CellDesigner Help

Import / Export SBML file

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.

To import SBML file:

If you import the SBML file created by other application, as the layout / graphical information valid for CellDesigner is missing, CellDesigner automatically generate the layout accordingly.

Auto Layout (new to 3.5)

Export a file to SBML:

CellDesigner can export the following pure SBML files.

* SBML Level-1 Version-1
* SBML Level-1 Version-2
* SBML Level-2 Version-1

Note that there are several versions in each level. For example, for SBML Level-1, there are "Version-1" and "Version-2".? The difference between each version is mainly bug fixes.

Note: For more details on the difference between SBML Level-1 Version-1, Version-2 and SBML Level-2 Version-1, please check the following URL: http://sbml.org/documents/ .
In the section "Specification Documents", you can download the specification documents.

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:

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.