Spatial behavioral modeling and simulation of metabolic pathways with Orion

Background: Systems biology, the formal description of the structure and of the dynamics of biomolecular systems, is acquiring capital importance in the modern, “-omics” based, life sciences. But the classical mathematical approaches to modeling and simulation of inter- and intra- cellular processes reveal inadequate to tame the inherent complexity of life’s molecular basis. Formal approaches from theoretical computer science appear more promising, permitting to describe the structure and the behavior of the complex biological systems composing the structure and the behavior of its components. Results: We present a novel approach, based on the behavioral paradigm, for modeling and simulation of metabolic pathways. Each enzyme, metabolite and complex involved in a pathway is represented by an autonomous software agent. We abstract the molecules at the mesoscale as spheres with a radius proportional to their weight. The molecules move with Brownian motion in a 3D virtual cell space. When an enzyme or a complex encounters an affine substrate for a metabolic reaction, than such reaction can take place, according to Michaelis-Menten kinetics. Conclusions: The system, named Orion, has been implemented as a society of agents on a mobile computing middleware and can be therefore executed on a network of computers. All the necessary biochemical knowledge is acquired from the SBML file of a pathway and from a custom XML database that organizes the biochemical information about enzymes, metabolites and their reactions.