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Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

GraphPad Prism is a powerful combination of basic biostatistics, curve fitting and scientific graphing in one comprehensive program. More than 100,000 scientists in over 100 countries rely on Prism to analyze, graph and present their scientific data.

the prefuse visualization toolkitPrefuse is a set of software tools for creating rich interactive data visualizations. The original prefuse toolkit provides a visualization framework for the Java programming language. The prefuse flare toolkit provides visualization and animation tools for ActionScript and the Adobe Flash Player.NOTE: Prefuse development has been opened up to the community and the source has moved from SourceForge to a new home on GitHub. Both Prefuse and Flare are now available on GitHub.Prefuse supports a rich set of features for data modeling, visualization, and interaction. It provides optimized data structures for tables, graphs, and trees, a host of layout and visual encoding techniques, and support for animation, dynamic queries, integrated search, and database connectivity. Prefuse is written in Java, using the Java 2D graphics library, and is easily integrated into Java Swing applications or web applets. Prefuse is licensed under the terms of a BSD license, and can be freely used for both commercial and non-commercial purposes.The visualization gallery and demonstration video provide numerous examples of the types of applications that can be built with the prefuse toolkit.To learn more about prefuse, take a look at the user's manual or the frequently asked questions. For users of the alpha version of the toolkit, there is also a porting guide for migrating to the beta version.Need help? Visit the Help Forum on SourceForge.net (You'll need a SourceForge login to post). Please be sure to include detailed information (e.g., stack traces, source code, etc) if you need debugging help.If you are interested in tools for ActionScript and Flash, see the prefuse flare project instead. »