Computational Methods in Systems Biology: International Conference CMSB 2004, Paris, France, May 26-28, 2004, Revised Selected Papers

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Vincent Danos, Vincent Schachter
Springer Science & Business Media, 24.03.2005 - 282 Seiten
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.
 

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Inhalt

Long Papers
1
Beta Binders for Biological Interactions
20
Biomimetic in Silico Devices
34
Introduction
58
Processing of Complex Immunogenetics Knowledge
73
Modeling the Molecular Network Controlling Adhesion Between Human
104
Modelling Metabolic Pathways Using Stochastic Logic ProgramsBased
119
Projective Brane Calculus
134
The Biochemical Abstract Machine BIOCHAM
172
Towards Reusing Model Components in Systems Biolog
192
A VIrtual CEll
207
Short Papers
221
Combining StateBased and ScenarioBased Approaches in Modeling
236
Proposals for Development
242
General Stochastic Hybrid Method for the Simulation of Chemical Reaction
248
Invited Contributions
257

Residual Bootstrapping and Median Filtering for Robust Estimation of Gene
149
Spatial Modeling and Simulation of Diffusion in Nuclei of Living Cells
161

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