Template:Cell Cycle Exercises

From Computational Cell Biology

Exercise 1

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

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?

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

Write notes 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 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.