BIOL398-04/S15:Week 7

This journal entry is due on Tuesday, March 3 at midnight PST (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

NOTE: this page is under construction.

Individual Journal Assignment

• Store this journal entry as "username Week 7" (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: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
  • 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 "BIOL398-04/S15" category to the end of your wiki page.
• Your electronic lab notebook detailing the work you did on your mathematical model goes on this page.

Partners

Tuesday

• TBA
• TBA
• TBA

Thursday

• TBA
• TBA

Research Project

We are focused in this project on Nitrogen metabolism in S. Cerevisiae as discussed in “The Concentration of Ammonia Regulates Nitrogen Metabolism in Saccharomyces cerevisiae,” by terSchure et al. We have successfully modeled two curves in Figure 1 A of the paper, namely biomass and residual ammonia. This modeling is at the level of the chemostat. We have also discussed models of metabolic activity within the cell, examining alpha-ketogluterate, glutamine, and glutamate. In this project we will consider a simplified model of the three reaction metabolic system:

Presentation Guidelines

• You will prepare a 15-20 minute PowerPoint presentation that will present your mathematical model of nitrogen metabolism in yeast. Please follow these guidelines when creating your presentation. You will need approximately 15 slides (1 slide per minute) for your presentation. You will be graded according to this rubric.
• Your presentation should cover the following content:
  • Purpose and significance of the model
  • A list and explanation of the state variables needed to model the process of interest.
  • Your system of differential equations that model the dynamics.
  • An explanation of the terms in your equations.
  • A list and explanation of all the parameters your model requires for numerical simulation.
  • The output (graphs) of your numerical simulation.
  • A discussion of your results and how they relate to the Journal of Bacteriology and Microbiology papers by ter Schure et al. (1995).
  • What future directions might you take.

Shared Journal Assignment

• Store your shared journal entry in the shared Class Journal Week 7 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 "BIOL398-04/S15" category to the end of the wiki page (if someone has not already done so).

Reflection