From Petri Nets to Differential Equations – An Integrative Approach for Biochemical Network Analysis

DOI10.1007/11767589_11MaRDI QIDQ3618705zbMATH OpenOpenAlexDBLPWikidataFDO

Authors David Gilbert, Monika Heiner

Publication date 2 April 2009

Published in Petri Nets and Other Models of Concurrency - ICATPN 2006 (Search for Journal in Brave)

Full work available at URL http://eprints.gla.ac.uk/3476/1/gilbert.3476.pdf

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Packaged methods for numerical algorithms (65Y15) Numerical methods for ordinary differential equations (65L99) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85)

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Cited in

(16)

• A survey of gene regulatory networks modelling methods: from differential equations, to Boolean and qualitative bioinspired models
• Hybrid Petri net based modeling for biological pathway simulation
• Efficient modelling of yeast cell cycles based on multisite phosphorylation using coloured hybrid Petri nets with marking-dependent arc weights
• Charlie -- an extensible Petri net analysis tool
• Two wrongs do not make a right: the assumption that an inhibitor acts as an inverse activator
• IDD-based model validation of biochemical networks
• Hybrid representation and simulation of stiff biochemical networks
• Petri nets for modelling metabolic pathways: a survey
• A Petri net approach to the study of persistence in chemical reaction networks
• Petri Nets for Modelling and Analysing Trophic Networks
• How Petri nets might enhance your systems biology toolkit
• Individuals, populations and fluid approximations: a Petri net based perspective
• Modeling biological gradient formation: combining partial differential equations and Petri nets
• Time Petri nets for modelling and analysis of biochemical networks
• PoCaB: A Software Infrastructure to Explore Algebraic Methods for Bio-chemical Reaction Networks
• Preface

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Uses Software

• GEPASI

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