UDA stands for Universal Descriptive Algebra. It consists of a Java package handling universal algebras and relational structures as description systems.
JFunctionViewer is a simple and fast OpenSource function plotter. Since it is written in Java it is Platform independend and can even be run from inside a Browser.
Visually build and simulate boolean logic circuits
Visually build boolean logic circuits and then simulate their operation. Create custom components from user-designed circuits. Written in Java for cross-platform functionality.
NOTE: This project has moved to Bitbucket at http://bitbucket.org/kwellwood/circuitsandbox
QTnew is a universal Queueing Theory simulator. Different types of serving disciplines, time distributions, routes are supported. Simulation is extremely flexible: any custom simulation can be performed with JavaScript.
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MASQOT-GUI is an open-source, platform-independent application for two-channel microarray spot quality control. Included is a set of tools for gridding, segmentation, quantification, multivariate spot quality assessment and data visualization.
Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical represetations from Gene Ontology (GO) annotated interactions maintained by the BioGRID.
Graph Theorizer will be a java application that will help to teach and research Graph Theory. We will support Windows, Linux, and Mac in our first releases, while hopefully moving towards any platform that supports Java Standard Editon.
MirkE is a platform-independent Java application using Hibernate, HSQLDB and Colt designed to facilitate common but tedious calculations on spectrophotometric and colormetric data for molecular and cellular biology assays.
MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic
Chart construction kit for the Java(TM) platform. A small (<100Kb) library and framework for scientific charts and plots. It runs under JDK(TM) 1.1 and PersonalJava(TM) platforms. Renderers for Graphics context, Graphics2D context, and SVG exist.
A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.
GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work
Cytoscape is a software platform for computational biology and
bioinformatics, useful for integrating data, and for visualizing and
performing calculations on molecular interaction networks
The jXUL project is an open source project to integrate the XUL language into the Java Platform. There are multiple ways in which this integration will take place. In fact, this project will expand as its members find new ways to integrate these two techn
The co-simulation adapation platform serves as programming framework and middleware to enable coupling of distributed, heterogeneous numerical models. The framework facilitates the adaptation and integration of new sub-models into a common simulation platform.