CAGEN: Critical Assessment of Genetically Engineered Networks

From OpenWetWare
Revision as of 14:37, 18 May 2010 by Murrayrm (talk | contribs) (Timeline for 2011 CAGEN competition)
Jump to: navigation, search

The Critical Assessment for Genetically Engineered Networks (CAGEN) competition is intended to drive new approaches to designing robust, synthetic biological circuits. The competition involves teams of established researchers designing circuits that implement a given function and the assessment of their circuit's performance across a set of multiple operating environments.

The CAGEN competition is sponsored by the Keck Foundation, as part of the National Acadamies Keck Futures Initiative (NAKFI).

Overview of the Competition

The Critical Assessment for Genetically Engineered Networks (CAGEN, pronounced ``cajun) is a new competition designed to improve the robustness and performance of human-designed biological circuits and devices operating in cells. The competition is intended to bring together leading research groups in biological circuit design to compete to demonstrate their abilities at designing circuits that perform in a prescribed manner in a variety of cellular contexts. Each year, a steering committee will propose a challenge problem that involves the design of an increasingly complex set of biological functions in a range of environments. Teams must submit their sequences, plasmid DNA implementing their circuit and data characterizing the performance of their system against a specified test suite. The top 3-5 designs will be submitted to the NSF BIOFAB for final characterization, and the winner will be selected based on a set of quantifiable metrics.

As part of a recent NAKFI proposal funded by the Keck Foundation, we are implementing the first iteration of the competition, including selecting the challenge problem, implementing a set of reference test protocols, announcing and publicizing the competition, implementing the selection process and choosing a winner. If successful, we believe that the competition can be proposed for continued funding from other sources and that over the medium term (5--10 years) CAGEN could lead toward a more robust set of biological design methods that allow human-designed circuits and devices to perform at levels closer to their biological counterparts.

Timeline for 2011 CAGEN competition

  • July 2010: first steering committee meeting; selection of draft competition specifications
  • November 2010: refinement of specifications completed; call for participation released
  • November 2011: submission deadline and selection of finalists
  • June 2012: Workshop for finalists; competition results announced

CAGEN steering committee

The CAGEN steering committee consists of:

  • Adam Arkin (UC Berkeley)
  • Barry Canton (Ginkgo BioWorks)
  • Peter Carr (MIT Media Lab)
  • James Collins (Boston University)
  • Drew Endy (Stanford)
  • Eric Klavins (U. Washington)
  • Richard Murray (Caltech; PI)
  • Georg Seelig (U. Washington)
  • Pamela Silver (Harvard)
  • David Sprinzak (Caltech/Tel-Aviv University)

How to Participate

Details on participation in the competition will be posted here at a future date.

External Resources

More information

Other critical assessment experiments and competitions

  • CASP - Critical Assessment of Techniques for Protein Structure Prediction
  • CAPRI - Critical Assessment of Prediction of Interactions