Template:Cell Cycle Exercises
From Computational Cell Biology
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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. | ||
| - | 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] | ||
| + | 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]]==== |
| - | 1. | + | 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). |
| - | + | 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: | |
| - | + | ||
| - | 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. | ||
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3. What questions came up if any? | 3. What questions came up if any? | ||
| - | Exercise version | + | Exercise version 7/30/07 |
| + | |||
| + | 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.
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
