Rule-Based Modelling, Symmetries, Refinements

DOI10.1007/978-3-540-68413-8_8MaRDI QIDQ3506871zbMATH OpenOpenAlexFDO

Authors Vincent Danos, Jerome Feret, Walter Fontana, Russell S. Harmer, Jean Krivine

Publication date 17 June 2008

Published in Formal Methods in Systems Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-540-68413-8_8

zbMATH Keywords

cellular signallingPetri netsignalling system

Mathematics Subject Classification ID

Applications of graph theory (05C90) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

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(30)

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• Chromar, a rule-based language of parameterised objects
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• Chromar, a language of parameterised agents
• Sustainability of RNA-interference in rule based modelling
• An algebraic approach for inferring and using symmetries in rule-based models
• Complete characterization for the fit-preserving data refinement of mass-action reaction networks
• Rule-based programming for integrative biological modeling. Application to the modeling of the \(\lambda\) phage genetic switch
• An excursion through quantitative model refinement
• Improving Discrete Model Representations via Symmetry Considerations
• Transformation and refinement of rigid structures
• Combinatorial conversion and moment bisimulation for stochastic rewriting systems
• Rule-Based Modelling of Cellular Signalling
• Lumpability abstractions of rule-based systems
• Solving moment hierarchies for chemical reaction networks
• Equilibrium and termination. II: The case of Petri nets
• A knowledge representation meta-model for rule-based modelling of signalling networks
• scientific article; zbMATH DE number 7453087 (Why is no real title available?)
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• Rule-based modelling and tunable resolution
• Fit-preserving data refinement of mass-action reaction networks
• Quantitative model refinement as a solution to the combinatorial size explosion of biomodels
• Stochastic bigraphs
• Beyond fitness: the information imparted in population states by selection throughout lifecycles

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