State-Sensitive Computational Modeling

Bioscape^P defines a new modeling language for a state-dependent stochastic simulation of parallel processes in 3D space. The contributions of the language are as follows. Normally a modeling language describes an initial concentration of entities after which all changes are driven by a simulation of reactions. We instead design "conditional simulation commands" which depend on a "global state". Our contribution is a new command in the form "when R run A1...An", which will cause A1...An entities to be added to the system when property R in the context of a global state is satisfied. Reactions are further equipped with "user-defined update functions" to produce "side effects" on the global state that includes a simulation clock to enable time dependent computation. Bioscape^P matches the realistic nature of experimentation by defining uncertainty from two sources: stochastic movement generating reactions on proximity, and probabilistic choice where an entity has the ability to be involved in more than one reaction. To capture the notion of state dependent conditional commands, we define a system of "multi-level semantics" broken into two parts, "World Level Semantics" and "Individual Level Semantics". Both levels take turns to evaluate their respective domains such that World Level Semantics evaluates the aforementioned conditional commands, while Individual Level Semantics simulates reactions, entity movement, and the update of the simulation clock and timed entities.