Dynamic Slicing of Reaction Systems Based on Assertions and Monitors

Brodo, Linda; Bruni, Roberto; Falaschi, Moreno

doi:10.1007/978-3-031-24841-2_8

Cited by 7 publications

(2 citation statements)

References 27 publications

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“…As future work, we want to study the combination of the forward slicing algorithm with the backward one which we have defined in [37]. We believe that this integration can improve the quality of the analysis, allowing for more erroneous/unexpected behaviours to be detected.…”

Section: Discussionmentioning

confidence: 99%

“…None of these approaches are suitable for RSs, which have a completely different computation behavior based on the non-monotonic enabling mechanism of reactions. In [37], we extended BioReSolve with a slicing algorithm which proceeds backwards. Some entities in the last state of a computation of an RS are selected and then the algorithm proceeds backwards, simplifying the computation and leaving only the entities which are essential to derive the selected ones.…”

Section: Related Workmentioning

confidence: 99%

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Modeling and Analyzing Reaction Systems in Maude

Ballis,

Brodo,

Falaschi

2024

Electronics

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Reaction Systems (RSs) are a successful computational framework for modeling systems inspired by biochemistry. An RS defines a set of rules (reactions) over a finite set of entities (e.g., molecules, proteins, genes, etc.). A computation in this system is performed by rewriting a finite set of entities (a computation state) using all the enabled reactions in the RS, thereby producing a new set of entities (a new computation state). The number of entities in the reactions and in the computation states can be large, making the analysis of RS behavior difficult without a proper automated support. In this paper, we use the Maude language—a programming language based on rewriting logic—to define a formal executable semantics for RSs, which can be used to precisely simulate the system behavior as well as to perform reachability analysis over the system computation space. Then, by enriching the proposed semantics, we formalize a forward slicer algorithm for RSs that allows us to observe the evolution of the system on both the initial input and a fragment of it (the slicing criterion), thus facilitating the detection of forward causality and influence relations due to the absence/presence of some entities in the slicing criterion. The pursued approach is illustrated by a biological reaction system that models a gene regulation network for controlling the process of differentiation of T helper lymphocytes.

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Section: Discussionmentioning

confidence: 99%

Section: Related Workmentioning

confidence: 99%