HRSSA
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 Rejectionbased 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 timevarying 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 
Standard Articles
1 Publication describing the Software, including 1 Publication in zbMATH  Year 

HRSSA  efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks. Zbl 1349.92070 Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong 
2016

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