Petri nets for modelling metabolic pathways: a survey

DOI10.1007/s11047-010-9180-6zbMath1206.68209OpenAlexW2013911710MaRDI QIDQ609029

Andrea Marin, Nicoletta Cocco, Marta Simeoni, Paolo Baldan

Publication date: 30 November 2010

Published in: Natural Computing (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s11047-010-9180-6

zbMATH Keywords

toolsPetri netsmetabolic pathwaysqualitative and quantitative analysis

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85)

Related Items (9)

Modeling and targeting an essential metabolic pathway of \textit{Plasmodium falciparum} in apicoplast using Petri nets ⋮ Parameterized Analysis of Immediate Observation Petri Nets ⋮ Preface: Petri nets for systems and synthetic biology ⋮ Analysis and design of molecular machines ⋮ How Might Petri Nets Enhance Your Systems Biology Toolkit ⋮ Preface: Petri nets for systems and synthetic biology ⋮ IDD-based model validation of biochemical networks ⋮ Unnamed Item ⋮ Flatness and Complexity of Immediate Observation Petri Nets

Uses Software

• Design/CPN
• PNML
• PetriNets
• SNOOPY
• MetaCyc
• TRANSPATH
• KEGG
• Reactome
• BRENDA

Cites Work

• Petri net modelling of biological regulatory networks
• Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets
• Persistence of vector replacement systems is decidable
• Petri nets and regular languages
• Analysis issues in Petri nets with inhibitor arcs
• An analysis of the Petri net based model of the human body iron homeostasis process
• Unfoldings: A partial-order approach to model checking.
• Introduction to Generalized Stochastic Petri Nets
• From Many Places to Few: Automatic Abstraction Refinement for Petri Nets
• From Petri Nets to Differential Equations – An Integrative Approach for Biochemical Network Analysis
• Recoverability of Communication Protocols--Implications of a Theoretical Study
• Discrete, Continuous, and Hybrid Petri Nets
• Free Choice Petri Nets
• The Petri Net Markup Language
• Applications and Theory of Petri Nets 2004
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