Accelerating stochastic simulations of mechanistic models of biological systems: Advantages and issues in the parallelization on Graphics Processing Units
Published in Quantitative Biology: Theory, Computational Methods, and Models (MIT Press), 2018
This chapter discusses how the stochastic simulation of mechanistic models of biological systems can be accelerated on Graphics Processing Units (GPUs). It reviews the advantages offered by GPU-based parallelization for the computationally demanding task of running large numbers of stochastic simulations, as well as the practical issues that arise when porting stochastic simulation algorithms to these massively parallel architectures.
Recommended citation: Cazzaniga P., Nobile M.S., Tangherloni A., Besozzi D. (2018). Accelerating stochastic simulations of mechanistic models of biological systems: Advantages and issues in the parallelization on Graphics Processing Units. In Quantitative Biology: Theory, Computational Methods, and Models, 423-440, MIT Press.