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PhyloPattern is a Java/Prolog API, helpful to simulate human reading of phylogenetic trees. Bioinformatician can: annotate trees, apply complex patterns to a tree to search specific architectures or extract information, compare trees with dynamically gen
jamod is an object oriented implementation of the Modbus protocol, realized 100% in Java. It allows to quickly realize master and slave applications in various transport flavors (IP and serial).
To help math students visualize the prufer code and/or discover anything new about the prufer code not already present. Examples and live applet on webiste.
Seems to be closely related to Cellular automaton, except this creates a complex pattern from a mathematical function you input. See website for examples/live applets. This program makes use of an old GPL version of the JEP equation parser.
This project is a compilation of tools/libraries to help with tasks related to Text Analytics mainly in Java. These tools range from simple wrappers to sophisticated mining tasks that can improve the productivity of researchers and engineers.
Program described in the paper: MUDE: A new approach for optimizing sensitivity in the target-decoy
search strategy for large-scale peptide/protein identification, 2010.
By Cerqueira, Fabio; Graber, Armin; Schwikowski, Benno; Baumgartner, Christian.
Blogspread is an open platform for the developmend of applications that analyze data from websites like blogs and forums. Blogspread is jointly developed by the University of Mannheim, Germany, the UFPE, Recife, Brasil and the UFAL, Maceio, Brasil.
NG4J - 'Named Graphs API for Jena' is an extension to the Jena Semantic Web framework for parsing, manipulating and serializing sets of Named Graphs. For details about Named Graphs see http://www.w3.org/2004/03/trix/
A graphical MatLab framework for estimating the parameters of, modeling and simulating static and dynamic linear and polynomial systems in the errors-in-variables context with the intent of comparing various estimation strategies.
UbikSim is an infrastructure to study complex AmI (Ambient Intelligence) applications which involve a large number of users. It is a MABS (multi-agent based simulation) programmed in MASON and aims to be as descriptive as possible.
CommonMap is an open source map project, forked from OpenStreetMap by a licence problem. CommonMap needs original softwares tuned for CommonMap. Most of software would be useful for any other open source map projects, too.
Biodiversity Information Group develops software tools and data standards that enable herbaria and museums to create dynamic distributed queries of their online databases. See http://bit.ly/bfirSh and http://bit.ly/bwpnSY for latest developments.
HealthAgents is an open source web-based distributed decision support system (DSS)
which provides hospitals and organisations with a reliable tool to aid in the diagnosis of brain tumours and their prognosis aiming to avoid invasive surgical
procedures
Maui is a multi-purpose automatic topic indexing algorithm. Given a document, Maui automatically identifies its topics. Depending on the task topics are tags, keywords, keyphrases, vocabulary terms, descriptors or Wikipedia titles.
GRad is a standalone solar radiation model, programmed in Java. It is capable of the calculation of potential (clear sky) and actual (real sky) irradiance and total irradiation for single and multiple geographical locations.
Note that, while fully functional, this application is currently not developed any further.
OpenDMAP (Open Source Direct Memory Access Parser) is a natural language processing (text mining) application: a semantic parser for information extraction.
Phenomenological Simulation of Electrical Conductivity in Ceramic Superconductors using High Performance Java (MPJ Express).
The source code for this project would be free to download and develop further
QSAR is a project that aims to build a GUI that enables people to build quantitative structure activity (or property) relationship models. It will use parts of CDK (cdk.sf.net), JOELib (joelib.sf.net), R (www.r-project.org) and other projects.
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