Computational Methods in Systems Biology: First International Workshop, CMSB 2003, Rovereto, Italy, February 24-26, 2003 : Proceedings

Cover
Springer Science & Business Media, 07.02.2003 - 214 Seiten
0 Rezensionen
Molecularbiologyhasuntilnowmainlyfocussedonindividualmolecules,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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
 

Was andere dazu sagen - Rezension schreiben

Es wurden keine Rezensionen gefunden.

Inhalt

Cells as Computation
1
A ScenarioBased Approach
4
Causal π Calculus for Biochemical Modelling
21
Graphs for Core Molecular Biology
34
Example from Pseudomonas Aeruginosa
47
Bisimulation and Collapsing
57
Multiscale Modeling of Alternative Splicing Regulation
75
A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information
88
Recreating Biopathway Databases towards Simulation
168
How to Synthesize an Optimized Genetic λ Switching System? A SystemTheoretic Approach Based on SQP
170
Simulation Sudy of the TNFα Mediated NF κB Signaling Pathway
171
Detection and Analysis of Unexpected State Components in Biological Systems
172
Model Validation of Biological Pathways Using Petri Nets Demonstrated for Apoptosis
173
An Overview of Data Models for the Analysis of Biochemical Pathways
174
Discrete Event Systems and ClientServer Model for Signaling Mechanisms
175
Enhanced Operational Semantics in Systems Biology
178

Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data
104
Discrete Event Simulation for a Better Understanding of Metabolite Channeling A System Theoretic Approach
114
Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway
127
Application to Escherichia Coli
142
Symbolic Model Checking of Biochemical Networks
149
Coupled Oscillator Models for a Set of Communicating Cells
163
Representing and Simulating Protein Functional Domains in Signal Transduction Using Maude
164
A Core Modeling Language for the Working Molecular Biologist Abstract
166
Integrating Simulation Packages via Systems Biology MarkUp Language
167
Issues in Computational Methods for Functional Genomics and Systems Biology
182
Integrating Biological Process Modelling with Gene Expression Data and Ontologies for Functional Genomics Position Paper
187
Computer Simulation of Protocells
194
How to Solve Semantic Puzzles of Systems Biology
198
Evolution as Design Engineer
202
Inference Modeling and Simulation of Gene Networks
207
Author Index
212
Urheberrecht

Andere Ausgaben - Alle anzeigen

Häufige Begriffe und Wortgruppen

Bibliografische Informationen