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JSys is a simple to use graphical package for simulating continuous dynamical systems. It was created for use in a first level undergraduate introduction to systems thinking for students of Information Technology and Information Systems.
Diagram (JGraph) driven simulator. Bondgraphs > nonlinear differantial system > plot: implemented for economics and ecology. Network analysis: emergy propagation implemented. Would also fit for electronics, mechanics, cost, GWP, footprint analysis.
YABI93 is an Interpreter for the esoteric programming language Befunge, version "Befunge93". It is written in Java 1.5 and uses Swing for its graphical interface. YABI supports a multilanguage GUI.
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GeoWidgets is a set of reusable UI widgets for geographic applications (GIS), such as referencing dialogs, legends, styling widgets or map panes. The project is based on GeoTools (in Java) and supports several GUI toolkits (e.g Swing, SWT).
Note that, while functional, this library is not developed any further.
A game/toy that simulates a world environment with organisms to survive: game of life with more complex rules. Every programmer can make his/her own organisms and compete with others. Hopefully in the future it will support genetics.
B.O.T.S (Bots Tactical Simulation) is a programming game, where players "code" the behaviour of their bot and watch them fight with others bots in a arena. It comes with a full environnement in Java/Swing, for coding, debugging, playing matchs, etc ...
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Formicidae is the official simulator and visualizer for the Ant-Wars competitive programming site, written in Java and SISC. The site is hosted at www.ant-wars.net.
Io (ISREC ontologizer) is a program to classify high-throughput genomics data (e.g. microarray results) in the Gene Ontology. Io includes a statistical estimation of the significance of data in the GO nodes and reannotation files for Affymetrix chips.
graphite: a portable graphics library, written in Java, JOGL and Postscript that allows rapid generation of high-quality graphs using an efficient, compact Java engine.
CryptoHelper is a Java program designed to aid in the decryption of classical ciphers, ie pre WWII ciphers. It brings together tools like frequency analysis, friedman tests, enciphering/deciphering for several clasical ciphers, and brute force algorithm
ISYS (Integrated SYStem) is a Java-based plugin framework for loosely-coupled integration of independently developed components. It provides both service-oriented and event-based communication whose semantics may be contributed by component developers.
Wordcorr automates the tedious and risky process of tabulating and managing the sound correspondences used in working out the historical development of natural languages. Initial support was from NSF.
msgnet is a library that implements a simulation framework with visualisation for message passing networks.
This might be useful for teachers and students of distributed systems courses.
CRANKS is an Java application that uses the Swing toolkit to provide an interactive environment for the animation and kinematic synthesis of four-bar mechanisms created through a series of geometrical constructions.
neochip is a collection of algorithms for high-density oligonucleotide microarrays. The current version contains heuristic algorithms that attempt to improve the quality of arrays by re-designing their layout (the location of the probes on the chip).
qsh is a shell for any operating system. It is coded in java so it inherits the pros and cons of java. It is in a very nascent stage, but all the regular commands work: Directory navigation, file tasks etc.
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
ISAS is a configurable computer instruction set architecture simulator, written in Java, that can be used to quickly define, test and measure performance of computer instruction set architectures.
DNAGalaxy is an attempt to produce an open-source bioinformatics software alternative to the expensive DNAStar Lasergene software. Its features currently include Blast and Entrez searching, a frontend to clustal and a sequence editor. It requires java1.5