Stochastic simulation is in widespread use for analyzing biological pathways. Due to the limited efficiency of a straightforward direct implementation such as the Gillespie algorithm, various improvements and approximate algorithms have been developed. For user-friendliness it is important to have efficient implementations available in software tools. Another important issue is the statistical ...

The master equation of chemical reactions is solved by first approximating it by the Fokker–Planck equation. Then this equation is discretized in the state space and time by a finite volume method. The difference between the solution of the master equation and the discretized Fokker–Planck equation is analyzed. The solution of the Fokker–Planck equation is compared to the solution of the master...

With Systems Biology, a promising new application area for modelling and simulation emerges. Today’s biologists are facing huge amounts of data delivered at different levels of detail by a multitude of advanced experimentation techniques. The Systems Biology approach copes with this information by cycling through phases of forming hypotheses, constructing models, experimenting with or analysing...

The present models and simulation algorithms of intracellular stochastic kinetics are usually based on the premise that diffusion is so fast that the concentrations of all the involved species are homogeneous in space. However, recents experimental measurements of intracellular diffusion constants indicate that the assumption of a homogeneous well-stirred cytosol is not necessarily valid even f...

Hybrid algorithms are a promising approach to speed-up the execution of multi-scale biochemical reaction networks, i.e., networks with reactions that operate on different time scales. The basic idea is to use the quasi-steady state distribution of the fast reactions, computed either analytically or empirically, to update the propensities of slow reactions and to apply a stochastic simulation al...

NoisySim is an open source Java library to simulate Gillespie-like intrinsically stochastic chemically reacting systems affected by extrinsic bounded noises. Noises are synthesized by (state-dependent) Langevin systems, in turn affecting the jump rates of a Markov process. Hence, the overall process is doubly stochastic (i.e. hybrid time-inhomogenous). NoisySim implements an exact simulation al...