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GiANT is a graphical interface for computer algebra systems (OS X/UNIX/Win). Currently GiANT lets the user work with number fields via KASH, but we aim to develop it into a GUI Library to run on top of any CAS and expose any of its functions.
Java Randomness Test Suite is a gui application to run randomness tests on random stream resource (file or algorithm). Application can be run in command line. Includes general statistical tests, NIST and DIEHARD tests.
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xPG was about an OpenPGP-GUI in Java. Some source-code is still available for reference purposes. See http://www.cryptix.org/ for a current implementation of OpenPGP for Java.
A secure PKI-based client/server encrypted chat engine under development in Java. Encryption will be supported via JCE and PKCS#11. A simple Java interface can be implemented by other projects wishing to develop a Java GUI or CLI for the client.