A Formalism for the Description of Protein Interaction Dedicated to Jerzy Tiuryn on the Occasion of his 60th Birthday

Authors:
Roberto Barbuti;Andrea Maggiolo-Schettini;Angelo Troina;Mariangiola Dezani-Ciancaglini;Paolo Milazzo
Affiliations:
Dipartimento di Informatica, Università/ di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy. barbuti@di.unipi.it/;Dipartimento di Informatica, Università/ di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy. maggiolo@di.unipi.it;Dipartimento di Informatica, Università/ di Torino, Corso Svizzera 185, 10149 Torino, Italy. troina@di.unito.it;(Correspd.) Dipartimento di Informatica, Università/ di Torino, Corso Svizzera 185, 10149 Torino, Italy. dezani@di.unito.it;Dipartimento di Informatica, Università/ di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy. milazzo@di.unipi.it
Venue:
Fundamenta Informaticae - From Mathematical Beauty to the Truth of Nature: to Jerzy Tiuryn on his 60th Birthday
Year:
2010

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Abstract

The Calculus of Looping Sequences is a formalism for describing evolution of biological systems by means of term rewriting rules. We propose to enrich this calculus by labelling elements of sequences. Since two elements with the same label are considered to be linked, this allows us to represent protein interaction at the domain level. Well-formedness of terms are ensured by both a syntactic constraint and a type system: we discuss the differences between these approaches through the description of a biological system, namely the EGF pathway.