Petri Nets for Modelling and Analysing Trophic Networks

Baldan, Paolo; Bocci, Martina; Brigolin, Daniele; Cocco, Nicoletta; Heiner, Monika; Simeoni, Marta

doi:10.3233/fi-2018-1673

Cited by 11 publications

(11 citation statements)

References 31 publications

(25 reference statements)

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“…The main originality of our work not only lies in the use of discrete models (e.g. Petri nets) in ecology, as some other studies started to explore the promising avenue of discrete models too (Baldan et al, ; Ewing et al, ; Gaucherel et al, , ). Rather, it concerns the discrete and qualitative conception of the integrated ecosystem forming, we think, the backbone of any ecosystem.…”

Section: Discussionmentioning

confidence: 99%

“…Petri nets are similar to Boolean networks (Kauffman, 1969;Thomas & Kaufman, 2001), as they are well-adapted to formalize network topological changes. To our knowledge, such discrete and qualitative models have rarely been used in ecology (but see Ewing, Yandell, Barbieri, Luck, & Forster, 2002;Cordier, Largouët, & Zhao, 2014;Baldan, Bocci, Brigolin, Cocco, & Simeoni, 2015;Gaucherel, Théro, Puiseux, & Bonhomme, 2017). Among discrete models, Petri nets are powerful tools that enable the rigorous formalization of exhaustive changes in an ecosystem's structure.…”

Section: Several Models Have Been Proposed To Describe Resilience Andmentioning

confidence: 99%

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Using discrete systems to exhaustively characterize the dynamics of an integrated ecosystem

Gaucherel

Pommereau

2019

Methods Ecol Evol

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To understand long‐term ecosystem dynamics, several concepts have been recently proposed that consider ‘basins of attraction’ to express resilience and ‘tipping points’ that express sharp change in an ecosystem's behaviour. However, these temporal features remain difficult to identify and quantify because current models usually focus only on a part of the whole ecosystem behaviour, whereas a holistic approach should be preferred. We propose an original family of models based on discrete systems and designed to comprehensively characterize ecosystem dynamics holistically and over the long term. We developed a qualitative model based on Petri nets, made up of a relational graph (interaction network) that was then rigorously handled using transition rules. Unlike traditional modelling and graph theory approaches, transition rules can strongly modify the graph structure (i.e. a dynamic topology occurs). We examined the value of Petri nets when applied to the simple ecosystem of a termite colony. A termite colony comprises of abiotic and biotic components and processes that we explored along all of their possible trajectories. Several temporal features, such as basins of attraction (i.e. strongly connected states), tipping points (critical transitions along trajectories) and various kinds of collapses (functioning systems whose structures were nevertheless fixed), were easily detected and quantified. We propose that Petri nets developed for more complex ecosystems will provide original insights into their holistic behaviour.

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Section: Discussionmentioning

confidence: 99%

Section: Several Models Have Been Proposed To Describe Resilience Andmentioning

confidence: 99%

Using discrete systems to exhaustively characterize the dynamics of an integrated ecosystem

Gaucherel

Pommereau

2019

Methods Ecol Evol

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“…abrupt physical changes possibly occurring at irregular intervals (Cassandras and Lafortune, 2008). These models, and most notably Asynchronous Boolean Networks (Thomas, 1991), have been used for a long time in systems biology to model regulation networks (Chabrier and Fages, 2003;Kauffman, 1969;Thomas, 1991Thomas, , 1973, but only recently in ecology (Baldan et al, 2015;Campbell et al, 2015;Gaucherel and Pommereau, 2019; but see Gronewold and Sonnenschein, 1998). In the EDEN approach, the values of ecological interaction parameters are not required (i.e.…”

Section: Discrete-event and Rule-based Modellingmentioning

confidence: 99%

East-African savanna dynamics: from a knowledge-based model to the possible futures of a social-ecological system

Cosme¹,

Hély

Pommereau

et al. 2021

Preprint

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Sub-Saharan savanna ecosystems are undergoing transitions such as bush encroachment, desertification or agricultural expansion. Such shifts and persistence of land cover are increasingly well understood, especially bush encroachment which is of major concern in pastoral systems. Although dominant factors can explain such transformations, they often result from intertwined causes in which human activities play a significant role. Therefore, in this latter case, these issues may require integrated solutions, involving many interacting components. Ecosystem modelling has proved appropriate to support decision-makers in such complex situations. However, ecosystem models often require lots of quantitative information for estimating parameters and the precise functional form of interactions is often unknown. Alternatively, in rangeland management, States-and-Transitions Models (STMs) have been developed to organize knowledge about system transitions and to help decision-makers. However, these conceptual diagrams often lack mathematical analyzing tools, which strongly constrains their complexity. In this paper, we introduce the Ecological Discrete-Event Network (EDEN) modelling approach for representing the qualitative dynamics of an East-African savanna as a set of discrete states and transitions generated from empirical rules. These rules are derived from local knowledge, field observations and scientific literature. In contrast with STMs, EDEN generates automatically every possible states and transitions, thus enabling the prediction of novel ecosystem structures. Our results show that the savanna is potentially resilient to the disturbances considered. Moreover, the model highlights all transitions between vegetation types and socio-economic profiles under various climatic scenarios. The model also suggests that wildlife diversity may increase socio-economic resistance to seasonal drought. Tree-grass coexistence and agropastoralism have the widest ranges of conditions of existence of all vegetation types and socio-economic profiles, respectively. As this is a preliminary use of EDEN for applied purpose, analysis tools should be improved to enable finer investigation of desirable trajectories. By translating local knowledge into ecosystem dynamics, the EDEN approach seems promising to build a new bridge between managers and modellers.

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“…Petri net are a tool that can be effectively used for modeling natural processes, including LCA. There are studies that deal with modeling of food chains using Petri nets [18]. Likewise, Petri's nets are a favorite tool for Workflow Management, which is aimed at controlling, monitoring, optimizing, and supporting business processes [19].…”

Section: Literature Reviewmentioning

confidence: 99%

Modelling of Biofuel Potential as a Tool for Public Managers

Baťa

Fuka

2018

Sustainability

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Developing the efforts to implement sustainability policies in the energy field requires the most accurate information on the potential of available resources to properly implement concrete policies. Total net energy yields are interpreted in isolation, and studies providing information on yields of specific energy crops in net values are relatively rare. This article, therefore, provides a tool based on methodology combining Lifecycle Assessment (LCA) approaches and a model implemented in a stochastic Petri net environment to support managerial decision-making at a national and regional level. This tool allows for the comparison of net yields of more energy crops used in Central Europe. Additional crops can be added to the model. For the purpose of comparison, it is also possible to customize the model parameters for particular crops and the way they are cultivated. In comparison with oilseed rape, sugar beet, and wheat, the model shows best results in terms of net energy yields for sugar beet.

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Petri Nets for Modelling and Analysing Trophic Networks

Cited by 11 publications

References 31 publications

Using discrete systems to exhaustively characterize the dynamics of an integrated ecosystem

Using discrete systems to exhaustively characterize the dynamics of an integrated ecosystem

East-African savanna dynamics: from a knowledge-based model to the possible futures of a social-ecological system

Modelling of Biofuel Potential as a Tool for Public Managers

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