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Computational Methods in Systems Biology

International Conference CMSB 2004, Paris, France, May 26-28, 2004, Revised Selected Papers

  • Conference proceedings
  • © 2005

Overview

Editors:
  1. Vincent Danos

    1. CNRS, Université Paris Diderot, France

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    You can also search for this editor in PubMed   Google Scholar

  2. Vincent Schachter

    1. CNRG Genoscope, Evry, France

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    You can also search for this editor in PubMed   Google Scholar

Part of the book series: Lecture Notes in Computer Science (LNCS, volume 3082)

Part of the book sub series: Lecture Notes in Bioinformatics (LNBI)

Included in the following conference series:

Conference proceedings info: CMSB 2004.

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Table of contents (24 papers)

  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
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Other volumes

  1. Computational Methods in Systems Biology

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About this book

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.

Editors and Affiliations

  • CNRS, Université Paris Diderot, France

    Vincent Danos

  • CNRG Genoscope, Evry, France

    Vincent Schachter

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