Computational Methods in Systems Biology

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.

Inhalt

Long Papers.- An Explicit Upper Bound for the Approximation Ratio of the Maximum Gene Regulatory Network Problem.- Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis.- Beta Binders for Biological Interactions.- Biomimetic in Silico Devices.- Building and Analysing an Integrative Model of HIV-1 RNA Alternative Splicing.- Graph-Based Modeling of Biological Regulatory Networks: Introduction of Singular States.- IMGT-Choreography: Processing of Complex Immunogenetics Knowledge.- Model Checking Biological Systems Described Using Ambient Calculus.- Modeling the Molecular Network Controlling Adhesion Between Human Endothelial Cells: Inference and Simulation Using Constraint Logic Programming.- Modelling Metabolic Pathways Using Stochastic Logic Programs-Based Ensemble Methods.- Projective Brane Calculus.- Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data.- Spatial Modeling and Simulation of Diffusion in Nuclei of Living Cells.- The Biochemical Abstract Machine BIOCHAM.- Towards Reusing Model Components in Systems Biology.- VICE: A VIrtual CEll.- Short Papers.- Biological Domain Identification Based in Codon Usage by Means of Rule and Tree Induction.- Black Box Checking for Biochemical Networks.- CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems.- Combining State-Based and Scenario-Based Approaches in Modeling Biological Systems.- Developing SBML Beyond Level 2: Proposals for Development.- General Stochastic Hybrid Method for the Simulation of Chemical Reaction Processes in Cells.- The Biodegradation Network, a New Scenario for Computational Systems Biology Research.- Invited Contributions.- Brane Calculi.