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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.
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
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.
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OSIOSS (Open Source Integrated Observing System Software) is a collection of code which can be used for geospatial observing systems merging data collection, management and products solutions with ocean observing systems (OOS) as an initial focus.
This is a framework to develop Contexts and Agents and a Container to run them. The Container lets each Agent interact with the Context and other Agents. The agents are deployed in jar files and each one runs in an exclusive sandbox.
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.
brCluster is a class library, written in java, that implements generic clustering algorithms carefully designed to allow its aplication in any kind of data. The algorithms implemented are K-means and Hierarchical Clustering (Simple and Complete Link).
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.
GiANT is a graphical interface for computer algebra systems (OS X/UNIX/Win). Currently GiANT lets the user work with number fields via KASH, but we aim to develop it into a GUI Library to run on top of any CAS and expose any of its functions.
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.
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
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
The Linear Algebra class library for Java provides a full set of tools to programmers who need linear algebra operations to use in their own projects.
Currently the library supports elementary matrix operations.