BIOL398-01/S10:Class Journal Week 3

Kristoffer Chin
Week 3 journal Entry

Week 3 Assignment Page

Lab Reflection
--Kristoffer T. Chin 00:06, 8 February 2010 (EST)
 * 1) The Purpose of the assignment was to better understand the techniques in searching science articles through specific search engines. These search engines helps find a a reliable source rather than using a generic one like Google.  THe enginges used were PubMed, Google Scholar and, ISI Web of Knowledge.  The assignment also helped exercise reading and imporving analysis on scientific journal articles to become a critical reviewer.
 * 2) Prior to the assignment, I already had some experience in using the PubMed search engine along with Google Scholar and ISI Web of Knowledge. That part was easy, but I did have a difficult time finding a review article.  I am more used to finding primary sources rather than review articles and this helped me with that.  I am learned how to actively read a scientific journal through outlining it and taking time rather than rushing.
 * 3) I understood the assignment pretty well, but I do not really understand the need for review articles. I know that they can help with accompanyment in reading the primary source, but I alwasy thought it is better to read that instead of a review.

Salomon Garcia

 * 1) The purpose of this assignment was to get used with using the database and finding relevant information on HIV-1.
 * 2) The important aspects that I learned from this assignment was how to use pubmed, being my first time and all it was an interesting experience. Especially when so many different articles showed with the search.
 * 3) For the most part I understood everything from this assignment, the only part where I had some problem was when it came to the article of Markham, to interpret the stats that is to be presented to the class even though we noticed many significant aspects and characteristics that are relevant and hard to explain.

Angela Garibaldi

 * 1) The purpose of this assignment was to practice reading through a scientific journal article on a topic that we have little knowledge of in order to get in the habit of looking up terms we do not know in order to better understand the experiment that was conducted and its importance. It was also meant to teach us how important it is to understand the tables and figures that convey data and to look at the paper and the data with a critical eye.
 * 2) I learned that it is important to look up terms I don't know immediately because it really helped to understand what was being explained. I also learned that in some papers the author tries to fit as much information into one sentence in the most concise way possible which means that it can sometimes be really unclear and takes a lot of time to decipher. However, I found that it is these sentences that seem to be the most important to understand because they pack so much information in even though it was very frustrating at times.
 * 3) I understand the assignment pretty well although I would like to spend more time learning the immunological mechanisms involved in fighting viruses. I also couldn't find seroconversion as word in the biological dictionaries and had to go to an outside source. Angela A. Garibaldi 23:46, 7 February 2010 (EST)


 * Week 3 Journal Entry
 * Week 3 Assignment Page

Alex George

 * 1) The purpose of this assignment was to learn how to use Biological databases to find relevant information to our search topic.  Also, we learned how to distinguish between a secondary review paper and a primary source.
 * 2) From this class, I learned how to navigate around databases such as PubMed and the ISI Web of Knowledge.  In addition, I learned HIV-1 is a virus that attacks the CD4-receptor T-cells in the body.  Finally, I realized the importance of HIV-1 study because of the large amount of research that is dedicated to it.  In addition, we learned a little background information about the HIV-1 virus and the Markham article went into further detail into examining the reasons why HIV-1 virus causes CD4 T-cell decline.
 * 3) In terms of databases, I didn't realize that the abstracts of articles can be published online before the physical paper is published.

Alex J. George 20:02, 4 February 2010 (EST)

J'aime Moehlman
J&#39;aime C. Moehlman 22:37, 7 February 2010 (EST)
 * Week 3 Journal Entry
 * Week 3 Assignment Page
 * 1) What was the purpose of this assignment? The main purpose of this assignment was to be able to navigate a research database and search for an article or topic that we are interested in. It also helped us learn how to analyze someones research.
 * 2) What did I learn from this assignment (head, hands, heart)? I learned how to properly analyze and summarize a research article. I also learned how to use the PubMed database in order to find something specific that I was looking for. This assignment was actually really helpful and I think that studying HIV over the course of this class is going to be something I really enjoy.
 * 3) What did I not understand (yet) about this assignment? This assingment was pretty straight forward, the only thing I can think of that I don't quite understand fully is how to use google scholar or the ISI research database.

KP Ramirez
Individual week 3
 * 1) The purpose of this assignment really reinforced how bioinformatics is used in the scientific community. Biological databases like PubMed serve as the forefront for new developments in studies on diseases and genomics. This session allowed everyone in class to practice actually using the databases, including specifying the searches and relevance.
 * 2) From this assignment I learned how to navigate through databases and analyze research articles. It was also a good experience to use the ISI Web of Knowledge that is utilized at LMU. We began to understand more about HIV-1 through our article including background information as well as how it attacks the CD4 T cells in the body. This was the introduction to our first large assignment.
 * 3) What I didn't understand (yet) was figures 3-4 in the article. But other then that this assignment went very well.

