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Puppeteer is a web-based planning and instruction generation system for synthetic biology. Puppeteer comprises 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 the Assembly. A Plan is a set of Tasks, and each Task is a set of Instructions. The Instructions are generated in CHRIS --- an intermediate Common Human Robot Instruction Set intended to standardize low-level protocol instructions across Instruments in synthetic biology. The Puppeteer Compiler translates CHRIS into low level instructions executable by Technicians, Robots, and other Instruments.


  • Puppeteer is a web-based tool for protocol automation in synthetic biology.
  • Puppeteer users assume one of the following roles:
  • Puppeteer is built in a layered way around the following stack:

Previous work with TASBE

Click here to see some of our previous work on Puppeteer in the context of the DARPA TASBE project.


  • S.Bhatia, J. Fernandes, A. P. Lechuga, D. Densmore, "Puppeteer: Protocol Automation Software for Synthetic Biology," accepted to the BioBricks Foundation's 6th International Meeting on Synthetic Biology, April 2013 (declined).




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