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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.
A UML-based spec (implemented in Java and soon in C++) for managing geometric/geographic objects. See <a href="http://geobject.org">geobject.org</a> (<a href="http://geobject.org/GeobjectPublicLicenseV1_0.htm">Geobject Public License 1.0</a>)
Atavi is an interactive genealogical data visualization tool. It uses XSLT to transform XML data into SVG (Scable Vector Graphics) images. Deploy it as a Javaservlet and explore visualizations from a browser that supports SVG. GEDCOM import is planned.
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CAVOR is an engine for building apps that involve both graphic and text/numeric data. Primarily GIS is the initial focus, but consider also CAD, CASE, project management (eg PERT charts), and others. Built-in scripting, C API, also supports Tcl and Java.
CrimeStat is an web-application which analyses the police's press releases of Berlin and visualizes the different criminal offences on a map of Berlin. It also shows different statistics about the crimes.
The Integrative Biology VRE is a web-based graphical user interface and repository that provides an environment where biological simulation experiments can be constructed without the need for any knowledge of unix, cluster computing, or shell scripting.