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Cyberinfrastructure Shell (CIShell) is an open source, community-driven framework/application for the integration and utilization of datasets, algorithms, tools, and computing resources. Algorithms can be integrated using most programming languages.
A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.
LogicAnalyzer is a framework as well as an application to operate a PC based logic analyzer. It's built using the Eclipse RCP and designed with extensibiliy in mind. Integrating new devices or creating completely new functionality is easy.
Automata Based Programming Tool for implementing logic for J2SE, J2EE and Sybmian applications. Consists of Java FSM Framework and Eclipse Plugin parts. Plugin implements UML model editor, visual debugger, validator, compiler and interpreter for Eclipse
Guanxi is a robust analysis and simulation application for Social Network Analysts. Guanxi allows researchers in the field to create, import, and export an endless array of networks, analyze their structure, and run custom dynamics over them.
OntoModel is a UML-based editor that works with OWL ontologies. The usage of the UML extension mechanism makes it possible to develope and maintain OWL ontologies with MDA technologies. Implemented as NeOn Toolkit (http://www.neon-toolkit.org) plugin.
A eclipse plugin for the history of a single file. The history is fetched from the repository and visualized based on annotations. The color describes the authorship or the changes and can be changed. It comes with a powerful metric extension point.
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A Mac OS X framework implemented in Objective-C 2.0 that reads and parses ASCII DXF files. The framework returns an array of custom entity objects that can be used as needed by the program implementing this library.
OpenReports is a powerful, flexible, and easy to use web reporting solution that provides browser based, parameter driven, dynamic report generation and flexible report scheduling capabilities. Supports JasperReports, JFreeReport, JXLS, and Eclipse BIRT
A lightweight, browsing-based, 100% Python, federated data integration framework. Users may create custom schemas for disparate sources, query and expand results across sources to find related data; for use in fields such as bioinformatics and datamining
CallMesh is an eclipse plugin visualizing call graphs in java projects with the help of the zest toolkit. It allows easy navigation around you classes. Additionally, call graphs can be exported as dot-files as understood by graphvis.
DiscriAlign implements a novel algorithm that aligns a set of biological interaction networks.It identifies both functionally conserved and dissimilar regions.
Jaude is "Java pour les Astronomes Utilisateurs de Detecteurs Electroniques". Jaude is Eclipse RCP and plugin based. So it will provide an Eclipse interface for JSky library (http://archive.eso.org/JSky/).
3D cellular automata modelling software for large general purpose simulations. Uses custom scripts for rules and can distribute processing over several machines.
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
HyPhy is a comprehensive environment for maximum likelihood statistical analysis of genetic sequence data. It includes a large collection of out of the box analyses, a feature-rich graphical user interface for custom data analysis and a scripting languag