Therefore, stochastic simulation is very accurate compared to approximate approaches (e.g., approximate stochastic methods and deterministic ones). Stochastic simulation methods consider reaction firings as a random process and each reaction is executed individually. However, all available algorithms can be grouped into four categories: stochastic, approximate stochastic, deterministic, and hybrid simulation approaches. There are various approaches to capture reaction firings as well as their effects on the system state.
The chosen simulation procedure determines how the system state vector is updated as well as the progression of the simulation time. A vector representing the state of a system serves to track the species concentrations and/or the corresponding number of molecules as the simulation advances with respect to time. In order to study the dynamics of biological models, a simulation procedure is usually employed to emulate reaction firings.
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