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Extracts dependencies and OO metrics from Java class files produced by most Java compilers. Computes API differences between versions. No source needed. Includes both Swing and command-line interfaces, with XSL stylesheets for formatting output.
The Dataverse Network is a Java EE5 app that enables researchers to share data on-line. It provides data citation standards, facilitates preservation, distribution and replication of data, and includes statistical analysis. More at: http://thedata.org
JCommons provides generally re-usable Java tools and components. Some things included are: code generation, data and object conversions such as EDI to XML, visualizing object instances as FreeMind mindmaps and a framework for generating factories.
ProteinArchitect facilitates the visual exploration of the architecture of proteins, including conserved domains, secondary structure elements and structurally flexible regions, e.g. in the context of the analysis of protein superfamilies.