Computational Methods in Systems Biology: First International Workshop, CMSB 2003, Rovereto, Italy, February 24-26, 2003 : ProceedingsSpringer Science & Business Media, 07.02.2003 - 214 Seiten 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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . |
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 |
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Computational Methods in Systems Biology: First International Workshop, CMSB ... Corrado Priami Eingeschränkte Leseprobe - 2003 |
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abstract activity algorithm analysis approach automaton behavior Berlin Heidelberg 2003 biochemical biological systems biologists bisimulation calculus causal cell cycle cellular CMSB complex components Computer Science concurrent constraint programming databases defined described differential equations domain dynamic Bayesian network enzymes ERK-PP example experimental experiments fluxes formal formula framework function gene expression gene expression data gene network genetic Genome glycolysis graph graphic hybrid automata hybrid automaton initial interaction interface isotopomer distributions kinase labels language linear LNCS LSCs maps metabolic network metabolite method microarray model checking modeling and simulation molecular molecules network and nonparametric nonparametric regression NuSMV parameter estimation Petri nets phase phosphorylation Priami processes production properties proteins qualitative quantitative reactants reaction reduction semantics regulation represent representation RKIP rules S-system sequence set of traces signaling pathway specific Springer-Verlag Berlin Heidelberg stochastic structure systems biology temporal logic tion transition values variables vector vulval