Efficient modelling of yeast cell cycles based on multisite phosphorylation using coloured hybrid Petri nets with marking-dependent arc weights

Herajy, Mostafa; Liu, Fei; Heiner, Monika

doi:10.1016/j.nahs.2017.09.002

Cited by 15 publications

(12 citation statements)

References 35 publications

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“…Besides, some other hybrid models with HSDMs can be found, e.g. the hybrid model of the Yeast cell cycle based on multisite phosphorylation in [ 66 ], and the hybrid model of calcium dynamics inside a dendritic spine in [ 67 ].…”

Section: Hybrid Modelling Methodsmentioning

confidence: 99%

Hybrid modelling of biological systems: current progress and future prospects

Liu

Heiner

Gilbert

2022

Briefings in Bioinformatics

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Integrated modelling of biological systems is becoming a necessity for constructing models containing the major biochemical processes of such systems in order to obtain a holistic understanding of their dynamics and to elucidate emergent behaviours. Hybrid modelling methods are crucial to achieve integrated modelling of biological systems. This paper reviews currently popular hybrid modelling methods, developed for systems biology, mainly revealing why they are proposed, how they are formed from single modelling formalisms and how to simulate them. By doing this, we identify future research requirements regarding hybrid approaches for further promoting integrated modelling of biological systems.

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Section: Hybrid Modelling Methodsmentioning

confidence: 99%

Hybrid modelling of biological systems: current progress and future prospects

Liu

Heiner

Gilbert

2022

Briefings in Bioinformatics

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“…Furthermore, they are supported by a wide range of simulation and analysis tools and offer several extensions. In order to model biochemical networks, different extensions of Petri nets are proposed in [7][8][9][10][11][12][13][14]. Some application examples of studying and analysing such systems are also given in [7,8,[15][16][17].…”

Section: Problems and Issuesmentioning

confidence: 99%

Modelling and Simulation of Biochemical Processes Using Petri Nets

Cherdal

Mouline

2018

Processes

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Systems composed of many components which interact with each other and lead to unpredictable global behaviour, are considered as complex systems. In a biological context, complex systems represent living systems composed of a large number of interacting elements. In order to study these systems, a precise mathematical modelling was typically used in this context. However, this modelling has limitations in the structural understanding and the behavioural study. In this sense, formal computational modelling is an approach that allows to model and to simulate dynamical properties of these particular systems. In this paper, we use Hybrid Functional Petri Net (HFPN), a Petri net extension dedicated to study and verify biopathways, to model and study the Methionine metabolic pathway. Methionine and its derivatives play significant roles in human bodies. We propose a set of simulations for the purpose of studying and analysing the Methionine pathway’s behaviour. Our simulation results have shown that several important abnormalities in this pathway are related to sever diseases such as Alzheimer’s disease, cardiovascular disease, cancers and others.

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“…Besides, ColPNs can be further enriched to include marking-dependent arcs, i.e. the arc multiplicities are allowed to be marking-dependent expressions of various types in terms of a transition’s preplaces [29], which facilitates the modelling of some special biological scenarios such as cell division [30, 31]. ColPNs and ColXPNs can be analysed using a variety of techniques, such as structural analysis (confined to models without special arcs extending the modelling power) [12] or state space analysis based on computational tree logic (CTL), which is a branching time temporal logic [32] matching the needs for analysing reachability graphs (model checking).…”

Section: Coloured Petri Netsmentioning

confidence: 99%

Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems

Liu

Heiner

Gilbert

2017

Briefings in Bioinformatics

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Owing to the availability of data of one biological phenomenon at different levels/scales, modelling of biological systems is moving from single level/scale to multiple levels/scales, which introduces a number of challenges. Coloured Petri nets (ColPNs) have been successfully applied to multilevel, multiscale and multidimensional modelling of some biological systems, addressing many of these challenges. In this article, we first review the basics of ColPNs and some popular extensions, and then their applications for multilevel, multiscale and multidimensional modelling of biological systems. This understanding of how to use ColPNs for modelling biological systems will assist readers in selecting appropriate ColPN classes for specific modelling circumstances.

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Efficient modelling of yeast cell cycles based on multisite phosphorylation using coloured hybrid Petri nets with marking-dependent arc weights

Cited by 15 publications

References 35 publications

Hybrid modelling of biological systems: current progress and future prospects

Hybrid modelling of biological systems: current progress and future prospects

Modelling and Simulation of Biochemical Processes Using Petri Nets

Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems

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