LEADER 12094nam 22007815 450 001 9910143879403321 005 20251116234259.0 010 $a3-540-36481-1 024 7 $a10.1007/3-540-36481-1 035 $a(CKB)1000000000211934 035 $a(SSID)ssj0000322040 035 $a(PQKBManifestationID)11277386 035 $a(PQKBTitleCode)TC0000322040 035 $a(PQKBWorkID)10283243 035 $a(PQKB)10333510 035 $a(DE-He213)978-3-540-36481-8 035 $a(MiAaPQ)EBC3072732 035 $a(PPN)155176390 035 $a(BIP)8159140 035 $a(EXLCZ)991000000000211934 100 $a20121227d2003 u| 0 101 0 $aeng 135 $aurnn|008mamaa 181 $ctxt 182 $cc 183 $acr 200 10$aComputational Methods in Systems Biology $eFirst International Workshop, CMSB 2003, Roverto, Italy, February 24?26, 2003 /$fedited by Corrado Priami 205 $a1st ed. 2003. 210 1$aBerlin, Heidelberg :$cSpringer Berlin Heidelberg :$cImprint: Springer,$d2003. 215 $a1 online resource (IX, 214 p.) 225 1 $aLecture Notes in Computer Science,$x0302-9743 ;$v2602 300 $aBibliographic Level Mode of Issuance: Monograph 311 08$a3-540-00605-2 320 $aIncludes bibliographical references at the end of each chapters and index. 327 $aInvited Papers -- Cells as Computation -- Formal Modeling of C. elegans Development: A Scenario-Based Approach -- Regular Papers -- Causal ?-Calculus for Biochemical Modelling -- Graphs for Core Molecular Biology -- Contribution of Computational Tree Logic to Biological Regulatory Networks: Example from Pseudomonas Aeruginosa -- Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing -- Multiscale Modeling of Alternative Splicing Regulation -- A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information -- Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data -- Discrete Event Simulation for a Better Understanding of Metabolite Channeling - A System Theoretic Approach -- Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway -- A Method to Identify Essential Enzymes in the Metabolism: Application to Escherichia Coli -- Symbolic Model Checking of Biochemical Networks -- Presentation Abstracts -- Coupled Oscillator Models for a Set of Communicating Cells -- Representing and Simulating Protein Functional Domains in Signal Transduction Using Maude -- A Core Modeling Language for the Working Molecular Biologist (Abstract) -- Integrating Simulation Packages via Systems Biology Mark-Up Language -- Recreating Biopathway Databases towards Simulation -- How to Synthesize an Optimized Genetic ?-Switching System? A System-Theoretic Approach Based on SQP -- Simulation Sudy of the TNF? Mediated NF-?B Signaling Pathway -- Detection and Analysis of Unexpected State Components in Biological Systems -- Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis -- An Overview of Data Models for the Analysis of Biochemical Pathways -- Discrete Event Systems and Client-Server Model for Signaling Mechanisms -- Position Papers -- Enhanced Operational Semantics in Systems Biology -- Issues in Computational Methods for Functional Genomics and Systems Biology -- Integrating Biological Process Modelling with Gene Expression Data and Ontologies for Functional Genomics (Position Paper) -- Computer Simulation of Protocells -- How to Solve Semantic Puzzles of Systems Biology -- Evolution as Design Engineer -- Inference, Modeling and Simulation of Gene Networks. 