Lumping BlenX

Chapter 1 Introduction A peculiarity of scientific understanding is the representation of every natu- ral phenomenon with a suitable model and an appropriate abstraction. An abstraction reduces an observable phenomenon by maintaining its essential properties and ignoring the others. In the field of molecular biology, many types of abstractions have acquired widespread acceptance, such as, for ex- ample, “DNA as string” (to see a sequence of nucleotides in a filament DNA as a string composed only of the letters A, C, G and T, which represent the four different kinds of nucleotides) and “protein-as-three-dimensional- labelled-graph”. In the last few years, a new successful abstraction has been found to represent complex biological systems: “cells as computation” [27]. This new type of abstraction has given rise to the fields of computational and systems biology, whose principal aim is to model, simulate and ana- lyse complex biological systems by describing their behaviour in terms of the interactions between their components. For this purpose, some com- puter science theories, in particular process calculi and visual formalisms such as the pi-calculus [15, 14, 28], Petri Nets [16] and Statecharts [9], orig- inally developed to represent the behaviour of interacting systems (such as distributed and mobile systems), are now being adapted to model the inter- actions among biological entities [23]. The approach we are interested in is based on a variant of the process cal- culus Beta-binders [19, 20, 4, 26, 24], which constitutes an adaptation of pi-calculus to the applicative domain of life sciences. In this calculus, en- tities are represented by boxes with an internal process that contains the information that drives the behaviour of the box and some binders that permit the interaction with other biological components. The novelty of the calculus resides in the new form of interaction that these binders can guarantee. Indeed, differently from other process calculi, in which commu- nication is based on the complementarity of interacting components, the communication between binders of different boxes is based on the notion of compatibility (or affinity).