Download PDF by Jakob Ruess, John Lygeros (auth.), Ashutosh Gupta, Thomas A.: Computational Methods in Systems Biology: 11th International

By Jakob Ruess, John Lygeros (auth.), Ashutosh Gupta, Thomas A. Henzinger (eds.)

This booklet constitutes the complaints of the eleventh foreign convention on Computational tools in structures Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 common papers integrated during this quantity have been rigorously reviewed and chosen from 27 submissions. They take care of computational versions for all degrees, from molecular and mobile, to organs and whole organisms.

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Extra resources for Computational Methods in Systems Biology: 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013. Proceedings

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Continuous-time Markov Chains: An Applications-Oriented Approach. Springer (1991) 2. : Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected escherichia coli cells. Genetics 149, 1633–1648 (1998) 3. : Computer Methods for Ordinary Differential Equations and Differential-Algebraic Equations. SIAM (1998) 4. : Stochastic Simulation: Algorithms and Analysis. Springer (2007) 5. : Elements of the Theory of Markov Processes and Their Applications. McGraw-Hill (1960) 6. : Noise in eukaryotic gene expression.

Sandmann, and V. Wolf function by this factor, independent of the specific state in which the reaction occurs. The factors are collected in the biasing parameter vector γ = (γ1 , . . , γM ). Note that γj = 1 for each reaction Rj whose propensity function is not changed. In order to keep the choice of the guidance functions as simple as possible, we do not change all propensity functions α1 , . . , αM but only those for which an increase or decrease obviously increases the probability of the rare event of interest.

3 The Fission Yeast Model The fission yeast model [21] represents the cell division and mating process of fission yeast cells. It comprises intracellular as well as intercellular reactions and contains a simple grid-based spatial level to describe specific diffusion reactions. In this model, a cell species contains two attributes, representing the volume and the phase of the cell. Further species types describe different pheromones and proteins. However, initial experiments show that τ -leaping performs worse for this model than the SSA.

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