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LiveGraph is a framework for real-time data visualisation, analysis and logging. It has a real time plotter that can automatically update graphs of your data while it is still being computed by your application. LiveGraph reads files in a simple CSV-style format. For applications developed in Java, LiveGraph additionally provides an API that handles all data logging and persistency issues.
HyperGraphDB is a general purpose, open-source data storage mechanism based on a powerful knowledge management formalism known as directed hypergraphs. While a persistent memory model designed mostly for Knowledge management, Artificial Intelligence and Semantic web projects, it can also be used as an embedded object-oriented database for Java projects of all sizes. It could also be used as graph database or as (non-SQL) relational database.
Rickshaw provides the elements you need to create interactive graphs: renderers, legends, hovers, range selectors etc. It's all based on d3 underneath, so graphs are drawn with standard SVG and styled with CSS.
Virtual Spaces MWN is a Java tool developed at the MPIWG for the structured representation of knowledge. Texts, images and hyperlinks can be organized in 2D graphs. These graphs are used to generate HTML, PDF or RTF files to create virtual tours.
Logrep is a tool for collection and presentation of information from various logfiles including snort, squid, postfix, apache, sendmail, iptables/ipchains and nt eventlogs. HTML-reports, multi dimensional analysis, ssh and graphs are available.