Computational Methods in Systems Biology

6th International Conference CMSB 2008, Rostock, Germany, October 12-15, 2008. Proceedings

  • Monika Heiner
  • Adelinde M. Uhrmacher
Conference proceedings CMSB 2008
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5307)

Table of contents

  1. Front Matter
    PDF
  2. Qualitative Modeling and Simulation of Bacterial Regulatory Networks
    Hidde de Jong
    Pages 1-1
  3. Integrated Analysis from Abstract Stochastic Process Algebra Models
    Jane Hillston, Federica Ciocchetta, Adam Duguid, Stephen Gilmore
    Pages 2-4
  4. An Exact Brownian Dynamics Method for Cell Simulation
    Koichi Takahashi
    Pages 5-6
  5. Multiscale Modelling of Neuronal Signalling
    Nicolas Le Novère
    Pages 7-7
  6. Systems Biology of Halophilic Archaea
    Dieter Oesterhelt
    Pages 8-8
  7. A Partial Granger Causality Approach to Explore Causal Networks Derived From Multi-parameter Data
    Ritesh Krishna, Shuixia Guo
    Pages 9-27
  8. Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe
    Alexander Ullrich, Christoph Flamm
    Pages 28-43
  9. Component-Based Modelling of RNA Structure Folding
    Carsten Maus
    Pages 44-62
  10. A Language for Biochemical Systems
    Michael Pedersen, Gordon Plotkin
    Pages 63-82
  11. The Attributed Pi Calculus
    Mathias John, Cédric Lhoussaine, Joachim Niehren, Adelinde M. Uhrmacher
    Pages 83-102
  12. The Continuous π-Calculus: A Process Algebra for Biochemical Modelling
    Marek Kwiatkowski, Ian Stark
    Pages 103-122
  13. Automatic Complexity Analysis and Model Reduction of Nonlinear Biochemical Systems
    Dirk Lebiedz, Dominik Skanda, Marc Fein
    Pages 123-140
  14. Formal Analysis of Abnormal Excitation in Cardiac Tissue
    Pei Ye, Radu Grosu, Scott A. Smolka, Emilia Entcheva
    Pages 141-155
  15. The Distribution of Mutational Effects on Fitness in a Simple Circadian Clock
    Laurence Loewe, Jane Hillston
    Pages 156-175
  16. SED-ML – An XML Format for the Implementation of the MIASE Guidelines
    Dagmar Köhn, Nicolas Le Novère
    Pages 176-190
  17. On Parallel Stochastic Simulation of Diffusive Systems
    Lorenzo Dematté, Tommaso Mazza
    Pages 191-210
  18. Large-Scale Design Space Exploration of SSA
    Matthias Jeschke, Roland Ewald
    Pages 211-230
  19. Statistical Model Checking in BioLab: Applications to the Automated Analysis of T-Cell Receptor Signaling Pathway
    Edmund M. Clarke, James R. Faeder, Christopher J. Langmead, Leonard A. Harris, Sumit Kumar Jha, Axel Legay
    Pages 231-250
  20. On a Continuous Degree of Satisfaction of Temporal Logic Formulae with Applications to Systems Biology
    Aurélien Rizk, Grégory Batt, François Fages, Sylvain Soliman
    Pages 251-268

About these proceedings

Introduction

This book constitutes the refereed proceedings of the 6th International Conference on Computational Methods in Systems Biology, CMSB 2008, held in Rostock, Germany, in September 2008.

The 21 revised full papers presented together with the summaries of 5 invited papers were carefully reviewed and selected from more than 60 submissions. The papers cover theoretical or applied contributions that are motivated by a biological question focusing on modeling approaches, including process algebra, simulation approaches, analysis methods, in particular model checking and flux analysis, and case studies.

Keywords

3D modeling agent based modeling aggregation biochemical reactions bioinformatics compositional analysis distributed simulation evolution formal methods markov chain metabolism model checking modeling modularity parallel algorithms

Editors and affiliations

  • Monika Heiner
    • 1
  • Adelinde M. Uhrmacher
    • 2
  1. 1.Department of Computer ScienceBrandenburg University of TechnologyCottbusGermany
  2. 2.University of RostockRostockGermany

Bibliographic information

  • DOI 10.1007/978-3-540-88562-7
  • Copyright Information Springer Berlin Heidelberg 2008
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-540-88561-0
  • Online ISBN 978-3-540-88562-7
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349