BIOL398-03/S13:Week 13

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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 19 at midnight PDT (Thursday night/Friday 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 13" (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.


  • Open the estimation_driver script in matlab and run it.
  • Paste the graphs of the individual genes into a powerpoint presentation.
  • Upload your powerpoint to openwetware.

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 13 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).


Look over the excel workbook input file.

  • How might you change the network to add more genes/transcription factors?
  • How might you run a computer experiment to examine the deletion of a gene?

Return to the chemostat.

  • In concept, without worrying about creating matlab code, how might you use the least squares technique to get parameters from the ter Schure et al experiments?

Read over the Vu and Vhoradsky paper in this week's reading list.

  • Is the method of the paper different from that in class? If so, in what ways?