Computational Methods in Systems Biology

1. Front Matter

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2. Long Papers

   1. An Explicit Upper Bound for the Approximation Ratio of the Maximum Gene Regulatory Network Problem

      • Sergio Pozzi, Gianluca Della Vedova, Giancarlo Mauri

      Pages 1-8

   2. Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis

      • Matthew D. Onsum, Adam P. Arkin

      Pages 9-19

   3. Beta Binders for Biological Interactions

      • Corrado Priami, Paola Quaglia

      Pages 20-33

   4. Biomimetic in Silico Devices

      • C. Anthony Hunt, Glen E. P. Ropella, Michael S. Roberts, Li Yan

      Pages 34-42

   5. Building and Analysing an Integrative Model of HIV-1 RNA Alternative Splicing

      • A. Bockmayr, A. Courtois, D. Eveillard, M. Vezain

      Pages 43-57

   6. Graph-Based Modeling of Biological Regulatory Networks: Introduction of Singular States

      • Adrien Richard, Jean-Paul Comet, Gilles Bernot

      Pages 58-72

   7. IMGT-Choreography: Processing of Complex Immunogenetics Knowledge

      • Denys Chaume, Véronique Giudicelli, Kora Combres, Chantal Ginestoux, Marie-Paule Lefranc

      Pages 73-84

   8. Model Checking Biological Systems Described Using Ambient Calculus

      • Radu Mardare, Corrado Priami, Paola Quaglia, Oleksandr Vagin

      Pages 85-103

   9. Modeling the Molecular Network Controlling Adhesion Between Human Endothelial Cells: Inference and Simulation Using Constraint Logic Programming

      • Eric Fanchon, Fabien Corblin, Laurent Trilling, Bastien Hermant, Danielle Gulino

      Pages 104-118

   10. Modelling Metabolic Pathways Using Stochastic Logic Programs-Based Ensemble Methods

       • Huma Lodhi, Stephen Muggleton

       Pages 119-133

   11. Projective Brane Calculus

       • Vincent Danos, Sylvain Pradalier

       Pages 134-148

   12. Residual Bootstrapping and Median Filtering for Robust Estimation of Gene Networks from Microarray Data

       • Seiya Imoto, Tomoyuki Higuchi, SunYong Kim, Euna Jeong, Satoru Miyano

       Pages 149-160

   13. Spatial Modeling and Simulation of Diffusion in Nuclei of Living Cells

       • Dietmar Volz, Martin Eigel, Chaitanya Athale, Peter Bastian, Harald Hermann, Constantin Kappel et al.

       Pages 161-171

   14. The Biochemical Abstract Machine BIOCHAM

       • Nathalie Chabrier-Rivier, François Fages, Sylvain Soliman

       Pages 172-191

   15. Towards Reusing Model Components in Systems Biology

       • Adelinde M. Uhrmacher, Daniela Degenring, Jens Lemcke, Mario Krahmer

       Pages 192-206

   16. VICE: A VIrtual CEll

       • D. Chiarugi, M. Curti, P. Degano, R. Marangoni

       Pages 207-220

3. Short Papers

   1. Biological Domain Identification Based in Codon Usage by Means of Rule and Tree Induction

      • Antonio Neme, Pedro Miramontes

      Pages 221-224

   2. Black Box Checking for Biochemical Networks

      • Dragan Bošnački

      Pages 225-230

   3. CMBSlib: A Library for Comparing Formalisms and Models of Biological Systems

      • Sylvain Soliman, François Fages

      Pages 231-235

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.

• Ensembl
• In silico
• Microarray
• Processing
• Simulation
• biochemical net
• bioinformatics
• computational systems biology
• concurrency
• formal methods
• logic
• microarray data analysis
• modeling
• natural computing
• object oriented design

• CNRS, Université Paris Diderot, France

  Vincent Danos

• CNRG Genoscope, Evry, France

  Vincent Schachter

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