CellDesigner Help

Save a Model

CellDesigner stores all the information of the model you created to an SBML format file.
The CellDesigner's specific information will be stored under <annotation> tag.
Instead, if you only want to save the basic SBML information, you can export the model to a pure SBML file.

To save a model

  1. Select File then Save, Save As... or Save All.
  2. Type the name of your choice.
  3. CellDesigner automatically adds the .XML extension on saving the file.
  4. The Name you type in this dialog will be not only the file name but the model id in the xml file when you select FileSave in the Menu. Therefore, the Name needs to conform to SBML convention.

    e.g. If you specify "sample" here, the file name will be "sample.xml", in which <model id="sample"> is written.

    However, if you select FileSave As … in the Menu, you can give a file name different from the id property of the model element in the xml file.

    e.g. If you save as "sam ple", the file name will be "sam ple.xml" but the model id is still <model id="sample">.

    See the file name has a space in it but the model id does not.

    Naming Convention
    The model id only accepts the Type Sid defined in SBML specification as follows:

    letter ::= ’a’..’z’,’A’..’Z’
    digit ::= ’0’..’9’
    idChar ::= letter | digit | ’_’
    SId ::= ( letter | ’ ’ ) idChar*

    The difference between saving and exporting:
    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 Save a Model with SBO terms

    CellDesigner can save the SBO Term automatically. Check SBO topic for details.

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

  1. Export "pure (which doesn't contain <annotations> tags)" SBML document from CellDesigner.
  2. Then retrieve the exported file by another SBML compliant application.


Here is the summary on CellDesigner's "export" / "SBML" functions:

  • CellDesigner stores all information only to SBML file.
  • Though SBML does not support layout information, CellDesigner stores layout information inside <annotations> tags in SBML, which is CellDesigner specific extension.
  • Though these extension is enclosed in <annotations> tags, generated SBML files are still "SBML Validated" documents.
  • CellDesigner has a feature to export "pure" SBML document which doesn't contain any layout information. You may use this feature if you find any trouble when you tried to open your SBML document with other SBML compliant software.

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