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)

Salomon Garcia

1. The purpose of this assignment was to formulate a question that is significant enough to answer and make a power point presentation out of it, and at the same time use our previous knowledge of Biology Workbench for this presentation.
2. The most important aspect that I learned was that it isn't easy formulating a question, as a matter fact its difficult and tough to formulate a reasonable question.
3. Thus, far all of the aspects of this assignment are understood and it's just a matter of time until the answering of the question occurs. (Salomon Garcia Valencia 22:35, 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

Alex George

1. The purpose of the assignment was to come up with a good, testable question in relation to the Markham paper. We also used the databases to find relative articles that would support our hypotheses.
2. I have further learned how to use the research databases at my disposal. Also, my group members and I realized the pitfalls that can come with forming a hypothesis on given data.
3. As for questions, the assignment is relatively clear. I will probably have a few questions once we get into the data analysis.

Alex J. George 22:16, 22 February 2010 (EST)

J'aime Moehlman

BIOL398-01/S10:Week 5 Week 5 Journal Entry

1. The purpose of this assignment was to come up with a group question based on the Markham et al. paper. It was also another opportunity for us to use the ISI to help search for an article related to our specific project question.
2. This assignment is actually really exciting for me, I'm really looking forward to starting the research and comparisons for our groups question. Also, I feel like I am getting better at using the different research databases to find even more articles related to this topic.
3. This week I don't have any big questions about what we did, I'm still finding using the workbench a bit difficult, however I think that I'm starting to understand what its' different functions are a lot better.

J'aime C. Moehlman 20:54, 22 February 2010 (EST)

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

Michael Piña

1. What was the purpose of this assignment?
   • I believe that the purpose of this assignment was to get us thinking about what it might be like to carry out our own research based on the work and data of the scientific community; so that we might be able to add information and discover new things that other people might not have looked at.
2. What did I learn from this assignment (head, hands, heart)?
   • With my head, I really thought hard about what I wanted to look into more specifically in the paper and what the possible discoveries could be that would be beneficial information about the HIV Virus.
   • I did not do too much with my hands this week, but I’m sure I will be this upcoming week.
   • With my heart, I got to see what another person saw as an area of interest in the paper. I thought that this was important because they may have seen something that didn’t occur to me or vice versa
3. What did I not understand (yet) about this assignment?
   • I can’t really say because this week I was just generation thoughts, ideas, and possible questions regarding the paper and not really looking into them.

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)

Bobak Seddighzadeh

1. What was the purpose of this assignment? The purpose of this assignment was to start us on the path of developing our own bioinformatics projects that is relevant to the paper and topics we have been covering in class. The assignment started was designed to get us to develop a question in which we can begin to design our project around. This is very realistic and relevant to how scientists use the scientific method for scientific discovery. This assignment will make me more familiar with practicing science.
2. What did I learn from the assignment (hands, head, heart)? From this assignment, I learned how to use ISI Web of Science as a tool much better. Furthermore, I learned that formulating a scientific question requires a lot of thought, and is very fundamental to the project because essentially the whole project is built around your question. Therefore, I learned the importance of taking the time to devise a very thoughtful question.
3. What did I not understand from this assignment? I felt that the procedure, purpose, and design of this week's assignment was very clear. I have no questions from this week's assignment.

• Week 5 Assignment Page

• Week 5 Journal

Amanda Wavrin

• Week 5 Assignment Page
• Amanda N. Wavrin Week 5

1. What was the purpose of this assignment? The purpose of this assignment was to work together as a group to formulate a relevant testable question to research for our HIV project.
2. What did I learn from this assignment (head, hands, heart)? During this assignment I learned how to work with my group and cooperate together to pool our ideas and come up with a research project idea. I also got to work more with the ISI in an effort to find relevant HIV articles.
3. What did I not understand (yet) about this assignment? This week there were no real difficulties, we were able to formulate a question and find more HIV related articles. I fear that the real confusion will come next week as we work more with our project during lab.

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