Michael Piña

 * 1) What was the purpose of this assignment?
 * 2) *The purpose of this weeks assignment was to begin familiarizing ourselves both with biological databases and scientific literature.
 * 3) What did I learn from this assignment (head, hands, heart)?
 * 4) *With my head, I got quite a bit of practice going through a primary source. Often times I find myself skimming through these types of articles because I have hard time trying to decipher through the information that is presented because its so densely written. Allowing myself to take time with the article and summarize it in my own words allowed for greater absorption of the material.
 * 5) *With my hands I learned how to navigate myself through PubMed and how to better narrow down my searches to find something thats more relevant to what I'm looking for.
 * 6) *With my heart I learned that I am not as fast with reading through articles as I would like to be and it is something that I would like to improve upon in the future.
 * 7) What did I not understand (yet) about this assignment?
 * 8) *I didn't completely understand the methods section of the article, though I believe that I got the gist of it.

Individual Week 3

Janelle N. Ruiz

 * 1) What was the purpose of this assignment? The purpose of this assignment was to get us to start thinking about HIV and what we already might know about the virus, what we do not already know, and what we would like to know. It also allowed us to become comfortable with online databases such as PubMed.
 * 2) What did I learn from this assignment (head, hands, heart)? I learned how to navigate the online database Web of Science, which I have never used before (never even knew it existed). I also learned that it is useful to use more than one database for a give search. It was interesting to see the vast differences in interest among my classmates in terms of which review articles they selected. I got some indight into the diversity of our class in terms of background and interest.
 * 3) What did I not understand (yet) about this assignment? I did not understand the last in-class question as well as I should have and had to ask for help from Kevin.

Janelle N. Ruiz 22:59, 7 February 2010 (EST)

Janelle N. Ruiz Assignment 3

Bobak Seddighzadeh

 * 1) What was the purpose of this assignment? The purpose of this assignment was self explore different methods of discovering research articles for the purpose of gaining experience and comfort in finding research articles that may be pertinent to our research or this class.
 * 2) What did I learn from this assignment (head, hands, heart)? I became more comfortable with using PubMed and furthermore I learned about another website that hosts a database of research called ISI Web of Knowledge. I also learned that articles in certain databases will have an ID number that I can reference on my wiki page, and it'll link me directly to the page.
 * 3) What did I not understand (yet) about this assignment? The assignment is very clear for the most part. What I did not understand though was Table 1. I didn't understand how the non-progressors had some of the smallest CD4 T cell count. That seems counterintuitive.

Amanda Wavrin

 * Week 3 Journal Entry
 * Week 3 Assignment Page


 * 1) What was the purpose of this assignment? The purpose of this assignment was to get us working with the online databases. During this lab we were able to familiarize ourselves with the databases, such as PubMed, and we learned how to efficiently search for research articles. We also learned how to recognize the differences between primary and review articles.
 * 2) What did I learn from this assignment (head, hands, heart)? With my head and my hands I got to familiarize myself with the online databases. Before this lab my computer skills were limited so it is a good opportunity for me to become more comfortable using these online biological databases and the computer in general. I also learned how to conduct searches to find scholarly papers/articles. Bioinformatics for Dummies was extremely helpful in this lab and I can see how it will come in handy throughout this course. With my heart I learned that I can finish anything if I am motivated and dedicated.  Understanding the HIV article and writing an outline on it was a challenge but I was able to complete it successfully after some of time and effort.
 * 3) What did I not understand (yet) about this assignment? After this lab I felt very comfortable using PubMed and Google scholar but I am not as comforatble using the ISI online database. The search tactics seemed more complex and not as easy to work.  Hopefully in time and with some practice I will become more familiar and comfortable with that website.

Ryan Willhite

 * 1) What was the purpose of this assignment?
 * The purpose of this assignment was to familiarize ourselves with biological databases such as PubMed. Reading Bioinformatics for Dummies also allowed us to see the differences created in such a short amount of time. Technology is always changing for the better. Change was apparent when trying to follow directions from the book yet seeing something completely different on the screen in front of us. Also, we prepared for the HIV Evolution project utilizing the new skills we acquired from the Bioinformatics for Dummies book on databases.


 * 1) What did I learn from this assignment (head, hands, heart)?
 * I learned a lot from this assignment. As far as the head, I learned how to search different articles using databases. I learned how to do advanced searches and really familiarized myself with newer tools I learned from the help menu. I tried to use knowledge from the book as well as the help menu to find what I was interested in as far as HIV. As far as my hands, typing different keywords got me no where at first. I got so frustrated because at first I could not find what I was looking for. Later, with the click of a mouse, I could find what I wanted exactly through advanced and more specific searches which I did not know was an option when first starting. In my heart, I know this will help me find anything I want with a reliable source. Often times on the internet there are so many people with different opinions and not considered too reliable. Learning about this database gives me a chance to look up articles and either do further studies or provide reports or essays with reliable sources. This was truly beneficial.

Ryan N. Willhite 13:12, 4 February 2010 (EST)
 * 1) What did I not understand (yet) about this assignment?
 * At the time when I first started I did not know that PubMed had such a great advanced search engine. I liked google scholar simply because I thought their advnaced search engine was great. However, the database we used for the in-class assignment had drop down arrows that even allowed me to narrow down the articles to only those that were review articles. This is important because now I will know for certain whether or not the sources are primary, secondary,etc.


 * Week 3 Assignment Page


 * Week 3 Journal