Nonlinear pattern matching in rule-based modeling languages

DOI10.1007/978-3-030-85633-5_12zbMath1491.92067OpenAlexW3199415441MaRDI QIDQ2142118

Tom Warnke, Adelinde M. Uhrmacher

Publication date: 25 May 2022

Full work available at URL: https://doi.org/10.1007/978-3-030-85633-5_12

zbMATH Keywords

formal semanticspattern matchingrule-based modeling

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08) Systems biology, networks (92C42)

Uses Software

• Haskell
• BioNetGen

Cites Work

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• Generalizing Gillespie's direct method to enable network-free simulations
• Chromar, a language of parameterised agents
• Biochemical Reaction Rules with Constraints
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• Multi-level modelling via stochastic multi-level multiset rewriting
• Associative-commutative discrimination nets
• Semantics and Efficient Simulation Algorithms of an Expressive Multilevel Modeling Language
• A uniform definition of stochastic process calculi

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