Automated biofoundries are powered by scheduling software which integrates independent instruments and robotic arms into a fully functional platform. System operators program individual instruments and coordinate full processes via workflow development on scheduling software. This status quo for biofoundry operation and high throughput workflow development sets a substantial barrier to entry as expert-level knowledge of many highly complex instruments and software suites is required. Development of a successful cloud biofoundry thus requires a method for users to describe custom workflows in a higher-level environment without in-depth knowledge of individual instruments and software. Ideally, the workflows and protocols developed by external users could then be implemented at any biofoundry possessing the functionality described within the protocol. We therefore aim to establish these high-level frameworks for cloud-based platform-agnostic workflow development, enabling full user access to biofoundry instrumentation, operations, and workflows.