To save a model:
1. Select [File] then [Save], [Save As] or [Save All].
[Save] and [Save As] is just as same as other application's [Save] and [Save As] menu.
[Save As] can specify different file name. [Save All] will save all the files opened with CellDesigner.
2. Type the name of your choice.
CellDesigner automatically add the .XML extension on saving the file.
Note: Naming Convention
Model ID or/and the File Name only accept the following characters:
(_|[a-z]|[A-Z])(_|[a-z]|[A-Z]|[0-9])*. No blank space is accepted.
This is the SBML convention.
Note: The differences between saving and exporting:
CellDesigner stores all information to SBML file, so you don't have to save in another format.
CellDesigner stores all layout information and interaction information to SBML file.
But the current SBML versions do not support storing "layout" nor "graphical" information in SBML.
To accommodate these layout functions, CellDesigner has extended SBML to support such kind of information.
These extensions are stored inside <annotations> tags, which means it would not break the definition of SBML.
CellDesigner creates completely "valid" SBML document.
If you want to open the xml file with other application, you should export the model to pure SBML files.
To retrieve the model created by CellDesigner to the other SBML compliant application::
1. Export "pure (which doesn't contain <annotations> tags)" SBML document from CellDesigner.
2. Then retrieve the exported file to the other SBML compliant application.
Summary:Here is the summary on CellDesigner's "export" / "SBML" functions:
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