CellDesigner Help

To import the reaction information from SABIO-RK database

1. Import the model TCA cycle from pantherdb.org. We will use the model as a sample throughout this walkthrough.
   

Import Models from pantherdb.org

2. On the Draw Aera, select Malate Dehydrogenase.
   
3. In the Menu, select Database - Import reaction information from SABIO-RK...
4. The SABIO Reaction Kinetics Database dialog will appear.
5. Verify that Malate Dehydrogenase is already been typed in Search Enzyme textbox.
6. Click Search by name button.
7. From Selected Enzyme drop-down list, select Malate Dehydrogenase
8. Verify that Enzyme radio button is selected and click Search Reaction.
9. From the returned list, select a row where rid is 143.
10. Click Get KineticLaw.
11. KineticLaws will be displayed.
    
    

    Click to enlarge.

12. On the Draw Area, click the Reaction r20.
    
13. In the SABIO Reaction Kinetics Database dialog, click Import KineticLaw.
14. Mapping SpeciesReferences ID dialog will appear. Imported data from SABIO-RK is displayed on the right side of the dialog.
    
    

    (left)CellDesigner; (right)SABIO-RK

15. If necessary, click Swap Reactants/Products to exchage the imported Reactants and Products.
    
    

    After Swap Reactants/Pruducts button is pessed, the imported Reactants and Products are swapped.

16. Confirm that the type of each Species on the left side (CellDesigner side) meets that of the right side (SABIO-RK side). If not, select another Species from the drop-down list.
17. Click Apply.
18. In the Confitmation Dialog, read the message and click OK.
19. In the SABIO Reaction Kinetics Database dialog, click Close.
20. On the Draw Area, right-click on the Reaction r20.
21. Select Edit KineticLaw from the list.
22. In the KineticLaw dialog, confirm that the Kinetic Law is successfuly imported.

Setting the Kinetic Laws / Parameters (The KineticLaw dialog)/p>

Test results of models from BioModels.net

• BioModels.net Simulation Results with CellDesigner 4.01(As of 2008/8.)
• BioModels.net Simulation Results with CellDesigner 3.5.2 (As of 2007/12.)

There are some models which have problems in simulating with CellDesigner. As the models on the BioModels.net are periodically updated, the status may change in the near future.