This plugin allows users to export and import pathways in BioPAX format. The plugin support BioPAX level 3. The import functionality is limited (pathways might need manual rearranging of objects).

License: http://www.apache.org/licenses/LICENSE-2.0.html
Website: http://developers.pathvisio.org/wiki/BiopaxPluginHelp

Version 1.0.0

  • initial release
  • export to BioPAX level 3
  • basic import functionality from BioPAX level 3 format


  1. Download and start PathVisio
  2. Open the Plugin Manager: Plugins » Plugin Manager
  3. Click the Install button for BioPAX3 plugin
  4. On success the plugin will be displayed in "installed plugins". If some error happens a message is displayed
  5. You can now use the plugin. Check out the plugin page to get started

If you have problems installing this plugin, please contact us.



2 thoughts on “BioPAX3 plugin

  1. BioPax3 plugin can’t be installed directly from the PathVisio plugin manager or it cannot be executed from the java file directly.
    Any suggestion to fix it?
    Thanks!

    Reply
    • Hi Simon,
      Import of BioPAX files is still in beta and does not work for all BioPAX files, but export of BioPAX files should work. The installation of the plugin works for me through the plugin manager. Can you tell me which error occurs? Which operating system are you using?
      Tina

      Reply

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