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Java Modelling Tools is a suite of scientific tools for performance analysis and modelling using queueing theory and colored stochastic Petri nets. Models are solved either with analytical, asymptotic or simulation methods; workload characterization tools are also included in the suite.
See the project website for more details: http://jmt.sf.net
Pocket Cube J3D is a simulator of a Pocket Cube, in Java language and Java 3D graphics API. Java 3D is available at: http://www.oracle.com/technetwork/java/javase/tech/index-jsp-138252.html
Energy-, mass- or money-flows are described with simular balances. Usually many upsetting tables are used to calculate the balance. The Software Flow visualizes the data in a grafic, zoomable and animated way.
JCreme is an automated interface to the CREME96 modeling web app (https://creme96.nrl.navy.mil/). It allows the user to send multiple requests to the CREME96 website and retrieve the results. CREME stands for "Cosmic Ray Effects on Micro Electronics"
Ciclope Planetarium is a web-based planetarium that provides a simulation of the sky from any location at any time and date. Developed using Google Maps API & AJAX. Available in PHP & J2EE. Integrated in the Ciclope Stars project (www.ciclope.info/stars)
The Integrative Biology VRE is a web-based graphical user interface and repository that provides an environment where biological simulation experiments can be constructed without the need for any knowledge of unix, cluster computing, or shell scripting.