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Predictive Models for Cellular Signaling Networks

  • Dagmar IberEmail author
  • Georgios Fengos
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 880)

Abstract

This chapter provides an introduction to the formulation and analysis of differential-equation-based models for biological regulatory networks. In the first part, we discuss basic reaction types and the use of mass action kinetics and of simplifying approximations in the development of models for biological signaling. In the second part we introduce phase plane and linear stability analysis to evaluate the time evolution and identify the long-term attractors of dynamic systems. We then discuss the use of bifurcation diagrams to evaluate the parameter dependency of qualitative network behaviors (i.e., the emergence of oscillations or switches), and we give measures for the sensitivity and robustness of the signaling output.

Key words

Mathematical modeling ODE models Signaling models 

Notes

Acknowledgments

We thank members of the Iber group for the critical reading of the manuscript. This work was financially supported by SystemsX, the Swiss Initiative for Systems Biology, with an iPhD grant and an RTD grant through the InfectX project.

References

  1.  1.
    Murray JD (2003) Mathematical biology. Springer, New YorkGoogle Scholar
  2.  2.
    Keener J, Sneyd J (2001) Math PhysiolGoogle Scholar
  3.  3.
    Behar M, Hao N, Dohlman HG, Elston TC (2007) Mathematical and computational analysis of adaptation via feedback inhibition in signal transduction pathways. Biophys J 93(3):806–821PubMedCrossRefGoogle Scholar
  4.  4.
    Ma W, Trusina A, El-Samad H, Lim WA, Tang C (2009) Defining network topologies that can achieve biochemical adaptation. Cell 138(4):760–773PubMedCrossRefGoogle Scholar
  5.  5.
    Novák B, Tyson JJ (2008) Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 9(12):981–991PubMedCrossRefGoogle Scholar
  6.  6.
    Tyson JJ, Chen KC, Novak B (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15(2):221–231PubMedCrossRefGoogle Scholar
  7.  7.
    Kauffman SA (1993) The origins of order: self organization and selection in evolution. Oxford University Press, OxfordGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Biosystems, Science, and Engineering (D-BSSE)ETH ZurichBaselSwitzerland

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