Continuous flow-based microfluidic biochips use actively controlled valves to manipulate the flow of fluids through components and channels to automate biochemical protocols. The current state-of-the-art design practices require biochemists with no engineering experience to manually design these devices. This process severely limits the realistic complexity a device can have, limiting the applications they can be used for. These devices can be viewed as a netlist of components and their interconnections, along with a protocol to be performed, similar to a how an integrated circuit can be abstracted. This thesis introduces an end to end tool-chain capable of taking a high level biochemical protocol and automatically generating a device design that can be fabricated to perform that experiment. This is done through the use of design automation algorithms adapted from the electronic design automation (EDA) industry.