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Transactions on Computational Systems Biology XI

Computational Models for Cell Processes

  • Book
  • © 2009

Overview

Editors:
  1. Corrado Priami

    1. Centre for Computational and Systems Biology, The Microsoft Research - University of Trento, Povo, Italy

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  2. Ralph-Johan Back

    1. Department of Information Technologies, Åbo Akademi University, Turku, Finland

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    You can also search for this editor in PubMed   Google Scholar

  3. Ion Petre

    1. Computational Biomodelling Laboratory, Turku Center for Computer Science, Turku, Finland

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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 5750)

Part of the book sub series: Transactions on Computational Systems Biology (TCSB)

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Table of contents (13 chapters)

  1. Front Matter

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  2. Computational Models for Cell Processes

    1. Process Algebra Modelling Styles for Biomolecular Processes

      • Muffy Calder, Jane Hillston
      Pages 1-25

    2. Simple, Enhanced and Mutual Mobile Membranes

      • Bogdan Aman, Gabriel Ciobanu
      Pages 26-44

    3. Bio-PEPA with Events

      • Federica Ciocchetta
      Pages 45-68

    4. In Silico Modelling and Analysis of Ribosome Kinetics and aa-tRNA Competition

      • D. Bošnački, T. E. Pronk, E. P. de Vink
      Pages 69-89

    5. Qualitative and Quantitative Analysis of a Bio-PEPA Model of the Gp130/JAK/STAT Signalling Pathway

      • Maria Luisa Guerriero
      Pages 90-115

    6. Rule-Based Modelling and Model Perturbation

      • Vincent Danos, Jérôme Feret, Walter Fontana, Russ Harmer, Jean Krivine
      Pages 116-137

    7. Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments

      • Monika Heiner, Sebastian Lehrack, David Gilbert, Wolfgang Marwan
      Pages 138-163

    8. A Projective Brane Calculus with Activate, Bud and Mate as Primitive Actions

      • Maria Pamela C. David, Johnrob Y. Bantang, Eduardo R. Mendoza
      Pages 164-186

    9. Accepting Networks of Non-inserting Evolutionary Processors

      • Jürgen Dassow, Victor Mitrana
      Pages 187-199

    10. Discrete Modeling of Biochemical Signaling with Memory Enhancement

      • John Jack, Andrei Păun
      Pages 200-215

    11. Dynamical Systems and Stochastic Programming: To Ordinary Differential Equations and Back

      • Luca Bortolussi, Alberto Policriti
      Pages 216-267

    12. Computing Equilibrium Points of Genetic Regulatory Networks

      • Graziano Chesi
      Pages 268-282

    13. Code, Context, and Epigenetic Catalysis in Gene Expression

      • Rodrick Wallace, Deborah Wallace
      Pages 283-334

  3. Back Matter

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Keywords

About this book

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena.

This special issue on Computational Models for Cell Processes is based on a workshop with the same name that took place in Turku, Finland, on May 27, 2008. The accepted papers, which have passed through a separate peer-review process, span an interesting mix of approaches to systems biology, ranging from quantitative to qualitative techniques, from continuous to discrete mathematics, from deterministic to stochastic methods, and from computational models for biology to computing paradigms inspired by biology. Also included in this issue are three regular submissions dealing with the relationship between ODEs and stochastic concurrent constraint programming, with the equilibrium points of genetic regulatory networks, and with probability models describing how epigenetic context affects gene expression and organismal development.

Reviews

From the reviews:

“It is a multidisciplinary collection of research papers, by researchers, for researchers. The papers target specialists in particular formalisms. … papers were presented at a satellite workshop of the 15th International Symposium on Formal Methods at Turku, in 2008. The goal of the research is to supplement ‘wetlab’ science (in vitro or in vivo) by in silico or in numero studies. … In conclusion, this book is for specialists … .” (Richard Botting, ACM Computing Reviews, November, 2010)

Editors and Affiliations

  • Centre for Computational and Systems Biology, The Microsoft Research - University of Trento, Povo, Italy

    Corrado Priami

  • Department of Information Technologies, Åbo Akademi University, Turku, Finland

    Ralph-Johan Back

  • Computational Biomodelling Laboratory, Turku Center for Computer Science, Turku, Finland

    Ion Petre

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