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From a Biological Hypothesis to the Construction of a Mathematical Model

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In Silico Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1021))

Abstract

Mathematical models serve to explain complex biological phenomena and provide predictions that can be tested experimentally. They can provide plausible scenarios of a complex biological behavior when intuition is not sufficient anymore. The process from a biological hypothesis to a mathematical model might be challenging for biologists that are not familiar with mathematical modeling.

In this chapter we discuss a possible workflow that describes the steps to be taken starting from a biological hypothesis on a biochemical cellular mechanism to the construction of a mathematical model using the appropriate formalism. An important part of this workflow is formalization of biological knowledge, which can be facilitated by existing tools and standards developed by the systems biology community.

This chapter aims at introducing modeling to experts in molecular biology that would like to convert their hypotheses into mathematical models.

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Acknowledgements

We are grateful for receiving funding from the European Union’s Seventh Framework Programme (FP7/2007-2013) under grant agreement n°259348. DC, IK, EB, AZ, and LC are members of the team “Computational Systems Biology of Cancer” Equipe labellisée par la Ligue Nationale Contre le Cancer. We would also like to thank Nicolas Le Novère for discussions on different types of diagrams and for providing Fig. 1.

Author information

Authors and Affiliations

  1. Institut Curie, Paris, France

    David Cohen, Inna Kuperstein, Emmanuel Barillot, Andrei Zinovyev & Laurence Calzone

  2. INSERM, U900, Paris, France

    David Cohen, Inna Kuperstein, Emmanuel Barillot, Andrei Zinovyev & Laurence Calzone

  3. Mines ParisTech, Fontainebleau, France

    David Cohen, Inna Kuperstein, Emmanuel Barillot, Andrei Zinovyev & Laurence Calzone

Authors
  1. David Cohen
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  2. Inna Kuperstein
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  3. Emmanuel Barillot
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  4. Andrei Zinovyev
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  5. Laurence Calzone
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Editor information

Editors and Affiliations

  1. The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom

    Maria Victoria Schneider

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Cohen, D., Kuperstein, I., Barillot, E., Zinovyev, A., Calzone, L. (2013). From a Biological Hypothesis to the Construction of a Mathematical Model. In: Schneider, M. (eds) In Silico Systems Biology. Methods in Molecular Biology, vol 1021. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-450-0_6

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  • DOI: https://doi.org/10.1007/978-1-62703-450-0_6

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-449-4

  • Online ISBN: 978-1-62703-450-0

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