Case Study I: Chemical Reaction Networks

Zusammenfassung

This chapter shows how the methods developed in chapter 4 to 8 can be applied to stochastic simulation algorithms (SSA), which have already been discussed briefly in section 1.3.1 (p. 7). JAMES II offers several kinds of simulators for the field of computational systems biology (see [308]). Some of them–e.g., those for models expressed in stochastic π-calculus [200]–rely on SSA implementations as well. At the same time, the performance of different SSA implementations is still fairly unexplored, particularly when it comes to different model properties and different sub-algorithms, e.g., RNGs or event queues (see discussion in [158]). Their relative merits are even debated in the literature (e.g., [281, p. 21]). Therefore, applying the algorithm selection methodology developed in part two of the thesis seems to be particularly beneficial in this setting.