Prefuse!

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.

Wandora is a general purpose information extraction, management and publishing application based on Topic Maps and Java. Wandora has graphical user interface, layered and merging information model, multiple visualization models, huge collection of information extraction, import and export options, embedded HTTP server with several output modules and open plug-in architecture. Wandora is a FOSS application with GNU GPL license.Wandora is well suited for constructing ontologies and information mashups. Wandora is capable of extracting and converting a wide range of open data feeds to topic map formats (see image below). Beyond topic map conversion, this feature allows Wandora user to aggregate multidimensional information mashups where information from Flickr interleaves with information from GeoNames and YouTube, for example. »

TouchGraph is the producer of data visualization software TouchGraph Navigator 2. With TouchGraph Navigator 2, users can upload data and create "interactive network visualizations."[1] Users can purchase licenses for either a TouchGraph Navigator Desktop version or TouchGraph Navigator Web, where the user hosts visualizations on their server and views the visualization on a web browser.[1]

Pathomx is a workflow-based tool for the analysis and visualisation of experimental data. Initially created as a tool for metabolomic data analysis is has been extended and can now be used for any scientific and non-scientific data analysis. The software functions as a hybrid of workflow and script-based approaches to analysis. Using workflows it is possible to construct rapid, reproducible analysis constructs for experimental data. By combining this with custom inline scripting it is possible to perform any analysis imaginable. Workflows can be dynamically re-arranged to test different approaches and saved to track the development of your approach. Saved workflows can also be shared with other users or groups, allowing instant reproduction of results and methods. Tools can export images as publication-ready high resolution images in common formats. »