BIOL398-01/S11:Week 14

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BIOL398-01: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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This journal entry is due on Tuesday, April 26 at midnight PDT (Monday night/Tuesday morning). NOTE new due date and that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Individual Journal Assignment

  • Store this journal entry as "username Week 14" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.)
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL398-01/S11" category to the end of your wiki page.

Preparation for Final Paper

The purpose of this week's assignment is to prepare you for the final paper and presentation due during Finals week.

  • Your final presentation will take place on Thursday, May 5, at 8:00AM.
  • Your final paper is due by 5:00PM on Friday, May 6.
  • Your milestone for this week's journal assignment is to prepare a rough draft of your final paper according to the guidelines below. To do this, you will be compiling and interpreting the results from the last few journal assignments. Compiling all of the figures and tables will also assist you with preparing for your final presentation, but you will just be turning in the rough draft of the paper.
  • E-mail your rough draft to Drs. Dahlquist and Fitzpatrick if it is < 10MB in size. If the file is larger, please post it on Lionshare and provide us the link.

Style Sheet

Use the following guidelines when formatting your paper.

  • 1" margins
  • double-spaced
  • Times New Roman, 12 point font
  • Number the pages
  • Title page should include a descriptive title for your project, your name, the course number and name, and the date of submission


The function of the title is to identify the main topic of the paper. It should be as specific as possible and name the organism. It can be a phrase or a sentence. What is the main result of your paper that you want to convey with the title?


The introduction gives the background information necessary to understand your paper. The introduction should be in the form of a logical argument that "funnels" from broad to narrow:


  • States importance of the problem
    • Why are we studying gene regulation and cold shock?
  • States what is known about the problem
    • Introduce the DNA microarray experiment that was performed.
  • States what is unknown about the problem
    • Little is known about which transcription factors regulate the early response to cold shock
  • States clues that suggest how to approach the unknown
    • Introduce the workflow of performing statistical analysis of the microarray data, clustering and GO term analysis, and finding candidate transcription factors with YEASTRACT
  • States the question the paper is trying to address
    • Using the model to estimate the relative contribution of each transription factor to the regulation of gene expression
  • Be sure to cite your sources according to the Guidelines for Literature Citations in a Scientific Paper instructions on the course home page. A good rule of thumb is that each paragraph should have at a minimum, two in text citations.


  • This section will summarize the entire workflow for the project. This needs to be a narrative description of what you actually did, but it is not a protocol or recipe. For each step, describe in words what you did and why.
  1. A description of the experimental design for your assigned microarray dataset
  2. The steps you performed in Excel
  3. Using STEM
  4. Using YEASTRACT
  5. Using the model

Results & Discussion

The text of the Results & Discussion section should be a narrative that describes and interprets each of the results from your DNA microarray modeling project. In particular, include the items listed below and describe each of the figures/tables in words in your text.

  • Number each of the figures sequentially; number each of the tables sequentially.
  • Write a descriptive legend for each figure and table that briefly states what the figure/table is and gives a brief key to any labels and abbreviations.
  • Create a table that reports the results of the DNA microarray analysis
    • How many genes were significantly increased and decreased at the different p value cut offs (see your Week 11 Assignment)?
    • How do you interpret the p values?
  • From the STEM analyis, include as figures the overall results (the screenshot showing all of the clusters) and then focus on the one you interpreted for your Week 12 Assignment.
    • Include a table showing the GO results for that cluster (just the narrowed down list of terms that you have interpreted).
    • Discuss what the p values for the cluster and for the GO term list mean. Discuss the interpretation of these results.
  • Include a table that lists the transcription factors that you are working with and include a picture of the network that you downloaded from YEASTRACT. Explain why you chose to include the transcription factors that you did.
  • Include the table that shows the output of your model: the optimized threshholds.
    • Show the individual plots for each transcription factor which compares the model to the actual data.
    • Interpret the results of the model simulation. 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? Which transcription factors are most likely to regulate the cold shock response and why?
  • What future directions would you take if you were to continue this project?


Acknowledge anyone that helped with your work (i.e., your classmates, instructors, and anyone else you had discussions with).


Presentation Guidelines

  • You will prepare a 15 minute PowerPoint presentation that will present the results of your microarray modeling project. Please follow these guidelines when creating your presentation. You will need approximately 15 slides (1 slide per minute) for your presentation.
  • Your presentation should cover the same content as your paper, but in a presentation format.
  • You are not required to turn in a rough draft of your slides for the Week 14 Assignment, they are due at the time of your presentation.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 14 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).


Reflect back on your learning for this project and for the entire semester and answer the following:

  1. What is the value of combining biological and mathematical approaches to scientific questions?
  2. Looking back on your reflections on the Janovy and Steward readings from the Week 1 Class Journal, do you have any further insights to share? Have your answers changed to those original reflection questions? Why or why not?