Biomolecular Agents as Multi-behavioural Concurrent Objects

In recent years, there has been increasing interest in computational models of biological systems based on various calculi of communicating processes, such as the stochastic pi-calculus. These models make it possible to simulate and eventually visualize the dynamic evolution of complex biosystems in time and under varying environmental conditions.While the elegance of the pi-calculus lies in its minimality, this is also a drawback when it comes to modeling because much effort must be devoted to encoding high-level ideas into the low-level means that the language affords us.In this paper, we describe an on-going effort to design a new higher-level programming language that provides direct ontological support for the concepts which are used to formulate, organize and structure models of biomolecular systems.Our language has an object-oriented flavour where we view molecular components as agents with finite sets of behaviours (states). Reactions are modeled as exchanges over connected ports that may cause agents to switch states.