By Eugenio Cinquemani, Alexandre Donzé
This ebook constitutes the refereed complaints of the fifth overseas Workshop on Hybrid structures Biology, HSB 2016, held in Grenoble, France, in October 2016.
The eleven complete papers provided during this e-book have been conscientiously reviewed and chosen from 26 submissions. They have been geared up and provided in four thematic periods additionally mirrored during this publication: version simulation; version research; discrete and community modelling; stochastic modelling for organic systems.
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Additional info for Hybrid Systems Biology: 5th International Workshop, HSB 2016, Grenoble, France, October 20-21, 2016, Proceedings
The generated trajectories are stochastically identical to those of the standard Gillespie algorithm . Popular simulation tools like NFSim  or KaSim  use agentbased simulations, during which each individual molecule is tracked instead of populations of molecules. According to a few rules with known propensities, the reacting monomers can be chosen directly, and the reaction can be performed or it is rejected, because the corresponding product of the reaction is not possible in reality.
Phys. 227(1), 100–122 (2007) 14. : Hybrid representation and simulation of stiﬀ biochemical networks. J. Nonlinear Anal. Hybrid Syst. 6(4), 942–959 (2012) 15. : A steering server for collaborative simulation of quantitative Petri nets. , Kindler, E. ) PETRI NETS 2014. LNCS, vol. 8489, pp. 374–384. Springer, Heidelberg (2014) 16. : Coloured hybrid Petri nets for systems biology. In: Proceedings of the 5th International Workshop on Biological Processes & Petri Nets (BioPPN), Satellite Event of PETRI NETS 2014, CEUR Workshop Proceedings, vol.
However, for hybrid simulation it is compulsory to repeatedly clear the solution history each time an event occurs. Unfortunately, even for simple hybrid models there are thousands of such events (cf. Table 2). Accelerated Simulation of Hybrid Biological Models 29 Therefore, reducing the number of times the ODE solver is reinitialised will inevitably improve the performance of hybrid simulation. Nevertheless, the hybrid simulation approaches in [1,11] require the simultaneous integration of the cumulative propensity (Eq.