The stochastic simulation of large-scale biochemical reaction networks is of
great importance for systems biology since it enables the study of inherently
stochastic biological mechanisms at the whole cell scale. Stochastic Simulation
Algorithms (SSA) allow us to simulate the dynamic behavior of complex kinetic
models, but their high computational cost makes them very slow for many
realistic size problems. We present a pilot service, named WebStoch, developed
in the context of our StochSoCs research project, allowing life scientists with
no high-performance computing expertise to perform over the internet stochastic
simulations of large-scale biological network models described in the SBML
standard format. Biomodels submitted to the service are parsed automatically
and then placed for parallel execution on distributed worker nodes. The workers
are implemented using multi-core and many-core processors, or FPGA accelerators
that can handle the simulation of thousands of stochastic repetitions of
complex biomodels, with possibly thousands of reactions and interacting
species. Using benchmark LCSE biomodels, whose workload can be scaled on
demand, we demonstrate linear speedup and more than two orders of magnitude
higher throughput than existing serial simulators.Comment: The 2017 International Conference on High Performance Computing &
Simulation (HPCS 2017), 8 page