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Programming Languages with Applications to Biology and Security pp 183–201Cite as

A Declarative View of Signaling Pathways

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9465))

Abstract

Due to the inherent limitations of wet-lab techniques, the experimental data regarding cellular signaling pathways often consider single pathways or a small subset of them. We propose a methodology for composing signaling pathways data in a coherent framework. Our method consists in specifying the signaling pathway as a computationally executable model. We rely on the timed concurrent constraint language ntcc to represent the system in hand as a set of stoichiometric-like equations resembling the essential features of molecular interactions. The main advantages of our approach stem from the use of constraints (formulas in logic) and from modeling of discrete time clocks in ntcc. We can deal with partial information, representing the fact that several features of the biological system may be undetermined. We can explicitly represent the time needed for a reaction to occur. We model and simulate some well known cross-talking networks, such as the TNF\(\alpha \), the EGF and the insulin signaling pathways as well as their interactions.

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Notes

  1. 1.

    This is the more general case. It may happen that the consumption of a reactant does not lead to the production of other molecules or that, as in the case of enzymes, a molecule takes part to a reaction but is not consumed by it.

  2. 2.

    Proteins are composed by chains of aminoacyds. For biochemical reasons, aminoacyds are often called residues.

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Acknowledgements

We thank the anonymous referees for their helpful comments.

Author information

Authors and Affiliations

  1. Department of Theory and Bio-Systems, Max Planck Institute for Colloids and Interfaces, Potsdam, Germany

    Davide Chiarugi

  2. Dipartimento di Ingegneria dell’Informazione e Scienze Matematiche, Università di Siena, Siena, Italy

    Moreno Falaschi

  3. ECT, Universidade do Rio Grande do Norte, Natal, Brazil

    Carlos Olarte

  4. INRIA and LIX, École Polytechnique, Paris, France

    Catuscia Palamidessi

Authors
  1. Davide Chiarugi
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  2. Moreno Falaschi
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  3. Carlos Olarte
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  4. Catuscia Palamidessi
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Corresponding author

Correspondence to Moreno Falaschi .

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Editors and Affiliations

  1. Dipartimento di Informatica, Università di Pisa, Pisa, Italy

    Chiara Bodei

  2. Dipartimento di Informatica, Università di Pisa, Pisa, Italy

    Gianluigi Ferrari

  3. Università degli Studi di Trento, Povo, Italy

    Corrado Priami

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Chiarugi, D., Falaschi, M., Olarte, C., Palamidessi, C. (2015). A Declarative View of Signaling Pathways. In: Bodei, C., Ferrari, G., Priami, C. (eds) Programming Languages with Applications to Biology and Security. Lecture Notes in Computer Science(), vol 9465. Springer, Cham. https://doi.org/10.1007/978-3-319-25527-9_13

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  • DOI: https://doi.org/10.1007/978-3-319-25527-9_13

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