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Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models

hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
hal.structure.identifierModels and Algorithms for the Genome [ MAGNOME]
dc.contributor.authorSOUEIDAN, Hayssam
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
dc.contributor.authorSUTRE, Grégoire
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
hal.structure.identifierModels and Algorithms for the Genome [ MAGNOME]
dc.contributor.authorNIKOLSKI, Macha
dc.contributor.editor21
dc.date.accessioned2024-04-15T09:50:46Z
dc.date.available2024-04-15T09:50:46Z
dc.date.created2009
dc.date.issued2009
dc.date.conference2009
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/198372
dc.description.abstractEnQuantitative models in Systems Biology depend on a large number of free parameters, whose values completely determine behavior of models. These parameters are often estimated by fitting the system to observed experimental measurements and data. The response of a model to parameter variation defines qualitative changes of the system's behavior. The influence of a given parameter can be estimated by varying it in a certain range. Some of these ranges produce similar system dynamics, making it possible to define general trends for trajectories of the system (e.g. oscillating behavior) in such parameter ranges. Such trends can be seen as a qualitative description of the system's dynamics within a parameter range. In this work, we define an automata-based formalism to formally describe the qualitative behavior of systems' dynamics. Qualitative behaviors are represented by finite transition systems whose states contain predicate valuation and whose transitions are labeled by probabilistic delays. Biochemical system' dynamics are automatically abstracted in terms of these qualitative transition systems by a random sampling of trajectories. Furthermore, we use graph theoretic tools to compare the resulting qualitative behaviors and to estimate those parameter ranges that yield similar behaviors. We validate this approach on published biochemical models and show that it enables rapid exploration of models' behavior, that is estimation of parameter ranges with a given behavior of interest and identification of some bifurcation points.
dc.language.isoen
dc.publisherSpringer Verlag
dc.source.titleProc. 7th Int. Conf. on Computational Methods in Systems Biology (CMSB'09), Bologna, Italy, Aug.-Sep. 2009
dc.title.enQualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models
dc.typeCommunication dans un congrès
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
bordeaux.page313--327
bordeaux.volume5688
bordeaux.hal.laboratoriesLaboratoire Bordelais de Recherche en Informatique (LaBRI) - UMR 5800*
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionBordeaux INP
bordeaux.institutionCNRS
bordeaux.conference.titleComputational Methods in Systems Biology (CMSB'09)
bordeaux.countryIT
bordeaux.title.proceedingProc. 7th Int. Conf. on Computational Methods in Systems Biology (CMSB'09), Bologna, Italy, Aug.-Sep. 2009
bordeaux.conference.cityBologna
bordeaux.peerReviewedoui
hal.identifierhal-00408909
hal.version1
hal.invitednon
hal.proceedingsoui
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-00408909v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.btitle=Proc.%207th%20Int.%20Conf.%20on%20Computational%20Methods%20in%20Systems%20Biology%20(CMSB'09),%20Bologna,%20Italy,%20Aug.-Sep.%202009&rft.date=2009&rft.volume=5688&rft.spage=313--327&rft.epage=313--327&rft.au=SOUEIDAN,%20Hayssam&SUTRE,%20Gr%C3%A9goire&NIKOLSKI,%20Macha&rft.genre=unknown


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