User talk:Alondra Vega

Week 12 Journal Feedback

• I've responded to your interpretation of the GO terms on your Week 12 journal page. You are on the right track--I just clarified some things for you.
• You have a good description of why you chose your additional transcription factors.
• I did not receive the PowerPoint file that was supposed to be turned in with this assignment, but I was at least able to see some of your figures in the rough draft of the paper you turned in for Week 14, so that's OK.

— Kam D. Dahlquist 23:54, 27 April 2011 (EDT)

Week 11 Journal Feedback

• Thank you for turning this assignment in on time (although you were a little late with one of your reflection questions).
• As I indicated in class, you did all of the calculations in your spreadsheet correctly, good job!
• In answer to the question about why we use the "$" when referring to the cells containing the chip average and standard deviation, your answer is correct, but more precisely, we do that so Excel does not change the cell we are referencing in the equation as we copy and paste it into other cells. If we allowed it to change the cell it was referencing, then we would not be adjusting the log ratios on each chip correctly. This will help us with the statistics in the sense that all of the log ratios will be on the same scale with each other.
• The gene with the lowest p value in your dataset was actually YJL145W at t90. The gene that you described has a small p value, but this one is actually lower. For the gene you interpreted, the proteasome is responsible for getting rid of proteins that the cell no longer needs. The expression is increased at t90. Why would the cell need to increase proteasomes when the cell is recovering from cold shock?
• Your electronic lab notebook was good; it would be better if you had intermixed the pertenant details (e.g. functions) from the copied protocol with your notes. Ideally, an electronic lab notebook should be like a paper notebook and have enough information so that you or someone else can reproduce what you did.
• Regarding your response to the question about NSR1. At every time point where the p value for NSR1 is < 0.05, it can be considered to have a "significant" gene expression change. In this case, you are not comparing the time points to each other, but you are comparing the average log fold change of NSR1 at a particular time point to what it would be if there was no change, 0. So, in your case, the expression of NSR1 is significantly different from zero at t15, t30, and t60, but not at t90 or t120 at a 95% confidence level.
• Please let me know if there is any further assistance I can give you with interpreting this portion of the project.

— Kam D. Dahlquist 19:27, 25 April 2011 (EDT)

Announcement Concerning Matlab

The computers (24 iMacs) on the first floor of Hannon Library have matlab installed. You should be able to access them most of the weekend (hannon hours). Ben G. Fitzpatrick 20:48, 4 February 2011 (EST)

Shared Journal Comments

Feel free to put your class journal comments on the page linked to the syllabus. I formatted all future assignments to make it easier for the class. :)

Sarah Carratt 20:22, 30 January 2011 (EST)

Week 5 Journal Feedback

• The work is somewhat vague. Since you did not provide any plots or quantitative results, it is difficult for me to judge exactly what you did. Statements like "changing these parameters did not change the shape of the graph much" beg for fuller description. Not much means what? I would encourage you to come see me so that you can show me more of what you did here. I would also welcome a more complete posting.
• Some parameters are missing. Each rate constant should be mentioned.
• When the two state variables, yeast and nutrient concentration, start changing in a coupled way, the exponential function definitions you give are no longer valid (which is why we need to go to the trouble of using matlab).

Ben G. Fitzpatrick 16:39, 16 February 2011 (EST)

Week 4 Journal Feedback

• Sorry about the tardy review.
• Terminology is mostly on target. The chemostat bit is fuzzy. After reading the handout for Assignment 5, you may want to revisit this term.
• Your matlab plots are good.
• The Lineweaver-Burk computation is correct.
• Thanks for your feedback in the shared journal about the matlab. I hope this will continue to get better for you. We are in fact simulating the concentrations of substrates, enzymes, complexes, and products as they change over time. We have a "full model" based on mass action, and the Michaelis Menten model, which assumes complex and enzyme concentrations are in equilibrium.

Ben G. Fitzpatrick 16:39, 16 February 2011 (EST)

Week 3 Journal Feedback

• Sorry about the tardy review.
• Terminology is good. Not entirely sure about homeostasis, though.
• Equations are very close. There are equations for A and B in first problem, and they are the negative of the one for C. In the second problem, the loss of C back to A and B is missing from the C equation. The third and fourth equations should have fraction factors instead of fraction powers. What you said in words is good, but it did not get translated into equations correctly. Please check my worked assignment 3.
• The matlab pictures look good.
• Your self assessment is quite accurate.

