Our solution comprises a five-layer stack as illustrated in the figure on the right. Using the Clotho platform, we develop two applications for specifying and executing biological protocols. The Assembly Planner is the end-point of an end-to-end design workflow that produces an assembly plan for synthetic biological devices, with each assembly step annotated with the name of a biological protocol. Each such protocol itself may be fully specified using another Clotho application called PuppetShow, which provides an environment for writing, testing, debugging, and executing biological protocols. The protocols are written in a new python-based high-level language called Puppeteer. The Language layer comprises the Puppeteer interpreter and linker. A protocol specified in Puppeteer may contain Puppeteer instructions as well as references to previously created Puppeteer programs available in a library. The Language layer expands and translates a Puppeteer protocol to a sequence of low-level commands expressed in a Common Human Robot Instruction Set (CHRIS). CHRIS provides a standardized instruction set that high level biological protocol languages like Puppeteer may assume to be supported by any robot. Any high-level language may produce CRIS programs and any robot vendor may support a superset of CHRIS: this decouples robot hardware details from biological protocol and specification details and supports our goal of portability and protocol library reuse. The Hardware Layer---the external control and I/O interface of a robot---is wrapped under a Hardware Abstraction Layer (HAL). Vendor-provided software for programming the robot may be proprietary and is used to control the robot. An interface to it is provided by a software bridge, which maps protocols expressed in CRIS to sequences of native robot instructions. The Resource Management layer maintains resource state information and provides a standardizable high-level interface for initializing, requesting, naming, aggregating, and accessing resources to the Language layer, analogous to a ``system call'' suite. This interface supports our goal of removing the minutiae of resource management from the protocol specification language.