BIOL398-04/S15:Class Journal Week 12

Lucia I. Ramirez

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

All the parts that had to do with Excel came most easily to me. Also copying and pasting data into the software was not too hard.

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

Troubleshooting was one of the biggest challenge. Even though most of these were repetitious, a small simple mistake can create errors when running the software.

• What (yet) do you not understand?

I really didn't understand the difference between the three sets of networks generated through the GRN software. Also, why were we looking at the degree distribution? Lucia I. Ramirez 02:58, 14 April 2015 (EDT)

Lucia I. Ramirez 02:59, 14 April 2015 (EDT)

William A. C. Gendron

1. What aspect of this assignment came most easily to you?
   • The steps were quite easy although there were some issues along the way, like being unable to access them for most of Sunday.
2. What aspect of this assignment was the most challenging for you?
   • The dCIN5 had limited significant transcription factors so I had to run all of them to attempt to create enough overlap between mine and the wildtype. We ended up only having 5 overlaps and mine had only had 11 significant TFs. I combined most of the two groups and removed some arbitrarily to keep it a bit below 30. We may increase the size of this later to make sure we have the full picture for this section of the network.
3. What (yet) do you not understand?
   • I do not understand why we include CIN5 in the dCIN5 comparison or how these values are going to be weighted. Will this be using data from the lab or is it relying on information from previous studies? How complete of a network should we aim for? I used all the significant ones from dCIN5 and a portion from the wild type. What questions should we be asking with this model?

• William A. C. Gendron 22:58, 13 April 2015 (EDT):

Tessa A. Morris

1. What aspect of this assignment came most easily to you?
   • The part that came easiest to me was manipulating the data in Excel because I am very familiar with the program.
2. What aspect of this assignment was the most challenging for you?
   • The aspect that was most challenging to me was the analysis of the data and the end.
3. What (yet) do you not understand?
   • I would like to talk more about how to interpret the data especially the plots from GRNsight.

Tessa A. Morris 23:58, 13 April 2015 (EDT)

Kristen M. Horstmann

1. What aspect of this assignment came most easily to you?
   • I felt like the excel aspect was easiest, especially after last weeks excel practice, most of this week's was very straightforward and explanatory.
2. What aspect of this assignment was the most challenging for you?
   • I felt like the majority of the assignment and the analyzing was fairly straightforward although I had some difficulty with understanding what the frequency meant and how to approach that aspect of the assignment. However, was it was explained, it was very simple and easy to do. I feel like my biggest struggle is a deeper understanding of all of this, like the terms and connections, which doesn't interfere with the assignments now, but might be an issue when the final paper is due.
3. What (yet) do you not understand?
   • As mentioned above, I think I would like to understand how all these transcription factors and genes fit together better and what the edges mean. While the GRNsight program was very easy to use and gave a nice map of the connections, unfortunately, my cell and biology background isn't quite strong enough to understand the entirety of what's happening.

Kristen M. Horstmann 23:17, 13 April 2015 (EDT)

Alyssa Gomes

1. What aspect of this assignment came most easily to you?
   • The YEASTRACT analysis and numerical values came easily to me. Because I am a math major I am much more apt to work with numbers and comparing values than biological terms. After (slowly) processing the Week 11 Excel work, most of the work seemed to fall into place.
2. What aspect of this assignment was the most challenging for you?
   • Defining the transcription values and why/how they worked with this gene regulation was a bit more difficult for me. As I searched the transcription factor terms last week, each answer came up with more terms that I needed definitions for. Also, it was to make sure that I wrote my methods as accurately as possible to ensure that readers could do the same procedure.
3. What (yet) do you not understand?
   • I still do not quite understand the purpose of the gene regulatory networks. I am not sure how to analyze the GRNSight graphs and understand a bigger picture from them. I know it says that having more than 40-50 factors for make the graph too dense to analyze, but as I cannot interpret any of them, I cannot distinguish what graphs are easier/harder to interpret.

