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Computation in Cells and Tissues

Perspectives and Tools of Thought

  • Book
  • © 2004

Overview

Editors:
  1. Ray Paton
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  2. Hamid Bolouri

    1. Institute for Systems Biology, Seattle, USA

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  3. Mike Holcombe

    1. Department of Computer Science, University of Sheffield, Sheffield, UK

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  4. J. Howard Parish

    1. School of Biochemestry and Molecular Biology, University of Leeds, Leeds, UK

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  5. Richard Tateson

    1. Future Technologies Group, Intelligent Systems Lab, BTexact Technologies, Ipswich, UK

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  • Deals with the growing interface between cellular systems, computational modelling and biologically inspired computing
  • Unique blend of topical contributions
  • Highly multidisciplinary but written for a general readership to understand
  • Contributions from biologists, computer scientists and mathematicians
  • Reflects recent/current trends and developments
  • Presents the state of the art in the emerging field of computation in cells and tissues
  • Includes supplementary material: sn.pub/extras

Part of the book series: Natural Computing Series (NCS)

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Table of contents (18 chapters)

  1. Front Matter

    Pages I-XV
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  2. CytoComputational Systems — Perspectives and Tools of Thought

    • R. Paton
    Pages 1-7

  3. Cells in Telecommunications

    • R. Tateson
    Pages 9-26

  4. Symbiogenesis as a Machine Learning Mechanism

    • L. Bull, A. Tomlinson
    Pages 27-50

  5. An Overview of Artificial Immune Systems

    • J. Timmis, T. Knight, L. N. de Castro, E. Hart
    Pages 51-91

  6. Embryonics and Immunotronics: Biologically Inspired Computer Science Systems

    • A. Tyrrell
    Pages 93-116

  7. Biomedical Applications of Micro and Nano Technologies

    • C. J. McNeil, K. J. Snowdon
    Pages 117-124

  8. Macromolecules, Genomes and Ourselves

    • S. B. Nagl, J. H. Parish, R. C. Paton, G. J. Warner
    Pages 125-148

  9. Models of Genetic Regulatory Networks

    • M. Schilstra, H. Bolouri
    Pages 149-159

  10. A Model of Bacterial Adaptability Based on Multiple Scales of Interaction : COSMIC

    • R. Gregory, R. Paton, J. Saunders, Q. H. Wu
    Pages 161-184

  11. Stochastic Computations in Neurons and Neural Networks

    • Jianfeng Feng
    Pages 185-210

  12. Spatial Patterning in Explicitly Cellular Environments: Activity-Regulated Juxtacrine Signalling

    • N. Monk
    Pages 211-225

  13. Modelling the GH Release System

    • D. J. MacGregor, G. Leng, D. Brown
    Pages 227-249

  14. Hierarchies of Machines

    • M. Holcombe
    Pages 251-268

  15. Models of Recombination in Ciliates

    • P. Sant, M. Amos
    Pages 269-276

  16. Developing Algebraic Models of Protein Signalling Agents

    • M. J. Fisher, G. Malcolm, R. C. Paton
    Pages 277-288

  17. Categorical Language and Hierarchical Models for Cell Systems

    • R. Brown, R. Paton, T. Porter
    Pages 289-303

  18. Mathematical Systems Biology: Genomic Cybernetics

    • O. Wolkenhauer, W. Kolch, K.-H. Cho
    Pages 305-325

  19. What Kinds of Natural Processes can be Regarded as Computations?

    • C. G. Johnson
    Pages 327-336

  20. Back Matter

    Pages 337-345
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Keywords

About this book

The field of biologically inspired computation has coexisted with mainstream computing since the 1930s, and the pioneers in this area include Warren McCulloch, Walter Pitts, Robert Rosen, Otto Schmitt, Alan Turing, John von Neumann and Norbert Wiener. Ideas arising out of studies of biology have permeated algorithmics, automata theory, artificial intelligence, graphics, information systems and software design. Within this context, the biomolecular, cellular and tissue levels of biological organisation have had a considerable inspirational impact on the development of computational ideas. Such innovations include neural computing, systolic arrays, genetic and immune algorithms, cellular automata, artificial tissues, DNA computing and protein memories. With the rapid growth in biological knowledge there remains a vast source of ideas yet to be tapped. This includes developments associated with biomolecular, genomic, enzymic, metabolic, signalling and developmental systems and the various impacts on distributed, adaptive, hybrid and emergent computation. This multidisciplinary book brings together a collection of chapters by biologists, computer scientists, engineers and mathematicians who were drawn together to examine the ways in which the interdisciplinary displacement of concepts and ideas could develop new insights into emerging computing paradigms. Funded by the UK Engineering and Physical Sciences Research Council (EPSRC), the CytoCom Network formally met on five occasions to examine and discuss common issues in biology and computing that could be exploited to develop emerging models of computation.

Reviews

From the reviews:

"This book provides a particularly rich source of insights into the future of computing, and of new notions of computation. This multi-disciplinary book brings together biologists, biochemists, bioinformaticians … who offer their insights into the paradigms emerging from modern biology. It contains 17 essays, for an audience of researchers working in biological information processing." (W. Richard Stark, Computing Reviews, February, 2005)

Editors and Affiliations

  • Institute for Systems Biology, Seattle, USA

    Hamid Bolouri

  • Department of Computer Science, University of Sheffield, Sheffield, UK

    Mike Holcombe

  • School of Biochemestry and Molecular Biology, University of Leeds, Leeds, UK

    J. Howard Parish

  • Future Technologies Group, Intelligent Systems Lab, BTexact Technologies, Ipswich, UK

    Richard Tateson

About the editors

Ray Paton trained originally as a biologist and for the last 12 years has worked in Computer Science. He is currently a Senior Lecturer in Dept Computer Science, University of Liverpool. He was the director of the CytoCom project on which this book is based.

Hamid Bolouri, PhD Microelectronics , Brunel Univ. 1990 Currently Professor of Computational Biology, Inst. for Systems Biology , Seattle, WA98103

Mike Holcombe is a Professor of Computer Science, University of Sheffield.

Howard Parish is a Senior Lecturer in the Biochemistry.

Richard Tateson has worked on nature-inspired computation at BTexact since 1997, applying ideas from cell biology, developmental biology and evolution to problems in telecommunications. Prior to that he was at Cambridge University doing a BA in biochemistry and a PhD in developmental biology.

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