BIOL398-03/S13:Week 13

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=== Tasks ===
=== Tasks ===
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# Download the matlab files
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* Download the matlab files
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* [http://openwetware.org/images/9/94/Estimation_driver.m estimation driver code]
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** [http://openwetware.org/images/9/94/Estimation_driver.m estimation driver code]
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* [http://openwetware.org/images/e/e1/General_parameter_estimation_function.m estimation function]
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** [http://openwetware.org/images/e/e1/General_parameter_estimation_function.m estimation function]
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* [http://openwetware.org/images/f/f3/General_least_squares_error.m least squares error function]
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** [http://openwetware.org/images/f/f3/General_least_squares_error.m least squares error function]
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* [http://openwetware.org/images/f/f5/General_network_dynamics.m dynamical system function]
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** [http://openwetware.org/images/f/f5/General_network_dynamics.m dynamical system function]
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* [http://openwetware.org/images/7/77/Full_schade_data.xls sample data input file]
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** [http://openwetware.org/images/7/77/Full_schade_data.xls sample data input file]
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# Open the estimation_driver script in matlab and run it.
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* Open the estimation_driver script in matlab and run it.
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# Paste the graphs of the individual genes into a powerpoint presentation.
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* Paste the graphs of the individual genes into a powerpoint presentation.
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# Upload your powerpoint to openwetware.
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* Upload your powerpoint to openwetware.
== Shared Journal Assignment ==
== Shared Journal Assignment ==
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Look over the excel workbook input file.
Look over the excel workbook input file.
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# How might you change the network to add more genes/transcription factors?
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* How might you change the network to add more genes/transcription factors?
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# How might you run a computer experiment to examine the deletion of a gene?
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* How might you run a computer experiment to examine the deletion of a gene?
Return to the chemostat.
Return to the chemostat.
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# 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?
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* 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?

Revision as of 10:42, 16 April 2013

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.

Contents

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.

Tasks

  • 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).

Reflection

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?
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