Formal Modeling in Systems Biology: an Approach from Theoretical Computer Science

Cell Biology, the study of the morphological and functional organization of cells, is an established field in biochemical research. Computer Science can provide biologists with models able to describe complex systems such as cells. This approach belongs to the new research field called Systems Biology. Many formalisms developed to model interactive systems have been applied to Biology. Formal models avoid ambiguity, that is often a problem of the notations used by biologists. Moreover, they allow the development of simulators and the verification of properties by means of tools that are widely used in other application fields of Computer Science, but unknown to biologists. The aim of this work is to study a new formalism, the Calculus of Looping Sequences, with a simple notation and able to describe systems at different abstraction levels. Formal analysis and stochastic simulation tools are developed and applied to examples of real biological systems. This book is addressed to computer scientists interested either in bioinformatics or in formal methods. It can be used by biologists as an introduction to the application of Theoretical Computer Science means to biological systems.