Simulation of caspases apoptotic signalling pathway in a tuple space-based bioinformatics infrastructure

Understanding intracellular communication processes is essential, since they allow the cell to perform the totality of its functions. Among them each cell has a self-destruction system that starts and operates in a regulated manner. It is called apoptosis, and includes the decision to start self-destruction as well as the proper execution of the apoptotic program. Caspases, a family of cysteine proteases, are the central regulators of apoptosis. As such, it requires the coordinated activation and execution of multiple sub programmes. Historically, different modelling approaches have been developed to deal with intracellular signalling pathways, from mathematical models – mainly Ordinary Differential Equations (ODEs) – to computational models —process algebra such as stochastic π-calculus (Priami, 1995) and κ-calculus (Danos et al., 2007). Accordingly, different simulation tools have been developed, from mathematical ones – see a survey in (Alves et al., 2006) – to computational ones such as SPiM (Phillips, 2007). While they typically address scenarios with a single compartment, in recent years a trend has emerged which moves from the single global approach to mechanisms and constructs tackling the multi-compartment scenario. In this paper, we adopt a simulation approach based on the notion of Biochemical Tuple Spaces for Self-Organising Coordination (BTS-SOC), introduced in (Viroli and Casadei, 2009), and then show how it can be applied to the simulation of the caspases signalling pathway (MacFarlane and Williams, 2004), which plays a crucial role in the transduction and execution of the apoptotic signal induced by various stimuli.