BIOL398-03/S13:Week 14

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Revision as of 21:54, 22 April 2013 by Kam D. Dahlquist (talk | contribs) (Creating your model input file: finished degradation rates, started production rates)
BIOL398-03: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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This journal entry is due on Friday, April 26 at midnight PDT (Thursday night/Friday morning). NOTE 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 "BIOL398-03/S13" category to the end of your wiki page.


Creating your model input file

Your first task will be to create a model input file using the Dahlquist lab data you have been working with.

  1. Your file will be similar to the sample data input file that you used last week, but with your expression data and network. You should download this file, change the name, and edit it to include your data.
  2. The first thing you need to do is determine the transcription factors that you are including in your network. You are going to use the "transposed" Regulation Matrix that you generated from YEASTRACT in the Week 12 Assignment.
    • Copy the transposed matrix from your Regulation Matrix file and paste it into the worksheets called "network", "network_weights", and "network_thresholds".
    • Note that the transcription factor names have to be in the same format across the top row and first column, like CIN5, not Cin5p, so you will need to change the format of the names in the top row.
    • It may be easier for you if you put the transcription factors in alphabetical order (using the sort feature in Excel), but whether you leave your list the same as it is from the YEASTRACT assignment or in alphabetical order, make sure it is the same order for all of the worksheets.
  3. The next worksheet to edit is the one called "degradation_rates".
    • Paste your list of transcription factors from your "network" sheet into the column named "StandardName". You will need to look up the "SystematicName" of your genes. YEASTRACT has a feature that will allow you to paste your list of standard names in to retrieve the systematic names here.
    • Next, you will need to look up the degradation rates for your list of transcription factors. These rates have been calculated from protein half-life data from a paper by Belle et al. (2006). Look up the rates for your transcription factors from this file and include them in your "degradation_rates" worksheet.
  4. The next worksheet to edit is the one called "production_rates".

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 "BIOL398-03/S13" 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?