Template:Cell Cycle Exercises

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===Concept Maps and System Statements===
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===Modeling the Cell Cycle Exercise===
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Modeling the Cell Cycle: Concept Maps and Rate Equations
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Introduction to Stella: Done as Live Presentation
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Directions
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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.
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A. Draw flow diagrams or concept map for the statements provided below.
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====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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* inactive MPF becomes active MPF
* inactive MPF becomes active MPF
* Active MPF becomes inactive MPF
* Active MPF becomes inactive MPF
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2.Concept map the following:
2.Concept map the following:
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* Cyclin stimulates inactive MPF to become active MPF
* Cyclin stimulates inactive MPF to become active MPF
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B. Create the same concept maps in Stella.
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====B. Create the same concept maps in Stella.====
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[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]
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C. What goes in the boxes?
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How do we create a reaction in Stella? What are the factors in a reaction?
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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?
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====C. What goes in the boxes? Reaction rates [[Exercise rationale]]====
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2. Values for cyclin and MPF range from 0.1 to 2. Choose at least three values to examine.
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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).  
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3. Use the at least two of following set of rate constants: 0.05, 0.1, 1.0, 2.0
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2. Use two of following set of rate constants in the rate equation: 0.05, 0.1, 1.0
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Write notes containing the following:
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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.
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1. Describe the characteristics of at least one set of simulation results.
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Write a notes (report) containing the following:
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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?
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===Creating with Stella===
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Exercise version 7/30/07
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[http://webster.cs.uga.edu/%7Ecs1210/Lectures/Stella/Intro.html Intro to Stella Controls]
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===Playing with Existing Models===
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Exercise using an existing model of Goldbeter in Stella Demo
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Purpose: To become oriented with the model and the software. This exercise was designed to work with Stella Demo or Player.
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Click through the levels of the model (interface to model and equations) using the up and down arrows in the top left corner.
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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.
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Exploration
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1. Run the simulation with the slider for “Vmax Cyclin degradation” to the far left (0.02).
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What results do you see in the graphs?
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How are the reaction velocities changed?
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Does it matter if you change the initial values of the variables?
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2. Re-run the simulation with the slider for “Vmax Cyclin degradation” placed to the far right (0.6)?
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What results do you see?
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How are the reaction velocities changed?
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Does it matter if you change the initial values of the variables?
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At what ~value of Vmax cyclin degradation are oscillations lost?
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Note: Non-degradable cyclin is one of the experimental tools used to characterize cell cycle dynamics.
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For additional work, try entering additional kinetic reactions and paramter values from the [[Media:GoldbeterParamterValues.pdf| table]]

Latest revision as of 04:38, 31 July 2007

Contents

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

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