BIOL398-01/S10:Class Journal Week 5

Kristoffer Chin

Kristoffer Chin: Week 5

BIOL398-01/S10:Week 5

1. The purpose of this assignment was to create a question from the given information that was recorded by the Markham experiment to allow data analysis through the form of ClustalW. Its purpose was also to understand more about the Markham paper and put us in the scenario of research and experimentation.
2. In this assignment I learned to brainstorm on a previous research and ask a question about it. I did not think we would be able to set up an experiment, but it is better than working without data. It also helped me hone my searching skills in articles using the ISI Web of knowledge. I was able to find papers that cited the Markham article easier by looking through the amount of times it has been cited on its ISI Web of knowledge page.
3. At the moment, there is nothing that I do not understand except the question we have asked and that we will hopefully find the answer to in week 6

--Kristoffer T. Chin 19:47, 21 February 2010 (EST)

Angela Garibaldi

1. The purpose of this assignment was to practice analyzing the research presented in a scientific paper and coming up with an additional question to answer. It also allowed for practice of finding the raw sequencing data collected by the researchers to answer a related question. Further, we also got great practice in searching for other related and more recent work on the topic, which, is important to get in the habit of for the future when developing our own original research.
2. From this activity I learned how to use WebScience and found it to be incredibly useful. I learned that sometimes it's just a matter of understanding the search algorithm enough to come up with terms or parameters that will best retrieve the most comprehensive and relevant results. I found that it was a little difficult to come up with a completely different question to answer but it really helped to have another person coming up with ideas also. Devising the methods was pretty fun and forced me to really consider every detail possible in order to do something in a scientifically sound way.
3. I'm unclear as to how detailed we should make the procedures. Also, are we aiming to write all of the parts of our journal for the hypothesis, etc in a manner that will be best suited to make it into a scientific paper style or just for notations for ourselves. Angela A. Garibaldi 17:47, 21 February 2010 (EST)

Personal Journal Week 5

KP Ramirez

1. The purpose of the assignment this week was to prepare us to being our first real individual bioinformatics project. This involves taking a new approach to an experiment. In the past couple of weeks we have looked into the Markham article and how that experiment was used to approach subjects with different TCell counts and their progression with HIV. This time we have been given the freedom to come up with our own question and experiment using their data.
2. What I learned from this week was learning how to categorize data into forming a cohesive hypothesis. Initially it was very easy to find issue with how the subjects were categorized, but it was another thing entirely to do it yourself. Janelle and I worked together to come up with a good hypothesis as well as categories which can be seen on our individual assignment pages listed below.
3. For the most part I understand everything so far, i feel that the difficulties will come next week with our data.

KP Ramirez 2:05 February 21 2010

Individual week 5

Janelle N. Ruiz

1. The purpose of the assignment this week was to help us discover our own research question regarding the HIV evolution paper and use bioinformatics to help answer that question.
2. What I learned from this week was learning the significance of the statistical tests we performed on the data from last week (pun :P). I also learned ways in which we can analyze the data from the paper to answer our own research question.
3. I feel comfortable so far with our question and the direction we are planning to take with our data analysis.

Janelle N. Ruiz Assignment 5

Janelle N. Ruiz 21:49, 21 February 2010 (EST)

Ryan Willhite

• What was the purpose of this assignment? The purpose of this assignment is to further our knowledge of database usage as well as helping us use the scientific method in order to create our own experiment based off observations or questions of the data presented in Markham's paper.

• What did I learn from this assignment (head, hands, heart)? I learned a lot while doing this. First, generating a question is extremely tough especially wording it in the right way to cover all of what we want to study. I learned how to generate a decent questions based off the Markhem paper and it was kind of fun. It is giving us a chance to research something we are really interested in ourselves using the tools we learned in class and data given to us.

• What did I not understand (yet) about this assignment? I am not sure what I do not understand yet because a lot was just generating our own question and predictions. However, I am sure tuesday or the week after will bring some questions and uncertainties while conducting the experiment.

Ryan N. Willhite 21:11, 21 February 2010 (EST)

• Week 5 Assignment Page

• Week 5 Journal