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Computational Modeling of Signal Transduction Networks: A Pedagogical Exposition

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Computational Modeling of Signaling Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 880))

Abstract

We give a pedagogical introduction to computational modeling of signal transduction networks, starting from explaining the representations of chemical reactions by differential equations via the law of mass action. We discuss elementary biochemical reactions such as Michaelis–Menten enzyme kinetics and cooperative binding, and show how these allow the representation of large networks as systems of differential equations. We discuss the importance of looking for simpler or reduced models, such as network motifs or dynamical motifs within the larger network, and describe methods to obtain qualitative behavior by bifurcation analysis, using freely available continuation software. We then discuss stochastic kinetics and show how to implement easy-to-use methods of rule-based modeling for stochastic simulations. We finally suggest some methods for comprehensive parameter sensitivity analysis, and discuss the insights that it could yield. Examples, including code to try out, are provided based on a paper that modeled Ras kinetics in thymocytes.

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Author information

Authors and Affiliations

  1. Chemical and Biological Engineering, School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA

    Ashok Prasad

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  1. Ashok Prasad
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Correspondence to Ashok Prasad .

Editor information

Editors and Affiliations

  1. Dept. Chemistry & Biochemistry, University of Colorado, Boulder, Boulder, 80309-0215, Colorado, USA

    Xuedong Liu

  2. Dept. Physics, University of Colorado, Boulder, Boulder, 80309, Colorado, USA

    Meredith D. Betterton

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© 2012 Springer Science+Business Media, LLC

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Prasad, A. (2012). Computational Modeling of Signal Transduction Networks: A Pedagogical Exposition. In: Liu, X., Betterton, M. (eds) Computational Modeling of Signaling Networks. Methods in Molecular Biology, vol 880. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-833-7_10

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  • DOI: https://doi.org/10.1007/978-1-61779-833-7_10

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-832-0

  • Online ISBN: 978-1-61779-833-7

  • eBook Packages: Springer Protocols

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