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From a Biological Hypothesis to the Construction of a Mathematical Model

  • David Cohen
  • Inna Kuperstein
  • Emmanuel Barillot
  • Andrei Zinovyev
  • Laurence Calzone
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Network diagram Mathematical model ODE Boolean Formalism 

Notes

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.

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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • David Cohen
    • 1
    • 2
    • 3
  • Inna Kuperstein
    • 1
    • 2
    • 3
  • Emmanuel Barillot
    • 1
    • 2
    • 3
  • Andrei Zinovyev
    • 1
    • 2
    • 3
  • Laurence Calzone
    • 1
    • 2
    • 3
  1. 1.Institut CurieParisFrance
  2. 2.INSERM, U900ParisFrance
  3. 3.Mines ParisTechFontainebleauFrance

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