Currently it is required to include the whole PathVisio core module which is much bigger and already contains PathVisio specific visualization aspects, also with the current data model it is difficult to find out the connections between two elements in the pathway. This automatically makes any graph algorithms which could be used to analyse the pathway very inefficient.

A general GPML library should only contain the data model, the functionality to read and write GPML files and relevant importers and exporters to other often used file formats so it can be easily integrated in other applications.

The main goal of this project is to create a separate GPML library to read and write GPML files in Java which can be used by PathVisio, the WikiPathways app for Cytoscape and many other applications.


Saurabh Kumar


  • Martina Summer-Kutmon
  • Alexander Pico