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Biomodel Engineering – From Structure to Behavior

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Transactions on Computational Systems Biology XII

Part of the book series: Lecture Notes in Computer Science ((TCSB,volume 5945))

Abstract

Biomodel engineering is the science of designing, constructing and analyzing computational models of biological systems. It forms a systematic and powerful extension of earlier mathematical modeling approaches and has recently gained popularity in systems biology and synthetic biology. In this brief review for systems biologists and computational modelers, we introduce some of the basic concepts of successful biomodel engineering, illustrating them with examples from a variety of application domains, ranging from metabolic networks to cellular signaling cascades. We also present a more detailed outline of one of the major techniques of biomodel engineering – Petri net models – which provides a flexible and powerful tool for building, validating and exploring computational descriptions of biological systems.

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Author information

Authors and Affiliations

  1. Groningen Bioinformatics Centre, University of Groningen, Kerklaan 30, 9751, NN Haren, The Netherlands

    Rainer Breitling

  2. Bioinformatics Research Centre, University of Glasgow, Glasgow, G12 8QQ, UK

    Robin A. Donaldson & David R. Gilbert

  3. School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, UB8 3PH, UK

    David R. Gilbert

  4. Dept. of Computer Science, Brandenburg University of Technology at Cottbus, Postbox 10 13 44, D 03013, Cottbus, Germany

    Monika Heiner

Authors
  1. Rainer Breitling
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  2. Robin A. Donaldson
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  3. David R. Gilbert
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  4. Monika Heiner
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Editor information

Editors and Affiliations

  1. Centre for Computational and Systems Biology, The Microsoft Research - University of Trento, Piazza Manci, 17, 38050, Povo (TN), Italy

    Corrado Priami

  2. Groningen Bioinformatics, University of Groningen, Centre, Kerklaan 30, 9751 NN, Haren, The Netherlands

    Rainer Breitling

  3. School of Information Systems, Brunel University, Kingston Lane, UB8 3PH, Uxbridge, UK

    David Gilbert

  4. Computer Science Institute, Brandenburg University of Technology, Walther-Pauer-Str. 2, 03046, Cottbus, Germany

    Monika Heiner

  5. Institute of Computer Science, University of Rostock, Joachim-Jungius-Str.10, 18059, Rostock, Germany

    Adelinde M. Uhrmacher

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© 2010 Springer-Verlag Berlin Heidelberg

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Breitling, R., Donaldson, R.A., Gilbert, D.R., Heiner, M. (2010). Biomodel Engineering – From Structure to Behavior. In: Priami, C., Breitling, R., Gilbert, D., Heiner, M., Uhrmacher, A.M. (eds) Transactions on Computational Systems Biology XII. Lecture Notes in Computer Science(), vol 5945. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-11712-1_1

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  • DOI: https://doi.org/10.1007/978-3-642-11712-1_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-11711-4

  • Online ISBN: 978-3-642-11712-1

  • eBook Packages: Computer ScienceComputer Science (R0)

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