Geographic library
Open Source Computer Vision Library
Toolkit for working with and mapping geospatial data
An object relational-mapping (ORM) library for Java
An interactive viewer for three-dimensional chemical structures.
Open source cross-platform Java Visual Traceroute
Open source Health IT for the planet
Robocode is a programming tank game for Java
BBMap short read aligner, and other bioinformatic tools.
Symja - Java computer algebra language & symbolic math library
Cross-platform DICOM implementation
Data Analysis, Simulations and Visualization on the Sphere