Probabilistic model checking of complex biological pathways
Probabilistic model checking is a formal verification technique that has been successfully applied to the analysis of systems from a broad range of domains, including security and communication protocols, distributed algorithms and power management. In this paper we illustrate its applicability to a...
| Main Authors: | , , , , |
|---|---|
| Format: | Journal article |
| Language: | English |
| Published: |
Elsevier
2008
|
| _version_ | 1797104498739511296 |
|---|---|
| author | Heath, J Kwiatkowska, M Norman, G Parker, D Tymchyshyn, O |
| author_facet | Heath, J Kwiatkowska, M Norman, G Parker, D Tymchyshyn, O |
| author_sort | Heath, J |
| collection | OXFORD |
| description | Probabilistic model checking is a formal verification technique that has been successfully applied to the analysis of systems from a broad range of domains, including security and communication protocols, distributed algorithms and power management. In this paper we illustrate its applicability to a complex biological system: the FGF (Fibroblast Growth Factor) signalling pathway. We give a detailed description of how this case study can be modelled in the probabilistic model checker PRISM, discussing some of the issues that arise in doing so, and show how we can thus examine a rich selection of quantitative properties of this model. We present experimental results for the case study under several different scenarios and provide a detailed analysis, illustrating how this approach can be used to yield a better understanding of the dynamics of the pathway. Finally, we outline a number of exact and approximate techniques to enable the verification of larger and more complex pathways and apply several of them to the FGF case study. © 2007 Elsevier Ltd. All rights reserved. |
| first_indexed | 2024-03-07T06:34:35Z |
| format | Journal article |
| id | oxford-uuid:f7298026-548f-4ef2-b61e-65e921b002e8 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T06:34:35Z |
| publishDate | 2008 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | oxford-uuid:f7298026-548f-4ef2-b61e-65e921b002e82022-03-27T12:40:45ZProbabilistic model checking of complex biological pathwaysJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:f7298026-548f-4ef2-b61e-65e921b002e8EnglishSymplectic Elements at OxfordElsevier2008Heath, JKwiatkowska, MNorman, GParker, DTymchyshyn, OProbabilistic model checking is a formal verification technique that has been successfully applied to the analysis of systems from a broad range of domains, including security and communication protocols, distributed algorithms and power management. In this paper we illustrate its applicability to a complex biological system: the FGF (Fibroblast Growth Factor) signalling pathway. We give a detailed description of how this case study can be modelled in the probabilistic model checker PRISM, discussing some of the issues that arise in doing so, and show how we can thus examine a rich selection of quantitative properties of this model. We present experimental results for the case study under several different scenarios and provide a detailed analysis, illustrating how this approach can be used to yield a better understanding of the dynamics of the pathway. Finally, we outline a number of exact and approximate techniques to enable the verification of larger and more complex pathways and apply several of them to the FGF case study. © 2007 Elsevier Ltd. All rights reserved. |
| spellingShingle | Heath, J Kwiatkowska, M Norman, G Parker, D Tymchyshyn, O Probabilistic model checking of complex biological pathways |
| title | Probabilistic model checking of complex biological pathways |
| title_full | Probabilistic model checking of complex biological pathways |
| title_fullStr | Probabilistic model checking of complex biological pathways |
| title_full_unstemmed | Probabilistic model checking of complex biological pathways |
| title_short | Probabilistic model checking of complex biological pathways |
| title_sort | probabilistic model checking of complex biological pathways |
| work_keys_str_mv | AT heathj probabilisticmodelcheckingofcomplexbiologicalpathways AT kwiatkowskam probabilisticmodelcheckingofcomplexbiologicalpathways AT normang probabilisticmodelcheckingofcomplexbiologicalpathways AT parkerd probabilisticmodelcheckingofcomplexbiologicalpathways AT tymchyshyno probabilisticmodelcheckingofcomplexbiologicalpathways |