Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors

Details Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors

2010-11-02

arxiv.org/abs/1011.0490v1

EPTCS 40, 2010, pp. 39-53

Computer Science

Computational Engineering, Finance, and Science

In Proceedings MeCBIC 2010, arXiv:1011.0051

Scientific paper

10.4204/EPTCS.40.4

In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving example. Starting from an existing Ordinary Differential Equations (ODEs) model, we implement the G-protein cycle in the stochastic Pi-calculus using SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also provide a high-level notation to abstract away from communication primitives that may be unfamiliar to the average biologist, and we show how to translate high-level programs into stochastic Pi-calculus processes and chemical reactions.

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