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.
Author(s): Sergio Pozzi, Gianluca Della Vedova, Giancarlo Mauri (auth.), Vincent Danos, Vincent Schachter (eds.)
Series: Lecture Notes in Computer Science 3082 : Lecture Notes in Bioinformatics
Edition: 1
Publisher: Springer-Verlag Berlin Heidelberg
Year: 2005
Language: English
Pages: 282
Tags: Simulation and Modeling; Bioinformatics; Computer Appl. in Life Sciences; Software Engineering; Database Management; Computation by Abstract Devices
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 -
