CellDesigner Help

Setting the Kinetic Laws / Parameters

To set a kinetic law to a reaction:

In the Reactions tab in the List area, select the target Reaction and click Edit button.
The Reaction dialog will appear.
Click Create or Edit button in KineticLaw field.
Or click on the target Reaction on canvas with right-mouse button, then select Edit KineticLaw... menu.
The KineticLaw dialog will appear.
Set the Kinetic Law in the math textbox.

Note: In the math textbox, Species IDs, not Speices Names, should be specified to make a formula.

Note:When you select the Math checkbox, the formula will be in the View mode, and fractions will be visually formatted.

Note:When you select the Name checkbox, the formula will be in the View mode, and Species names instead of id's will be displayed in the formula.

Note:The formula is NOT editable in the View mode.

To enter a Species ID in the math textbox, you can click the target Species on canvas, and press copy button below the math textbox. The ID will be automatically put in the textbox.
Or, in Species tab at the bottom of KineticLaw dialog, select a Species and click copy button.

To set a local parameter:

Select Parameters tab at the bottom of the KineticLaw dialog.
Click New button.
In the Parameter dialog, specify id, name, value and units for the new parameter.

To set a global parameter:

Select Parameters tab in the List area.
Click New button.
In the Parameter dialog, specify id, name, value and units for the new parameter.

Note: CellDesigner supports subset of MathML representation of functions,which is defined in SBML Level 2 specification. You can see the list of supported functions in Section 3.6.1 of SBML Level2 spec which is available from the following URL:
http://sbml.org/Special/specifications/sbml-level-2/version-1/sbml-level-2-v1.pdf

To view all the Kinetic Laws set to the reactions in the model:

You can check all the reactions and kinetic laws set to the reactions in the list view.