By Jakob Ruess, John Lygeros (auth.), Ashutosh Gupta, Thomas A. Henzinger (eds.)
This ebook constitutes the lawsuits of the eleventh foreign convention on Computational tools in platforms Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 average papers incorporated during this quantity have been rigorously reviewed and chosen from 27 submissions. They care for computational versions for all degrees, from molecular and mobile, to organs and full organisms.
Read or Download Computational Methods in Systems Biology: 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013. Proceedings PDF
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Extra resources for Computational Methods in Systems Biology: 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013. Proceedings
Helms et al. because they have to be executed recursively along the hierarchy of the model. Thereby, each species is treated individually, because it is assumed that even identical species probably have diﬀerent numbers of reaction ﬁrings during a τ leap. , the context which is not enclosed by a species: 1. Compute the number of reaction ﬁrings for the current reaction context rc and τ . 2. Remove all reaction reactants from rc. 3. For each remaining enclosed species of rc, execute this algorithm.
In Table 3 we list the probabilities P (A) for three diﬀerent choices of as well as the size of the set Sig of signiﬁcant states. For the parameter biasing vector we chose γ = (1, 1, γ3 , 1, 1, 1/γ3), as explained before. In Table 4 we list the relative error of the approximated rare event probability and the size of the set Sig of signiﬁcant states for diﬀerent values of γ3 , δ and . Note that a relative error of one corresponds to approximating the rare event probability as zero. This is actually the same as what happens in direct simulation when due to the small probability the rare event is not observed and the probability of the nonobserved event is estimated as zero.
Catenin (inside the nucleus) Number of Species Number of Species Phosphorylized Actin 12000 8000 4000 0 0 50 100 150 Simulation Time 200 300 200 100 0 0 50 100 150 200 Simulation Time Fig. 4. , the least accurate conﬁguration we used) of the species amount of phosphorylized Actin proteins and of β-catenin proteins inside the nucleus for the Wnt/β-catenin pathway model with one cell. However, the interesting aspect is how much accuracy is traded for this gain of eﬃciency and especially due to their impact on the execution time how is the impact of the parameters and μ on the accuracy.