A compositional approach for modeling and simulation of bio-molecular systems

The simulation of biological systems is a challenge to modeling methodologies. Living entities are supported by a complex hierarchical network of chemical reactions. The accurate representation of organisms require the use of stochastic chemical equations (SCE) organized into compartments in order to reflect the organization into cells, tissues and organs. In this paper we introduce a modeling and simulation framework based on the Heterogeneous Flow System Specification formalism (HFSS). HFSS provides an hybrid representation of dynamic systems, being able to describe sampled and discrete event systems. These features enable a modular representation of stochastic chemical reactions. In particular, we show that SCE require only two types of HFSS models defined in this paper: molecule holders, and chemical reactors. We provide a description of a HFSS implementation based on pluggable software units (PUs), a component-based framework that supports the development of SCE libraries.