CellDesigner Help

Import the Reaction Information from SABIO-RK database

The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modellers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. Information about reactions and their kinetics can be exported in SBML format.

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.
    pantherdb.org dialog
  2. Import Models from pantherdb.org

  3. On the Draw Aera, select the reaction r19.
    Malate Dehydrogenase in TCA cycle
  4. In the Menu, select Database - Import reaction information from SABIO-RK...
  5. The Import KineticLaw from SABIO-RK dialog will appear.
  6. Verify that Malate Dehydrogenase is already been typed in Search Query textbox.
  7. Specify Organism and Tissue where appropriate.
    Note: You can skip this step but will take more time for search.
  8. Click Search button.
  9. From the returned list, select a row where rid is 23613.
    SABIO Reaction Kinetics Database dialog

    Click to enlarge.

  10. Click Import KIneticLaw button.
  11. Mapping SpeciesReferences ID dialog will appear. Imported data from SABIO-RK is displayed on the right side of the dialog.
  12. 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.

  13. 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.
  14. Click Apply.
  15. In the Confitmation Dialog, read the message and click OK.

  16. In the SABIO Reaction Kinetics Database dialog, click Close.
  17. On the Draw Area, right-click on the Reaction r19.
  18. Select Edit KineticLaw from the list.
  19. In the KineticLaw dialog, confirm that the Kinetic Law is successfuly imported.
  20. Setting the Kinetic Laws / Parameters (The KineticLaw dialog)/p>

Test results of models from BioModels.net

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.

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