From OpenWetWare
Jump to navigationJump to search
BIOL398-03: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

Home       People        LionShare       Help      

  • Your final presentation will take place on Thursday, May 9, at 8:00AM.
  • Your final paper is due by 5:00PM on Friday, May 10.

Final Paper

  • Your final paper for this course is an individual assignment.
  • Prepare 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.

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 9 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

  • The presentation will be given as a group with your project partner. Partners are as follows:
  • You and your partner 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.
  • Upload your presentation slides to the OpenWetWare wiki and link to them from your User page and from this page.