Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks.
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| Title: | Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks. |
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| Authors: | Herajy, Mostafa1 mherajy@sci.psu.edu.eg, Heiner, Monika2 monika.heiner@informatik.tu-cottbus.de |
| Source: | Fundamenta Informaticae. 2014, Vol. 129 Issue 1-2, p49-67. 19p. |
| Subjects: | Computational steering (Computer science), Petri nets, Computer simulation, Remote control, Parameters (Statistics), Stochastic analysis, Mathematical models |
| Abstract: | Computational steering is an interactive remote control of a long running application. The user can adopt it, e.g., to adjust simulation parameters on the fly. Simulation of large-scale biochemical networks is often computationally expensive, particularly stochastic and hybrid simulation. Such extremely time-consuming computations necessitate an interactive mechanism to permit users to try different paths and ask 'what-if-questions' while the simulation is in progress. Furthermore, with the progress of computational modelling and the simulation of biochemical networks, there is a need to manage multi-scale models, which may contain species or reactions at different scales. In this context, Petri nets are of special importance, since they provide an intuitive visual representation of reaction networks. In this paper, we introduce a framework and its implementation for combining Petri nets and computational steering for the representation and interactive simulation of biochemical networks. The main merits of the developed framework are: intuitive representation of biochemical networks by means of Petri nets, distributed collaborative and interactive simulation, and tight coupling of simulation and visualisation. [ABSTRACT FROM AUTHOR] |
| Copyright of Fundamenta Informaticae is the property of Polskie Towarzystwo Matematyczne and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Links: – Type: pdflink Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 94006993 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Herajy%2C+Mostafa%22">Herajy, Mostafa</searchLink><relatesTo>1</relatesTo><i> mherajy@sci.psu.edu.eg</i><br /><searchLink fieldCode="AR" term="%22Heiner%2C+Monika%22">Heiner, Monika</searchLink><relatesTo>2</relatesTo><i> monika.heiner@informatik.tu-cottbus.de</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Fundamenta+Informaticae%22">Fundamenta Informaticae</searchLink>. 2014, Vol. 129 Issue 1-2, p49-67. 19p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Computational+steering+%28Computer+science%29%22">Computational steering (Computer science)</searchLink><br /><searchLink fieldCode="DE" term="%22Petri+nets%22">Petri nets</searchLink><br /><searchLink fieldCode="DE" term="%22Computer+simulation%22">Computer simulation</searchLink><br /><searchLink fieldCode="DE" term="%22Remote+control%22">Remote control</searchLink><br /><searchLink fieldCode="DE" term="%22Parameters+%28Statistics%29%22">Parameters (Statistics)</searchLink><br /><searchLink fieldCode="DE" term="%22Stochastic+analysis%22">Stochastic analysis</searchLink><br /><searchLink fieldCode="DE" term="%22Mathematical+models%22">Mathematical models</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Computational steering is an interactive remote control of a long running application. The user can adopt it, e.g., to adjust simulation parameters on the fly. Simulation of large-scale biochemical networks is often computationally expensive, particularly stochastic and hybrid simulation. Such extremely time-consuming computations necessitate an interactive mechanism to permit users to try different paths and ask 'what-if-questions' while the simulation is in progress. Furthermore, with the progress of computational modelling and the simulation of biochemical networks, there is a need to manage multi-scale models, which may contain species or reactions at different scales. In this context, Petri nets are of special importance, since they provide an intuitive visual representation of reaction networks. In this paper, we introduce a framework and its implementation for combining Petri nets and computational steering for the representation and interactive simulation of biochemical networks. The main merits of the developed framework are: intuitive representation of biochemical networks by means of Petri nets, distributed collaborative and interactive simulation, and tight coupling of simulation and visualisation. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Fundamenta Informaticae is the property of Polskie Towarzystwo Matematyczne and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
| PLink | https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=94006993 |
| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.3233/FI-2014-960 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 19 StartPage: 49 Subjects: – SubjectFull: Computational steering (Computer science) Type: general – SubjectFull: Petri nets Type: general – SubjectFull: Computer simulation Type: general – SubjectFull: Remote control Type: general – SubjectFull: Parameters (Statistics) Type: general – SubjectFull: Stochastic analysis Type: general – SubjectFull: Mathematical models Type: general Titles: – TitleFull: Petri Net-Based Collaborative Simulation and Steering of Biochemical Reaction Networks. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Herajy, Mostafa – PersonEntity: Name: NameFull: Heiner, Monika IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Text: 2014 Type: published Y: 2014 Identifiers: – Type: issn-print Value: 01692968 Numbering: – Type: volume Value: 129 – Type: issue Value: 1-2 Titles: – TitleFull: Fundamenta Informaticae Type: main |
| ResultId | 1 |
