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International Conference on the Theory and Practice of Natural Computing

TPNC 2021: Theory and Practice of Natural Computing pp 15–32Cite as

Exploiting Modularity of SOS Semantics to Define Quantitative Extensions of Reaction Systems

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 13082))

Abstract

Reaction Systems (RSs) are a successful natural computing framework inspired by chemical reaction networks. A RS consists of a set of entities and a set of reactions. Entities can enable or inhibit each reaction, and are produced by reactions or provided by the environment. In a previous paper, we defined an original labelled transition system (LTS) semantics for RSs in the structural operational semantics (SOS) style. This approach has several advantages: (i) it provides a formal specification of the RS dynamics that enables the reuse of many formal analysis techniques and favors the implementation of tools, and (ii) it facilitates the definition of extensions of the RS framework by simply modifying some of the SOS rules in a modular way. In this paper, we demonstrate the extensibility of the framework by defining two quantitative variants of RSs: with reaction delays/durations, and with concentration levels. We provide a prototype logic programming implementation and apply our tool to a RS model of \( Th \) cells differentiation in the immune system.

Research supported by University of Pisa PRA_2020_26 Metodi Informatici Integrati per la Biomedica, by MIUR PRIN Project 201784YSZ5 ASPRA–Analysis of Program Analyses, and by University of Sassari Fondo di Ateneo per la ricerca 2020.

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Notes

  1. 1.

    To ease the presentation, we impose \(n \in \mathbb {N}^+\) on the linear epression e to guarantee that its evaluation into a positive number, even when \(x=0\). Alternative choices are possible to relax this constraint.

  2. 2.

    https://www3.diism.unisi.it/~falaschi/ReactionSystemsQuantities.

  3. 3.

    https://www3.diism.unisi.it/~falaschi/reactionsConcentrationLevels.txt.

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Author information

Authors and Affiliations

  1. Dipartimento di Scienze Economiche e Aziendali, Università di Sassari, Via Muroni 25, Sassari, Italy

    Linda Brodo

  2. Dipartimento di Informatica, Università di Pisa, Largo B. Pontecorvo 3, Pisa, Italy

    Roberto Bruni, Roberta Gori, Francesca Levi & Paolo Milazzo

  3. Dipartimento di Ingegneria dell’Informazione e Scienze Matematiche, Università di Siena, Via Roma 56, Siena, Italy

    Moreno Falaschi

Authors
  1. Linda Brodo
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  2. Roberto Bruni
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  3. Moreno Falaschi
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  4. Roberta Gori
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  5. Francesca Levi
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  6. Paolo Milazzo
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Corresponding author

Correspondence to Roberta Gori .

Editor information

Editors and Affiliations

  1. Graduate School of Systems and Information Engineering, University of Tsukuba, Tsukuba, Japan

    Claus Aranha

  2. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

    Carlos Martín-Vide

  3. School of Technology, University of Extremadura, Cáceres, Spain

    Miguel A. Vega-Rodríguez

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Brodo, L., Bruni, R., Falaschi, M., Gori, R., Levi, F., Milazzo, P. (2021). Exploiting Modularity of SOS Semantics to Define Quantitative Extensions of Reaction Systems. In: Aranha, C., Martín-Vide, C., Vega-Rodríguez, M.A. (eds) Theory and Practice of Natural Computing. TPNC 2021. Lecture Notes in Computer Science(), vol 13082. Springer, Cham. https://doi.org/10.1007/978-3-030-90425-8_2

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  • DOI: https://doi.org/10.1007/978-3-030-90425-8_2

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