This book constitutes the refereed proceedings of the International Workshop on Computational Methods in Systems Biology, CMSB 2003, held in Rovereto, Italy, in February 2003.
The 11 revised full papers presented together with 2 invited papers, 7 position papers, and 11 abstracts were carefully reviewed and selected from 30 submissions. Among the topics addressed are modeling languages for systems biology, concurrency in biological systems, constraint programming, logical methods in systems biology, formal methods for the analysis of biomolecular systems, quantitative analysis of biomolecular systems, and simulation and modeling techniques for systems biology.
Author(s): Amitai Regev, Ehud Shapiro (auth.), Corrado Priami (eds.)
Series: Lecture Notes in Computer Science 2602
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2003
Language: English
Pages: 214
Tags: Computation by Abstract Devices; Algorithm Analysis and Problem Complexity; Mathematical Logic and Formal Languages; Simulation and Modeling; Bioinformatics; Evolutionary Biology
Cells as Computation....Pages 1-3
Formal Modeling of C. elegans Development: A Scenario-Based Approach....Pages 4-20
Causal π-Calculus for Biochemical Modelling....Pages 21-34
Graphs for Core Molecular Biology....Pages 34-46
Contribution of Computational Tree Logic to Biological Regulatory Networks: Example from Pseudomonas Aeruginosa....Pages 47-56
Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing....Pages 57-74
Multiscale Modeling of Alternative Splicing Regulation....Pages 75-87
A Method for Estimating Metabolic Fluxes from Incomplete Isotopomer Information....Pages 88-103
Dynamic Bayesian Network and Nonparametric Regression for Nonlinear Modeling of Gene Networks from Time Series Gene Expression Data....Pages 104-113
Discrete Event Simulation for a Better Understanding of Metabolite Channeling - A System Theoretic Approach....Pages 114-126
Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway....Pages 127-141
A Method to Identify Essential Enzymes in the Metabolism: Application to Escherichia Coli ....Pages 142-148
Symbolic Model Checking of Biochemical Networks....Pages 149-162
Coupled Oscillator Models for a Set of Communicating Cells....Pages 163-163
Representing and Simulating Protein Functional Domains in Signal Transduction Using Maude....Pages 164-165
A Core Modeling Language for the Working Molecular Biologist (Abstract)....Pages 166-166
Integrating Simulation Packages via Systems Biology Mark-Up Language....Pages 167-167
Recreating Biopathway Databases towards Simulation....Pages 168-169
How to Synthesize an Optimized Genetic λ-Switching System? A System-Theoretic Approach Based on SQP....Pages 170-170
Simulation Sudy of the TNFα Mediated NF-κB Signaling Pathway....Pages 171-171
Detection and Analysis of Unexpected State Components in Biological Systems....Pages 172-172
Model Validation of Biological Pathways Using Petri Nets - Demonstrated for Apoptosis....Pages 173-173
An Overview of Data Models for the Analysis of Biochemical Pathways....Pages 174-174
Discrete Event Systems and Client-Server Model for Signaling Mechanisms....Pages 175-177
Enhanced Operational Semantics in Systems Biology....Pages 178-181
Issues in Computational Methods for Functional Genomics and Systems Biology....Pages 182-186
Integrating Biological Process Modelling with Gene Expression Data and Ontologies for Functional Genomics (Position Paper)....Pages 187-193
Computer Simulation of Protocells....Pages 194-197
How to Solve Semantic Puzzles of Systems Biology....Pages 198-201
Evolution as Design Engineer....Pages 202-206
Inference, Modeling and Simulation of Gene Networks....Pages 207-211
