PathwayNexus

The project formerly known as PathwayMatrix, started in collaboration with the Leist group.

Contains a Vanted extension that evolved from the Master's thesis of Philipp Eberhard.

Project members: Falk Schreiber, Michael Aichem, Karsten Klein, Philipp Eberhard, Benjamin Moser, Martin Kern (TBC).

Documentation

• A comprehensive overview from a programmer's perspective can be found in /doc/Docs-MA.pdf. This also includes documentation on the Pinboard feature and pathway scoring.
• Slides at doc/presentation.pdf.
• See the project wiki (accessible via the sidebar on GitLab)
• See the VANTED wiki

Development

• Latest stable state is on main.

Getting Started

• You can start VANTED with the Add-On by invoking the main method in the class StartVantedWithAddon.

Distribution

• Generate jar-file under use of ant-script "createAdd-on.xml" (in Eclipse right-click and choose "Run As -> Ant Build").

Jar-files can be installed from users by starting VANTED, choosing sidepanel "help -> settings", opening Addon-manager and choosing "Install Add-on".

Additional Materials

• Example data file that can be used for testing can be found on the PathwayNexus website