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The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!
A basic quadratic equation calculator written in Java with a command-line interface. Handles fractions and imaginary roots. Thanks to Doug Lea at SUNY Oswego for his work on the Fraction class.
MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web userinterface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
JCrocus is a GUI (Graphical UserInterface) that allows representing the network topology definition of microwave cavity filters based on the coupling matrix approach as well as simulating and plotting its frequency response
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Example-based Modeling (EMO) is an tool to create data models, with examples, using a web interface. You interactively create a web-accessible database of models and samples for those models. A white paper describes the underlying assumptions.
An Interactive Fiction Player written for Java Virtual Machine. It implements the Z-machine and Glulx specifications and can be used either standalone or as an applet. The Z-Code/Glulx interpreter runs adventures made by Infocom and contemporary Inte
netcdf-tools is a set of tools for creating netCDF files. It supports command line use on both Windows and Unix as well as use directly as a Java library. Written by CSIRO Australia and funded by the ANDS Australian Research Data Commons Project
Trial Criteria Online Data Entry (trialCODE): a Java-based userinterface that codifies eligibility requirements used to automate the screening of potential subjects to clinical trials. Used for caMATCH screening engine on BreastCancerTrials.org site.
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
Ex-Crawler is divided into 3 subprojects (Crawler Daemon, distributed gui Client, (web) search engine) which together provide a flexible and powerful search engine supporting distributed computing. More informations: http://ex-crawler.sourceforge.net
PowerTalk automatically speaks Microsoft PowerPoint presentations. For presenters who find speaking difficult, audiences containing people with visual impairments and fun educational uses. Uses synthesised computer speech provided with Windows
This project will be a Java Application for the Parallax Microntrollers, It will eventualy implement Code Snippets, and javadocs when completed. If you are experianced and interested in Java, please help this project.
PORIS toolkit allows describing graph-based systems and their behavior in a snapshot. It provides a web
editor for a domain visual specific language (DSL) and transformation tools to generate software prototypes, system configurations, ...
h2:www is an easily extendable online interface for bioinformatical command-line tools, providing convenient project-oriented working facilities for multiple users.
This is an open, cross platform SCADA system. SCADA stands for Supervisory Control and Data Acquisition, and is used to create software front-ends to control processes in industry. Created in Java, it has a headless server and uses Swing GUI controls
Code for the SALAMANDER environmental sensor project. SALAMANDERs are wireless motes (Crossbow TelosB with MSP430 processor) with a string of sensors attached. Mote code is in nesC. DataGetter java code enables mobile phones to collect sensor data.
Moara is a biological text mining tool and consists of a Java library and some auxiliary MySQL databases for gene/protein training and extraction of mentions and its further normalization and disambiguation.
This project is a compilation of tools/libraries to help with tasks related to Text Analytics mainly in Java. These tools range from simple wrappers to sophisticated mining tasks that can improve the productivity of researchers and engineers.
Sanchay is a collection of tools and APIs for language researchers. It has some implementations of NLP algorithms, some flexible APIs, several user friendly annotation interfaces and Sanchay Query Language for language resources.
"Java Textual Desktop" project stands for the classical TEXT screen with java implementation inspired with Curcus which used for decades in the history of UNIX (linux).