A Biochemically-inspired Coordination-based Model for Simulating Biochemical Patterns

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Given the prominence of the interaction issues in the simulation of complex systems, coordination models and infrastructures have the potential to work as the core of non-trivial simulation frameworks. In particular, self-organising, nature-inspired coordination models are seemingly well-suited for the simulation of complex biochemical systems, where molecules massively interact arising patterns that underlie cell functioning.
In this paper we adopt a self-organising coordination model based on biochemical tuple spaces (BTS-SOC), and show how it can be straightforwardly and effectively applied to the simulation of complex interaction patterns of intracellular signalling pathways. We discuss the model and the high-level simulation architecture, where tuples represent chemical substances, coordination rules evolve tuple concentrations over time, tuple spaces represent single-compartment solutions, and a network of tuple spaces resemble a set of compartments in a biological system. Then we develop and discuss a simple case study, that is, a single signalling pathway from the complex network of the Ras signalling pathways.

keywordsSelf-organising coordination; Simulation; Biochemical tuple spaces; Computational Biology; Intracellular signalling pathways