Our mission at Ginkgo Bioworks is to make biology easier to engineer. We believe that biology is a powerful manufacturing technology, but engineering organisms for this purpose today requires creating and testing many prototype designs. We have created advanced biological foundries at Ginkgo to facilitate this process, balancing often competing requirements of flexibility and scale. This talk will cover some of the tools, methods, and systems we have built and used at Ginkgo over the years to automate our synthetic biology workflows. We'll discuss the challenges we have attempted to address in the design of these systems, and how we hope to continue to improve our solutions.