbench we ran several multiple sequence alignments and distance matrices. We then interpreted our results and presented them in our powerpoint. I also got more work using ISI and relating our results to those results of the article we found.
3. What did I not understand (yet) about this assignment? This assignment cleared up my confusions from last week about how we were going to complete and interpret our research. However, the results of our research were not completely satisfactory and I wish we had discovered more.

Amanda N. Wavrin 22:40, 28 February 2010 (EST)

Ryan Willhite

1. What was the purpose of this assignment? The purpose was to take a paper and try and create our own questions we would like to research using the same tools that the authors of the original paper used.
2. What did I learn from this assignment (head, hands, heart)? I learned a lot through this assignment. Mainly I learned not to take a person's article for what it says completely. In Markam's paper, after doing the research, I realized that their categorization of the progressors and non progressors seemed a bit flawed. There are so many different aspects to be viewed besides the CD4 T cell count at the end of the experiment. This is apparent when looking at more recent studies like Hill's paper I added to my journal 5 and 6 page. This includes variable regions and nucleotides from both RNA and DNA to really get into the diversity of this progressive disease.
3. What did I not understand (yet) about this assignment? I can only say that in my experiment, there is no definite answer, right, or wrong, however a lot of insight as to what Markham could have investigated instead of simply basing the categories on CD4 T cell counts; it just isn't enough.

Ryan N. Willhite 02:24, 1 March 2010 (EST)

• Week 6 Assignment Page

• Week 6 Journal

Angela Garibaldi

1. The purpose of this assignment was to practice carrying through with the analysis necessary in order to answer a question. It was also meant to get us in the habit of creating a powerpoint presentation based on our question and results in a more scientific format.
2. I learned how difficult it can be to interpret results that aren't necessarily clear. I also learned to become more comfortable with Benchworks, how limited this program can be, yet how simple and easy to use it is. I also learned to be more careful after losing a paper I've searched for when trying to relocate it. I accidentally posted the wrong paper and later realized I had posted an irrelevant paper but quickly found the correct one.
3. I am unclear as to which test would be best suited to test significance for the data we collected. Angela A. Garibaldi 01:03, 1 March 2010 (EST)

Week 6 Journal

Week 6 Assignment Page