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ODE Analysis of Biological Systems

  • Chapter
Formal Methods for Dynamical Systems (SFM 2013)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 7938))

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.

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Authors and Affiliations

  1. Computational Biomodeling Laboratory, Turku Centre for Computer Science, Åbo Akademi University, Turku, Finland

    Diana-Elena Gratie, Bogdan Iancu & Ion Petre

Authors
  1. Diana-Elena Gratie
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  2. Bogdan Iancu
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  3. Ion Petre
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Editor information

Editors and Affiliations

  1. Dipartimento di Scienze di Base e Fondamenti, Università di Urbino "Carlo Bo", , ,, Piazza della Repubblica 13, 61029, Urbino, Italy

    Marco Bernardo

  2. Department of Mathematics and Computer Science, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ, Eindhoven, The Netherlands

    Erik de Vink

  3. Dipartimento di Informatica,, Università di Verona, Ca’ Vignal 2, Strada le Grazie 15, 37134, Verona, Italy

    Alessandra Di Pierro

  4. Department of Computing, Imperial College London, Huxley Building,180 Queen’s Gate, SW7 2BZ, London, UK

    Herbert Wiklicky

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Gratie, DE., Iancu, B., Petre, I. (2013). ODE Analysis of Biological Systems. In: Bernardo, M., de Vink, E., Di Pierro, A., Wiklicky, H. (eds) Formal Methods for Dynamical Systems. SFM 2013. Lecture Notes in Computer Science, vol 7938. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38874-3_2

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  • DOI: https://doi.org/10.1007/978-3-642-38874-3_2

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-38873-6

  • Online ISBN: 978-3-642-38874-3

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