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A plugin for the VANTED system, called Glyph-based Link Exploration of Pathways (GLIEP). It helps to guide the navigation and exploration process of interconnected pathway visualization as well as insight into the overall interconnectivity.
Jep is a Java package for parsing and evaluating mathematical expressions. It currently supports user defined variables, constants, and functions. The open-source Jep project was halted in favor of commercial development of version 3.0 upwards.
Intrepid Bioinformatic's Integrative Genomics Viewer (IGV) modifications for viewing NGS files on IGV with data located on remote servers, accessed by web services.
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Worldlines visualizes special relativity, as particles near lightspeed trace paths in a 3D slice of 4D Minkowski spacetime. Scenes illustrate time dilation, the twin paradox, length contraction, and Bell's spaceship paradox.
PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.
Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.
The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html
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
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
The Quantitative Finance Framework (QFF) supports the development of software libraries in mathematical finance. The main field of applications are the pricing of derivatives and the management of financial risks.
PSIGHOS is a Java-based simulation library. PSIGHOS is focused on the simulation of business processes and comprises a parallel core so to reduce the execution time for large models.
Siafu simulates individual agents and their context, from home to city-wide scenarios. As a developer, you use the API to write your simulation for the purposes of data-set generation, test or visualization, optionally hooking it to your own application.
This project provides a java implementation of the Captcha project ( see http://www.captcha.net ). A CAPTCHA is a program that can generate and grade tests that: -Most humans can pass. -Current computer programs can't pass.
IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.
Chisio is a free editing and layout tool for compound or hierarchically structured graphs based on the Eclipse Graph Editing Framework (GEF) that can be customized to build application-specific graph visualization tools by modifying its code-base.
!!! For latest version, please see !!!
http://code.google.com/p/chied
A Java library and set of tools to quickly and easily manipulate graphs (set of nodes and edges) and dynamic graphs. The principal trait of this library is its ability to manage (create, edit, layout, display) continuously evolving graphs.
The development of this project now takes place on Github. Visit the official Graphstream website at http://graphstream-project.org
JGraph is the most powerful, lightweight, feature-rich, and thoroughly documented open-source graph component available for Java. See the project homepage at www.jgraph.com for information and downloads.
JSatTrak is a Satellite tracking program written in Java. It allows you to predict the position of any satellite in real time or in the past or future. It uses advanced SGP4/SDP4 algorithms developed by NASA/NORAD to propagate the satellite orbits.