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OrthoInspector is a new software system for orthology/paralogy analysis. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.
Semtinel is an application framework for the semi-automatic creation, maintenance and analysis of hierarchical concept schemes (thesaurus, classification or ontology). Semtinel supports the development of new analysis methods and visualization techniques
Implementation of the Weight Spherical Centroidal Voronoi Tessellation described in http://arxiv.org/abs/0912.3974
It uses this implementation of convex hull: http://www.cs.ubc.ca/~lloyd/java/quickhull3d.html
On The Mark is a video and image scoring system that allows one to mark any number of events and durations through a simple, easy-to-use graphical interface.
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JTreeMap is a Swing Component which represents a tree structure with rectangles (a TreeMap. See http://www.cs.umd.edu/hcil/treemap/). KTreeMap is the SWT component for treemapping (see http://en.wikipedia.org/wiki/Treemapping). It is an Eclipse plugin.
Kabeja is a java library for parsing DXF and converting to SVG (dxf2svg). The library supports the SAX-api and can integrated into other applications (Cocoon,Batik). Tools for converting svg to jpeg, tiff, png and pdf are included .
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.
Solvere4D is a powerful, open-source, freely available post-processor that makes it easy for anyone to generate 3D animations of 3D rigid body kinematics and kinetics, with many visualization options.
JEuclid is a complete MathML rendering solution, consisting of: a MathViewer application, command line converters from MathML to other formats, an ant task for autmated conversion, display components for AWT and Swing and a component for Apache Cocoon
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.
MedioVis is concerned with the user-centred development of next generation visual information seeking systems for novice and nonexpert users. Various Browsing-oriented data exploration strategies are supported (overview & detail, filtering, zooming etc.)
Intrepid Bioinformatic's Integrative Genomics Viewer (IGV) modifications for viewing NGS files on IGV with data located on remote servers, accessed by web services.
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.
VR Juggler is a virtual platform for virtual reality application development created at the Virtual Reality Applications Center at Iowa State University. Applications developed in VR Juggler can transparently move between a wide range of VR systems.
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