Modelling biochemical pathways through enhanced π-calculus

  • Authors:
  • M. Curti;P. Degano;C. Priami;C. T. Baldari

  • Affiliations:
  • Dipartimento di Informatiea, Università di Pisa, Via Filippo Buonarroti, 2, I-56127 Pisa, Italy and Dipartimento di Informatica, Università di Pisa, Via Sommarive, 14, Povo, TN I-38050, ...;Dipartimento di Informatiea, Università di Pisa, Via Filippo Buonarroti, 2, I-56127 Pisa, Italy;Dipartimento di Informatica e Telecomunicazioni, Università di Trento, Via Sommarive, 14, I-38050 Povo, TN, Italy;Dipartimento di Biologia Evolutiva, Università di Siena, Via Mattioli, 4, I-53100 Siena, Italy

  • Venue:
  • Theoretical Computer Science - Special issue: Computational systems biology
  • Year:
  • 2004

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Abstract

We use the π-calculus to model the evolution of biochemical systems, taking advantage of their similarities with global computation applications. First, we present a reduction semantics for the π-calculus from which causality and concurrency can be mechanically derived. We prove that our semantics agrees with the causal definitions presented in the literature. We also extend our semantics to model biological compartments. Then, we show the applicability of our proposal on a couple of biological examples.