Exact simulation of stochastic chemically reacting systems with extrinsic noises made easy

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 algorithm to realize such a process; this allows to approximate (with arbitrary precision) the solution of the differential Chapman-Kolgomorov equation describing the probability of the system to be in some state. Custom noises can be implemented in NoisySim; the library already provides a ready-to-use implementation of five noises with different features. NoisySim defines a abstract model; its concrete specification can be either hand-coded or automatically generated by NoisySim model generator, provided a textual description of the model.