330 $aMolecularbiologyhasuntilnowmainlyfocussedonindividualmolecules,on theirpropertiesasisolatedentitiesorascomplexesinverysimplemodelsystems. However,biologicalmoleculesinlivingsystemsparticipateinverycomplexn- works,includingregulatorynetworksforgeneexpression,intracellularmetabolic networksandbothintra-andintercellularcommunicationnetworks. Suchn- worksareinvolvedinthemaintenance(homeostasis)aswellasthedi'erentiation ofcellularsystemsofwhichwehaveaveryincompleteunderstanding. Nevertheless,theprogressinmolecularbiologyhasmadepossiblethedetailed descriptionofthecomponentsthatconstitutelivingsystems,notablygenesand proteins. Large-scalegenomesequencingmeansthatwecan(atleastinpr- ciple)delineateallmacromolecularcomponentsofagivencellularsystem,and microarrayexperimentsaswellaslarge-scaleproteomicswillsoongiveuslarge amountsofexperimentaldataongeneregulation,molecularinteractionsand cellularnetworks. Thechallengeofthe21stcenturywillbetounderstandhow theseindividualcomponentsintegrateintocomplexsystemsandthefunction andevolutionofthesesystems,thusscalingupfrommolecularbiologytos- temsbiology. Bycombiningexperimentaldatawithadvancedformaltheories fromcomputerscience,"theformallanguageforbiologicalsystems"tospecify dynamicmodelsofinteractingmolecularentitieswouldbeessentialfor:(i)- derstandingthenormalbehaviourofcellularprocesses,andhowchangesmay a'ecttheprocessesandcausedisease-itmaybepossibletocorrelategenetic propertiesandsymptomsinnewandmoree'cientways,basedonanactual- derstandingofhowvariousprocessesinteract;(ii)providingpredictabilityand ?exibilitytoacademic,pharmaceutical,biotechnologyandmedicalresearchers studyinggeneorproteinfunctions. Inparticular,itmaysavetimebyreducing thenumberofexperimentsneeded,ifinadequatehypothesescanbeexcludedby computersimulation. Inresponsetothecallforpapers39weresubmittedtoCMSB2003. Allthe submittedpaperswerereviewedandtheprogrammecommittee(listedbelow) selected11high-qualitypapersforpublicationinthisvolume. Thecareofthe reviewersandoftheprogrammecommitteemembersinreviewingthepapers wassurelyvaluable. Afurther11paperswereselectedonlyforpresentationat theworkshopinordertostimulatediscussions(anabstractisincluded). AttheworkshopEhudShapiroandMichaelSterngavetwoinvited talks whosetopicsaredescribedinpapersincludedinthisvolume. Theprogramme committeedecidedtoacceptforpublicationinthisvolumealsosomeposition papers that highlight the research trends in this new ?eld of computational methodsinsystemsbiology. Thereasonisthatbecausethisisthe'rstedition ofaworkshopinthisfast-growing'eldalargeviewofpotentialtopicsofresearch wasconsideredextremelyimportant. Rovereto,December2002 CorradoPriami ProgrammeCommitteeofCMSB 2003 CorradoPriami(Chair),UniversityofTrento(Italy), CharlesAu'ray,CNRS,Villejuif(France), CosimaBaldari,Universit`adiSiena(Italy), AlexanderBockmayr,Universit´eHenriPoincar´e(France), LucaCardelli,MicrosoftResearchCambridge(UK), VincentDanos,Universit´eParisVII(France), PierpaoloDegano,Universitad ` iPisa(Italy), Francois ¸ Fages,INRIA,Rocquencourt(France), DrabløsFinn,NorwegianUniversityofScienceandTechnology,Trondheim(N- way), MonikaHeiner,BrandenburgUniversityofTechnologyatCottbus(Germany), InaKoch,UniversityofAppliedSciencesBerlin,(Germany), JohnE. Ladbury,UniversityCollegeLondon(UK), PatrickLincoln,SRI(USA), SatoruMiyano,UniversityofTokyo(Japan), GordonPlotkin,UniversityofEdinburgh(UK), SimonPlyte,PharmaciaCorporation(Italy), AvivRegev,WeizmannInstituteofScience(Israel), MagaliRoux-Rouqui´e,BSMIPasteurInstitute(France), VincentSchachter,HybrigenicsParis(France), MasaruTomita,KeioUniversity(Japan), AdelindeUhrmacher,UniversityofRostock(Germany), AlfonsoValencia,CNB-CSIC,CentroNacionaldeBiotecnologia(Spain), OlafWolkenhauer,UMIST,Manchester(UK) Local Organizing Committee Corrado Priami, Linda Brodo, Michela de Concini, Debora Schuch da Rosa Machado,andtheUniversityofTrentoEventsandMeetingsO'ce. List ofReferees F. Abascal,N. Chabrier,A. Cimatti,M. Curti,M. D. Devignes,S. Gnesi, J. Guijarro,K. Hafez,E. Klipp,C. Laneve,P. LopezRomero,F. Luccio, R. Marangoni,M. Padron,M. C. Pinotti,R. Rizzi,S. Tini. Acknowledgement TheworkshopwassponsoredandpartiallysupportedbytheUniversityofTrento, ComunediRovereto,APT,andtheEUprojectIST-32072-DEGAS. Table of Contents IInvitedPapers CellsasComputation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 AmitaiRegevandEhudShapiro FormalModelingofC. elegansDevelopment:AScenario-BasedApproach . . . 