1. A computer-program product for selective memory restoration of a simulation comprising: a non-transitory computer-readable medium encoded with computer-executable instructions that, as a result of being executed by a computer, control the computer to perform a method for selective memory restoration of a simulation based on an indexing scheme, the method comprising: (a) generating an expected simulation result of a biological process by executing a block diagram model of the biological process with a simulation engine, wherein the simulation engine provides one or more states or parameters associated with the block diagram model and the block diagram model is associated with a first memory layout; (b) registering memory locations in the computer based on an indexing scheme that identifies a specific memory location used by a simulation context, and assigning a unique identifier to the memory location, wherein the memory location constitutes the simulation context for a subsystem in the block diagram model, wherein the simulation context comprises one or more values associated with the one or more states or parameters established during the simulation (c) gathering experimental data directly from an in situ experimental device conducting an ongoing in situ experiment of the biological process; (d) comparing the expected simulation result to the experimental data using an analysis environment that is in communication with the simulation engine; (e) updating the block diagram model based on the comparison to generate a modified block diagram model comprising one or more states and parameters, the modified block diagram model associated with a second memory layout; and (f) selectively restoring the simulation to a steady-state by re-initializing the simulation using the modified block diagram model comprising the one or more states or parameters and associated with the second memory layout.