Modeling Cell Cycle Lab Exercise

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

I. Live presentation of Stella

Instructor:

Create stocks and flows.
Enter values for stocks and rate equations for flows.
Add converters and connectors, modify rate equations accordingly.
Open and plot data on a graph and table.
See U. of Georgia Intro page for additional instructions.

II. Concept Mapping Statements

Hand draw (or use your favorite concept mapping tool) flow diagrams/concept map for the statements provided below.

1.Create a concept map in stella that model 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

III. Working with Stella.

Create concept map in Stella. Make any needed changes.

IV. Draft rate equations and values

This is designed for you to try multiple scenarios of reaction rates and variable “concentrations”. There is no correct value in this exercise. The variable values are arbitrary and assumed to have the same units. Do you get different behaviors? Assume the following for reactions and variables and enter them to your Stella model:

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 2. 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

V. Report(s)

As a group, create a report including 1-4 below. Individually respond to 5-8.

1. Screen shots of the Stella concept maps.
2. Screen shot of Stella work screen that shows equations for your model
3. Present in table format the parameter/variable values that you chose to simulate
4. Screen shot of results from simulations

5. Describe the characteristics of at least one set of simulation results.
6. Describe briefly (min. paragraph) why you think you obtained the results you did?
7. Is there something you need that you did not have for this lab?
8. What questions came up if any?