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Dynamic Slicing of Reaction Systems Based on Assertions and Monitors

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Practical Aspects of Declarative Languages (PADL 2023)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 13880))

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Abstract

Reaction Systems (RSs) are a successful computational framework inspired by biological systems. RSs can involve a large number of reactions and entities, which makes it difficult the debugging of quite long computations that traverses complex states. Slicing is a technique which is useful for simplifying a debugging process, by selecting a portion of the program containing the faulty code. We define the first dynamic slicer for RSs and show that it can help the user to detect the origins of bugs and also to inspect more closely the behavior of the model, highlighting the parts that need more investigation. Our slicer allows to select part of a (faulty) state and then eliminates from the computation the information which is not relevant for the selected items. We show how to use the slicer on some biological models in RSs. Our dynamic backward slicer is based on an SOS semantics of RSs. In order to automatize the slicing process we describe how to use monitors for identifying the states which violate a safety specification and hence are suitable to start the slicing. We have integrated our slicer in BioResolve, a prototype implementation in Prolog which provides also other features such as computations represented as colored graphs, and verification of properties.

Research supported by Università degli Studi di Sassari Fondi di Ateneo per la ricerca 2020, by MIUR Project Programma di Sviluppo - Dipartimenti di Eccellenza 2018–2022, by MIUR PRIN Project 201784YSZ5 ASPRA–Analysis of Program Analyses, and by the INdAM - GNCS Project CUP_E55F2200027001 Proprietà qualitative e quantitative di sistemi reversibili.

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Notes

  1. 1.

    http://www.di.unipi.it/~bruni/LTSRS/slicingBioReSolve.zip.

  2. 2.

    http://www.di.unipi.it/~bruni/LTSRS/.

  3. 3.

    http://www.di.unipi.it/~bruni/LTSRS/wrongspec.pl.

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Acknowledgment

We thank the anonymous reviewers for their comments and suggestions that helped us to improve our paper.

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Authors and Affiliations

  1. Dipartimento di Scienze economiche e aziendali, Università di Sassari, Sassari, Italy

    Linda Brodo

  2. Dipartimento di Informatica, Università di Pisa, Pisa, Italy

    Roberto Bruni

  3. Dipartimento di Ingegneria dell’Informazione e Scienze Matematiche, Università di Siena, 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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Correspondence to Moreno Falaschi .

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Editors and Affiliations

  1. University of Kiel, Kiel, Germany

    Michael Hanus

  2. Miami University, Oxford, OH, USA

    Daniela Inclezan

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Brodo, L., Bruni, R., Falaschi, M. (2023). Dynamic Slicing of Reaction Systems Based on Assertions and Monitors. In: Hanus, M., Inclezan, D. (eds) Practical Aspects of Declarative Languages. PADL 2023. Lecture Notes in Computer Science, vol 13880. Springer, Cham. https://doi.org/10.1007/978-3-031-24841-2_8

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  • DOI: https://doi.org/10.1007/978-3-031-24841-2_8

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