A problem in the SBML export of the stable release COPASI 4.3 (Build 25) has been reported by Marvin Schulz on April 28, 2008. The problem has been confirmed to affect all platforms.
On April 28, 2008, Marvin Schulz reported a problem in the SBML export of the stable release COPASI 4.3 (Build 25). We are grateful to Marvin for bringing this problem to our attention. The problem has been verified and it affects all platforms. It occurs when a model has been imported from an SBML file, new elements were added and the model is reexported. On reexport, it can happen that new elements get the same id as elements that already existed, making the exported file invalid. The chances of this bug occurring are very high if the original SBML model has already been created with COPASI. The problem also occurs when the model is stored as a COPASI file in between import and export because the original ids are stored in the COPASI file.
As a workaround, you can safe the model as a COPASI file, remove the section where the SBML ids are stored with a text editor, reload the model and then export it to SBML.
We are very sorry for the inconveniences this might cause. We are currently working on correcting this problem and will release a new version of COPASI once the fix has been tested.