User talk:Sarah Carratt

Week 12 Journal Feedback

• Thank you for turning in you complete assignment on time.
• Your electronic notebook recording your work this week is very good.
• I see that you had a little trouble with interpreting your GO terms; hopefully it helped when we went over it in class. As I said, you can change the ones you interpret for your paper if you want.
• Also, you should look up the individual transcription factors that you added to the model at SGD to see if there is any further connection with these transcription factors and cold stress.

— Kam D. Dahlquist 00:02, 28 April 2011 (EDT)

Week 11 Journal Feedback

• Thank you for turning this assignment in on time.
• 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.
• When you determined how many genes met the filter of p < 0.05 and were either increased or decreased, I meant that you should find this out for the regular p values, not the Bonferroni corrected p values. It would be best if you found this out for inclusion in the table in your final report.
• 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 instead of just copying it at the bottom of your page.
• Your analysis of NOP8 was good; the cells need to make more ribosomes during cold shock because the existing ribosomes are rendered nonfunctional when subjected to cold temperatures.
• Please let me know if there is any further assistance I can give you with interpreting this portion of the project.

— Kam D. Dahlquist 18:31, 19 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 20:45, 4 February 2011 (EST)

Week 5 Journal Feedback

• Your response to the basic questions of state variables and parameters are good. The only thing I'd tweak is that, once the two concentrations (yeast and nutrient) change simultaneously, the formulas you provide are no longer valid.
• Your observation about the lack of a death phase is a good one.
• The discussion of the parametric studies is rather thin: it would be helpful to see some graphs to illustrate more clearly what you saw in any simulations you conducted. I would welcome a fuller discussion.

Ben G. Fitzpatrick 17:54, 16 February 2011 (EST)

Week 4 Journal Feedback

• Sorry about the long delay for the feedback.
• Terminology for this assignment are little sketchy. The Michaelis Menten equation specifically assumes the complex is in equilibrium, and the Lineweaver-Burk technique is a means of determining the rate parameters in the Michaelis Menten model. While e^x is the archetypal exponential function, the key ingredient of exponential growth is the definition of the growth rate: the population's rate of change is proportional to the population size. The included picture was nice as an illustration!
• The plots of the simulated reactions are good.
• The Lineweaver Burk computation is correct.
• Hang in there on the matlab... you'll get the hang of it. Please feel free to come to my office or email me with questions.

Ben G. Fitzpatrick 17:54, 16 February 2011 (EST)

Week 3 Journal Feedback

• Sorry about the long delay for the feedback.
• Your terminology bit is very well done.
• The equations of mass action are good. The first two are exactly right. The third problem has a power of (1/2) instead of the factor of (1/2)in the C equation. The fourth one has powers of (1/2) and (1/3) instead of factors in the A and B equations. Please see the worked assignment 3 for more information.
• Your matlab simulation results are good.
• Thanks for the feedback on matlab. I understand it's a challenge to learn new math/chemistry/biology at the same time as learning a software package.
• Your discussion of homeostasis and equilibrium was quite nice.

Ben G. Fitzpatrick 17:54, 16 February 2011 (EST)

Week 2 Journal Feedback

• Thanks for making some of the requested changes to your User page. However, I do still strongly suggest that you move your tables of links to the weekly assignments and your individual and shared journal pages over to your template. Also you should add the category "BIOL398-01/S11" to your template. That way, each time you create an individual journal assignment, you can add just your template to that page and all of your links will be there automatically.
• Your definitions and outline are complete.
• For the figure you are presenting in class, you could have had a little more detail analyzing the plots.
• For future reference, you can work the answers to the questions into your outline.
• 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 19:51, 25 January 2011 (EST)

Week 1 Journal Feedback

• Thank you for submitting your assignment on time.
• Your assignment is complete with a couple of minor omissions/suggestions:
  • Please let us know if you have any worries or concerns about the course or if there is anything else you want us to know. If the answers to these questions are "no", then please let us know that as well.
  • You have completed all of the wiki skills, I have a couple of suggestions for improving your page:
    • For your external link to the Passions magazine, use the magazine title as the label for your hyperlink so that you hide the URL. It's OK the way it is, but it will make your paragraph look nicer if you do it this way.
    • Ditto for your link to your PDF schedule. It will look nicer with a label instead of seeing the wiki syntax for the link.
    • For your Week 1 Assignment, you linked to the Class Journal Page. For this first week of class, we didn't have an individual assignment because it was to create your User Page, but for subsequent weeks, you will have an individual journal page to link to. You can create a separate table of links for the Class Journals to make that distinction clear. Also, you could add this table of links 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.

— Kam D. Dahlquist 18:45, 17 January 2011 (EST)

Responses to Instructor Questions

You asked: "Hey there Dr. Fitzpatrick! How did you become interested in biology and math? What inspired you to teach both? Sarah Carratt 16:58, 16 January 2011 (EST) "

I answered: Ben G. Fitzpatrick 17:19, 16 January 2011 (EST) My dad's a veterinarian, so I have long experience in "applied biology," especially biological waste products. I went to college planning to study engineering, but I found math (and the math professors) a lot more interesting. I returned to an interest in biology as a grad student. My adviser was collaborating with some biologists and agricultural engineers, and those problems were very cool. When I came to LMU, the math department was eager to re-energize biomathematics, and the faculty in bio seemed interested in collaborating. In both disciplines, puzzling out the structure and function of things is at the heart of inquiry. Such questions always seem to draw me in. Bringing biology concepts into math courses seems very natural to me in that regard.

You asked: "Hey Dr. Dahlquist!! Why did you choose to co-teach a math class instead of merely staying in the field of biology? Sarah Carratt 16:56, 16 January 2011 (EST)"

I answered: The short answer is that Dr. Fitzpatrick and I do research together and we were both interested in sharing our common interest with students in a class. As to why I am interested in biomathematics in the first place, the field that I work in has become math-intensive in order to analyze and model the data. What we are able to do by combining our efforts in biology and mathematics is much greater than what either of us would be able to achieve alone using just biology or mathematics. Research is becoming more and more interdisciplinary as the problems get larger and larger and require expertise from different areas to solve. — Kam D. Dahlquist 18:53, 17 January 2011 (EST)