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Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)
A C++ library for machine learning within dynamic systems. It provides methods such as the Kalman, unscented Kalman, and particle filters and smoothers, as well as useful classes such as common probability distributions and stochastic processes.
Simulates and visualizes swarming algorithms with limited communication. Also provides an interface to animate particle motion by playback (with pause, fastforward, and rewind) of path information from files. Can output EPS figures and avi frames.
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Partgen is a simple particle system generator and simulator. It's intended to have a 3D scene description language, and batch processing mode. Support for some scripting languages like ruby is also planned