Puppeteer is a web-based planning and instruction generation tool which automates the task of DNA assembly by tracking, managing, and controlling laboratory tasks, reagents, and equipment. It is designed to translate protocols into sets of human- and machine-readable instructions, reducing the labor cost of building genetic devices.

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By generating control instructions based on established protocols, Puppeteer is able to increase the utility of laboratory robotics platforms in the synthetic biology workspace, such as the Tecan Freedom Evo series, by automating liquid handling tasks that would normally be carried out by manual pipetting.

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Puppeteer also manages the assignment of laboratory tasks, optimizing the use of limited-capacity laboratory resources by assigning operators to carry out processes.

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Puppeteer is comprised of a Planner and a Compiler. The Puppeteer Planner takes an Assembly Specification, Laboratory Resources, and formal Protocols, and translates them into a Plan for executing an Assembly. A Plan is a set of Tasks, and each Task is a set of Instructions. Instructions are generated in CHRIS — an intermediate Common Human Robot Instruction Set — which standardizes protocol instructions across laboratory instruments and procedures. The Puppeteer Compiler translates CHRIS into low-level instructions, which can then be executed by Technicians, Robots, and other Instruments.