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


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

CellDesigner 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.