BioPAX 3 Plugin for PathVisio

The Plugin is currently still in Beta stage. It won't work reliably under all circumstances, and should not be used for production work.

Only BioPAX Level 3 is supported. There are no plans to support older levels.

How to use

To access the plugin, you can use this special webstart link to access the plugin:  http://pathvisio.org/webstart/Biopax3GPML/Biopax3GPML.jnlp

To export a GPML pathway, first open it with File->Open and then export it using File->Export (Select BioPAX level 3 from the drop-down list).

To import a pathway, use File->Import (Select BioPAX level 3 form the drop-down list). Imported pathways can be saved as GPML using File->Save as.

Reporting bugs

Please report all bugs on our MailingLists When you report a crash bug, please also include the Log file. You can find the log file in the .PathVisio directory in your home folder (so /home/user/.PathVisio on linux or C:\Documents and Settings\User\.PathVisio on windows)

Implementation

The plugin uses Emek Demir's  PaxTools library. The source code is available on our open subversion server here:  http://svn.bigcat.unimaas.nl/pvplugins/trunk/Biopax3GPML/