Exploiting Modularity of SOS Semantics to Define Quantitative Extensions of Reaction Systems
| Autor: | Linda Brodo, Roberto Bruni, Francesca Levi, Moreno Falaschi, Roberta Gori, Paolo Milazzo |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Theoretical computer science
Semantics (computer science) Computer science Natural computing Bioinformatics RSS computer.file_format Logic programming Reaction systems SOS rules Modularity Operational semantics Formal specification Transition system Bioinformatics SOS rules Reaction Systems Logic programming computer |
| Zdroj: | Theory and Practice of Natural Computing ISBN: 9783030904241 TPNC |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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