BIOL388/S19:Class Journal Week 3

Ava's Response

1. What aspect of this assignment came most easily to you?
   • I found that finding unfamiliar words or phrases in the paper and then defining them came easily.
2. What aspect of this assignment was the most challenging for you?
   • Interpreting the figures in the paper was challenging as some were a bit ambiguous or not super easy to understand.
3. What (yet) do you not understand?
   • I still do not fully understand figure 4 (which is not good because that is what I am presenting on!) This figure feels like it tried to include way too much data and it is not clear as to what is being shown. There are two different sub-sections of microarrays and one is labeled wild type vs the name of the mutants and I do not understand what it is trying to signify.

Avalekander (talk) 18:08, 3 February 2019 (PST)

Alison S King Reflection

What aspect of this assignment came most easily to you?

• Creating the outline was the easiest aspect of the assignment for me because the wiki syntax is extremely easy to use for this purpose. The headers and bulleting system are perfect for outlines.

What aspect of this assignment was the most challenging for you?

• Understanding the figures and trying to interpret them was difficult for me. It took time to find out what the axes meant, what the trends in the data were, and what the authors of the study wanted us to take away from each figure.

What (yet) do you not understand?

• I don't feel like I fully understand the implications of the study. I would like more information on why this study is important and where it will lead.

Alison S King (talk) 18:39, 6 February 2019 (PST)

Fatimah Alghanem

• What aspect of this assignment came most easily to you?

Finding the definitions for the words that I didn't understand was the easiest aspect of the assignment.

• What aspect of this assignment was the most challenging for you?

Summarizing the Article was the most challenging for me.

• What (yet) do you not understand?

I think by far I have understood everything.

Desiree Gonzalez

1. What aspect of this assignment came most easily to you?
   • The formatting of the layouts of the Wiki Pages was the aspect that came most easily to me. I think I am getting used to the Wiki syntax since it has begun to be second nature; for example, I can now determine the way the page will look without having to press the preview button all the time.
2. What aspect of this assignment was the most challenging for you?
   • The most challenging aspect of this assignment was actually reading the paper and interpreting the data on the figures. The small text size, the use of experimental procedures that I have never heard of, and the various transcription factor names made the article hard to follow. I had to reread portions of it in order to gain a better understanding of what was going on in the experiments.
3. What (yet) do you not understand?
   • I would want to clarify the difference between ESR genes and LCR genes. Are only their response time and functions what makes them different?

Desireegonzalez (talk) 17:36, 6 February 2019 (PST)

Angela Abarquez's Reflection

1. The easiest part of this assignment was creating an outline summary of the article.
2. The most challenging part of the assignment was summarizing the figures, as they took a long time for me to interpret.
3. I still don't understand how the hierarchical clusters are made to make visuals out of the microarray data. I understand how to read them but am unclear on the process to create them out of raw data.

Angela Abarquez

Angela C Abarquez (talk) 13:41, 6 February 2019 (PST)

Brianna N. Samuels

1. The easiest part of the assignment was defining the terms and making the outline
2. The most challenging part of the assignment was understanding and summarizing the figures in the paper.
3. I don't understand how to visualize the microarray data ratios still as well as how the hierarchical clusters played a role in the figures I was assigned.

Brianna N. Samuels Briannansamuels (talk) 16:59, 6 February 2019 (PST)

Austin Dias Reflection

1. The easiest aspect of this assignment was finding the 10 terms that I was unclear of and defining them.
2. Trying to interpret all of the figures and learning every aspect of each one was the most difficult part of the assignment. It took a lot of time and active thinking to figure out each and every one.
3. I am still quite unclear on some of the statistical methods and applications used and how the data is normalized. Specifically I am interested to learn how they turned the raw data they collected into the figures that were presented in the paper. I do not completely understand figure 4. I get the left hand portion of the figure showing the wild type transcription from 30 C to 10 C, but I am confused on what the right hand part of figure 4 is expressing.

Austindias (talk) 21:49, 6 February 2019 (PST)

Leanne's Response

1. Identifying the 10 terms I did not understand was the easiest part of this assignment.
2. The most challenging part of this assignment was combing through the methodology used. The methods section is usually the portion of scientific articles that I skim at best, as it is very dense. Also, most of the software used to analyze and quantify the microarrays were foreign and confusing to me.
3. I am still unsure of how to interpret the transcriptional profiles, specifically Figure 1 with the dendrogram. I understand the color system used, however this doesn't seem to be the best way to analyze the data (at least by eye) as different people will interpret the various genes to be different intensities of green or red. I also am still unsure of how the cDNA hybridizes to the microarray correctly. I understand that it uses the concept of complementary base pairing, but it seems to me that the different gene sequences would simply bind wherever it had a base pair, regardless of it being the correct gene.

Leanne Kuwahara (talk) 23:40, 6 February 2019 (PST)

Edward's Response

1. Finding 10 new terms and defining them. Finding definitions for some of the words from proper biology sources was not the easiest, so I had to find other words that could be searched in the biology dictionaries. Good thing I did not know a lot of words.
2. The figures were definitely the most difficult things to try to understand. While I did have to think critically about each of them for the assignment, I still do not believe that I got the answers to each figure correct.
3. Again, the figures were very difficult to understand, and I do not believe I would have come to the correct conclusions if it were not for the discussion of the results.

EdwardRyanTalatala (talk) 23:55, 6 February 2019 (PST)

Sahil's Response

1. The easiest part of this assignment for me was probably reading and understanding the article and then making the outline.
2. The part that was the most challenging for me was grasping the figures at first but once I read the description I understood exactly what it was talking about.
3. There is still some terminology that I am not 100% comfortable with as of yet, however I feel the more we read these types of articles the more accustomed I will get with it.

Sahil Patel (talk) 08:25, 7 February 2019 (PST)