Pattern graphs and rule-based models: the semantics of Kappa

DOI10.1007/978-3-642-37075-5_1MaRDI QIDQ4910408zbMATH OpenOpenAlexFDO

Authors Jonathan Hayman, Tobias Heindel

Publication date 18 March 2013

Published in Lecture Notes in Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-642-37075-5_1

Mathematics Subject Classification ID

Applications of graph theory (05C90) Grammars and rewriting systems (68Q42) Computational methods for problems pertaining to biology (92-08) Cell biology (92C37) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

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Cited in

(16)

• Rewriting theory for the life sciences: a unifying theory of CTMC semantics
• Reachability analysis via orthogonal sets of patterns
• Chromar, a rule-based language of parameterised objects
• Nonlinear pattern matching in rule-based modeling languages
• Rigid geometric constraints for Kappa models
• An algebraic approach for inferring and using symmetries in rule-based models
• Rule-based programming for integrative biological modeling. Application to the modeling of the \(\lambda\) phage genetic switch
• Moment semantics for reversible rule-based systems
• Transformation and refinement of rigid structures
• Complex functional rates in rule-based languages for biochemistry
• Constraining rule-based dynamics with types
• Efficient reduction of Kappa models by static inspection of the rule-set
• Abstract Interpretation of Cellular Signalling Networks
• Counters in Kappa: semantics, simulation, and static analysis
• Computational category-theoretic rewriting
• Computational Category-Theoretic Rewriting

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