Alyssa N Gomes 23:26, 13 April 2015 (EDT)

Lauren M. Magee

1. What aspect of this assignment came most easily to you?
   • I think working and formatting in Excel came easiest to me, because I am very familiar with the program. The directions are clearly laid out for us on our assignment page and while it requires you to have a keen eye for detail, Excel is a very user friendly program and you will notice almost immediately when you make an error.
2. What aspect of this assignment was the most challenging for you?
   • Working with Yeastract was the most challenging part of this assignment for me, because its functions were completely foreign to me. I think it's easy to follow an instructor in class, when you are going through the task, but doing it on your own is much more challenging. Of course, the directions given were very clear, but because it was so new, it took me a while to adjust to the format. I found this assignment to be relatively easy, as it was many just following direction and plugging numbers and files into an online system. The complications, however, come in when you receive and error message or something doesn't look exactly right. I find these small issues to happen to me quite often, which may be a commentary on my inability to focus on the detailing in an assignment.
3. What (yet) do you not understand?
   • I am looking forward to understanding the significance of these pathways in the future. While I understand the importance of transcription factors, it will be interesting to see how cold shock and the deletion of the HMO1 gene effect there expression and presence in interaction pathways. I don't know if I completely understand the graphs created by STEM, but that may be due to the fact that I was only able to effectively use STEM today and have not had a chance to sit down and analyze the figures yet.

Lauren M. Magee 01:58, 14 April 2015 (EDT)

Natalie Williams

1. What aspect of this assignment came most easily to you?
   • Most of the homework came easy to me just because I do this weekly for research, so I know the ins and outs of the system. It is nice to be around familiar territory.
2. What aspect of this assignment was the most challenging for you?
   • A difficult aspect of this assignment is just setting up the degree tab in the worksheet. Because I had 41 genes, it took a while to calculate ad input equations for some of the information.
3. What (yet) do you not understand?
   • I am confused about in degree and out degree. My understanding was that the in degree was for genes controlling or the columns. They are the input and therefore the in degree. The out degree was the rows which equivocates to the output of the genes being regulated.

23:39, 13 April 2015 (EDT)

Kara M Dismuke

1. What aspect of this assignment came most easily to you?
   • Working within Excel came fairly easily to me because I have worked a lot within the program before, and because the work we were doing within the software was pretty simple and straightforward.
2. What aspect of this assignment was the most challenging for you?
   • Organizing my files and saving them with the proper file extensions proved to be the most difficult part of the assignment for me. It created extra work for me when I lost some of the sheets and graphs due to my negligence to ensure I was saving using the proper file extensions.
3. What (yet) do you not understand?
   • I am still a little confused about the meaning of the "Function" column and the "In-degree", and "Out-degree" rows/columns. I am not quite sure what these mean.

--Kara M Dismuke 00:10, 14 April 2015 (EDT)

Jeffrey Crosson

1. What aspect of this assignment came most easily to you?
   • The manipulations in excel.
2. What aspect of this assignment was the most challenging for you?
   • Understanding all of the biological phenomena.
3. What (yet) do you not understand?
   • I'm not sure exactly how the two strains are being compared? Are we finding what gene networks they share for responding to cold shock?

Jeffrey Crosson 2:54, 14 April 2015 (EDT)

Karina Alvarez

1. What aspect of this assignment came most easily to you?
   • The YEASTRACT analysis and building a gene regulatory matrix from the YEASTRACT came the most easily to me because it helped me visualize the genes that we were working with. Starting from over 6000 genes was overwhelming but being able to whittle them down to the most significant ones and see how they were related was not too difficult and was also very helpful.
2. What aspect of this assignment was the most challenging for you?
   • For me, it was most difficult to just work with the Zip files. Perhaps it is because I was not very familiar with these tools that I was challenged, but I had trouble using and handling these files from week to week.
3. What (yet) do you not understand?
   • I do not quite yet understand how we will compare the two networks for each of the strains that we have, but I look forward to understanding how these genes play roles in different organisms and strains.