Gephi the open graph Viz platform
DBMS supporting graph, document, full-text and geospatial models
A premier mind-mapping software written in Java
3D Network Traffic Visualisation
An Enclosure+Connection Visualization Technique for Hierarchical Data
Particle Image Velocimetry
Relative entropy optimization network layout plugin
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
jchart2d is a real-time charting library written in java.