The Beta Workbench

This paper presents a system to model and simulate biological processes. It is based on process calculi theory and incorporates a language, a compiler, the execution environment and some graphical interface components. The language is based on Beta-binders, a recently introduced process algebra bio-inspired and developed to be suitable for the biological applicative domain. The runtime environment is based on a stochastic abstract machine that extends and improve the classical Gillespie’s approach. The quantitative aspects included in the stochastic information associated with the language allow to simulate and plot quantitative parameters of the system under investigation. We define the syntax, semantics and implementation of the language comparing our design choices with the most common features of process calculi applied to biology. A relevant part of this work is the description of design patterns for the most common biological features in molecular interactions. This is an important aspect in exploiting the expressive power of the language and in providing a preliminary guide to the use of the compositional properties of process calculi.