An Engineering Biology Approach to Automated Workflow and BioDesign

Abstract

The paper addresses the application of engineering biology strategy and techniques to the automation of laboratory workflow - primarily in the context of biofoundries and biodesign applications based on the Design, Build, Test and Learn paradigm. The trend towards greater automation comes with its own set of challenges. On the one hand, automation is associated with higher throughput and with higher replicability. On the other hand, implementation of an automated workflow requires an instruction set that is far more extensive than for a manual workflow. Automated tasks must also be conducted in the order specified in the workflow, with the right logic, utilising suitable biofoundry resources, and at scale - whilst simultaneously collecting measurements and associated data. The paper describes an approach to automated workflow that is being trialled at the London Biofoundry at SynbiCITE. The solution represents workflows with directed graphs, uses orchestrators for their execution and relies on existing standards. The approach is highly flexible and applies to not only workflow automation in single locations but also distributed workflows (e.g for biomanufacturing). The final section presents an overview of the implementation - using the simple example of an assay based on a dilution, measurement and data analysis workflow.