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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.
JGraphT is a free Java class library that provides mathematical graph-theory objects and algorithms. JGraphT supports a rich gallery of graphs and is designed to be powerful, extensible, and easy to use.
Gremlin is a graph traversal language. Gremlin works over those graph databases or frameworks that implement the Blueprints property graph data model. It works beter with graph database like TinkerGraph, Neo4j, OrientDB, DEX, Rexster, and Sail RDF Stores. This language has application in the areas of graph query, analysis, and manipulation.
JGraphT is a Java graph library that provides mathematical graph-theory objects and algorithms. It includes directed, undirected, weighted, unweighted etc. Graphs could be created based on Strings, URLs, XML documents.
Prolog+CG is a Java implementation of Prolog with extensions implementing a subset of the Conceptual Graph (CG) theory of John Sowa. CGs are first-class datatypes on a par with terms. Object oriented extensions are also included.
Titan is a scalable graph database optimized for storing and querying graphs containing hundreds of billions of vertices and edges distributed across a multi-machine cluster. Titan is a transactional database that can support thousands of concurrent users executing complex graph traversals. It is a native Blueprints enabled graph database and as such, it supports the full TinkerPop stack of technologies.