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

 Overview GUI Compounds Reactions Kinetic Model Simulation Panel Example  

=Set-up a Kinetic Simulation=

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.