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CallMesh is an eclipse plugin visualizing call graphs in javaprojects with the help of the zest toolkit. It allows easy navigation around you classes. Additionally, call graphs can be exported as dot-files as understood by graphvis.
Cube Platform is a decentralized grid computing system that uses P2P Pastry protocol for communication between nodes. It's a big data storage written in Java.
OpenFakt is an open source Java invoicing and billing system using XML definition files for various forms (address book, articles, invoices, stock management). It is language, database and platform independent and aims at small to big companies.
Java Inventor is a Java interface to Open Inventor. Open Inventor (http://oss.sgi.com/projects/inventor/) is a popular API for developers of 3D applications. Java Inventor uses the Java Native Interface (JNI) to access the Open Inventor C++ libraries.
JNeuron is an analysis tool for multi-neuronal spike train analysis. The tool will allow scientists to organize their spike train data analysis into projects. The tool will implement standard spike train analysis algorithms and also datamining algorithms