Digital microfluidic biochips allow the execution of biochemical protocols on a chip-scaled device delivering cost and performance advantages over the traditional benchtop wet-laboratory processes. Several microfluidic high-level programming languages have been proposed, but none is currently adopted as a standard since their compilers and execution engines often target specific platforms. To address this issue and favor standardization, we propose a biochip-independent execution engine and low-level target language. The execution engine supports the execution of parallel synchronized tasks allowing each droplet or process to be controlled by an independent task. The target language run by the engine is inspired by traditional computer instruction set architectures and offers instructions covering the full range of low-level functionalities offered by digital biochips. The versatility of the proposed solution and its ability to support the selection and iteration control structures commonly used in programs is demonstrated with a real-life case study that sorts droplets based on real-time measurements of their color.