Functionality of the plugin manager

Until PathVisio 3 it was complicated to install plugins and there was no central collection of PathVisio plugins. With PathVisio 3 we introduce the new plugin repository. This repository will contain plugins that run with PathVisio 3 or higher. The plugin manager allows the user to install plugins from this repository directly from PathVisio without restarting the application (although some plugins might still need that).

The goal of the plugin manager is to provide a user-friendly and easy to use interface to install plugins.


User manual


Download plugins from the repository

  • Download PathVisio 3
  • For installing plugins you need to be connected to the internet. After installation the plugins can be used offline as well.
  • Start PathVisio and open the plugin manager dialog (Plugins -> Plugin Manager).
  • Select the plugin you want to install in the list of available plugins (you can read more information about the plugin and the developers in the right side panel)
  • Click Install
  • If the plugin was installed correctly, the plugin will disappear from the available tab and will show up the installed tab.
  • In case an error occurred, please check the error tab in the plugin manager dialog.
  • If you have questions about the plugin, you can contact the mailing list or leave a comment on the plugins page directly.


Install plugins from a local directory

This option is only designed for plugins that are not present in the plugin repository. Make sure that you have all the necessary jar files in a local directory (the plugin jar itself and all dependencies that are not part of the PathVisio core application).

  • Download PathVisio 3
  • Start PathVisio and open the install local plugin dialog (Plugins -> Install local plugins).
  • Select the directory that contains all necessary jar files.
  • Click on Start
  • Make sure that you select the check box for all jar files in the directory that implement the PathVisio plugins interface.
  • Click Ok
  • If the plugin was installed correctly, the plugin will show up the installed tab.
  • In case an error occurred, please check the error tab in the plugin manager dialog.

Future work


The plugin manager was introduced in PathVisio 3 and can now be used to install plugins from the PathVisio plugin repository. More functionality will be added in the next releases:

  • Search: Functionality to search in the plugin manager dialog.
  • Categories: Browse plugins per tag.
  • Introducing profiles: Download a set of plugins for a specific use case (e.g. metabolomics, import/export,…).
  • Smart uninstalling: when uninstalling a plugin, remove all plugins that depend on it and clean up all libraries that are only used by this plugin.
  • Customizing: Allow custom plugin icons and banners.