A software-controlled chemical process emulation system and environment having individually-addressable and/or group-addressable software-controlled chemical system processing modules, software-controlled chemical system handling modules, and related components. The software-controlled modules may be designed and interconnected to emulate various fixed, configurable, and reconfigurable “Lab-on-a-Chip” (“LoC”) devices. The software-controlled modules may be designed as separate units with well-defined ports and interfaces that can be used in the construction of larger systems. Alternatively, the software-controlled modules may be integrated into more complex subsystems that can be used in similar or other ways. These aspects may be used to design a LoC device, develop software for the operation of a LoC device, or may be used together with actual LoC devices as part of a larger system. Some applications may be used to implement laboratory automation features in experimental set-ups and laboratory-scale chemical production.