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It is an open source scientific library that is focused on multi-agent simulations on graphs. It prepares basic toolkit for agents, models, timers, graphs, nodes and edges. It is also accompanied with tools for data processing.
Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes.
Please check our new repository: https://github.com/CNS-OIST/STEPS
Stochastic Pi Machine (SPiM), created by Microsoft, is a programming language for modeling biological processes. Two tools are available from Microsoft for simulation. A web application Visual SPiM, and a destkop application SPiM Player. Both simulation tools require to be run on a Windows platform.
Fortunately Microsoft has also released a command line version for Linux and Mac OS based on OCAML however this version will only output a CSV file for the simulation results.
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Simulation of stochasticprocesses and ODE models in biology.
SIMulation of Biological systems
(developed at the TU Munich)
This program allows to define ODE-models or stochastic compartemental models of biological processes, to simulate, to fit data and to do some statistics (fitting and statistics for deterministic models only).
...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 stochasticprocesses.
KStochastic gives the user the ability to create pictures of stochasticprocesses based on arbitrary probability distributions. Those pictures can then be used for illustration purposes in various publications treating random phenomena.