Template:Cell Cycle Exercises

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-	===Concept Maps and System Statements===	+	===Modeling the Cell Cycle Exercise===
-	===Creating with Stella===	+	Work in groups of 3. Work with people from different discipline. The goal of the lab is to become familiar with the software and the process of constructing a model.
-	[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]	+
-	===Playing with Existing Models===	+	====A. Draw flow diagrams or concept map for the statements provided below.====
-	Exercise using an existing model of Goldbeter in Stella Demo	+
-	Purpose: To become oriented with the model and the software. This exercise was designed to work with Stella Demo or Player.	+	1.Create a concept map of the following:
-	Click through the levels of the model (interface to model and equations) using the up and down arrows in the top left corner.	+	* inactive MPF becomes active MPF
		+	* Active MPF becomes inactive MPF
-	The values in the right hand column of the tables “Variable values” and “Vmax of other reactions” can be changed by typing directly into the cell.
-	Exploration	+	2.Concept map the following:
-	1. Run the simulation with the slider for “Vmax Cyclin degradation” to the far left (0.02).	+	* Cyclin is synthesized and degraded
		+	* Cyclin stimulates inactive MPF to become active MPF
-	What results do you see in the graphs?	+	====B. Create the same concept maps in Stella.====
-		+	[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]
-	How are the reaction velocities changed?	+
-	Does it matter if you change the initial values of the variables?	+	How do we create a reaction in Stella? What are the factors in a reaction?
		+	====C. What goes in the boxes? Reaction rates [[Exercise rationale]]====
-	2. Re-run the simulation with the slider for “Vmax Cyclin degradation” placed to the far right (0.6)?	+	1. Consider all reactions to be linear and based on the law of [http://eot.bu.edu/ccb/Kinetics/RateLaws/MassAction.htm mass action] (rate constant x substrate).
-	What results do you see?	+	2. Use two of following set of rate constants in the rate equation: 0.05, 0.1, 1.0
-	How are the reaction velocities changed?	+	3. Select initial concentration values for cyclin and MPF stocks in a range from 0.1 to 1. Choose at least three values to examine.
-	Does it matter if you change the initial values of the variables?	+	Write a notes (report) containing the following:
-	At what ~value of Vmax cyclin degradation are oscillations lost?	+	1. Describe the characteristics of one set of simulation results.
		+	2. Describe briefly why you think you obtained the results you did?
		+	3. What questions came up if any?
		+	Exercise version 7/30/07
-	Note: Non-degradable cyclin is one of the experimental tools used to characterize cell cycle dynamics.	+	For additional work, try entering additional kinetic reactions and paramter values from the [[Media:GoldbeterParamterValues.pdf| table]]

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Latest revision as of 04:38, 31 July 2007

Contents 1 Modeling the Cell Cycle Exercise 1.1 A. Draw flow diagrams or concept map for the statements provided below. 1.2 B. Create the same concept maps in Stella. 1.3 C. What goes in the boxes? Reaction rates Exercise rationale

Modeling the Cell Cycle Exercise

Work in groups of 3. Work with people from different discipline. The goal of the lab is to become familiar with the software and the process of constructing a model.

A. Draw flow diagrams or concept map for the statements provided below.

1.Create a concept map of the following:

• inactive MPF becomes active MPF
• Active MPF becomes inactive MPF

2.Concept map the following:

• Cyclin is synthesized and degraded
• Cyclin stimulates inactive MPF to become active MPF

B. Create the same concept maps in Stella.

Intro to Stella Controls

How do we create a reaction in Stella? What are the factors in a reaction?

C. What goes in the boxes? Reaction rates Exercise rationale

1. Consider all reactions to be linear and based on the law of mass action (rate constant x substrate).

2. Use two of following set of rate constants in the rate equation: 0.05, 0.1, 1.0

3. Select initial concentration values for cyclin and MPF stocks in a range from 0.1 to 1. Choose at least three values to examine.

Write a notes (report) containing the following:

1. Describe the characteristics of one set of simulation results. 2. Describe briefly why you think you obtained the results you did? 3. What questions came up if any?

Exercise version 7/30/07

For additional work, try entering additional kinetic reactions and paramter values from the table