Integrating diverse reaction types into stochastic models: a signaling pathway case study in the imperative π-calculus

Authors:
Orianne Mazemondet;Mathias John;Carsten Maus;Adelinde M. Uhrmacher;Arndt Rolfs
Affiliations:
University of Rostock, Gehlsheimerstr, Rostock, Germany;University of Rostock, Albert-Einstein-Str, Rostock, Germany;University of Rostock, Albert-Einstein-Str, Rostock, Germany;University of Rostock, Albert-Einstein-Str, Rostock, Germany;University of Rostock, Gehlsheimerstr, Rostock, Germany
Venue:
Winter Simulation Conference
Year:
2009

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Abstract

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 π-Calculus based approach by deploying the Imperative π-Calculus.