User talk:James P. McDonald

Week 12 Journal Feedback

• Thank you for submitting your assignment on time.
• It was a little difficult to review your GO terms since you only listed the GO ID, not the name of the term itself.
• Remember, from our journal club paper and the review articles, it is known that ribosome biogenesis is a process that is up-regulated during cold shock.

— Kam D. Dahlquist 12:38, 18 April 2013 (EDT)

Week 12 Shared Journal Feedback

• With regard to question 4: The individual gene's p value just tells us that we would see that big of a change in gene expression due to chance, that percentage of the time. The other factors that might influence that amount of change in gene expression could be technical issues with the experiment itself. Also, the Gene Ontology terms and transcription factors are two separate considerations. GO terms are associated with a group of genes who all play a part in that process the term describes. There are some terms related to transcription and transcription factors, but most GO terms are related to other parts of a cell's physiology. YEASTRACT tells us about which transcription factors regulate a group of genes.

— Kam D. Dahlquist 15:25, 19 April 2013 (EDT)

Week 1 Journal Feedback

• Thank you for submitting your assignment on time.
• There are a few of things that you need to fix on your individual user page and shared journal page. Please make these changes by next week's journal deadline (midnight, February 8) to earn back the points you missed on this assignment.
  1. You need to put the complete street address for your box at LMU.
  2. On the Week 1 shared journal page, put the link to your user page underneath the header for your section. Be sure to use a label for the link back to your user page. Instead of [[User:James P. McDonald]], use [[User:James P. McDonald | James P. McDonald]].
  3. You are writing something in the summary field most of the time; the goal is to fill it out every time you make a change.
  4. Your external link needs a label. What you did works, but it would be better to use the complete wiki syntax. I.e., use [http://www.lmu.edu LMU], which looks like this: LMU, instead of just http://www.lmu.edu.
  5. For the file you uploaded, you provided a journal article. While this is illustrative of your research, you need to be clear that you did not write this article. You should give the complete bibliographic citation of the article and say that it is related to your research. In addition, you need to find out if you are even allowed to post this article here. The article may be copyrighted by the journal, which means that you cannot repost it without permission. You will need to go to the journal web site to see if that is the case. If it is, you need to take it down. You can link to the article on the journal web site instead and you will need to provide a different file that you own for the assignment.

— Kam D. Dahlquist 01:52, 31 January 2013 (EST)

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James, I answered your question on my user talk page — Kam D. Dahlquist 15:57, 22 January 2013 (EST)

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You asked: "Hi Dr. Fitzpatrick, it appears that you have an extensive background in math, what got you interested in biology as well? James P. McDonald 21:21, 21 January 2013 (EST)"

My answer: My dad was a veterinarian, so I always had some interest. In graduate school, my thesis involved developing and applying so statistical techniques to study brain tissue, and as a young faculty member at UTK I discovered Murray's work on a math model of how leopards get their spots. That kind of thing really got me into it.

Ben G. Fitzpatrick 13:23, 3 February 2013 (EST)

Week 2 Journal Feedback

• Thank you for submitting your assignment on time.
• Your discussion is reasonable, but it would help tremendously to see graphs from some of your simulations. See Elizabeth's page for a good example of a single pdf file containing simulations that are well-annotated. See Ashley's page for figures embedded in the discussion.
• How might you include waste in the differential equation model?

Ben G. Fitzpatrick 13:33, 4 February 2013 (EST)