User talk:Lucia I. Ramirez

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).
  • I noticed on your PowerPoint that there were no differences in the production rates between runs. I looked at your output workbooks for both runs and saw that you had copied the initial guesses for the production rates instead of the optimized versions. The optimized versions can be found in the sheet called "out_production_rates". You will need to redo this bar chart. Also, it would be helpful to see the labels of the gene names on the x axis instead of numbers. It would also be helpful to put the genes in alphabetical order.
  • For your bar chart that contains the weights, not all of the labels for the genes are showing up on the x axis. You might need to split this up into two charts to make them show.
  • In your PowerPoint, it is a nice visual display to see the two plots for the genes side by side. However, make sure that the plots are the same size.
  • For your presentation, you may not want to show all of the genes, but instead pick out a few to highlight that have interesting properties (goodness/badness of fit, large dynamics in expression, divergence between strains).
  • 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?
    • I this case, the question is asking whether the line (the model) fits the experimental data. In other words, do the lines go through the average or center of the data points? When I look at your data, it seems that most genes have a pretty good fit, except for MSN4, ROX1, and YOX1. Do you agree? Why do you think that is?
  • 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?
    • To my eye, it looks like MSN4, ROX1, CIN5, HMO1, YOX1, and YLR278C showed the largest dynamics over the timecourse (nonzero log fold changes). You could look at the p values for the ANOVA you did in Week 11 to confirm this. A lot of your genes showed divergence between the wt and dHMO1 strain. HMO1 has an out-degree of 9, which means that it affects a lot of genes in the network both directly and indirectly.
  • 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?
    • Since the bar chart for the production rates needs to be corrected, I can't comment on this yet.
    • I agree that there aren't major differences between the weight values. Upon closer inspection, it seems that your labels are reversed. ROX1 has 4 incoming edges, but no outgoing edges. You need to label the weights from the controller to the target gene (i.e. outgoing to incoming).
  • Finally, as you prepare your slides, make sure that each slide has a meaningful title that gives the message for that slide.

— Kam D. Dahlquist 17:16, 1 May 2015 (EDT)

Week 13 Feedback

• Thank you for submitting your work on time.
• Your spreadsheet is complete and correct, although you need to save it as ".xlsx" instead of ".xls" for it to work with GRNsight.
• 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 substitute the specified value.

— Kam D. Dahlquist 18:39, 21 April 2015 (EDT)

Week 11 Feedback Part 1

• I have checked your spreadsheet and it is all correct!

— Kam D. Dahlquist 17:52, 25 March 2015 (EDT)

Week 7 Feedback

• Your Week 7 individual journal assignment was late by 1 hour and 36 minutes and your shared journal reflection was late by 1 hour and 4 minutes.
• You fulfilled all of the hyperlinks required for the assignment (back and forth to user page, to assignment, category).
• Your electronic notebook had no descriptive text at all. 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. In addition to the MATLAB files, you should have described what values you used for each run of the model and why you chose them. You should have had multiple plots and your interpretation of what they mean.
• Your handwritten notes on the analysis of the steady-state were good.

— Kam D. Dahlquist 12:49, 17 March 2015 (EDT)

Week 1 Redux

• I have reviewed the changes you made to your Week 1 Assignment; be careful to give yourself enough time to complete assignments so that you don't submit work after the deadline.
• I noted that your usage of the summary field has improved slightly; you have written comments in the summary field for 74% of the last 50 contributions you made. Remember, we are aiming for 100%.
• You did not finish all of the changes requested, including the external link, uploading and linking to a file, commenting out some of your code, and creating and using your template.
  • Correct usage of the template is important for all subsequent assignments in this class. Please take the time to create and use your template as directed; come see me if you need assistance.

— Kam D. Dahlquist 19:41, 10 February 2015 (EST)

Week 1 Feedback

Here is the feedback to your Week 1 journal assignment.

• Thank you for completing this 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). You are doing this approximately 50% of the time, but you should aim for 100%.
  • Please add in information about your future career interests and goals.
  • By the deadline for the Week 1 assignment, you had not created a link to a new wiki page, but you have since then.
  • 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.
  • Please upload an image and display it on your page (removing the double helix placeholder).
  • Please upload a file and link to it within your user page.
  • Please make sure you add the category BIOL398-04/S15 to your user page (Hint: put this on your template and then use your template on your page).
  • Please create a template and invoke it on your user page (you will then use this on all subsequent individual journal pages).

— Kam D. Dahlquist 20:42, 29 January 2015 (EST)

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

Dr. Fitzpatrick's answer to your question

You asked Hi Dr. Fitzpatrick, What is your favorite equation to solve?

dx/dt = a*x(t), like we did in class today. That's gotta be my favorite. Ben G. Fitzpatrick 01:53, 21 January 2015 (EST)