Table 1

Requirements for simulation of intracellular signalling pathways	Computational representation/abstractions and algorithms of the BTSSOC framework
Computational Abstraction	Tuple Spaces
Representation of intracellular compartments	Tuple centres
Representation of signalling components (i.e., membrane receptors, proteins, enzymes, and genes)	Chemical reaction sets
Representation of signalling molecules (i.e., first and secondary messengers), activation and deactivation signals	Reactants and concentrations recorded as tuples in the tuple centre
Type of chemical reaction allowed	Collaborative activation Alternative activation Complex formation Decomposition reactions Standard equation for enzymatic reaction Interaction from and to extracellular space
Model of chemical reactions	Discrete system model
Action selection mechanism for chemical reactions	Gillespie algorithm [13] – an algorithm typically used to simulate systems of chemical/biochemical reactions efficiently and accurately – to execute chemical reactions with the proper rate.
User interaction and visualization of the simulation	Graphical user interfaces, viewer components, graphical components

Table 1: Mapping requirements for simulation of intracellular signaling pathways onto BTSSOC abstractions.