BIOL398-01/S10:Class Journal Week 13

For this last Class Journal, please reflect on this class as a whole.
 * What was the most important thing that you learned this semester that you think will stay with you a year from now?
 * Please share anything else you'd like to say about the class.

Kristoffer Chin

 * Overall, this class has showed me new and interesting techniques that can be used in biology research. It is interestingbecause it helps combine the aspects of Biology and apply it to technology. it ismuch different from different labs, but was educaitonal.  A year from now, I belive the experiences from presenting and reading journals will remain intact along with how to use the Biology workbench.  The work using excel will also remain itact as it can be useful in all other applications rather than just biology.


 * I think the class is pretty well off at the moment, I think it would be more interesting if other subjects of biology are tackled besides the huge emphasis of HIV

--Kristoffer T. Chin 05:02, 26 April 2010 (EDT)

Kristoffer Chin: Week 13

BIOL398-01/S10:Week 13

Salomon Garcia
(Salomon Garcia Valencia 02:04, 26 April 2010 (EDT))
 * 1) My overall experience in this class was a great one I learned so many new things on how to use the web in order to find out the results that were needed for each presentation and project we made. Overall, I think that the most valuable aspect of the class that I will take is the usage of the different websites that were used throughout the class, I feel that knowing how programs like GenMAPP, MAPPFinder will be useful in the long run when it comes to the field of biology. Most of the programs and software that were used in the course I feel will stay with me in the long run.
 * 2) I feel that the overall class was great the structure and the material were something that I know and feel will be of my use in the near future. I feel though we could have spend less time on the Markham paper and more time in protein structure. But, other than that I thought the class was great and it taught me many fundamental aspects on how answers in biology are reached.

Alex George
Alex J. George 02:54, 23 April 2010 (EDT)
 * 1)  Learning how to analyze and interpret data in different ways was probably the most important thing I took from this class.  It is interesting to see the ways data can be analyzed (and almost manipulated) to make it fit what you want to happen.  I will look at scientific papers more critically from now on and not just be willing to accept results.  With that in mind, this class helped me realize the amount of work and time that goes into creating an experiment and finding useful results.
 * 2)  As for the class, I don't know how crazy I am about everything being online.  It definitely makes finding assignments easier and sharing information easier, but I guess I am 'old school' in the sense that I like using pen and paper.

J'aime Moehlman
J&#39;aime C. Moehlman 05:00, 26 April 2010 (EDT) J'aime C. Moehlman's Week 13
 * What was the most important thing that you learned this semester that you think will stay with you a year from now?
 * I think that the most important thing I will take away from this class is learning how to analyze datasets while using different computer based programs will stick with me. I was only used to analyzing simple data that I found in my own experiments until this class. I also think that I gained a much better knowledge of how to read scientific articles and how a journal club worked, and I think that will definently play a significant role in other classes.
 * Please share anything else you'd like to say about the class.
 * This class was definitely a huge challenge for me, and I don't think that working with a computer is something I have still gotten the hang of yet, but I really did enjoy studying and listening to other peoples projects based off of the HIV virus.

KP Ramirez

 * The most important thing I learned this semester was how to properly interpret and understand DNA microarray research and more effectively how to present my findings knowledgeably. This included learning how to best structure presentations and allocating how much time is spent interpreting tables and structures in a formal presentations.


 * This was an interesting course to take, even though the university structures it as a Lab to correspond with Biological Databases, in some ways it felt more like a follow up to that course and expanded considerably as far as presenting your findings. This semesters presentations were much more precise and structured then the ones I completed last semester. However, there were also some downsides as well. Having a public OpenWetWare wiki had issues, such as not being able to post all of the files that we wanted, and thus relying on lionshare. However, besides that issue this wiki was similar to last semesters and worked effectively as a way to quickly be able to maintain the data being worked on. As a whole this was a successful followup to Biological databases.

KP Ramriez 05:26 April 25 Individual week 13

Michael Piña
1. This project was essentially the culmination of the lab. We took all of the tools and techniques we've learned and used throughout the semester and applied our own knowledge of Biology to interpret our findings and suggest possible reasons for our results.

2. I believe that this week gave some true insight on what it means to be a scientist; the data isn't always clear cut and there is a lot of room for interpretation.

3. I find many of the Gene Ontology terms to be very vague, so it was somewhat difficult to interpret our results. Overall I think that this project put everything in to perspective so there wasn't really anything else that I'm unsure of or didn't understand.

Individual Week 13 Michael R. Pina 00:38, 26 April 2010 (EDT)

Bobak Seddighzadeh
1. The purpose of this assignment is to learn how to interpret and analyze data. Furthermore, to learn how to use excel as a useful tool in doing so. Also, the assignment was designed to use your biology intuition and reasoning to interpret data. 2. What did you learn? I learned how to fine tune my biological thinking skills by practicing analyzing the data of the GO terms for Nitrogen and Carbon limited cultures. 3. Any questions? I am still not sure as to why everything was either unregulated or down-regulated in the Nitrogen and Carbon limited cultures.

Amanda Wavrin

 * Amanda N. Wavrin Week 13
 * Week 13 Assignment Page


 * 1) I think that the most important thing I learned in this class was how to work with a group on biology related projects and give a proper presentation. I learned much about the biological database but I think a year from now what I will remember most is how to analyze and present data/results.  Excel is another program that I now have much more experience with.
 * 2) Even though the class was a lot of work and a lot of constantly learning new things, I can honestly say I took a lot away from it. Before this class I would not have been this comfortable working with computers on a regular basis and I have more confidence in my ability to use them.  I also have a greater understanding of bioinformatics and how important and useful it is today.

Amanda N. Wavrin 05:57, 26 April 2010 (EDT)

Ryan Willhite

 * 1) What was the purpose of this assignment?  The purpose of this assignment was to utilize GenMAPP as well as MAPPFinder to help organize data, filter, and overall make sense our information for analysis. Through this process color sets were created in order to highlight areas of increase and decrease and find terms that help further our reasoning as to why these genes were induced or repressed.
 * 2) What did I learn from this assignment (head, hands, heart)? I learned a lot through this process. It was not easy and needed more explanation but I eventually understood the reasoning for this process. These programs are used to help organize and filter data and acquire more knowledge as to why certain genes are induced or repressed during the cell wall biosynthesis according to our study on Staphylococcus aureus. Cell wall biosynthesis has a pathway that in a lot of ways can disrupted and can cause inhibition using antibiotics etc. but what is interesting is the information gathered about the genes that help theses processes occur. Filtering and finding these terms that related to our data were the most interesting part mainly because it allowed us to be creative and ask why is this happening? It also allowed us to do a bit of research and say to ourselves if i was a cell why would I induce or reduce this particular gene. It was really a great learning experience and I learned quite a bit. I also learned that it is not only helpful in our study but any study involving microarray analysis that can assist in our many questions about disease, etc.
 * 3) What did I not understand (yet) about this assignment? I still do not quite understand the 10 go terms versus the top ten terms based on increase/decrease and why they differ.

Ryan N. Willhite 16:15, 25 April 2010 (EDT)


 * Week 13 Assignment Page


 * Week 13 Journal