research-puppeteer Laboratory Automation for Synthetic Biology
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.

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.

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

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.

Key features

  • Track, manage, and control tasks, reagents, and equipment.
  • Define protocols for carrying out laboratory processes.
  • Generate standardized CHRIS instructions for use by robots and technicians.
  • Generate control scripts for laboratory robotics.
  • Manage laboratory roles and assign operators to perform tasks.

Funding

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Puppeteer is currently under development, and is not yet available to users.

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Selected Puppeteer publications:

  • V. Vasilev, C. Liu, J. Fernandes, E. Orozco, T. Haddock, S. Bhatia, A. Adler, F. Yaman, J. Beal, J. Babb, R. Weiss, and D. Densmore. A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering, poster presented at the SynBERC Fall Retreat, Harvard University, September 2011.
    [BibTeX]
    @MISC{VasilevSynBERC2011,
    author = {Vasilev, Viktor and Liu, Chenkai and Fernandes, Janoo and Orozco,
    Evelyn and Haddock, Traci and Bhatia, Swapnil and Adler, Aaron and
    Yaman, Fusun and Beal, Jacob and Babb, Jonathan and Weiss, Ron and
    Densmore, Douglas},
    title = {A Software Stack for Specification and Robotic Execution of Protocols
    for Synthetic Biological Engineering},
    howpublished = {poster presented at the SynBERC Fall Retreat, Harvard University},
    month = {September},
    year = {2011},
    __markedentry = {[Aaron Heuckroth:5]},
    keywords = {posters, puppeteer, synthetic biology},
    owner = {Aaron Heuckroth},
    timestamp = {2013.08.13}
    }

  • V. Vasilev, C. Liu, T. Haddock, S. Bhatia, A. Adler, F. Yaman, J. Beal, J. Babb, R. Weiss, and D. Densmore. A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering, talk presented at the International Workshop on Bio-Design Automation (IWBDA), June 2011.
    [BibTeX]
    @MISC{VasilevIWBDA2011,
    author = {Vasilev, Viktor and Liu, Chenkai and Haddock, Traci and Bhatia, Swapnil
    and Adler, Aaron and Yaman, Fusun and Beal, Jacob and Babb, Jonathan
    and Weiss, Ron and Densmore, Douglas},
    title = {A Software Stack for Specification and Robotic Execution of Protocols
    for Synthetic Biological Engineering},
    howpublished = {talk presented at the International Workshop on Bio-Design Automation
    (IWBDA)},
    month = {June},
    year = {2011},
    __markedentry = {[Aaron Heuckroth:5]},
    keywords = {puppeteer, synthetic biology, talks},
    owner = {Aaron Heuckroth},
    timestamp = {2013.08.13}
    }

Recent news stories for Puppeteer

CIDAR Project Lead
 

Swapnil Bhatia, PhD swapnilb@bu.edu

Swapnil Bhatia, PhD
swapnilb@bu.edu


Project Advisors
 


Undergraduate Collaborators
 

Janoo Fernandes

Janoo Fernandes


 
 

Eda Aslanoba

Eda Aslanoba


 
 

Alehandro Pelaez Lechuga

Alejandro Pelaez Lechuga


Denise Ortega

Denise Ortega


Puppeteer was originally developed as part of the Tool Chain to Accelerate Synthetic Biology (TASBE). For more information on the early phase of the Puppeeter project, please visit the CIDAR Wiki.