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Matthias Jeschke and Roland Ewald (2008)

Large-Scale Design Space Exploration of SSA

In: Computational Methods in Systems Biology, International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008, Proceedings, vol. 5307, pp. 211-230, Berlin / Heidelberg, Springer. Lecture Notes in Computer Science.

Stochastic simulation algorithms (SSA) are popular methods for the simulation of chemical reaction networks, so that various enhancements have been introduced and evaluated over the years. However, neither theoretical analysis nor empirical comparisons of single implementations suffice to capture the general performance of a method. This makes choosing an appropriate algorithm very hard for anyone who is not an expert in the field, especially if the system provides many alternative implementations. We argue that this problem can only be solved by thoroughly exploring the design spaces of such algorithms. This paper presents the results of an empirical study, which subsumes several thousand simulation runs. It aims at exploring the performance of different SSA implementations and comparing them to an approximation via τ-Leaping, while using different event queues and random number generators.

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