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Orianne Mazemondet, Mathias John, Carsten Maus, Adelinde M Uhrmacher, and Arndt Rolfs (2009)

Integrating Diverse Reaction Types Into Stochastic Models - A Signaling Pathway Case Study in the Imperative Pi-Calculus

In: Proceedings of the Winter Simulation Conference, ed. by M. D. Rossetti and R. R. Hill and B. Johansson and A. Dunkin and R. G. Ingalls, pp. 932-943, IEEE Computer Science.

We present a case study of reusing parameters and reactions of a deterministic model of a biochemical system in order to implement a stochastic one. Our investigations base on a model of the Wnt signaling pathway and aim to study the influence of the cell cycle on the pathway's dynamics. We report on our approaches to solve two major challenges: one is to gather and convert kinetic model parameters, e.g. constants for diffusion and enzymatic reactions. The second challenge is to provide the first implementation of reactions that exhibit Michaelis-Menten kinetics into a \picalc based approach by deploying the Imperative Pi-Calculus.

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