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VIKAMINE is a flexible environment for visual analytics, data mining and business intelligence - implemented in pure Java. It features several powerful visualization and mining methods, and can utilize background knowledge.
This open source software benchmarks the queries per second of an Apache Lucene index. It is an Java implementation and uses MultiFieldQueryParser to form a query.
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Now part of Apache's Mahout machine learning project at http://mahout.apache.org/-- please see there for latest info and code and releases and support!
Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)
Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program.
It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user
written MAEPlugins, documentation, tutorials, demo data.
This site is intended as a location containing a suite of tools to (1) Aid in the design of db APIs to be utilized in a J2EE environment and (2) generate stubs for the db API, Java classes and SQL DDL necessary to support the MVC pattern and the Data Own
TM4 is a suite of applications for managing and analyzing microarray data. TM4 provides data storage and tracking, image analysis, normalization, data filtering, clustering and statistical analysis capabilities. Includes MADAM, Spotfinder, MIDAS, and MeV.