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Mathematical Modeling of Biomolecular Network Dynamics

  • Alexander V. Ratushny
  • Stephen A. Ramsey
  • John D. Aitchison
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 781)

Abstract

Mathematical and computational models have become indispensable tools for integrating and interpreting heterogeneous biological data, understanding fundamental principles of biological system functions, genera­ting reliable testable hypotheses, and identifying potential diagnostic markers and therapeutic targets. Thus, such tools are now routinely used in the theoretical and experimental systematic investigation of biological system dynamics. Here, we discuss model building as an essential part of the theoretical and experimental analysis of biomolecular network dynamics. Specifically, we describe a procedure for defining kinetic equations and parameters of biomolecular processes, and we illustrate the use of fractional activity functions for modeling gene expression regulation by single and multiple regulators. We further discuss the evaluation of model complexity and the selection of an optimal model based on information criteria. Finally, we discuss the critical roles of sensitivity, robustness analysis, and optimal experiment design in the model building cycle.

Key words

Biomolecular network Differential equation Dynamical system Inverse problem Mathematical model Systems biology 

Notes

Acknowledgments

This work was supported by the National Institutes of Health through grants from the National Institute of General Medical Sciences (R01-GM075152 and P50-GM076547), the National Technology Centers for Networks and Pathways (U54-RR022220), and the National Heart, Lung, and Blood Institute (K25-HL098807 to S.A.R).

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Alexander V. Ratushny
    • 1
  • Stephen A. Ramsey
    • 1
  • John D. Aitchison
    • 1
  1. 1.Institute for Systems BiologySeattleUSA

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