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Gephi is the leading visualization and exploration software for all kinds of graphs and networks. Gephi is open-source and free. Gephi is an award-winning open-source platform for visualizing and manipulating large graphs. It runs on Windows, Mac OS X and Linux. Localization is available in English, French, Spanish, Japanese, Russian, Brazilian Portuguese, Chinese, Czech and German. Fast Powered by a built-in OpenGL engine, Gephi is able to push the envelope with very large networks. Visualize networks up to a million elements. All actions (e.g. layout, filter, drag) run in real-time. ...

mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.

JProGraM (PRObabilistic GRAphical Models in Java) is a statistical machine learning library. It supports statistical modeling and data analysis along three main directions: (1) probabilistic graphical models (Bayesian networks, Markov random fields, dependency networks, hybrid random fields); (2) parametric, semiparametric, and nonparametric density estimation (Gaussian models, nonparanormal estimators, Parzen windows, Nadaraya-Watson estimator); (3) generative models for random networks...