User talk:Laura Terada

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Week 12 Journal Feedback

  • Thank you for submitting your assignment on time.
  • Excellent job with the electronic notebook for the assignment!
  • Be careful about the difference between a gene and a GO term. The individual genes change expression; a GO term is associated with a group of genes.
  • Also be careful when discussing the 90 and 120 minute timepoints; the cells are at 30°C, recovering from the cold temperature, they are not acclimating to the cold.
  • There is an issue with your regulation matrix file from YEASTRACT. It should only include the transcription factors in the original network plus the new ones you chose to add. On the Generate Regulation Matrix page, you need to paste your list of transcription factors into both the "Transcripton Factors" and "ORFs/Genes" fields and do not check the box for "Check for all ORFs/Genes". Please remake this file and upload it to LionShare. Send me the link when you have done it.

Kam D. Dahlquist 18:33, 17 April 2013 (EDT)

Week 12 Shared Journal Feedback

  • For question 4 of the shared journal reflection, be careful in the way you state your answer. The profile and GO term p values do not refer to individual genes. The profile p value is a measure of the probability that you would see that many genes that fit that expression profile due to chance. The GO term p value is a measure of the probability that you would see that many genes in that profile associated with that GO term due to chance. The latter two p values are dealing with groups of genes, not individual genes. Also, the GO terms do not necessarily include transcription factors. There are GO terms specific for transcription, but most of the terms relate to other cellular processes. YEASTRACT was telling us about which transcription factors potentially regulate the genes in the cluster, not the GO terms.

Kam D. Dahlquist 13:38, 18 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. Please let us know on your user page or via e-mail if you have any worries/concerns about the class and if there is anything else you want us to know, even if the answer is "no".
    3. On your Biomathematical Modeling Course Links section of your wiki, you have a stray bullet point. This happens when you use two asterisks to start a list instead of just one. Only use two asterisks underneath where you already have one asterisk.
    4. Make sure that you use the summary field to record what you changed every time you make a change.
    5. Your template duplicates links that you put on your user page. You can delete the links you put there manually because you are using your template.
    6. On the Week 1 shared journal page, make your name the header of the section where you answered the questions. Make sure you make a label for the link to your user page, i.e., Laura Terada instead of just User:Laura Terada.
  • Please feel free to delete the welcome message from OpenWetWare below.

Kam D. Dahlquist 18:53, 30 January 2013 (EST)

Laura, I've answered your question on my User talk page. Kam D. Dahlquist 19:45, 21 January 2013 (EST)

You asked: "Hi Dr. Fitzpatrick, what are your thoughts in regards to the future of biomathematics in the medical field? What is your favorite aspect of biology? Thanks, Laura Terada 15:07, 17 January 2013 (EST)"

My answers: Mathematics and computation will become more important in medicine as we learn more about the operation of the human organism (especially at the level of genes and gene regulation). Math and computational models that are quantitatively accurate will help us experiment more safely and efficiently. Models and algorithms will aid in hardware/medical device design and operation, from replacement limbs to insulin pumps. On your second question, I'd have to say the evolution of patterns that can described simply in the presence of such complexity is what interests me about biology.

Ben G. Fitzpatrick 13:15, 3 February 2013 (EST)

Week 2 Journal Feedback

  • Thank you for submitting your assignment on time.
  • Thank you for fixing the broken return link, too!
  • Your discussion is a bit thin. You need to include a little more detail on the simulations you performed.
  • Graphs would be very helpful in backing up your discussion. See Elizabeth's page for a good example of a file containing some well-annotated simulations, or Ashley's for graphs embedded in the discussion. Paul's screencaps, while a bit difficult to view due to size, may also help you.
  • How might you model waste?

Ben G. Fitzpatrick 13:57, 4 February 2013 (EST)

Hello, Laura Terada! This is a welcome message from OpenWetWare. By the way, we've announced you on the home page! You can leave messages to any OWW member by editing their User_talk pages like this one. And don't forget to personalize your User Page so that we can get to know you better! We've included some tips below to get you started.

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