The Aquarium Herbarium: Adapting Human-in-the-Loop Automation for Plant Synthetic Biology Workflows

Human in the loop automation is the formalisation and automation of laboratory workflows while retaining human operators at the lab bench. The Aquarium system guides human technicians with a click-to-proceed screen interface, allowing undergrads with no prior experience to reliably perform molecular biology workflows. So far the power of this approach has not been adapated for plant synthetic biology. The expertise required for plant molecular biology workflows remains a high barrier for entry to the field.

We have adjusted the syntax of the Aquarium programming language, Krill, as well as adding a new vocabulary of plant protocols with which to construct plant synthetic biology workflows. This was also accompanied by development of low cost hardware solutions. The flagship worklflow is the creation of Arabdopsis thaliana transgenics. This will be integrated with the plasmid assembly capabilities of the UW BIOFAB offered as a service to academic and commercial users. In addition we are working with insititutional partners to develop starter kits that combine seed material with Aquarium workflows to provide hands-on educational experiences in Plant Genetics. In the long term we hope that human-in-the-loop automation will be a powerful approach to distill expertise in plant synthetic biology, lowering barriers to entry within the field.