A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-Models via Coloured Hybrid Petri Nets
Three-dimensional modelling of biological systems is imperative to study the behaviour of dynamic systems that require the analysis of how their components interact in space. However, there are only a few formal tools that offer a convenient modelling of such systems. The traditional approach to con...
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| Format: | Article |
| Language: | English |
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Wiley
2020-01-01
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| Series: | Modelling and Simulation in Engineering |
| Online Access: | http://dx.doi.org/10.1155/2020/4715172 |
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| author | Amr Ismail Mostafa Herajy Elsayed Atlam Monika Heiner |
| author_facet | Amr Ismail Mostafa Herajy Elsayed Atlam Monika Heiner |
| author_sort | Amr Ismail |
| collection | DOAJ |
| description | Three-dimensional modelling of biological systems is imperative to study the behaviour of dynamic systems that require the analysis of how their components interact in space. However, there are only a few formal tools that offer a convenient modelling of such systems. The traditional approach to construct and simulate 3D models is to build a system of partial differential equations (PDEs). Although this approach may be computationally efficient and has been employed by many researchers over the years, it is not always intuitive since it does not provide a visual depiction of the modelled systems. Indeed, a visual modelling can help to conceive a mental image which eventually contributes to the understanding of the problem under study. Coloured Hybrid Petri Nets (HPNC) are a high-level representation of classical Petri nets that offer hybrid as well as spatial modelling of biological systems. In addition to their graphical representations, HPNC models are also scalable. This paper shows how HPNC can be used to construct and simulate systems that require three-dimensional as well as hybrid (stochastic/continuous) modelling. We use calcium diffusion in three dimensions to illustrate our main ideas. More specifically, we show that creating 3D models using HPNC can yield more flexible models as the structure can be easily scaled up and down by just modifying a few parameters. This advantage of convenient model configuration facilitates the design of different experiments without the need to alter the model structure. |
| format | Article |
| id | doaj-art-e2b4f518a5204e30a56d04a7051acfb6 |
| institution | Kabale University |
| issn | 1687-5591 1687-5605 |
| language | English |
| publishDate | 2020-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Modelling and Simulation in Engineering |
| spelling | doaj-art-e2b4f518a5204e30a56d04a7051acfb62025-02-03T00:58:42ZengWileyModelling and Simulation in Engineering1687-55911687-56052020-01-01202010.1155/2020/47151724715172A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-Models via Coloured Hybrid Petri NetsAmr Ismail0Mostafa Herajy1Elsayed Atlam2Monika Heiner3Department of Mathematics and Computer Science, Faculty of Science, Port Said University, 42521-Port Said, EgyptDepartment of Mathematics and Computer Science, Faculty of Science, Port Said University, 42521-Port Said, EgyptFaculty of Computer Science and Engineering, Taibah University, Yanbu, Saudi ArabiaComputer Science Institute, Brandenburg University of Technology, Postbox 101344, 03013 Cottbus, GermanyThree-dimensional modelling of biological systems is imperative to study the behaviour of dynamic systems that require the analysis of how their components interact in space. However, there are only a few formal tools that offer a convenient modelling of such systems. The traditional approach to construct and simulate 3D models is to build a system of partial differential equations (PDEs). Although this approach may be computationally efficient and has been employed by many researchers over the years, it is not always intuitive since it does not provide a visual depiction of the modelled systems. Indeed, a visual modelling can help to conceive a mental image which eventually contributes to the understanding of the problem under study. Coloured Hybrid Petri Nets (HPNC) are a high-level representation of classical Petri nets that offer hybrid as well as spatial modelling of biological systems. In addition to their graphical representations, HPNC models are also scalable. This paper shows how HPNC can be used to construct and simulate systems that require three-dimensional as well as hybrid (stochastic/continuous) modelling. We use calcium diffusion in three dimensions to illustrate our main ideas. More specifically, we show that creating 3D models using HPNC can yield more flexible models as the structure can be easily scaled up and down by just modifying a few parameters. This advantage of convenient model configuration facilitates the design of different experiments without the need to alter the model structure.http://dx.doi.org/10.1155/2020/4715172 |
| spellingShingle | Amr Ismail Mostafa Herajy Elsayed Atlam Monika Heiner A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-Models via Coloured Hybrid Petri Nets Modelling and Simulation in Engineering |
| title | A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-Models via Coloured Hybrid Petri Nets |
| title_full | A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-Models via Coloured Hybrid Petri Nets |
| title_fullStr | A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-Models via Coloured Hybrid Petri Nets |
| title_full_unstemmed | A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-Models via Coloured Hybrid Petri Nets |
| title_short | A Graphical Approach for Hybrid Simulation of 3D Diffusion Bio-Models via Coloured Hybrid Petri Nets |
| title_sort | graphical approach for hybrid simulation of 3d diffusion bio models via coloured hybrid petri nets |
| url | http://dx.doi.org/10.1155/2020/4715172 |
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