Biofoundry Workflows

Overview

• Due to differences in terminology, concepts, and scope among biofoundry researchers, there are limitations in utilizing physically/logically standardized automated equipment and software
• Conceptually subdividing and structuring the processes required in biofoundries enables standardized execution and management of processes, thereby improving biofoundry performance
• We propose a 4-level abstraction hierarchy (Project, Service/Capability, Workflow, Unit Operation) to standardize biofoundries and streamline the DBTL cycle. This framework improves modularity, automation, and reproducibility while enabling better integration of AI tools, ultimately supporting a globally interoperable biofoundry network for collaborative synthetic biology. See Biofoundry Abstraction Hierarchy and its Supplement Information

Workflow Concepts

• Workflow: Defined as a logical, sequential flow of unit processes that can include part or all of the DBTL (Design-Build-Test-Learn) stages of experiments. Can be utilized as a basic unit for measuring biofoundry performance and developing automation levels.
• Unit Operation: The minimum unit process of experiments, where one unit operation is defined to correspond to one piece of equipment (UO) or one software (US)

Purpose of This Repository

• Definition and management of workflows and unit operations
• Concept updates through opinion exchange

Folder Structure

• workflows Contains types, definitions, and descriptions of workflows
• unit-operations Contains types, definitions, and descriptions of unit operations

Providing Feedback

• Use the issue for opinions and discussions