Process calculi for biological processes

Systems Biology is a research area devoted to de- veloping computational frameworks for modeling biologi- cal systems in a holistic fashion. Within this approach, the typical advantages of using computer systems and formal methodologies are applicable. Experiments can indeed be carried on in silico that turn out to be much quicker and less expensive than wet-lab experiments. This paper surveys a specific computational approach to Systems Biology, based on the so-called Process Calculi, a formalism for describing concurrent systems. After a gentle, intuitive introduction to both fields, we present the most successful process calculi designed and used for this purpose. We start from a basic process calculus that is then extended with increasingly ex- pressive features to better reflect the biological aspects of interest. We then compare the expressive power of the re- sulting calculi, mentioning if they are supported by software tools. From this comparison we derive some suggestions on the most suitable frameworks for dealing with specific cases of interest, with the help of three relevant case studies.