Modelling of biochemical reactions by stochastic automata networks

DOI10.1016/J.ENTCS.2007.05.017MaRDI QIDQ2864207zbMATH OpenOpenAlexFDO

Authors Verena Wolf

Publication date 6 December 2013

Published in Electronic Notes in Theoretical Computer Science (Search for Journal in Brave)

Copyright license Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International

Full work available at URL https://doi.org/10.1016/j.entcs.2007.05.017

zbMATH Keywords

Markov chainbiochemical reactionsstochastic automata networks

Mathematics Subject Classification ID

Formal languages and automata (68Q45) Biochemistry, molecular biology (92C40) Probability in computer science (algorithm analysis, random structures, phase transitions, etc.) (68Q87) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85)

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Cites work

• scientific article; zbMATH DE number 52118 (Why is no real title available?)
• scientific article; zbMATH DE number 2102728 (Why is no real title available?)
• scientific article; zbMATH DE number 3240796 (Why is no real title available?)
• A stochastic automata network descriptor for Markov chain models of instantaneously coupled intracellular Ca\(^{2+}\) channels
• Application of a stochastic name-passing calculus to representation and simulation of molecular processes
• Applications and Theory of Petri Nets 2004
• Formal molecular biology
• Stochastic approaches for modelling in vivo reactions
• Transactions on Computational Systems Biology IV

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(14)

• An improved robust delay-dependent stability criterion for genetic regulatory networks with interval time delays
• Automated generation of conditional moment equations for stochastic reaction networks
• Semi-quantitative abstraction and analysis of chemical reaction networks
• Emulating cellular automata in chemical reaction-diffusion networks
• Complexity results for autocatalytic network models
• Modelling biochemical reaction systems by stochastic differential equations with reflection
• scientific article; zbMATH DE number 2016515 (Why is no real title available?)
• Reaction-based models of biochemical networks
• Stochastic Semantics of Signaling as a Composition of Agent-view Automata
• Computational Probability for Systems Biology
• Hybrid representation and simulation of stiff biochemical networks
• scientific article; zbMATH DE number 6769232 (Why is no real title available?)
• A stochastic automata network description for spatial DNA-methylation models
• Teaching Concurrency Concepts to Freshmen

Describes a project that uses

Uses Software

• PEPA
• APNN-Toolbox
• PEPS

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