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Modeling in Systems Biology pp 3–18Cite as

Introduction

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Part of the book series: Computational Biology ((COBO,volume 16))

Abstract

This chapter gives a general introduction into the field of systems biology and the motivation for using Petri nets in this field. We consider modeling processes in the context of biological modeling approaches providing different examples. Starting from a general description of the purpose of a model and the modeling process, we cover the range from qualitative to quantitative modeling. We compile different modeling techniques at different abstraction levels, for example, at discrete, stochastic, and continuous levels. In this context, we introduce Petri nets and give the motivation for using Petri nets in particular for modeling biochemical systems. We describe the first applications of Petri nets in biology and give a brief overview of the progress made so far. Furthermore, we discuss the main public data resources for systems biology, giving an overview of microarray data repositories, protein–protein interaction databases, and pathway databases. Finally, we describe methods and tools for the visualization of biochemical systems and Petri net models.

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Authors and Affiliations

  1. Institute of Computer Science, Martin Luther University Halle-Wittenberg, Von Seckendorff Platz 1, 06120, Halle, Germany

    Falk Schreiber

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  1. Ina Koch
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  2. Falk Schreiber
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Correspondence to Ina Koch .

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Editors and Affiliations

  1. Institute for Computer Science, J.W. Goethe University Frankfurt, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany

    Ina Koch

  2. Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin, 10099, Germany

    Wolfgang Reisig

  3. Institute of Computer Science, Martin Luther Univ. Halle-Wittenberg, Von Seckendorff Platz 1, Halle, 06120, Germany

    Falk Schreiber

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Koch, I., Schreiber, F. (2011). Introduction. In: Koch, I., Reisig, W., Schreiber, F. (eds) Modeling in Systems Biology. Computational Biology, vol 16. Springer, London. https://doi.org/10.1007/978-1-84996-474-6_1

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  • DOI: https://doi.org/10.1007/978-1-84996-474-6_1

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