Computational Methods in Systems Biology

First International Workshop, CMSB 2003 Rovereto, Italy, February 24–26, 2003 Proceedings

Editors:

ISBN: 978-3-540-00605-3 (Print) 978-3-540-36481-8 (Online)

Table of contents (31 chapters)

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  1. Invited Papers

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      Book Chapter

      Pages 1-3

      Cells as Computation

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      Pages 4-20

      Formal Modeling of C. elegans Development: A Scenario-Based Approach

  2. Regular Papers

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      Book Chapter

      Pages 21-34

      Causal π-Calculus for Biochemical Modelling

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      Pages 34-46

      Graphs for Core Molecular Biology

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      Pages 47-56

      Contribution of Computational Tree Logic to Biological Regulatory Networks: Example from Pseudomonas Aeruginosa

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      Pages 57-74

      Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing

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      Pages 75-87

      Multiscale Modeling of Alternative Splicing Regulation

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      Pages 88-103

      A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information

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      Pages 104-113

      Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data

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      Pages 114-126

      Discrete Event Simulation for a Better Understanding of Metabolite Channeling - A System Theoretic Approach

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      Pages 127-141

      Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway

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      Pages 142-148

      A Method to Identify Essential Enzymes in the Metabolism: Application to Escherichia Coli

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      Pages 149-162

      Symbolic Model Checking of Biochemical Networks

  3. Presentation Abstracts

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      Book Chapter

      Pages 163-163

      Coupled Oscillator Models for a Set of Communicating Cells

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      Book Chapter

      Pages 164-165

      Representing and Simulating Protein Functional Domains in Signal Transduction Using Maude

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      Pages 166-166

      A Core Modeling Language for the Working Molecular Biologist (Abstract)

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      Pages 167-167

      Integrating Simulation Packages via Systems Biology Mark-Up Language

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      Pages 168-169

      Recreating Biopathway Databases towards Simulation

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      Pages 170-170

      How to Synthesize an Optimized Genetic λ-Switching System? A System-Theoretic Approach Based on SQP

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      Book Chapter

      Pages 171-171

      Simulation Sudy of the TNFα Mediated NF-κB Signaling Pathway

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