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

Orianne Mazemondet (1) , Mathias John (2) , Carsten Maus (2) , Stefan Leye (2) , Adelinde Uhrmacher (2) , Arndt Rolfs (3)

1 University of Rostock
2 Computer Science and Electrical Engineering
3 Albrecht-Kossel-Institut fur Neuroregeneration

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 pi-calculus based approach by deploying the imperative pi-calculus.

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Orianne Mazemondet, Mathias John, Carsten Maus, Stefan Leye, Adelinde Uhrmacher, et al.. Integrating Diverse Reaction Types into Stochastic Models - A Signaling Pathway Case Study in the Imperative Pi-Calculus. Winter Simulation Conference (WSC) '09, Dec 2009, Austin, Texas, United States. ⟨10.1109/WSC.2009.5429723⟩. ⟨hal-00656195⟩