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
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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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An Explicit Upper Bound for the Approximation Ratio of the Maximum Gene Regulatory Network Problem
1
Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis
9
Beta Binders for Biological Interactions
20
Biomimetic in Silico Devices
34
Building and Analysing an Integrative Model of HIV1 RNA Alternative Splicing
43
Introduction of Singular States
58
Processing of Complex Immunogenetics Knowledge
73
Model Checking Biological Systems Described Using Ambient Calculus
85
The Biochemical Abstract Machine BIOCHAM
172
Towards Reusing Model Components in Systems Biology
192
A VIrtual CEll
207
Biological Domain Identification Based in Codon Usage by Means of Rule and Tree Induction
221
Black Box Checking for Biochemical Networks
225
A Library for Comparing Formalisms and Models of Biological Systems
231
Combining StateBased and ScenarioBased Approaches in Modeling Biological Systems
236
Proposals for Development
242

Inference and Simulation Using Constraint Logic Programming
104
Modelling Metabolic Pathways Using Stochastic Logic ProgramsBased Ensemble Methods
119
Projective Brane Calculus
134
Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data
149
Spatial Modeling and Simulation of Diffusion in Nuclei of Living Cells
161
General Stochastic Hybrid Method for the Simulation of Chemical Reaction Processes in Cells
248
The Biodegradation Network a New Scenario for Computational Systems Biology Research
252
Interactions of Biological Membranes
257
Author Index
279
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