Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle

Herajy, Mostafa; Schwarick, Martin; Heiner, Monika

doi:10.1007/978-3-642-40465-8_7

Cited by 15 publications

(18 citation statements)

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“…The case studies range from simple to complex ones that involve many species and reactions. These include: a T7 phage model [ 8 ], a hybrid model of the eukaryotic cell cycle [ 29 ] based on the stochastic one in [ 7 ], the ATM/p53/NF- κ B model [ 31 ] which has been discussed in the “ Results ” section, and the simple hybrid calcium model provided in Fig. 2 .…”

Section: Discussionmentioning

confidence: 99%

“…Reactions are represented by transitions, while species are denoted by places. More information about hybrid Petri net notations can be found in [ 11 , 19 , 29 ] as well as in Snoopy’s hybrid simulator user manual [ 21 ]. In addition to specifying all reactions, the model editor provides other features to configure the model parameters as well as the initial state.…”

Section: Methodsmentioning

confidence: 99%

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Snoopy’s hybrid simulator: a tool to construct and simulate hybrid biological models

et al. 2017

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BackgroundHybrid simulation of (computational) biochemical reaction networks, which combines stochastic and deterministic dynamics, is an important direction to tackle future challenges due to complex and multi-scale models. Inherently hybrid computational models of biochemical networks entail two time scales: fast and slow. Therefore, it is intricate to efficiently and accurately analyse them using only either deterministic or stochastic simulation. However, there are only a few software tools that support such an approach. These tools are often limited with respect to the number as well as the functionalities of the provided hybrid simulation algorithms.ResultsWe present Snoopy’s hybrid simulator, an efficient hybrid simulation software which builds on Snoopy, a tool to construct and simulate Petri nets. Snoopy’s hybrid simulator provides a wide range of state-of-the-art hybrid simulation algorithms. Using this tool, a computational model of biochemical networks can be constructed using a (coloured) hybrid Petri net’s graphical notations, or imported from other compatible formats (e.g. SBML), and afterwards executed via dynamic or static hybrid simulation.ConclusionSnoopy’s hybrid simulator is a platform-independent tool providing an accurate and efficient simulation of hybrid (biological) models. It can be downloaded free of charge as part of Snoopy from http://www-dssz.informatik.tu-cottbus.de/DSSZ/Software/Snoopy.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-017-0449-6) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Snoopy’s hybrid simulator: a tool to construct and simulate hybrid biological models

et al. 2017

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“…This feature is called marking-dependent arc weights (Valk, 1978;Matsuno et al, 2003;Herajy et al, 2013). Implementing certain model semantics without the help of marking-dependent arc weights may become intricate and even impossible in certain circumstances.…”

Section: Marking-dependent Arc Weightsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Similarly, stochastic Petri nets (Ajmone et al, 1995) provide a graphical tool to permit the stochastic exploration of a constructed model. Nowadays, a variety of Petri nets with different extensions have been used to model various technical and biological systems (e.g., see Reddy et al, 1993;Matsuno et al, 2003;Fujita et al, 2004;Herajy et al, 2013).Hybrid Petri Nets (HPN ) (David and Alla, 2010) are another interesting class of Petri nets. HPN permit the integration of discrete and continuous variables (places) in addition to discrete and continuous processes (transitions) into one model.…”

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Modeling and simulation of multi-scale environmental systems with Generalized Hybrid Petri Nets

Herajy

Heiner

2015

Front. Environ. Sci.

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Predicting and studying the dynamics and properties of environmental systems necessitates the construction and simulation of mathematical models entailing different levels of complexities. Such type of computational experiments often require the combination of discrete and continuous variables as well as processes operating at different time scales. Furthermore, the iterative steps of constructing and analyzing environmental models might involve researchers with different background. Hybrid Petri nets may contribute in overcoming such challenges as they facilitate the implementation of systems integrating discrete and continuous dynamics. Additionally, the visual depiction of model components will inevitably help to bridge the gap between scientists with distinct expertise working on the same problem. Thus, modeling environmental systems with hybrid Petri nets enables the construction of complex processes while keeping the models comprehensible for researchers working on the same project with significantly divergent educational background. In this paper we propose the utilization of a special class of hybrid Petri nets, Generalized Hybrid Petri Nets (GHPN ), to model and simulate environmental systems exposing processes interacting at different time-scales. GHPN integrate stochastic and deterministic semantics as well as some other types of special basic events. To this end, we present a case study illustrating the use of GHPN in constructing and simulating multi-timescale environmental scenarios.Keywords: modeling and simulation, Hybrid Petri Nets, multi-scale environmental systems, Chagas disease, Triatoma infestans IntroductionThe process of constructing and analyzing environmental systems is increasingly becoming a complex procedure (Seppelt et al., 2009;Uusitalo et al., 2015). On the one hand, it can require the amalgamation of different simulation techniques to accurately and efficiently find a solution to the problem under consideration (see e.g., Gillet, 2008;Gregorio et al., 1999). On the other hand, complex environmental systems require the collection and analysis of various data and information that cannot be tackled by researchers coming from just one area of expertise (Seppelt et al., 2009).While the ordinary differential equations (ODEs) approach is widely used to construct and simulate many problems in the environmental domain, certain classes of such problems cannot be adequately addressed using this approach alone. For instance in Khoury et al. (2013) construct a simple, but elegant ODEs model to study food and population dynamics in honey bee colonies. However, such a continuous approach cannot capture the effect of seasonal variations Herajy and Heiner GHPN for multi-scale environmental systems on many parameters. Contrary, in Schmickl and Crailsheim (2007) and Russell et al. (2013) a discrete simulation of recurrence and difference equations has been deployed to emulate the discrete changes in bee population taking into account seasonal variations. Nevertheless, certain scenarios necessitate ...

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A Graphical Approach for Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets

Ismail

Herajy

Heiner

2019

Computational Biology

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Hybrid Petri Nets for Modelling the Eukaryotic Cell Cycle

Cited by 15 publications

References 21 publications

Snoopy’s hybrid simulator: a tool to construct and simulate hybrid biological models

Snoopy’s hybrid simulator: a tool to construct and simulate hybrid biological models

Modeling and simulation of multi-scale environmental systems with Generalized Hybrid Petri Nets

A Graphical Approach for Hybrid Modelling of Intracellular Calcium Dynamics Based on Coloured Hybrid Petri Nets

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