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Matthias Jeschke, Roland Ewald, Alfred Park, Richard Fujimoto, and Adelinde M Uhrmacher (2008)

A Parallel and Distributed Discrete Event Approach for Spatial Cell-Biological Simulations

ACM SIGMETRICS Performance Evaluation Review, 35(4):22-31.

As data and knowledge about cell-biological systems increases so does the need for simulation tools to support a hypothesis driven wet-lab experimentation. Discrete event simulation has received a lot of attention lately, however, often its application is hampered by its lack on performance. One solution are parallel, distributed approaches, however, their application is limited by the amount of parallelism available in the model. Recent studies have shown that spatial aspects are crucial for cell biological dynamics and they are also a promising candidate to exploit parallelism. Promises and specific requirements imposed by a spatial simulation of cell biological systems will be illuminated by a parallel and distributed variant of the Next-Subvolume Method (NSM), which augments the Stochastic Simulation Algorithm (SSA) with spatial features, and its realization in a grid-inspired simulation system called Aurora.

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