BIOL398-01/S11:Week 6

This journal entry is due on Tuesday, February 22 at midnight PST (Monday night/Tuesday morning). NOTE new due date and that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

Individual Journal Assignment

 * Store this journal entry as "username Week 6" (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 "BIOL398-01/S11" category to the end of your wiki page.

A Quantitative Look at Nitrogen Metabolism

 * List the state variables needed to model the process of interest.
 * Propose at least one system of differential equations you think will model the dynamics.
 * Discuss the terms in your equation(s) in order to justify your choices.
 * List all parameters your model requires for numerical simulation.
 * Discuss the relationship between the data in the papers by ter Schure et al and the state variables (and parameters).

Shared Journal Assignment

 * Store your journal entry in the shared Class Journal Week 6 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 "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).

Reflection on a Quantitative Look at Nitrogen Metabolism

 * 1) What was the purpose of this assignment?
 * 2) What aspect of this assignment came most easily to you?
 * 3) What aspect of this assignment was the most challenging for you?
 * 4) What (yet) do you not understand?

Read and Reflect

 * Compare the current ter Schure et al paper (Microbiology, 1995, 141, pp1101-1108) with the previously discussed J. Bacteriology (1995) 177, no. 22, pp6672-6675, paper.
 * In what ways are the goals of the papers different?
 * What things in the Microbiology paper help clarify methods in the Bacteriology paper?
 * Do you feel anything is lacking for the purposes of developing a math model and simulating nitrogen metabolism? If so, what?