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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.
The Information Visualization Cyberinfrastructure is a graphical tool with diverse modeling, analysis, and visualization algorithms for education and research. This tool is built on CiShell: Cyberinfrastructure Shell.
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.
SpOK - The Spectrum Organisation Kit, a program for the organisation and visualisation of spectral data written in Java. Sorry - this project is not being continued. All functionality was integrated into the Bioclipse project...
JavaCET is an API wrote in Java that allows to analyze Java source code and libraries, and control its execution and its trace in an integrated and comprehensible object-oriented way. It allows backwards execution.
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.
The Macro Agent Transport Event-based Simulator (MATES) is intended to efficiently investigate the behavior of distributed agent based systems over mobile ad hoc networks (MANETs). MATES provides an expandable environment for agent-based system testing.
Datastream Pro is a user friendly, 100% pure java, desktop application designed to interface to multiple RDBMS systems simultaneously. Easily browse and maintain data in your database, write queries and perform database entity maintenance.
PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.
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BibTeXlib is a BibTeX library written in JAVA. You can use it to extract information from BibTeX files, manipulate this information, and save it to BibTeX files.
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.
Nested pie chart is for tree visualization. Each node of the tree has a size and color attribute, enabling the chart to be used as a heatmap. Linear arrangement of the nodes in decreasing order of size is an advantage over rectangular heatmaps.
MobileMath is a software written by using J2ME technolology. It turns mobile into calculator supporting many operations such as : evaluate expression, plotting, differentiate & integrate expression... It can run on any mobiles supporting Java.
Xquetzal/Xitris Get, Process, Display, Store, Compress and Publish (In Web Page) Data from Analog Source Flux in Real Time using LabPC+ or Other A/D Convertor board.
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.
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.
Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.
Java3D 3DS FileLoader for platforms supporting JDK1.4 and Java 3D
Highly functional, multiplatform 3DS File format loader
Supports:
Heirarchical animation
Cameras
Point Lights
Directional Lights
Textures
Smooth Groups
and other features
A visual Domain-Specific Language for Data Transformations, which generates programs for non-programmer domain-experts. The generated program will extract data from one source and converts it into a meaningful format defined by the user.
ISpheres provide distributed interoperable metadata & digital object services. Each ISphere can publish multiple heterogeneous collections of digital objects (eg images, GIS data, etc) search other ISpheres, translate metadata, transform & serve objects.
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
Framework for storing and editing Forestry-related XML data, with a specialised graphical interface for each object type. Plug-in API for adding functionality. Coded in Java, uses WebStart for distribution, swing GUI, ~100k lines of code.