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Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other...

Java Data Processing Project aims to manipulate text file containing scientific data such as time/intensity scan or spectrum. Jdpp provide large flexibility to read all possible time duration and date format. It is originally design to treat MS data.

Sanchay is a collection of tools and APIs for language researchers. It has some implementations of NLP algorithms, some flexible APIs, several user friendly annotation interfaces and Sanchay Query Language for language resources.

RadDoom is a radiosity scene renderer that use "Dynamic Surface Subdivision". It's write in Java and Java3D. It enables, in real time, the user to travel in the 3D scene during rendering.