BIOL398-01/S10:Class Journal Week 8

Kristoffer Chin
Kristoffer Chin: Week 8

BIOL398-01/S10:Week 8


 * 1) The purpose of this assignment was to take a step forward in the HIV project from looking at sequences to actually looking at translation and protein folding. This week was mostly an introduction to the tools that we will be utilizing once  independent projects start.  These tools help analyze the sequences that were acquired from the Markham paper.
 * 2) I learned how to utilize the protein analysis tools that was shown by the Bioinformatics for Dummies book. I was surprised to see that there are these many resources online that helps with the analysis of the HIV and free.  I thought that there would be some programs that would be necessary to purchase for specific analysis.  I also learned that there are many more details that are in a single sequence of a protein that we have yet learned in undergraduate studies showing that there is still much to learn.
 * 3) I still do not understand the complete nature of all the tasks that was practiced in this week's assignment. I think practice will make it easier and perhaps a clarifications for the ORF and the purpose ofthe other tools that had vague explanations in the book

--Kristoffer T. Chin 01:38, 15 March 2010 (EDT)

Salomon Garcia
Salomon Garcia Valencia 02:11, 15 March 2010 (EDT)
 * 1) The purpose of this assignment was to familiarize ourselves with the new programs from the internet. We did this by following the Bioinformatics for Dummies instruction. Because these new tools will be needed for the following project on HIV.
 * 2) I learned how to use the tools as shown in the Bioinformatic Book for dummies. The instructions were straight forward and to the point.
 * 3) Overall, I understood the assignment I just think that I will need a bit of time to familarize myself with the tools and the only way that I will be able to achieve this is by practicing as these phase of the project moves on.

Angela Garibaldi
Angela A. Garibaldi 02:53, 15 March 2010 (EDT)
 * 1) The purpose of this assignment was to learn how to use these bioinformatics tools online that help to figure out a protein from sequence(primary structure) to its 3d structure.
 * 2) I learned that sometimes the way things are termed can be more of a hang up than the actual concepts. I kept getting confused as to which sequence I should use for these exercises, so I ended up just using one from the Markham clones.
 * 3) I feel that I understand the concepts of the programs pretty well but am still confused as to which sequences I should have been using during these exercises. Also, I definitely would need more time to learn the ins and outs of these different tools in order to make the most of them

Week 8 Assignment

Alex George

 * 1) The purpose of this assignment was to get us comfortable working with protein sequences so that we will be able to use these tools for our project.
 * 2) I learned a lot of helpful information from this assignment.  The book showed us how to obtain sequences from SWISS-PROT as well as how to test the amino acid sequence of the protein.  Also, the book showed us how to interpret the results using different tools, such as the transmembrane protein tool.
 * 3) I am still trying to figure out how we can use these tools for our particular project question.  Also, I didn't know if we were supposed to work through the entire chapter 6, or just the two bullet points you mentioned on the assignment.

J'aime Moehlman

 * Week 8 Assignment Page
 * J'aime C. Moehlman's Week 8


 * 1) What was the purpose of this assignment? The main purpose of this assignment was to help us become more comfortable with using different online tools, so that we can work with protein sequences.
 * 2) What did I learn from this assignment? I learned how to get amino acids from protein sequences, as well as how to use differnt web tools in order to learn different things about a protein sequence. I also am really enjoying the study of the HIV disease; I feel as though this could eventually lead me in a direction towards a research opportunity.
 * 3) What did I not understand about this assignment? I'm still a bit fuzzy on using each of the sites that the Bioinformatics book had us working with, but I think that the more I use them, the more comfortable I will get with them.

KP Ramirez

 * 1) What was the purpose of this assignment? The purpose of this assignment was to teach us how to use new online tools as well as understand more in the field of bioinformatics using our Bioinfomatics for dummies book.
 * 2) What did I learn from this assignment? This assignment taught me how to find amino acids from protein sequences,as well as the tools needed to analyze and understand them that we have at our disposal. I never appreciated how the bioinformatics book actually has a lot to offer, but walking through these practices helped me to plan out what I can use in my future assignment.
 * 3) What did I not understand about this assignment? Even though I feel this was a good excersize, i also feel that I need to practice this more to really understand it.

KP Ramirez 3:24 pm March 14 Individual week 8

Michael Piña
Week 8 Individual
 * 1) The purpose of this assignment was to get us familiar with the protein sequences and to practice with gene databases so that we can to begin to formulate our question for our project.
 * 2) I gained a good deal more practice with gene databases with this assignment. I really think that with this assignment we're getting to the core of what bioinformatics is about.
 * 3) I understood this assignment very well. I definitely need some more time to think about the question that I want to answer, but it's not necessarily something that I don't comprehend as of now.

Janelle N. Ruiz

 * 1) What was the purpose of this assignment? The purpose of this assignment was to demonstrate to us how to use online protein analysis tools to analyze our protein sequence.
 * 2) What did I learn from this assignment? I learned how to determine transmembrane domains, post-translational modifications, etc.
 * 3) What did I not understand about this assignment? I didn't understand the ORF task as well as I would have liked...I will need help with this on Tuesday.

Janelle N. Ruiz 22:00, 14 March 2010 (EDT) Janelle N. Ruiz Assignment 8

Bobak Seddighzadeh

 * 1) What was the purpose of this assignment? The purpose of this assingment was to learn how to use pro param tools to analyze our protein sequences.
 * 2) What did you learn form this assingment? I learned how to use expasy.org to retrieve protein sequences and create a SWISS-PROT entry. I also learned how to determine the open reading frame of my sequence, do a PROT Param and look for transmembrane proteins.
 * 3) What are your confused about? I am not sure exactly what all the graphs and results for each tool translate to.

Amanda Wavrin

 * Week 8 Assignment Page
 * Amanda N. Wavrin Week 8


 * 1) What was the purpose of this assignment? The purpose of this assignment was to move into the second part of the HIV project. This assignment introduced us to the HIV structure part of the HIV project.
 * 2) What did I learn from this assignment (head, hands, heart)? From this assignment I learned all about how to analyze protein strucutre. By following the instructions in the Bioinformatics for Dummies book, I was able to retrieve a protein sequence, run TMHMM, and use the NCBI ORF finder, among other things.  This assignment allowed me to work on my computer and bioinformatics understanding as well.
 * 3) What did I not understand (yet) about this assignment? Some of the instructions in chapter six were difficult to follow and complete at first.

Ryan Willhite

 * 1) What was the purpose of this assignment?  The purpose of this assignment was to follow the instructions included in the "Bioinformatics for Dummies" book. These instructions are involved with protein sequencing while using the ExPASy site.
 * 2)  What did I learn from this assignment (head, hands, heart)? I learned once again that the book's instructions have some differences. A whole section from the book was skipped because the site is extremely different from the book screen shots. Technology is constantly changing and this is apparent with the noticeable differences.
 * 3) What did I not understand (yet) about this assignment? I still do not understand fully every task in its entirety in the "Bioinformatics for Dummies" book.

Ryan N. Willhite 01:14, 15 March 2010 (EDT)

Week 8 Assignment

Ryan N. Willhite Week 8