Ben G. Fitzpatrick 16:39, 16 February 2011 (EST)

Week 2 Journal Feedback

• Thanks for making the suggested changes to your User page based on the feedback from Week 1.
• However, I think you misunderstood one of the things I said. The way that you had put your picture on the page was good, it was visible for us to see you. I was actually talking about the zip and PowerPoint files you had referred to under your "Presentations" section. That is where you want to say "Media" instead of "Image" because we want the link to function to automatically download the file. You actually do want to use the "Image" syntax to display your picture on the page.
• Thank you for submitting your Week 2 assignment on time.
• Remember, when you want to invoke your template so that the template content appears on your page, you need to use the curley brackets, {{ }} instead of the square brackets.
• You have a good level of detail in your description of Figure 1, but could use some more detail for Figures 2 and 3. Make sure you say what the units are and that you understand what they mean.
• You did not need to copy the references from the paper into your outline. References should only be included if you personally read the paper. For your outline, the only reference should be the ter Schure paper itself (unless you did read one or more of those other papers.)

— Kam D. Dahlquist 17:44, 26 January 2011 (EST)

Week 1 Journal Feedback

• Thank you for submitting your assignment on time.
• I have a few suggestions for improving your page.
  • Under your heading "Useful Links", one of your links (to the SGD CIN5 page) has the incorrect syntax for an external link. It just needs a singe set of square brackets. Also, you'll notice that since you did not put a label on the link, it just has a number. It would be more useful with a visible label.
  • When you link to a file that is not an image, please use the wiki syntax of [[Media:exact-name-of-file | visible label]]. Note the use of the word "Media" instead of "Image". When you use the word "Media", the file will automatically download when you click the link. When you use the word "Image", it takes you to the file information page. It is more direct to have the file automatically download.
  • You could add the table of links to the assignment pages to your template so that anytime you use your template on subsequent journal assignments, it will make your life easier. You could also add your Categories to your template so that it will automatically be added each time you use your template.
• You can also delete the automatically generated content from OpenWetWare from your talk page if you want.
• Also, thanks for letting us know about your concerns about reading primary research articles. It was very difficult for me as well when I was an undergraduate. Unfortunately, the only way to get better at it is to practice. Please be sure to come to office hours to go over the papers for the assignments, we are happy to do that.

— Kam D. Dahlquist 20:29, 17 January 2011 (EST)

Responses to Instructor Questions

You asked: Hi Dr. Fitzpatrick! I was wondering how many women were studying Math when you were an undergrad and/or in grad school?Alondra Vega 12:01, 16 January 2011 (EST)

I answered: Ben G. Fitzpatrick 13:54, 16 January 2011 (EST). My undergraduate class was about 25% women, and the grad program at Auburn (where I got my master's) was about the same. The strongest student in that program (by far) was a woman who was hired onto the Auburn faculty after getting her PhD. It's pretty unusual for a department to hire one of its own grads. In my PhD studies we had very few women, probably around 10% of the students. In my previous faculty positions, there were not so many women. At UT Knoxville, I worked a lot with Suzanne Lenhart, who was pretty much my mentor when I was starting out as a fresh assistant professor. She's a great mathematician, a great person, and a super role model for anyone in the profession. If you were to change your mind about nursing and get interested in biomath grad programs, I'd have you get in touch with her.

You asked: "Hi Dr. Dahlquist! I was wondering why you chose to study cell biology other than any other discipline in the Biology field?Alondra Vega 11:57, 16 January 2011 (EST)"

I answered: If you see my answer to Carmen's question above, I was intrigued by cells from when I was very little. I would more properly call myself a Molecular Biologist as opposed to a Cell Biologist because what I am particularly studying is gene regulation which falls more into the area of molecular biology. I am just really interested in how cells work at the molecular level. I am interested in other fields of biology as they intersect with cellular mechanisms. Now that DNA sequencing is so cheap, there are lots of opportunities for field and organismal biologists to ask cellular questions. — Kam D. Dahlquist 20:33, 17 January 2011 (EST)