To save a model
- Select File then Save, Save As... or Save All.
- Type the name of your choice.
- CellDesigner automatically adds the .XML extension on saving the file.
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 File – Save 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 File – Save 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.
