Template:Cell Cycle Exercises - Revision history

Raquell at 04:38, 31 July 2007

2007-07-31T04:38:46Z

← Older revision		Revision as of 04:38, 31 July 2007
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	[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]		[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html 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]]====		====C. What goes in the boxes? Reaction rates [[Exercise rationale]]====
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	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).		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).

-	~~How do we create a reaction~~ in ~~Stella? What are~~ the ~~factors in a reaction?~~	+	2. Use two of following set of rate constants in the rate equation: 0.05, 0.1, 1.0
-		+
-	2. ~~Set values for cyclin and MPF range from~~ 0.1 to 1. ~~Choose at least three values to examine.~~	+

-	3. ~~Use two of following set of rate constants: 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:		Write a notes (report) containing the following:
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	3. What questions came up if any?		3. What questions came up if any?

-	Exercise version 5/2/07	+	Exercise version 7/30/07

	For additional work, try entering additional kinetic reactions and paramter values from the [[Media:GoldbeterParamterValues.pdf\| table]]		For additional work, try entering additional kinetic reactions and paramter values from the [[Media:GoldbeterParamterValues.pdf\| table]]

Raquell: /* Modeling the Cell Cycle Exercise */

2007-07-31T04:34:31Z

Modeling the Cell Cycle Exercise

← Older revision		Revision as of 04:34, 31 July 2007
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	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.		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.	+	====A. Draw flow diagrams or concept map for the statements provided below.====

	1.Create a concept map of the following:		1.Create a concept map of the following:
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	* Cyclin stimulates inactive MPF to become active MPF		* Cyclin stimulates inactive MPF to become active MPF

-	B. Create the same concept maps in Stella.	+	====B. Create the same concept maps in Stella.====
	[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]		[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]


-	C. What goes in the boxes? Reaction rates [[Exercise rationale]]	+	====C. What goes in the boxes? Reaction rates [[Exercise rationale]]====

-	1. ~~All~~ reactions ~~are~~ linear and based on the law of mass action (rate constant x substrate).	+	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).

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

Raquell: /* Modeling the Cell Cycle Exercise */

2007-05-05T11:45:40Z

Modeling the Cell Cycle Exercise

← Older revision		Revision as of 11:45, 5 May 2007
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	Exercise version 5/2/07		Exercise version 5/2/07
		+
		+	For additional work, try entering additional kinetic reactions and paramter values from the [[Media:GoldbeterParamterValues.pdf\| table]]

129.44.184.27 at 21:36, 3 May 2007

2007-05-03T21:36:04Z

← Older revision		Revision as of 21:36, 3 May 2007
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-	===Exercise===	+	===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.		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.

129.44.184.27 at 21:34, 3 May 2007

2007-05-03T21:34:32Z

← Older revision		Revision as of 21:34, 3 May 2007
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	3. Use two of following set of rate constants: 0.05, 0.1, 1.0		3. Use two of following set of rate constants: 0.05, 0.1, 1.0

-	Write a notes containing the following:	+	Write a notes (report) containing the following:

	1. Describe the characteristics of one set of simulation results.		1. Describe the characteristics of one set of simulation results.

75.69.230.175: /* Exercise */

2007-05-03T00:00:04Z

Exercise

← Older revision		Revision as of 00:00, 3 May 2007
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-	C. What goes in the boxes? Reaction rates	+	C. What goes in the boxes? Reaction rates [[Exercise rationale]]

-	1. All reactions are linear and based on the law of mass action (rate constant x substrate). ~~How do we create a reaction in Stella? What are the factors in a reaction?~~	+	1. All reactions are linear and based on the law of mass action (rate constant x substrate).

-	~~2. Values for cyclin and MPF range from 0.1 to 1. Choose at least three values to examine.~~	+	How do we create a reaction in Stella? What are the factors in a reaction?

