License: Creative Commons Attribution 4.0 International license (CC BY 4.0)
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DOI: 10.4230/DagSemProc.06161.7
URN: urn:nbn:de:0030-drops-7061
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2006/706/
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Cavaliere, Matteo ; Sedwards, Sean

Modeling and Simulating Biological Processes with Stochastic Multiset Rewriting

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06161.CavaliereMatteo.ExtAbstract.706.pdf (0.4 MB)

Abstract

Membrane systems were originally introduced as models of computation inspired by the structure and the functioning of living cells. More recently, membrane systems have been shown to be suitable also to model cellular processes. Inspired by brane calculi, a new model of membrane system with peripheral proteins has been recently introduced. Such model has compartments (enclosed by membranes), floating objects, and objects attached to the internal and external surfaces of the membranes. The objects can be processed/transported inside/across the compartments and the transport is regulated by opportune objects attached to the membranes surfaces. We present a stochastic simulator of this model, with a style of syntax based on chemical reactions. We show that the simulator can be particularly useful in modelling biological processes that involve compartments, surface and integral membrane proteins, transport and processing of chemical substances. As examples we present the simulation of circadian clock and the G-protein cycle in yeast.

BibTeX - Entry

@InProceedings{cavaliere_et_al:DagSemProc.06161.7,
  author =	{Cavaliere, Matteo and Sedwards, Sean},
  title =	{{Modeling and Simulating Biological Processes with Stochastic Multiset Rewriting}},
  booktitle =	{Simulation and Verification of Dynamic Systems},
  pages =	{1--8},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{6161},
  editor =	{David M. Nicol and Corrado Priami and Hanne Riis Nielson and Adelinde M. Uhrmacher},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2006/706},
  URN =		{urn:nbn:de:0030-drops-7061},
  doi =		{10.4230/DagSemProc.06161.7},
  annote =	{Keywords: Systems biology, membrane systems, formal language, simulation}
}

Keywords: Systems biology, membrane systems, formal language, simulation
Collection: 06161 - Simulation and Verification of Dynamic Systems
Issue Date: 2006
Date of publication: 07.09.2006

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