User talk:Alyssa N Gomes

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Week 11 Part 2

  • I have some observations to make about your Week 11 assignment as you prepare for the final paper/presentation.
    • With regard to your stem results:
      • All of the terms in your list all have to do with ribosome biogenesis, the process of making new ribosomes. This is a "classic" response to cold shock by the cell. Cold temperatures stabilize RNA secondary structures. The ribosome is composed mostly of RNA and when the structure is stabilized, it gets "stuck" and cannot perform translation very well. Thus, the cell responds by making more ribosomes to compensate. Make sure you understand why I say that all of these terms are referring in some way to ribosome biogenesis and if you don't, please let me know. You should also talk to your partner about this. You both chose the same profile to analyze and you both got very similar results for that profile. It appears that the induction of ribosome biogenesis genes is very similar amongst the two strains you analyzed.
    • There appears to also be an error in the ANOVA table in your PowerPoint. You are reporting the same percentage for p < 0.0001 and the B-H p < 0.05. Also, please give the actual number of genes for each of the p values as well as the percentages in your table.
    • Your statements interpreting the percentages of genes that meet each p value cut-off are odd. The reason why we are counting how many genes with a certain p value cut-off is that we expect that at a p value of < 0.05, 5% of the genes will have a p value of < 0.05 by chance. 5% of 6189 is 309/ So, if more than 309 genes have a p value of < 0.05, then it is likely that some of them did not get that p value just by chance. The logic is is similar for the other p value cut-offs, just with different numbers.

Kam D. Dahlquist 13:44, 5 May 2015 (EDT)


  • The GRNsight home page has been fixed and is now working. Kam D. Dahlquist 18:50, 30 April 2015 (EDT)

Week 14 Feedback

  • I have some observations to make about your data as you prepare for the final paper/presentation (I'm copying both partners on this feedback).
  • Since you re-did your runs in class today, you don't have an interpretation of your data on your Week 14 page that actually matches your new data. Here are some observations that I have made.
    • Which genes in the model have the closest fit between the model data and actual data? Why do you think that is? How does this help you to interpret the microarray data?
      • There does seem to be a relationship between goodness of fit and noise in the data. In fact, instead of talking about which genes have a particularly good fit, there seems to be some ones that have a particularly bad fit, like MIG2. Also there seems to be a few cases where the data for the wt and dGLN3 strain diverge quite dramatically, but the model does not and therefore does not fit the individual strain data very well, like STB5, YHP1, YOX1, and ZAP1.
    • Which genes showed the largest dynamics over the timecourse? Which genes showed differences in dynamics between the wild type and the other strain your group is using? Given the connections in your network (see the visualization in GRNsight), does this make sense? Why or why not?
      • When we are talking the "largest dynamics" over the timecourse, it means which genes showed the largest changes in expression (non-zero log fold changes) at any timepoint and between timepoints. When I look at your graphs, it seems that CIN5, HMO1, INO4, MIG2, MSN4, PDR1, SFP1, SNF5, and YLR278C all show non-zero dynamics in terms of the model. As noted above, some of the model fits aren't very good and the data are actually showing some dynamics that the model is not capturing. How do you explain this?
    • Examine the bar charts comparing the weights and production rates between the two runs. Were there any major differences between the two runs? Why do you think that was? Given the connections in your network (see the visualization in GRNsight), does this make sense? Why or why not?
      • Your weights and production rates from the two runs are very similar to each other, as you expect because GLN3 is not actually controlling any other genes in the network. But as we noted above, the model does not seem to be capturing the dynamics of the differences between strains. How do you explain this?
    • As you prepare for your final presentation and paper, think about how you will display the graphs in your talk. You will probably want to focus in on the genes that illustrate points about the fit, dynamics, differences between the fixed b and estimated b runs, and the differences between genes. I like how you have put graphs for the same gene next to each other on the same slide so that they can be easily compared. Note that on your bar chart that compares the weights, only half of the labels are showing on the x axis. You might need to break this up into two charts so that those can be read.
    • Make sure that the titles of your slides convey a "message" or "result", not just the topic of the slide.

Kam D. Dahlquist 17:59, 30 April 2015 (EDT)

Week 13 Feedback

  • Thank you for submitting your work on time.
  • I have confirmed that you have made the changes requested to your spreadsheet. Make sure to go back and record the changes you made in your Week 13 electronic lab notebook.
  • Your electronic notebook is good, but could be improved by the following:
    • Link to your own individual assignment pages throughout the protocol when it refers to data coming from previous assignments.
    • You need to state which transcription factors did not have degradation rates in the file provided and which you had to subsitute the specified value.
    • Give the actual filename of your new spreadsheet.
  • You are missing the links from your individual journal page to the assignment page and to your user page. You are missing the category. Don't forget, this is part of every assignment.

