Open Source Java Scientific/Engineering Software - Page 20

Periodic table of the chemical elements for Java (J2ME) enabled devices. http://kenai.com/projects/periodic/pages/Home

This project is a “proof-of-concept” prototype that used diagrammatic visualization for presenting multi-dimensional port data, in relation to local and global events. The visualization emphasizes relations between land-side and wharf-side elements and thus conveys derivable knowledge on labor productivity and efficiency. It can be used to convey commodity flows through the port and state, modes of transport, facilities and their capacities, operational characteristics, intermodal operations, and parameters required for calculating system efficiency, benefits and costs.

ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.

PulsarHunter is a java based package for pulsar searching. It operates on a number of standard data formats. This package also includes the JReaper graphical candidate selection tool.

QASE is a Java-based API designed to provide all the functionality needed to create game agents in Quake 2. Powerful enough to facilitate high-end research, it is also suitable for undergrad courses geared towards classic AI and agent-based systems.

QRay is an interactive 3D modelling system in Java. It's built-in real-time raytracing engine implements the Quadric-CSG representation model and the Seed-Fill optimization method, which empower QRay to provide cool WYSIWYG 3D modelling functionalities.

SWARD (System for Weapon Allocation Research and Development) is a testbed for benchmarking weapon allocation algorithms against each other. It is intended for researchers within operations research, information fusion, and related areas.

A solar sail structure and flight simulator with accurate accounting for orbit perturbations and structural details. Geometric algebra is used for mathematical functions.

This project proposes a virtual laboratory for social scientists interested in the modelling, analysis and behavioral simulation of power relationships within organizations and more generally in systems of collective action. This software is grounded on the works lead by Sibertin-Blanc and Roggero on the formalization of the Sociology of Organised Action [Crozier and Freidberg]. Visit the homepage of the project on soclabproject.wordpress.com for tutorials, examples and further theoretical position.

GNAT is an open source, platform-independent MATLAB based toolbox. It is written in MATLAB and Java. It has been tested in Windows (Windows 7), Linux (Ubuntu), and Mac OS (X Lion) platforms. The original GNAT package (file GNAT.zip) provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks (citation [1]). The second version of this software (GNATv2beta.zip) upgrades the original GNAT program with additional features that are geared towards incorporating glycan-structure experimental data into the simulation environment. For information about GNAT installation and usage, please see the GettingStarted.pdf file enclosed in the package. To cite GNAT: [1] Gang Liu, Apurv Puri and Sriram Neelamegham, Glycosylation Network Analysis Toolbox (GNAT): a MATLAB based environment for systems glycobiology, Bioinformatics 2013 29: 404-406

TAS (Transcription Analysis System) is a multi-tier framework for running parameterized SQL queries. Users can analyze new data or new combinations of data with a few clicks in a GUI. Potentially complex/repetitive database interaction is all automated

TER implements the CCSDS Recommendation for Image Data Compression (CCSDS 122.0-B-1). TER also adds new features to the Recommendation. TER is designed and programmed with the aim to provide a good basis to test and develop the CCSDS Recommendation.

TIRfinder: A tool for mining class II transposons

The Text Annotation Environment (tae) can be used to annotate natural language text manually or automatically (UIMA Annotator) with meta information (tokens, part-of-speech, named entities, ...). Tae is based on Eclipse and IBM's UIMA.

A neuroscientific knowledge management system for the published literature

TinyOS is an operating system for embedded sensors and networks. Versions 2.0 and later of TinyOS should be downloaded from www.tinyos.net.

This is a simulation package developed for numerical simulation of ultrashort pulse propagation in optical media and pulse generation from mode-locked lasers. Although the code is primarily intended for investigations of fiber links, fiber amplifiers and fiber lasers, it can be applied to any other setting for which the governing equiations are valid. The physics included in the code is based on a generalized nonlinear Schrödinger equation, including higher order dispersion, stimulated Raman effect, gain with bandwidth limitation and saturation, loss, and saturable absorption. Disclaimer: The simulation code is provided free of charge for the use of the academic community only. We kindly ask the users to acknowledge use of the code in academic settings. We do not accept responsibility for any errors or omissions that may be present. Çağrı Şenel, Punya Prasanna Paltani, Fatih Ömer Ilday

Este aplicativo foi desenvolvido através de um trabalho de conclusão do curso de Engenharia Civil da Universidade do Extremo Sul Catarinense. Seu uso está restrito para fins educacionais e não deve ser reproduzido comercialmente. O usuário é responsável pelas conclusões dos resultados obtidos pelo aplicativo. O autor, orientador e instituição de ensino envolvidos no desenvolvimento desse aplicativo, não têm nenhum dever legal ou responsabilidade por danos causados de forma direta ou indireta pelo uso de alguma informação disponibilizada por esse aplicativo. Não existe nenhum compromisso ou garantia do bom funcionamento do aplicativo.

XNavigator is the online viewer for the OpenStreetMap Globe at http://osm-3d.org and much more. It is an interactive 3D viewer and integrated client for exploring virtual city and landscape models. A wide range of interaction and navigation possibilities makes it easy to visualize and analyze very detailed virtual urban environments. XNavigator is the first application that supports the Web3DService (W3DS) service interface.

GUI to configurate and start XPlanet easily. Adds a downloader to XPlanet to load clouds, images and marker files from the internet. Generates cmd (windows) and configuration files for XPlanet and the downloader. Hides in the System Tray.

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

DVKit provides an Eclipse-based integrated development environment (IDE) for common design-verification tasks, such as developing SystemVerilog, C++, TCL, Python, and shell code

The goal of the Ibis project at the Vrije Universiteit Amsterdam is to provide an efficient and flexible Java-based programming environment for Grid computing. Ibis provides several communication models, including a highly efficient RMI implementation.

A collection of plugins and tools for the ImageJ software. Contains modules for image filtering (directional filtering), segmentation, analysis (perimeter estimation, geodesic diameter...), or visualisation (image overlay).

jCAE is a JAVA based environment for CAE applications. It provides meshing and visualization capabilities. It is targetted to run on a maximal number of platform.