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PANTHER CellDesigner to BioPAX converter plugin supports CellDesigner version 4.1 and 4.2.

Steps for adding the PANTHER CellDesigner to BioPAX converter plugin.

1.  Download both BioPAX_Plugin.jar and paxtools-yyyymmdd.jar to your system where yyyymmdd stands for the date when the paxtools library was released.
2.  Go to your CellDesigner plugin director and copy BioPAX_Plugin.jar from step 1. into this directory.
3.  Go to your CellDesigner installation lib directory (Something like/Applications/Celldesigner4.*/lib).  Look for a file called paxtools.jar.  If file paxtools.jar is not in the lib directory,  no further action is necessary.  Else rename paxtools.jar to paxtools_do_not_use.jar.  Copy file paxtools-*.jar from step 1 into the lib directory.  Rename paxtools-*.jar to paxtools.jar.  This is because the CellDesigner team incorporated the old version of PaxTools  into their code and it is incompatible with the new PaxTools package.  Newer versions of CellDesigner will not contain the PaxTools package.


There are also instructions on the CellDesigner website on how to add plugins