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[This project is frozen, but has an offspring with more features: https://github.com/jeffhain/jadecy ] JCycles provides treatments to compute cycles, or just strongly connected components, in directed graphs in general, or in classes or packages dependencies graphs parsed from class files (major version <= 51, else does best effort). It uses Tarjan's algorithm for SCCs, and Johnson's for cycles, with continuations instead of recursion, which allows to handle large graphs (< Integer.MAX_VALUE vertices). ...

Moved to GitHub https://github.com/fedups Algebraic equation processing at run time for Java programs. Supports variables, functions with parameters, rate table lookups, an embedded "if" function... Infinitely extensible, very small footprint.

A rich client to analyse data from a liquid-feedback (http://liquidfeedback.org/) instance, for now it's a 3d graph explorer to inspect the delegations. It's an application based on the eclipse platform (indigo). To be precise its a directed weighted multi graph browser in 3d. Find out more in the wiki https://sourceforge.net/p/lqfbanalyser/wiki/Home/ . Generated reports https://sourceforge.net/p/lqfbanalyser/wiki/generated%20lqfb%20reports/ .

A software framework to build maps for Neurospora crassa genome based on probabilistic models of meiotic recombination. A netbeans platform application is built to incorporate the computations. Project issues are mainatined at https://freecode4susant.atlassian.net/browse/GENOMEMAP

The Systems Biology Ontology project (SBO) goal is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. !!!! Important Announcement !!!! We have moved the curation and development of Systems Biology Ontology (SBO) to a git-hub repository https://github.com/EBI-BioModels/SBO. Hence, this SourceForge SBO project has also been retired. Please use the Git-Hub issue tracker https://github.com/EBI-BioModels/SBO/issues to request the addition of new terms.

...The program is fully multiplatform (100% Java) and integrated with the Jython (Python) scripting language. Currently the project is known under the name DataMelt (https://datamelt.org)

This project has been moved to bitbucket.org: - https://bitbucket.org/vahidi/jbdd/wiki/Home - https://bitbucket.org/vahidi/jdd/wiki/Home It includes two libraries for working with decision diagrams: - JBDD: a Java interface to two popular BDD libraries, CUDD and BuDDy - JDD: a native Java library supporting BDD, Z-BDD

moved to https://github.com/Mithos/Euclid/wiki

...Once an expression is created the user can convert it into a variety of different linear syntax for mathematics, including MathML, LaTeX, Maple, Maxima or any user defined style. PLEASE NOTE: active code development has moved to GitHub. https://github.com/maths/dragmath

JUNG provides a common and extendible language for the modeling, analysis, and visualization of data that can be represented as a graph or network. New version now available on GitHub: https://github.com/jrtom/jung/releases/tag/jung-2.1

A project to help students calculate symbolic derivatives and integrals. Plus, a Java expression tree library for developers who may need to do such things in their programs. The project has moved to github: https://github.com/generalpenguin89/calchelper

directed rounding, rational arithmetic and arbitrary precision arithmetic based on regular continued fraction expansions Moved to https://exactarithmetic.dev.java.net/