4 Na''aman Kam,David Harel,Hillel Kugler, RamiMarelly, AmirPnueli, E. JaneAlbertHubbard, andMichael J. Stern IIRegularPapers Causal?-CalculusforBiochemicalModelling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Michele Curti,Pierpaolo Degano, andCosima Tatiana Baldari GraphsforCoreMolecularBiology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 Vincent Danos and Cosimo Laneve ContributionofComputationalTreeLogic toBiologicalRegulatoryNetworks: ExamplefromPseudomonasAeruginosa. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 SabinePeresandJean-PaulComet ModelingCellularBehaviorwithHybridAutomata: BisimulationandCollapsing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 Marco Antoniotti, Bhubaneswar Mishra, Carla Piazza, Alberto Policriti, andMarta Simeoni MultiscaleModelingofAlternativeSplicingRegulation. . . . . . . . . . . . . . . . . . . . . 75 Damien Eveillard, Delphine Ropers,Hidde deJong,Christiane Branlant, andAlexanderBockmayr AMethodforEstimatingMetabolicFluxes fromIncompleteIsotopomerInformation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88 JuhoRousu,AriRantanen,HannuMaaheimo, Esa Pitk¨ anen, KatjaSaarela, andEsko Ukkonen DynamicBayesianNetworkandNonparametricRegression forNonlinearModelingofGeneNetworks fromTimeSeriesGeneExpressionData. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 SunYongKim, SeiyaImoto, andSatoru Miyano VIII Table ofContents DiscreteEventSimulationforaBetterUnderstanding ofMetaboliteChanneling-ASystemTheoreticApproach. . . . . . . . . . . . . . . . 114 Daniela Degenring,Mathias Rohl, ¨ andAdelinde M. Uhrmacher MathematicalModelingoftheIn'uenceofRKIP ontheERKSignalingPathway. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 Kwang-HyunCho, Sung-YoungShin, Hyun-WooKim,Olaf Wolkenhauer, Brian McFerran,and WalterKolch AMethodtoIdentifyEssentialEnzymesintheMetabolism: ApplicationtoEscherichia Coli. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 410 0$aLecture Notes in Computer Science,$x0302-9743 ;$v2602 606 $aLife sciences 606 $aComputers 606 $aAlgorithms 606 $aLogic, Symbolic and mathematical 606 $aComputer simulation 606 $aBioinformatics 606 $aLife Sciences, general$3https://scigraph.springernature.com/ontologies/product-market-codes/L00004 606 $aComputation by Abstract Devices$3https://scigraph.springernature.com/ontologies/product-market-codes/I16013 606 $aAlgorithm Analysis and Problem Complexity$3https://scigraph.springernature.com/ontologies/product-market-codes/I16021 606 $aMathematical Logic and Formal Languages$3https://scigraph.springernature.com/ontologies/product-market-codes/I16048 606 $aSimulation and Modeling$3https://scigraph.springernature.com/ontologies/product-market-codes/I19000 606 $aBioinformatics$3https://scigraph.springernature.com/ontologies/product-market-codes/L15001 615 0$aLife sciences. 615 0$aComputers. 615 0$aAlgorithms. 615 0$aLogic, Symbolic and mathematical. 615 0$aComputer simulation. 615 0$aBioinformatics. 615 14$aLife Sciences, general. 615 24$aComputation by Abstract Devices. 615 24$aAlgorithm Analysis and Problem Complexity. 615 24$aMathematical Logic and Formal Languages. 615 24$aSimulation and Modeling. 615 24$aBioinformatics. 676 $a572.8/0285 702 $aPriami$b Corrado$4edt$4http://id.loc.gov/vocabulary/relators/edt 712 12$aCMSB 2003 906 $aBOOK 912 $a9910143879403321 996 $aComputational Methods in Systems Biology$92907803 997 $aUNINA