BIOL398-03/S13:Class Journal Week 8

James P. McDonald Week 6 Journal

James P. McDonald

Questions

1. What aspect of this assignment came most easily to you?
   • Determining what the color and shade of the spots would be on the chip when looking at the calculated ratios of the genes.
2. What aspect of this assignment was the most challenging for you?
   • No specific part of the assignment was especially difficult. It just took time to get through the paper and take out specific pieces of information that I analyzed to answer the assignment questions.
3. What (yet) do you not understand?
   • I don't think there was any part of this paper or the assignment that I did not understand. I don't know a lot about computer programming so I don't think I would understand how people have developed programs to interpret and simplify the massive amounts of data present on the microarray chips.
4. What aspect of microarrays would you like to know more about?
   • I would like to know how microarrays could someday be used to determine the the traits of a person or show how a person's genome could point to the potential for contracting diseases. I think this could be very interesting and useful information to have about a specific individual.

James P. McDonald 00:34, 14 March 2013 (EDT)

Ashley Rhoades Week 8

Ashley Rhoades

• What aspect of this assignment came most easily to you?
  • The reading of the chapter came easiest to me. It was a clear, well written chapter and I'm a good reader.
• What aspect of this assignment was most challenging to you?
  • I think the challenge for me was making sure I was going in the right direction with the ratios. I understand what they mena and what the colors mean but it's easy to get mixed up.
• What (yet) do you not understand?
  • I understand the process of producing a microarray in a basic sense but I think I could probably have a fuller understanding of how they are made.
• What aspect of microarrays would you like to know more about?

I would like to know more about the process of making the microarrays and the implications of expression profiles.

Ashley Rhoades 14:06, 14 March 2013 (EDT)Ashley RhoadesAshley Rhoades 14:06, 14 March 2013 (EDT)

Kevin McKay Week 8

Kevin McKay

• Analyzing the data on the graphs was the easiest part of the assignment to me.
• Choosing the correct color for the ratios was the hardest for me. It is pretty much up to the individual to tell where the ratio falls on the color scale.
• I had trouble understanding how to quantify the colored results so exactly.
• I would like to know more about the clustering in microarrays and similar expression profiles, and further applications of the microarray.

Kevin Matthew McKay 15:21, 14 March 2013 (EDT)

Laura Terada Week 8

Laura Terada

1. What aspect of this assignment came most easily to you?
   • Understanding the microarray concept was easiest.
2. What aspect of this assignment was most challenging to you?
   • The most challenging was understanding the ratio calculations and the reasoning behind it. Also matching up the ratio values with the colors and what they mean were confusing at first.
3. What (yet) do you not understand?
   • I have a good understanding on the microarray; however, I find it amazing that people can use computer programs for data analysis on such a large number of genes.
4. What aspect of microarrays would you like to know more about?
   • I would like to know more about expression profiles of specific genes and how they affect different processes. I think learning about how microarrays have been used for biomedical research would be interesting as well.

Laura Terada 15:56, 14 March 2013 (EDT)

Kasey E. O'Connor Week 6 Journal

Kasey E. O'Connor

Questions

1. What aspect of this assignment came most easily to you?
   • Understanding and analyzing all the graphs in the paper was the easiest part of the assignment.
2. What aspect of this assignment was the most challenging for you?
   • There was nothing too challenging about the assignment, however trying to get the ratio and color correct when they all look relatively similar.
3. What (yet) do you not understand?
   • I have basic understandings of how the microarrays work, but I would love to have more knowledge of how to actually make one, and how the process of determining the color ratios functions.
4. What aspect of microarrays would you like to know more about?
   • I would like to know how the microarrays are used for other living things, and what the results of microarrays for the human genome have been used for, especially in medical areas.

Kasey E. O'Connor 21:55, 14 March 2013 (EDT)

Salman Ahmad Week 8

Salman Ahmad

• What aspect of this assignment came most easily to you?
  • It was easy to decide what color would show up if a gene was overexpressed. The paper was also easy to read.
• What aspect of this assignment was most challenging to you?
  • It was hard to decide what colors to use for the rations because the scale only has three colors, and there’s a gradient.
• What (yet) do you not understand?
  • I want to know more about how microarrays can be used in the medical field, and if they are already being used, in what way.
• What aspect of microarrays would you like to know more about?
  • There was a part of the paper that talked about microarrays maybe being less accurate than what most people think. They were not sure if that was because of experiments being carried out differently or if there was some other factor. I would like to know if these problems have been fixed.

Salman Ahmad 22:48, 14 March 2013 (EDT)

Anthony J. Wavrin Week 8

Anthony J. Wavrin

1. What aspect of this assignment came most easily to you?
   • The idea of microarrays and how inducing and repressing genes is relayed with this method.
2. What aspect of this assignment was the most challenging for you?
   • The most challenging part was the actual questions. It was kind of confusing because some of the questions were answered directly in the reading which made me over think some of the responses.
3. What (yet) do you not understand?
   • I do not quite understand how we are going to model all of this information in to MATLAB. The examples in class helped today but, I feel there is much work to be done in that aspect.
4. What aspect of microarrays would you like to know more about?
   • How someone actually discovered an efficient way to create duplicates of genes and place them on a slide in a uniform manner. I feel like the creation of the slide is the most difficult portion.

Anthony J. Wavrin 23:04, 14 March 2013 (EDT)

Paul Magnano week 8

Paul Magnano

• What aspect of this assignment came most easily to you?
  • The idea of how microarrays work, especially since we did an overview in tuesdays class.
• What aspect of this assignment was most challenging to you?
  • The questions were difficult, mainly because it could get confusing. It was not too difficult, it just took me a lot of time to make sure I was not getting confused on some of the more involved questions like the one asking about repression or over expression resulting in repression of another gene.
• What (yet) do you not understand?
  • Im not sure how we will model this, because it seems more complicated than the other models like the metabolism model we created.
• What aspect of microarrays would you like to know more about?
  • I would like to know exactly how accurate microarrays are, in a quantifiable manner. For example in the microbio lab where I work we have machines that will determine the identity of an organism and give a percent confidence value such as 95%. I would like to learn if there is someway this could be applied to microarrays, so that you could better evaluate the results (example, a 95% confidence vs a 75% confidence value would greatly affect the value of the experiment).

Paul Magnano 23:14, 14 March 2013 (EDT)

Matthew E. Jurek Week 8

Matthew E. Jurek

1. What aspect of this assignment came most easily to you?
   • Microarrays look at gene expression and compare expression based on experimental conditions. In previous classes I've learned what exactly gene expression was. It was easy to follow along as the paper described how genes are overexpressed or silenced.
2. What aspect of this assignment was the most challenging for you?
   • I'm still working on understanding how to look at the different ratios of expression and when to use log2 vs. log10. I know the log system is used to make the ratios easier to understand. I'm working on fully understanding how to interpret the ratios based on expression or silencing.
3. What (yet) do you not understand?
   • Similar to my previous answer, I'm working on understanding the math side of the microarrays. I feel like I have the science down, for the most part, as we've discussed it in class several times. I'm working to understand how to fully interpret the results and what exactly the results mean.
4. What aspect of microarrays would you like to know more about?
   • At times it seems like all 6,000 spots are all on one microscope slide. Then in the reading it will say the robot has to read 12 slides within a certain amount of time, making me think the 6,000 spots are divided over several slides. Yet how we discussed this in class, it seems like all the spots are on one slide. I'm trying to figure out how it works exactly.

• Matthew E. Jurek 23:45, 14 March 2013 (EDT):