A compositional approach to the stochastic dynamics of gene networks

  • Authors:

  • Ralf Blossey;Luca Cardelli;Andrew Phillips

  • Affiliations:

  • Interdisciplinary Research Institute, Villeneuve d'Ascq, France;Microsoft Research, Cambridge, United Kingdom;Microsoft Research, Cambridge, United Kingdom

  • Venue:
  • Transactions on Computational Systems Biology IV
  • Year:
  • 2006

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Abstract

We propose a compositional approach to the dynamics of gene regu-latory networks based on the stochastic π-calculus, and develop a representation of gene network elements which can be used to build complex circuits in a transparent and efficient way. To demonstrate the power of the approach we apply it to several artificial networks, such as the repressilator and combinatorial gene circuits first studied in Combinatorial Synthesis of Genetic Networks [1]. For two examples of the latter systems, we point out how the topology of the circuits and the interplay of the stochastic gate interactions influence the circuit behavior. Our approach may be useful for the testing of biological mechanisms proposed to explain the experimentally observed circuit dynamics.