-	3. ~~Use the~~ at least two of following set of rate constants: 0.05, 0.1, 1.0	+	2. Set values for cyclin and MPF range from 0.1 to 1. Choose at least three values to examine.
		+
		+	3. Use two of following set of rate constants: 0.05, 0.1, 1.0

	Write a notes containing the following:		Write a notes containing the following:

75.69.230.175: /* Exercise 1 */

2007-05-02T22:50:13Z

Exercise 1

← Older revision		Revision as of 22:50, 2 May 2007
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-	===Exercise 1===	+	===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.		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.

75.69.230.175: /* Exercise 1 */

2007-05-02T22:49:54Z

Exercise 1

← Older revision		Revision as of 22:49, 2 May 2007
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	* inactive MPF becomes active MPF		* inactive MPF becomes active MPF
	* Active MPF becomes inactive MPF		* Active MPF becomes inactive MPF
		+

	2.Concept map the following:		2.Concept map the following:
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	B. Create the same concept maps in Stella.		B. Create the same concept maps in Stella.
	[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]		[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]
		+

	C. What goes in the boxes? Reaction rates		C. What goes in the boxes? Reaction rates
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	3. Use the at least two of following set of rate constants: 0.05, 0.1, 1.0		3. Use the at least two of following set of rate constants: 0.05, 0.1, 1.0

-	Write notes containing the following:	+	Write a notes containing the following:

	1. Describe the characteristics of one set of simulation results.		1. Describe the characteristics of one set of simulation results.

75.69.230.175 at 22:44, 2 May 2007

2007-05-02T22:44:21Z

← Older revision		Revision as of 22:44, 2 May 2007
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	Exercise version 5/2/07		Exercise version 5/2/07
-
-	~~===Exercise 2: Playing with Existing Models===~~
-	~~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.~~
-
-	~~Click through the levels of the model (interface to model and equations) using the up and down arrows in the top left corner.~~
-
-	~~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~~
-
-	~~1. Run the simulation with the slider for “Vmax Cyclin degradation” to the far left (0.02).~~
-
-	~~What results do you see in the graphs?~~
-
-	~~How are the reaction velocities changed?~~
-
-	~~Does it matter if you change the initial values of the variables?~~
-
-
-	~~2. Re-run the simulation with the slider for “Vmax Cyclin degradation” placed to the far right (0.6)?~~
-
-	~~What results do you see?~~
-
-	~~How are the reaction velocities changed?~~
-
-	~~Does it matter if you change the initial values of the variables?~~
-
-	~~At what ~value of Vmax cyclin degradation are oscillations lost?~~
-
-
-	~~Note: Non-degradable cyclin is one of the experimental tools used to characterize cell cycle dynamics.~~

128.197.41.230: /* Exercise 1 */

2007-05-02T11:35:29Z

Exercise 1

← Older revision		Revision as of 11:35, 2 May 2007
Line 18:		Line 18:
	[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]		[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]

-	C. What goes in the boxes?	+	C. What goes in the boxes? Reaction rates

	1. All reactions are linear and based on the law of mass action (rate constant x substrate). How do we create a reaction in Stella? What are the factors in a reaction?		1. All reactions are linear and based on the law of mass action (rate constant x substrate). How do we create a reaction in Stella? What are the factors in a reaction?

-	2. Values for cyclin and MPF range from 0.1 to 2. Choose at least three values to examine.	+	2. Values for cyclin and MPF range from 0.1 to 1. Choose at least three values to examine.

-	3. Use the at least two of following set of rate constants: 0.05, 0.1, 1~~.0, 2~~.0	+	3. Use the at least two of following set of rate constants: 0.05, 0.1, 1.0

	Write notes containing the following:		Write notes containing the following:

-	1. Describe the characteristics of ~~at least~~ one set of simulation results.	+	1. Describe the characteristics of one set of simulation results.
	2. Describe briefly why you think you obtained the results you did?		2. Describe briefly why you think you obtained the results you did?
	3. What questions came up if any?		3. What questions came up if any?
		+
		+	Exercise version 5/2/07

	===Exercise 2: Playing with Existing Models===		===Exercise 2: Playing with Existing Models===