# Imperial College/Courses/Spring2008/Synthetic Biology/Computer Modelling Practicals/CellDesigner Tutorial/Kinetic Simulation

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Synthetic Biology (Spring2008): Computer Modelling Practicals

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# Set-up a Kinetic Simulation

### Overview

 this section deals with preparing your model to kinetic simulations (time evolving simulations). CellDesigner offers a link to an ODE Solver.

### Minimum requirements for a simulation

• Compounds: 'initialAmount' might need to be changed for some compounds (zero by default)
• Reactions : define a kineticLaw for all reactions defined, write a formula with appropriate parameters.

### Defining a kinetic law for your reaction

• Double click on an item in the reaction list to display the “Reaction” dialog.
• You can also display “Reaction” dialog” by clicking on the reaction on canvas with right mouse button, then select “Edit Reaction” menu.
• Click “KineticLaw” Edit button to display “KineticLaw” dialog
• Enter “math” formulae and edit parameters by clicking in the “listofParameters” section
• Note: In “math” formulae, Species ID, not Species Name, should be specified
• To enter Species ID, you can click the target Species on canvas, and press [copy] button below the “math” field. The ID will be automatically input to the field.

### Defining a parameter used in the kinetic law

• Local parameter: To set a local parameter for the kinetic law formula, click [New] button in the above KineticLaw dialog window to specify the parameter id, name, value and units.
• Global parameter: From the "Parameters" tab in the list window, select [NEW] to create a new global parameter.