Kam D. Dahlquist 18:54, 21 April 2015 (EDT)

Week 11 Feedback Part 1

  • I reviewed your spreadsheet and all of the equations are correct. However, you did not do the last step of changing the Bonferroni p values that are > 1 to 1 (in column S).

Kam D. Dahlquist 18:03, 25 March 2015 (EDT)

Week 7 Feedback

  • Your Week 7 individual journal assignment was late by 8 minutes and your shared journal reflection was on time.
  • You are missing the link from your individual journal page to the assignment page.
  • Your electronic notebook is on the right track, but still needs improvement. The intent of an electronic notebook is to record what you did so that you or somebody else could reproduce what you did based on the information there. You did provide your MATLAB files and a description of what values you used for each run of the model. You needed to explain why you chose those values and show the the resulting plots on your wiki page, not just your handwritten notes. Go deeper in your interpretation of what they mean.
  • You needed to perform an analysis of the steady state.

Kam D. Dahlquist 13:06, 17 March 2015 (EDT)

Week 1 Redux

  • I have reviewed the changes that you made to the Week 1 assignment; thank you for submitting them on time.
  • I noted that your usage of the summary field has improved slightly; you have written comments in the summary field for 90% of the last 50 contributions you made. Remember, we are aiming for 100%.
  • You did not complete all requested changes, including creating third level subheadings and fixing the bulleted list.
  • I think there is also still some confusion regarding what needs to go on your template. Your template should include what you have now added to your user page under the header "Assignments". I.e., you need a list of links to each of the course assignment pages, a list of links to your individual journal entries, and a list of links to the class journal entries. Take a look at how some of your classmates have approached this and let me know if you need assistance. It is important to make these changes to fulfill your weekly assignments going forward in the course.

Kam D. Dahlquist 19:49, 10 February 2015 (EST)

Week 1 Feedback

Here is the feedback to your Week 1 journal assignment.

  • Thank you for submitting your Week 1 assignment on time.
  • The grade for this assignment is posted on the MyLMUConnect Grade Center for this course. You will be able to earn back the points you missed on this assignment by completing the requested revisions below by the Week 3 journal assignment deadline of midnight on Tuesday, February 3 (Monday night/Tuesday morning).
    • Every time you make a change to a wiki page, please type something in the summary field (found above the "Save page" button). I estimate you are doing this about 75% of the time. You want to aim for 100%.
    • You did not use and "third" level subheadings (three equals signs or more). Be sure to utilize this feature to organize content on your journal pages.
    • Your bulleted list did not format correctly because you used an initial space before the "*" of the subbullets. As you can see, an initial space on a line actually creates a different type of formatting using a fixed-width font. There are times that we may want this type of formatting, but this is not one of them. If you go back and remove the initial space, your bulleted list will look right.
    • I can see that you modeled your template after the main template for the course. Your template looks good, but does not have quite the information that I intended for student templates. I would like your template to contain a list of links to the Assignment pages, a list of links to your individual journal entries, and a list of links to the shared journal entries, as well as a link to your user page and the BIOL398-04/S15 category. I would prefer all of this information appear on your actual user page (and in subsequent weeks on your individual journal pages as well) and not on a separate page. The reason for this is that it helps me navigate the wiki while I am grading all 10 students' assignments. Having to go to an extra page takes additional time when I could just go there directly. You can still keep the header in place, but provide these links elsewhere on the page. Let me know if you need assistance formatting this. Also your "general" link to shared journal, just goes to the Week 1 journal, so it is labeled incorrectly.
    • The link to the Assignment page and to the Week 1 shared journal was not there as of the Week 1 deadline.
    • You can also remove the OpenWetWare automated text from the bottom of this talk page.

Kam D. Dahlquist 15:58, 29 January 2015 (EST)

I've answered your question on my User talk page. Kam D. Dahlquist 21:26, 29 January 2015 (EST)

Answer from Dr. Fitzpatrick

You asked what do you feel sets you apart from other math professors here, professionally as well as as a whole?

Hmm.. that's a tough one. Professionally, I'd say that I have a lot more applied and industrial experience. I've spent a significant amount of time working in industry (mostly aerospace and defense) in addition to my academic work. As a whole, it's very hard to say. Many of our faculty are pretty well-rounded, with outside interests like hiking, running, photography, music. I like to do woodworking and have made a bit of my own furniture. I have a truck that is older than I am. Those two are probably separators. Ben G. Fitzpatrick 01:22, 21 January 2015 (EST)