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JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.
The Embedded Data Display System provides a lightweight portable C++ server library and a PC (Windows, Linux, or Mac) based client that captures and graphically displays data generated by embedded devices such as medical or industrial instruments.
EdgeExpressDB (eeDB) is a federated data abstraction system designed for integrating, interpreting, and visualizing very large biology datasets. It is designed for scaling beyond Petabytes and 10^13 objects. http://fantom.gsc.riken.jp/4/edgeexpress
FElt is an open source system for finite element analysis, primarily for mechanical problems. FElt includes command line tools, an X11 interface for pre- and post-processing, and a Windows editor interface with some post-processing capabilities.
SYSTEM FOR DESIGNING AND SIMULATE CONCURRENT AND DISTRIBUTED PROGRAMS IN CLUSTER ARCHITECTURE Provides graphical interface for configuring relationships between cooperating, abstract processes and simulate it in real cluster environment, using MPI.
This library provides an easy interface to Gnuplot (http://www.gnuplot.info/) from OCaml (http://caml.inria.fr/) for static 2D and 3D graphs and simple animations. This library aims to be portable on all platforms OCaml runs on.
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Musical Notation System
Using a GUI with a built in text editor, one can create a score with the appropriate notations. All musical notations are then transformed into a graphical representation and can be exported into various formats (pdf, ps, eps).
The Optics Project on the Web (WebTOP) is a 3D, interactive computer graphics system that visualizes optical phenomena. Its purpose is to help instructors teach and students learn about optics. It is a platform independent Java application that uses X3D.
Vegetation3D is a library for realistic visualization of vegetation. Every phase of this process, such as plant topology generation (L-System) or mesh generation may be controlled and used separately.
Franklin Math is an open source Java symbolic computer algebra system (CAS), with similarities to commercial math packages such as MATLAB or Mathematica. It allows numeric and symbolic calculations, with built-in functions including plotting commands.
DemoScript runs commandline-based demos. It logs to a remote host (ssh), writes the password, and then writes the commands specified in a script. The tool mimics someone's typing: delay between each letter and intelligent command sending synchronisation.
The Olduvai bioinformatics visualization system allows side by side comparison of:
TreeJuxtaposer: evolutionary trees
SequenceJuxtaposer: genomic sequences
GParticles is a tool to simulate the growth behaviour of two- and three-dimensional nano particles based on a simple grid model, with adjustable (time-dependent) concentrations of the particle's different components.
Orthogonal (a.k.a manhattan) line routing is
a technique for rendering a human-readable
hierarchical diagram. Manhattanlines
implements an orthogonal line routing algorithm
that minimizes line length and crossings.
Software tools for building interactive information visualization applications. Prefuse supports a rich set of features for data modeling, visualization, animation, and interaction for both Java (prefuse) and Flash (prefuse flare).
glomp is an open source multipipe OpenGL library. Its intent is to automatically distribute 3D graphics computations over multiple graphics card on the same machine.
BINViz(Bidirectional Interactive Network Visualization) is a JavaScript library for network and graph visualization. The goal of this tool is to provide a better way to visualize complex graphical models and the underlying data in a web-based environ
StormForce is a free open source program written in Python/PyGame for the Boltek LD-250/StormTracker. StormForce works in FreeBSD, Linux, and Microsoft Windows.
Developed in Java programming language, this software lets its users view and manipulate hierarchical data structures represented as a hyperbolic trees.
The Parallel Compositing library enables developers to write scalable 3D graphics applications. The library does sort-last compositing, and works on both clusters and SMP machines. The API aims to be the MPI of parallel compositing.
The SESAME (Simulation of Embedded System Architectures for Multilevel Exploration) software system is an embedded system co-simulation environment and research tool which implements the ideas of the SESAME project at the University of Amsterdam.