Activity networks with delays an application to toxicity analysis

DOI10.3233/FI-2018-1677zbMATH Open1395.92061arXiv1608.07440OpenAlexW2425349372WikidataQ129888144 ScholiaQ129888144MaRDI QIDQ3174740FDOQ3174740

Authors: Franck Delaplace, Cinzia Di Giusto, Jean-Louis Giavitto, Hanna Klaudel, Antoine Spicher 

Publication date: 18 July 2018

Published in: Fundamenta Informaticae (Search for Journal in Brave)

Abstract: ANDy , Activity Networks with Delays, is a discrete time framework aimed at the qualitative modelling of time-dependent activities. The modular and concise syntax makes ANDy suitable for an easy and natural modelling of time-dependent biological systems (i.e., regulatory pathways). Activities involve entities playing the role of activators, inhibitors or products of biochemical network operation. Activities may have given duration, i.e., the time required to obtain results. An entity may represent an object (e.g., an agent, a biochemical species or a family of thereof) with a local attribute, a state denoting its level (e.g., concentration, strength). Entities levels may change as a result of an activity or may decay gradually as time passes by. The semantics of ANDy is formally given via high-level Petri nets ensuring this way some modularity. As main results we show that ANDy systems have finite state representations even for potentially infinite processes and it well adapts to the modelling of toxic behaviours. As an illustration, we present a classification of toxicity properties and give some hints on how they can be verified with existing tools on ANDy systems. A small case study on blood glucose regulation is provided to exemplify the ANDy framework and the toxicity properties.

Full work available at URL: https://arxiv.org/abs/1608.07440

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zbMATH Keywords

model checkingPetri netsreaction networkstoxicity

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Deterministic network models in operations research (90B10) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85)

Cited In (1)

• Detecting Toxicity Pathways with a Formal Framework Based on Equilibrium Changes

Uses Software

• ANDy

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