Dynamic Biological Modelling: a language-based approach

Abstract

Systems biology investigates the interactions and relationships among the components of biological systems to understand how they globally work. The metaphor “cells as computations”, introduced by Regev and Shapiro, opened the realm of biological modelling to concurrent languages. Their peculiar characteristics led to the development of many different bio-inspired languages that allow to abstract and study specific aspects of biological systems. In this thesis we present a language based on the process calculi paradigm and specifically designed to account for the complexity of signalling networks. We explore a new design space for bio-inspired languages, with the aim to capture in an intuitive and simple way the fundamental mechanisms governing protein-protein interactions. We develop a formal framework for modelling, simulating and analysing biological systems. An implementation of the framework is provided to enable in-silico experimentation.