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MTCoord Preliminary Version

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Niveau: Supérieur, Doctorat, Bac+8
MTCoord 2005 Preliminary Version Biomolecular agents as multi-behavioural concurrent objects Denys Duchier 1 Celine Kuttler 2 Interdisciplinary Research Institute (CNRS), Lille, France Abstract In recent years, there has been increasing interest in computational models of bi- ological systems based on various calculi of communicating processes, such as the stochastic pi-calculus. These models make it possible to simulate and eventually visualize the dynamic evolution of complex biosystems in time and under varying environmental conditions. While the elegance of the pi-calculus lies in its minimality, this is also a drawback when it comes to modeling because much effort must be devoted to encoding high- level ideas into the low-level means that the language affords us. In this paper, we describe an on-going effort to design a new higher-level pro- gramming language that provides direct ontological support for the concepts which are used to formulate, organize and structure models of biomolecular systems. Our language has an object-oriented flavour where we view molecular components as agents with finite sets of behaviours (states). Reactions are modeled as exchanges over connected ports that may cause agents to switch states. Key words: biological systems, stochastic pi-calculus, communicating agents, systems biology, simulation, programming 1 Introduction The interdisciplinary study of coordination [12] investigates processes of man- aging dependencies among activities.

  • pi calculus

  • protein interaction

  • makes models

  • all reactions

  • stochastic control

  • elaborating stochastic

  • models can

  • over time

  • system biology

  • protein can inactivate


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MTCoord2005PreliminaryVersionBiomolecularagentsasmulti-behaviouralconcurrentobjectsDenysDuchier1Ce´lineKuttler2InterdisciplinaryResearchInstitute(CNRS),Lille,FranceAbstractInrecentyears,therehasbeenincreasinginterestincomputationalmodelsofbi-ologicalsystemsbasedonvariouscalculiofcommunicatingprocesses,suchasthestochasticpi-calculus.Thesemodelsmakeitpossibletosimulateandeventuallyvisualizethedynamicevolutionofcomplexbiosystemsintimeandundervaryingenvironmentalconditions.Whiletheeleganceofthepi-calculusliesinitsminimality,thisisalsoadrawbackwhenitcomestomodelingbecausemucheffortmustbedevotedtoencodinghigh-levelideasintothelow-levelmeansthatthelanguageaffordsus.Inthispaper,wedescribeanon-goingefforttodesignanewhigher-levelpro-gramminglanguagethatprovidesdirectontologicalsupportfortheconceptswhichareusedtoformulate,organizeandstructuremodelsofbiomolecularsystems.Ourlanguagehasanobject-orientedflavourwhereweviewmolecularcomponentsasagentswithfinitesetsofbehaviours(states).Reactionsaremodeledasexchangesoverconnectedportsthatmaycauseagentstoswitchstates.Keywords:biologicalsystems,stochasticpi-calculus,communicatingagents,systemsbiology,simulation,programming1IntroductionTheinterdisciplinarystudyofcoordination[12]investigatesprocessesofman-agingdependenciesamongactivities.Onthesurface,researchersfromdiffer-entfieldsusethesameterminologyforthedescriptionofcomplexsystems:model,control,regulation,amplification,feedback.Eachlivingcellisainherentlycomplexsystems[6].Itisdenselypopulatedbytenthousandsmoleculeswithhighlyspecializedfunctionandinteractioncapabilities.Forexample,areceptormoleculeonabacterium’ssurfacemaybe1Email:denys.duchier@lifl.fr2Email:celine.kuttler@lifl.frThisisapreliminaryversion.ThefinalversionwillbepublishedinElectronicNotesinTheoreticalComputerScienceURL:www.elsevier.nl/locate/entcs