PhenoFam is a web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.
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
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.
MonteCarlo portfolio simulation - it can be used as stand-alone command line application - it takes simple XML file needed data as entry and creates simple XML file with output, also this stuff have JNI and ISAPI interface.
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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
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.
Maximally flat (maxflat) digital filter design in Java, with arbitrary numbers of poles and zeros. "Maximally flat" means that the magnitude frequency response has the maximum number of vanishing derivatives at 0 and pi.
Currently, all existing formal tools are designed to serve as formal verifiers, using one implementation or another. JTLV is a new tool aimed to facilitate and provide a unified framework to the development of formal verification algorithms.
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A version of the source I used in these videos on youtube: http://www.youtube.com/watch?v=5k6arok7zac http://www.youtube.com/watch?v=TaNu8-ObsXU and http://www.youtube.com/watch?v=7qAq61ATgqo . It requires Sunflow, JBullet, and Java.
The project "Sippie" is an additional tool for automatically converting Wireshark-Traces to XML - scenarios, which can be easily used as infile for the OpenSource SIPp test tool and traffic generator.
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.
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.
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.
Graph polynomials and view prime numbers on a ulam spiral graphing plot. Only integer numbers. Based on an old GPL version of the JEP equation parser. See website for additional examples/live applets Seems to be closely related to Cellular automaton.
The Minervan project aims at aiding intelligent software development. It integrates reporting, analysis and data mining to support better decision making.
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.
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/
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.