Stochastic rule-based modelling of biological systems using a parallel implementation of spatial Kappa

The Stochastic Simulation Algorithm (SSA) is a method to model the behaviour of a system whose constituent elements, modelled as particles, interact by random collisions. Originally introduced by D. Gillespie in 1977, SSA is currenlty used to model stochastic processes in biology such as chemical reactions, cellular signalling, gene regulation and metabolic pathways. During this talk, we will present PISKA, a parallel implementation of the SSA to execute spatially-explicit models coded in the Kappa formal language. Some biological models and their simulations using PISKA will be discussed. Among other important issues, time-travel and multiple clock synchronisation processes will be also presented.