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ODE analysis of biological systems

Diana-Elena Gratie, Bogdan Iancu, Ion Petre, ODE analysis of biological systems. In: Marco Bernardo, Erik de Vink, Alessandra Di Pierro, Herbert Wiklicky (Eds.), Formal Methods for Dynamical Systems, Lecture Notes in Computer Science 7938, 29–62, Springer, 2013.

Abstract:

This chapter aims to introduce some of the basics of modeling with ODEs in biology. We focus on computational, numerical techniques, rather than on symbolic ones. We restrict our attention to reaction-based models, where the biological interactions are mechanistically described in terms of reactions, reactants and products. We discuss how to build the ODE model associated to a reaction-based model; how to fit it to experimental data and estimate the quality of its fit; how to calculate its steady state(s), mass conservation relations, and its sensitivity coefficients. We apply some of these techniques to a model for the heat shock response in eukaryotes.

BibTeX entry:

@INBOOK{cGrIaPe13a,
  title = {ODE analysis of biological systems},
  booktitle = {Formal Methods for Dynamical Systems},
  author = {Gratie, Diana-Elena and Iancu, Bogdan and Petre, Ion},
  volume = {7938},
  series = {Lecture Notes in Computer Science},
  editor = {Bernardo, Marco and de Vink, Erik and Di Pierro, Alessandra and Wiklicky, Herbert},
  publisher = {Springer},
  pages = {29–62},
  year = {2013},
  keywords = {Biomodeling, reaction-based models, ODE-based models, ODE analysis, parameter estimation, model identifiability, model refinement, heat shock response.},
}

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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