swMATH ID: 18041
Software Authors: Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong
Description: HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks. This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.
Homepage: http://www.cosbi.eu/research/prototypes/hsimulator
Keywords: hybrid simulation; stochastic simulation; biochemical reaction networks; systems biology
Related Software: HSimulator; COPASI; STEPS; SHAVE; CERENA
Cited in: 6 Publications

Citations by Year