CellDesigner Help

Simulation Sample: MAPK.xml

We will use the sample file "MAPK.xml" to see how the data required for simulation is specified in the model.

To check the data required for simulation

  1. Open MAPK.xml. This file should be found in your CellDesigner's "samples" directory.
  2. Select the Species tab in the List area and observe the initial quantities.
    Species List
  3. Select the Reactions tab in the List area to see how the kinetic laws and parameters are specified.Reactions List
  4. In the Reactions list, double-click on the third row whose id is "J2".
    Reactions List
  5. The Reaction dialog will open.
    Reaction List
  6. You can also open the Reaction dialog by clicking on the Reaction on Draw Area with the right-mouse button, then select Edit Reaction... menu. If the Reaction ID is not displayed on Draw Area, select ViewShow Reaction Id in the Menu.
    Edit Reaction... context menu
  7. Click Edit to display KineticLaw dialog.
    KineticLaw dialog
  8. In the math text box, you can change the formula.
  9. In the Parameters tab, you can change the parameter values.
  10. Ticking Name checkbox will show the variables in the math text box in Species name rather than Species ID.
    math text box

    Ticking Math checkbox will show the variables in the math text box in fractional representation.
    math text box

To add a Species ID in the math text box

  1. In the KineticLaw dialog, in the SelectedReaction pane, select a Species (e.g. MKK_P).
  2. In the math text box, put the cursor to the place where you want to add the Species ID.
  3. Verify that the Math checkbox is NOT selected, otherwise you cannot edit the math expression.

  4. Press the copy button.
  5. Observe that the Species ID has been added.

To edit parameters

  1. Click on the Parameters tab at the bottom of the KineticLaw dialog.
  2. All the parameters related to the selected Reaction are listed.

To use a Predefined Function

You can use some predefined functions such as Mass Action or irreversible simple Michaelis-Menten, by using Predefined Functions section on the dialog.

To run the simulation

  1. After checking all the reactions and KineticLaw formulas, close the KineticLaw dialog and the Reaction dialog.
  2. You can double-check all the specified Reactions, Parameters, etc in the List area.
  3. Select SimulationControlPanel from the Menu, and then conduct the simulation. You can view the graph as well as the simulated values in the Graph and Table tabs respectively.
  4. "Running CellDesigner Simulation with ControlPanel" found in the documents folder.

To save or print the simulated Graph

  1. Select FileSave Image / Print menu.
  2. Image Config Dialog will be displayed.
  3. Click Config, and display Chart Properties dialog.
  4. Specify Title, Legend, Plot and Other, then click OK.
  5. Click either Save Image or Print.

To save the simulation results

  1. Click SaveAs button or select File - SaveAs menu.
  2. Specify where you save the results.
  3. Modified model as well as the simulation results (with .sim extension) are stored in the specified folder.
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