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MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic
Free Java monitoring library to easily instrument apps to measure performance detail over time with minimal overhead. Has dashboard, SVG graphs. Extends Jamon and its statistical data, same usage. http://www.e-peas.com/opensla/. JMX, SNMP planned.
A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.
GraPHPite is a highly customizable utility written in OO PHP for creating charts or graphs (Bar, Area, Pie, etc).
Users are encouraged to switch to PEAR::Image_Graph which is based on GraPHPite source. GraPHPite is in maintenance only state.
An Eclipse plug-in and KDE application to visually and interactively explore arbitrary graphs (collections of nodes and edges) specified in the Graph eXchange Language (GXL).
JPlot is a multi-purpose data plotting program for use as the graphic front-end of (scientific) software. JPlot is also available as a stand-alone application with a complete and easy-to-use graphic user interface (GUI).
ThunderGraph is another java charting library intended to draw 2D graphs. Additionally, it contains a package that presents a live component implementing zoomable, scrollable and 'hintable' graph. Written for JDK 1.1+, it may be used in MS IE applets.
An object oriented Java package that can be used to store 3-D graphs and perform various functions on them, arranging nodes with a spring embedder and generating VRML output. Visit http://vrmlgraph.i-scream.org.uk for documentation and examples.
NetGraph is a collection of java classes and beans that can visualize common network and dependency graphs. These graphs are built of nodes and connections between the nodes. See homepage for details.