A Language for Biochemical Systems: Design and Formal Specification

DOI10.1007/978-3-642-11712-1_3zbMath1275.92020OpenAlexW1495757226MaRDI QIDQ3068848

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Publication date: 18 January 2011

Published in: Transactions on Computational Systems Biology XII (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/978-3-642-11712-1_3

zbMATH Keywords

ordinary differential equationsPetri netscontinuous-time Markov chainsnondeterminismcoloured Petri netssubtypinglarge-scalecombinatorial explosionparametrised modules

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Systems biology, networks (92C42) Applications of continuous-time Markov processes on discrete state spaces (60J28)

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Uses Software

• Bio-PEPA
• PEPA
• BlenX
• Antimony

Cites Work

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• Statecharts: a visual formalism for complex systems
• A guide to membrane computing.
• BioAmbients: an abstraction for biological compartments
• Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks
• Rule-Based Modelling of Cellular Signalling
• Computational Methods in Systems Biology
• Brane Calculi
• Computational Methods in Systems Biology