BIOL398-01/S10:Class Journal Week 9

Kristoffer Chin
BIOL398-01/S10:Week 9

Kristoffer Chin: Week 9


 * 1) The purpose of this assignment was to independently study the HIV structure in a group. It was much like the HIV evolution project in which we were required to select HIV patient subjects, visits, and clones from the Markham study.  It lets use utilize bioinformatics tools to analyze the structure of these sequences that were given to us in order to understand the structure of the HIV.
 * 2) I learned how to better understand the ProtPram tool used for comparing amino acids and looking at the protein structures of amino acid sequence. I was also able to utilize past tools, such as the workbench which means that all of these tools are practiced on because they all work together
 * 3) At the moment, I have no questions.

Salomon Garcia
Salomon Garcia Valencia 19:17, 21 March 2010 (EDT)
 * 1) The overall objective of this assignment was to make sure to work as a group to figure out and comprehend the structure of HIV. In order to do this task we would need to work with previous information from the Markham paper as well with the previous tools that we learned such as the case with Biology Workbench and at the same time we learned to use new tools that helped with the creation of 3D models of the proteins we gathered.
 * 2) Some of things that I learned how to use quite well were how to use biology workbench and make a 3D model by making a boxshade once the sequence has been aligned and imported. One other thing that I learn to use but not quite as extensively was the ProtPram Tools.
 * 3) At this time I have no questions.

Angela Garibaldi
Personal Journal week 9

Angela A. Garibaldi 02:46, 22 March 2010 (EDT)
 * 1) The purpose of this was to utilize the tools we learned and apply them to our experiment carried on from the HIV evolution project. The point was basically to examine our questions on a structural level.
 * 2) I learned that this can be very frustrating working with structural programs with no experience with them previously. I also learned that the further into a project you get, the more you realize youd like to ask 5 more questions more in depth as your results prove interesting or uninteresting.
 * 3) I don't completely understand the 3d structure creation yet.

Alex George

 * 1) The purpose of this assignment was to work on our group structure projects.  Bobby and I came up with a question and used the tools from Bioinformatics for Dummies to analyze the data.
 * 2) From this class, I learned the difficulty of working with protein data.  I learned how to use the Expasy tools with out data and use the Cn3D application to analyze protein structure.
 * 3) I feel like I have finally understood the gist of our project.  I wasn't understanding the ultimate goal of our project at the beginning, but now it is much more clear.  However, I don't understand why we are using the Markham data because we have completely fallen away from the whole progressor/non-progressor idea.

Alex J. George 14:59, 22 March 2010 (EDT)

J'aime Moehlman
J&#39;aime C. Moehlman 00:29, 22 March 2010 (EDT)
 * 1) The purpose for this weeks assignment work on our HIV Structure project. Amanda and I decided to continue what we worked on for the HIV evolution project, only this time we were focusing on where we noticed differences between two subjects. We utilized some of the new tools such as prosite, PROTpram, Boxshade, as well as being able to analyze the 3D structure of the entire protein.
 * 2) The things we learned about were PROTpram, and how to use all of the other different tools from chapter 6 and 11. I feel like we found some really interesting data after analyzing our different protein structures from the 2 different subjects.
 * 3) Where we struggled was with accurately identifying the data we were uncovering for our project, however I think that eventually we really got the hang of using the tools we used on our protein structure. Also, we have a lot of information, but were not exactly sure where to include it within our powerpoint.

Week 9 Assignment

KP Ramirez

 * 1) The purpose of this weeks assignment was to work on our independent project on HIV-1 Structure. This allowed us to take time to go through our project and iron out exactly what we were going to explore. We decided to expand upon the work that we had completed on our last HIV project utilizing some of the things that we had learned from this project.
 * 2) This allowed both me and Janelle to use the PROTpram tool as well as looking at the actual structure in terms of how conformational changes could affect our studies depending on where they were.
 * 3) Further questions could deal with how to best present some of the additional information we found and incorporating that into the powerpoint.

KP Ramirez 8:27 pm March 21 Individual week 9

Michael Piña

 * 1) The purpose of this assignment was to observe how the amino acid sequence of the HIV-1 virus relates to it's physical structure, and ultimately see how that can be used to learn more about how the virus is involved in the immune system
 * 2) I've certainly gained some skills moving on to amino acid sequences from DNA sequences that we had been using up until now. I've also gained some practice with the Cn3D software.
 * 3) I don't understand entirely what's happening in the crystal structures that we were dealing with, partially because it's so new to me. I think that the more time I spend with it, however, the more I notice new things.

Individual Week 9

Janelle N. Ruiz

 * 1) The purpose of this week's assignment was to use what we had learned regarding our bioinformatics tools to analyze protein structure in our analysis of our V3 variants from out last Journal Club.
 * 2) I learned how to use these tools and apply this to our study.
 * 3) I feel good about our presentation and our study

Janelle N. Ruiz 03:05, 22 March 2010 (EDT) Janelle N. Ruiz Assignment 9

Bobak Seddighzadeh

 * 1) What was the purpose of this assignment? The purpose of this assignment was to teach us like real scientist how to design and start our own experiment. We are supposed to learn how to draw reasonable inferences from the data we collected so that if we were to actually conduct wet lab experiment we would have a good direction.
 * 2) What did you learn? I learned that forming an experiment takes a long time and its a big process. It takes a lot of thought and reflection and each day your thoughts become clearer and it does not just come overnight. I also learned how to properly present my research form office hours. Furthermore, I learned that I enjoyed doing such things and it became exciting at times trying to collect data and come to new inferences/discoveries.
 * 3) What do you not understand? I have a strong understanding of all my previous questions because I went to office hours twice. I still want to solidify how to do an outline for the presentation.

Amanda Wavrin

 * Week 9 Assignment Page
 * Amanda N. Wavrin Week 9


 * 1) What was the purpose of this assignment? The purpose of this assignment was to finish our HIV structure research project that we began two weeks ago. This projects was intended to allow us to analyze the relationship between protein structure and function.
 * 2) What did I learn from this assignment (head, hands, heart)? From this assignmnet I learned how to predict the secondary structures of proteins and analyze them using the actual 3-D structures of the proteins.  I also learned how to run a boxshade to help us analyze the amino acid differences.
 * 3) What did I not understand (yet) about this assignment? I had a tough time interpeting the results from the tests and programs we ran and understanding what further work we could do with them.

Ryan Willhite

 * 1) What was the purpose of this assignment? The purpose of the assignment was to rephrase our previous question but using protein sequences instead of nucleic sequences to further investigate the questions we had on the markham paper. Using workbench, and the book "Bioinformatics for Dummies," we were able to utilize these skills to experiment and test in the area of biochemistry.
 * 2) What did I learn from this assignment (head, hands, heart)? I learned so much from this task simply because I have never taken biochemistry before. It is a different world in my eyes and I am finding that nucleic sequences may not be the most efficient way of looking for clue but in the protein developed from these sequences. They function entirely different and this is apparent when looking at differences in results from the previous presentation with no to little answers, but some interesting findings to some sort of conclusion as to at least the best method of categorizing progression. Although, what we hoped to find was not found, I learned that these tools online are very informative and helpful in our research. I also feel a lot more comfortable using these programs.
 * 3) What did I not understand (yet) about this assignment? I thought that one of the programs we have used was a bit confusing and still unsure how to use this ProScan tool on the expasy.org site.

Ryan N. Willhite 15:32, 21 March 2010 (EDT)


 * Week 9 Assignment Page


 * Week 9 Journal