A Fast and Versatile Stochastic Simulator
Stochsim is a fast and versatile stochastic simulator. The simulator is written in C++, but also offers a convenient Matlab interface.
Different to many other stochastic simulators, stochsim provides functionality for
- both propensity and fixed time delay reactions (reactions firing a pre-defined time after a molecule was created).
- custom reaction rate/propensity definitions to implement non-mass action kinetic reactions (e.g. logarithmic growth).
- assigning-if required-a unique identity to each molecule of a species/state, for example to count the number of how often a given molecule participated in a reaction as a catalyst.
- probabilistic outcomes of reactions, e.g. A->B with probability 0.1, and A->C otherwise. This is especially useful when combined with fixed time delay reactions, or with molecules having each a unique identity (probabilities can depend on this identity).
The stochsim simulator can be accessed in three different ways:
- Directly adding the C++ source and header files, respectively the compiled static libraries and the header files, to a C++ project, and configuring and running the simulation directly via C++.
- Via a Matlab (mex) interface, mapping the C++ class structure directly to a (simplified) Matlab class structure which provides nearly the same capabilities as the C++ interface.
- By calling a provided standalone executable and providing the simulation configuration as an argument.
A simulation/model can be configured in two different ways:
- Directly via the native or Matlab interface by calling the respective functions.
- Via a cmdl model file, which is essentially a simple mini-language allowing to describe a stochsim model in an intuitive way (see below).
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16.03.2018 – New Homepage
We are currently preparing the stable release of stochsim 1.0. In preparation of this event, we created this new homepage for stochsim. Celebrate with us by running a stochastic simulation!