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TRMSim-WSN (Trust and Reputation Models Simulator for Wireless Sensor Networks) is a Java-based simulator aimed to test Trust and Reputation models for WSNs. It provides several Trust and Reputation models and new ones can be easily added.
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)
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4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
Cervelletto is a neural network simulator. It uses a new neural model based on biological, neurological and psychological studies. [it's not yet completed... just give me some weeks! sorry!]
The aim of GUINNEA (Graphical User Interfaced Neural Network Architecture) is to develop a comfortable and high-featured neural net simulator which is highly configurable and flexible. It will support many neural nets and visualization features for those
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An Evolution Simulator of Single Cells in a Pond. This shows a crosssection of
water with sun shining from above. A single cell is dropped in and has various genes. The cells multipy and evolve. See Files above for download and screenshot.