Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle

System level understanding of the repetitive cycle of cell growth and division is crucial for disclosing many unknown principles of biological organisms. The deterministic or stochastic approach – when deployed separately – are not sufficient to study such cell regulation due to the complexity of th...

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Published inTransactions on Petri Nets and Other Models of Concurrency VIII Vol. 8100; pp. 123 - 141
Main Authors Herajy, Mostafa, Schwarick, Martin, Heiner, Monika
Format Book Chapter
LanguageEnglish
Published Germany Springer Berlin / Heidelberg 2013
Springer Berlin Heidelberg
SeriesLecture Notes in Computer Science
Subjects
eukaryotic cell cycle
Generalised hybrid Petri nets
hybrid modelling
marking-dependent arc weight
Snoopy
Online AccessGet full text
ISBN9783642404641
3642404642
ISSN0302-9743
1611-3349
DOI10.1007/978-3-642-40465-8_7

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Abstract System level understanding of the repetitive cycle of cell growth and division is crucial for disclosing many unknown principles of biological organisms. The deterministic or stochastic approach – when deployed separately – are not sufficient to study such cell regulation due to the complexity of the reaction network and the existence of reactions at different time scales. Thus, an integration of both approaches is advisable to study such biochemical networks. In this paper we show how Generalised Hybrid Petri Nets can be used to intuitively represent and simulate the eukaryotic cell cycle. Our model captures intrinsic as well as extrinsic noise and deploys stochastic as well as deterministic reactions. Additionally, marking-dependent arc weights are biologically motivated and introduced to Snoopy – a tool for animating and simulating Petri nets in various paradigms.
AbstractList System level understanding of the repetitive cycle of cell growth and division is crucial for disclosing many unknown principles of biological organisms. The deterministic or stochastic approach – when deployed separately – are not sufficient to study such cell regulation due to the complexity of the reaction network and the existence of reactions at different time scales. Thus, an integration of both approaches is advisable to study such biochemical networks. In this paper we show how Generalised Hybrid Petri Nets can be used to intuitively represent and simulate the eukaryotic cell cycle. Our model captures intrinsic as well as extrinsic noise and deploys stochastic as well as deterministic reactions. Additionally, marking-dependent arc weights are biologically motivated and introduced to Snoopy – a tool for animating and simulating Petri nets in various paradigms.
Author Heiner, Monika
Herajy, Mostafa
Schwarick, Martin
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Snippet System level understanding of the repetitive cycle of cell growth and division is crucial for disclosing many unknown principles of biological organisms. The...
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StartPage 123
SubjectTerms eukaryotic cell cycle
Generalised hybrid Petri nets
hybrid modelling
marking-dependent arc weight
Snoopy
Title Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle
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