计算系统生物学中并行随机仿真方法研究进展

随机仿真是计算系统生物学中对随机离散模型进行仿真研究的一类重要方法。本文对随机仿真方法的原理及并行化研究的进展进行了论述,指出了并行化是解决随机仿真性能开销问题的重要途径,并依照细粒度并行和粗粒度并行分类,阐述了当前并行随机仿真方法的研究现状,重点针对空间并行性,介绍了反应-扩散系统随机仿真的方法和相关工具。最后,对并行随机仿真方法研究未来发展进行了展望。

Parallel Stochastic Simulation in Computational Systems Biology

Stochastic Simulation is a very important method for the research of discrete stochastic models in the field of Computational Systems Biology. In this paper, the principles and parallel approaches of Stochastic Simulation are reviewed. It is pointed out that parallel simulation is a significant approach to overcome the performance pitfalls in stochastic simulation. With the classification of coarse grain and fine grain, the status quo of the parallel stochastic simulation is surveyed firstly. Stressing on the spatial parallelism, the stochastic simulation of the reaction and diffusion system and the related tools are reviewed. Finally, the paper is covered by a discussion on the future work.