Synthetic biology is the process of forward engineering living systems. These systems can be used 13 to produce bio-based materials, agriculture, medicine, and energy. One approach to designing these 14 systems is to employ techniques from the design of embedded electronics. These techniques include 15 abstraction, standards, modularity, automated design, and formal semantic models of computation. 16 Together these elements form the foundation of "bio-design automation," where software, robotics, 17 and microfluidic devices combine to create exciting biological systems of the future. This paper 18 describes a "hardware, software, wetware" co-design vision where software tools can be made to 19 act as "genetic compilers" that transform high-level specifications into engineered "genetic circuits" 20 (wetware). This is followed by a process where automation equipment, well-defined experimental 21 workflows, and microfluidic devices are explicitly designed to house, execute, and test these 22 circuits (hardware). These systems can be used as either massively parallel experimental platforms 23 or distributed bioremediation and bio-sensing devices. Next, scheduling and control algorithms 24 (software) manage these systems' actual execution and data analysis tasks. A distinguishing feature 25 of this approach is how all three of these aspects (hardware, software, and wetware) may be derived 26 from the same basic specification in parallel and generated to fulfill specific cost, performance, and 27 structural requirements.