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swIMP (swig-based Interfaces for Mathematical Programming) provides Java wrappers for solvers written in C or C++. The current focus is on accessing OSI-compatible linear programming (LP) solvers from the Coin-OR-project (e.g. Clp, GLPK, MOSEK, CPLEX).
HATS (Haplotype Amplification in Tumor Sequences) is a tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. The amplified haplotype may reveal gene variants.
Numerical math is tool that demonstrates numerical math methods. It includes following areas: interpolation, numerical differentiation, numerical integration, root finding, linear systems, non-linear systems, differential equations.
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Tifad is a framework to deal with Natural Gas (NG) dispatching for thermoelectrical generation networks. Project blog can be browsed here: https://tifadframework.wordpress.com/
Enrich and query corpora in the TEI-XML vocabulary. CorpusReader manage very large corpora and corpora containing milestone annotation. It provides tools for enriching corpora with output of linguistic parsers, and for extracting quantitative information
TagSEA is a framework for tagging locations of interest within Eclipse. Visit our project page for more information - including downloads and documentation: tagsea.sourceforge.net
A program to calculate and create lists of possible variations (permutations) and selections (combinations) of a given set of elements. Creating the cartesian product of two sets is also possible.
Cougar Squared is a new Java library for machine learning and data mining research, supporting research needs of the community. It is written by researchers for researchers. It extends the WEKA and YALE machine learning frameworks.
TMAJ is software for Tissue MicroArrays (TMA's). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.
The system searches synonyms (and related words) in Wikipedia. WikIDF generates index database of Wikipedia (for Russian, English, and German). The continuation of this project is "wikokit" at code.google.com
Java based multi-agent platform built on an organizational model (agent, group, role). MadKit provides general agent facilities (lifecycle management, message passing, distribution, ...), and allows high heterogeneity in agents.
Volta is a suite of development tools for distributed, hard real-time systems. It includes Cascade, a control flow analysis tool for Java, and Clepsydra, a worst-case execution time analyzer. Also included is a Clepsydra plug-in for jEdit.
Editor for formal grammars. Attempts to be universal – customizable for any grammatical formalism and any syntax. Provides features such as syntax checking and highlighting, transformations (refactoring) and advanced rule editor.
VI Compute Server (VICS) is a collection of grid-enabled bioinformatics tools with HTTP (browser) and Web Services (scriptable) interfaces. JCVI VICS is licensed under the Perl Foundation Artistic License 2.0.
Parallel Colt is a multithreaded version of Colt - a library for high performance scientific computing in Java. It contains efficient algorithms for data analysis, linear algebra, multi-dimensional arrays, Fourier transforms, statistics and histogramming
Biomedical Information Management System (BIMS) is a modular multilayer object - oriented software architecture, which provides a flexible computational solution to capture and manage a heterogeneous biomedical data: textual and visual information.
The BE-Calculator is a Java application, written to ease the average diabetic's life. It currently only calculates how many I.U. you have to inject, but aims at providing a full, multilingual diabetic's diary.
This project has been superseded by GGC!
Geomajas is a web mapping GIS software with full vectorial editing capabilities, and support for custom attribute relation models in the browser. It has built-in support for any type of query, selection, filtering, snapping, printing, ...
The Java Code Clone Detection API (JCCD) allows to implement individual code clone detectors. These code clone detectors can be easily integrated into other Java applications. JCCD is based on a pipeline architecture which allows to replace whole par