Computational Methods in Systems Biology: International Conference CMSB 2004, Paris, France, May 26-28, 2004, Revised Selected Papers (Lecture Notes in Computer Science, 3082)

The Computational Methods in Systems Biology (CMSB) workshop series was established in 2003 by Corrado Priami. The purpose of the workshop series is to help catalyze the convergence between computer scientists interested in language design, concurrency theory, software engineering or program verification, and physicists, mathematicians and biologists interested in the systems-level understanding of cellular processes. Systems biology was perceived as being increasingly in search of sophisticated modeling frameworks whether for representing and processing syst- level dynamics or for model analysis, comparison and refinement. One has here a clear-cut case of a must-explore field of application for the formal methods developed in computer science in the last decade. This proceedings consists of papers from the CMSB 2003 workshop. A good third of the 24 papers published here have a distinct formal methods origin; we take this as a confirmation that a synergy is building that will help solidify CMSB as a forum for cross-community exchange, thereby opening new theoretical avenues and making the field less of a potential application and more of a real one. Publication in Springer's new Lecture Notes in Bioinformatics (LNBI) offers particular visibility and impact, which we gratefully acknowledge. Our keynote speakers, Alfonso Valencia and Trey Ideker, gave challenging and somewhat humbling lectures: they made it clear that strong applications to systems biology are still some way ahead. We thank them all the more for accepting the invitation to speak and for the clarity and excitement they brought to the conference. Front Matter....Pages - An Explicit Upper Bound for the Approximation Ratio of the Maximum Gene Regulatory Network Problem....Pages 1-8 Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis....Pages 9-19 Beta Binders for Biological Interactions....Pages 20-33 Biomimetic in Silico Devices....Pages 34-42 Building and Analysing an Integrative Model of HIV-1 RNA Alternative Splicing....Pages 43-57 Graph-Based Modeling of Biological Regulatory Networks: Introduction of Singular States....Pages 58-72 IMGT-Choreography: Processing of Complex Immunogenetics Knowledge....Pages 73-84 Model Checking Biological Systems Described Using Ambient Calculus....Pages 85-103 Modeling the Molecular Network Controlling Adhesion Between Human Endothelial Cells: Inference and Simulation Using Constraint Logic Programming....Pages 104-118 Modelling Metabolic Pathways Using Stochastic Logic Programs-Based Ensemble Methods....Pages 119-133 Projective Brane Calculus....Pages 134-148 Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data....Pages 149-160 Spatial Modeling and Simulation of Diffusion in Nuclei of Living Cells....Pages 161-171 The Biochemical Abstract Machine BIOCHAM....Pages 172-191 Towards Reusing Model Components in Systems Biology....Pages 192-206 VICE: A VIrtual CEll....Pages 207-220 Biological Domain Identification Based in Codon Usage by Means of Rule and Tree Induction....Pages 221-224 Black Box Checking for Biochemical Networks....Pages 225-230 CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems....Pages 231-235 Combining State-Based and Scenario-Based Approaches in Modeling Biological Systems....Pages 236-241 Developing SBML Beyond Level 2: Proposals for Development....Pages 242-247 General Stochastic Hybrid Method for the Simulation of Chemical Reaction Processes in Cells....Pages 248-251 The Biodegradation Network, a New Scenario for Computational Systems Biology Research....Pages 252-256 Brane Calculi....Pages 257-278 Back Matter....Pages -

This book constitutes the thoroughly refereed postproceedings of the International Conference on Computational Methods in Systems Biology, CMSB 2004, held in Paris, France in May 2004.

The 16 revised full papers and 7 revised short papers presented together with an invited paper went through two rounds of reviewing, selection and revision. The papers present a variety of techniques from computer science, such as language design, concurrency theory, software engineering, and formal methods, for biologists, physicists, and mathematicians interested in the systems-level understanding of cellular processes.