Membrane Systems and Petri Net Synthesis

Kleijn, Jetty; Koutny, Maciej; Pietkiewicz-Koutny, Marta; Rozenberg, Grzegorz

doi:10.4204/eptcs.100.1

Cited by 5 publications

(2 citation statements)

References 19 publications

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“…Examples of the Ąrst approach include [17] presenting the design a reaction system model for the heat shock response in such a way that the qualitative behavior of the result correlates well with the quantitative behavior of the corresponding ODE model of the heat shock response, and [31] developing a reaction system model inspired by the mechanistic model of within-cell signal transduction networks of [32]. Examples of the second approach include [33,34] presenting automated synthesis from behavioural speciĄcations into membrane systems which are a computational model carrying out calculations in cells using a biologically inspired abstraction, and [35,36] discussing tissue systems which provide a computational abstraction of biological reactions and transport of molecules in a tissue. In both cases the problem addressed was that of synthesising systems from speciĄcations of observed or desired behaviour given in the form of transition systems.…”

Section: Introductionmentioning

confidence: 99%

Reaction Mining for Reaction Systems

Męski

Koutny

Penczek

2018

Lecture Notes in Computer Science

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Reaction systems are a formal model for computational processing in which reactions operate on sets of entities (molecules) providing a framework for dealing with qualitative aspects of biochemical systems. This paper is concerned with reaction systems in which entities can have discrete concentrations, and so reactions operate on multisets rather than sets of entities. The resulting framework allows one to deal with quantitative aspects of reaction systems, and a bespoke linear-time temporal logic allows one to express and verify a wide range of key behavioural system properties. In practical applications, a reaction system with discrete concentrations may only be partially specified, and the possibility of an effective automated calculation of the missing details provides an attractive design approach. With this idea in mind, the current paper discusses parametric reaction systems with parameters representing unknown parts of hypothetical reactions. The main result is a method aimed at replacing the parameters in such a way that the resulting reaction system operating in a specified external environment satisfies a given temporal logic formula. This paper provides an encoding of parametric reaction systems in smt, and outlines a synthesis procedure based on bounded model checking for solving the synthesis problem. It also reports on the initial experimental results demonstrating the feasibility of the novel synthesis method.

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Section: Introductionmentioning

confidence: 99%

Reaction Mining for Reaction Systems

Męski

Koutny

Penczek

2018

Lecture Notes in Computer Science

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“…Automated synthesis from behavioural specifications is an attractive and powerful way of constructing correct concurrent systems [1][2][3]13]. The paper [9] considered the synthesis of membrane systems from (step) transition systems, and the paper [12] discussed the same problem for membrane systems. Both papers demonstrated how a solution to the synthesis problem of Petri nets, based on the notion of regions of a transition system, leads to a method for the automated synthesis of membrane systems.…”

Section: Maciej Koutnymentioning

confidence: 99%