Caleydo makes use of a range of open source tools, bioinformatics resources and pre-packages several datasets, which we gratefully acknowledge here.

Software Libraries

  • Bubble Sets - A Java implementation of the visualization technique.
  • CDK - The Chemistry Development Kit.
  • JGrahT - A graph library.
  • Jogl - Java bindings for OpenGL.
  • PathVisio - loading and parsing WikiPathways.
  • WordHoard - statistical utilities.

Bioinformatics Resources


  • CCLE - BROAD Institute Cancer Cell Line Encyclopedia.
  • TCGA - The Cancer Genome Atlas.


  • GitHub - Hosting our source code.
  • WebStorm - Free developer licenses for our web projects from JetBrains.