CellDesigner Help

Import / Export SBML file

The difference between Save and Export:

CellDesigner stores all information including layout information and interaction information to an SBML file but the current SBML versions do not support storing "layout" nor "graphical" information. To accommodate its layout and graphical information, CellDesigner has extended SBML to support such kind of information. These extensions are stored inside <annotations> tags, without violating the definition of SBML. Hence, CellDesigner creates a completely "valid" SBML document.
Nevertheless, if you create a model with CellDesigner and need to open it with another application, you should export the model to a pure SBML file.

To import SBML file

  1. Select File - Open.
  2. In the Open dialog, select an .sbml or .xml file.
  3. Click Open.
  4. If you import the SBML file created by other applications, as the layout / graphical information valid for CellDesigner is missing, CellDesigner will automatically generate the layout accordingly.

    Auto Layout (new in ver. 3.5)

To export a model to a pure SBML file (.sbml, .xml)

CellDesigner can export a model to the following pure SBML file.

  1. In the Menu, select File, then Export Pure Level x Version x....
  2. Save dialog opens.
  3. Specify a file name.
  4. Click Save.
  5. There are several versions in each level. For example, SBML Level-1 has "Version-1" and "Version-2". The difference between each version is mainly bug fixes.

    For more details on the difference between each version, please check the following URL: http://sbml.org/documents/ .
    In the section "Specifications", you can download the specification documents.

    To open the model created by CellDesigner with another SBML compliant application

To export a model to a BioPAX format file (.owl)

CellDesigner can export a model to the following BioPAX Level file.

  1. In the Menu, select File, then Export to BioPAX Level 3....
  2. In Export to BioPAX Level 3... dialog, change the file name if needed.
  3. By default, your file will be saved in .owl format.

  4. Click Save.
  5. Error dialog will list the Species that were not converted.
  6. Click OK.
  7. To check if your exported .owl file is valid, go to BioPAX Validator

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