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The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.
The main home page of the CDK is now at: http://cdk.github.io
Object Graph Visualizer is a tool primarily meant to be used in CS courses to help new students understand the Object Oriented paradigm and patterns. Classes and objects - that can be part of a software project - are visualised in 3D: The classes stay In the xz-plane in form of an UML class diagram. Directly above in the y-axis objects can be instantiated as an object diagram.
At an early stage of development. Application/middleware usage monitoring/reporting. Focus on business transactions/use cases to help communicate with users. Small footprint, easy to use GUI and a level of statistical analysis to summarise the data.