CAGEN: Critical Assessment of Genetically Engineered Networks

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(Overview of the Competition)
(Overview of the Competition)
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== Overview of the Competition ==
== Overview of the Competition ==
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The Critical Assessment for Genetically Engineered Networks (CAGEN, pronounced "cajun") is  a new competition designed to
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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 3-5 best performing designs will be selected as finalists and results will be reviewed and verified by the CAGEN steering committee, who will then select the overall winner based on a set of quantitative metrics.
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improve the robustness and performance of human-designed biological
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-
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
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-
counterparts.
+
 +
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.
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As a example of the type of problem specification that we envision, consider the  design of a circuit that is capable of tracking a specified time signal via some internal protein or species concentration.  For example, the competition could simply be to initiate and hold the concentration of a fluorescent reporter at specified level as quickly as possible after the introduction of an inducer molecule.  The performance of the circuit could be quantified in terms of the integrated square error between an ideal (but unachievable) step response and the measured response (which corresponds to minimizing the mean error and variance of the temporal response).  The circuit could be tested in a variety of cell strains and a variety of media, or just across multiple cell division cycles, with the overall score determined by combining the responses from the test suite.  Details such as the host organism (E. coli, yeast, both), performance metric and circuit environment variability would be decided by the steering committee.
As a example of the type of problem specification that we envision, consider the  design of a circuit that is capable of tracking a specified time signal via some internal protein or species concentration.  For example, the competition could simply be to initiate and hold the concentration of a fluorescent reporter at specified level as quickly as possible after the introduction of an inducer molecule.  The performance of the circuit could be quantified in terms of the integrated square error between an ideal (but unachievable) step response and the measured response (which corresponds to minimizing the mean error and variance of the temporal response).  The circuit could be tested in a variety of cell strains and a variety of media, or just across multiple cell division cycles, with the overall score determined by combining the responses from the test suite.  Details such as the host organism (E. coli, yeast, both), performance metric and circuit environment variability would be decided by the steering committee.
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* July 2010: first steering committee meeting; selection of draft competition specifications
* July 2010: first steering committee meeting; selection of draft competition specifications
* October 2010: internal distribution of draft proposals to steering committee
* October 2010: internal distribution of draft proposals to steering committee
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* <s>January</s> April 2011: request for comments posted
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* <s>January</s> April 2011: candidate proposals posted for comment
* <s>April</s> May 2011: selection of 2011 CAGEN challenged announced
* <s>April</s> May 2011: selection of 2011 CAGEN challenged announced
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* April 2012: submission deadline and selection of finalists
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* May 2012: submission deadline  
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* June 2012: selection of finalists
=== CAGEN steering committee ===
=== CAGEN steering committee ===
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* Georg Seelig (U. Washington)
* Georg Seelig (U. Washington)
* Pamela Silver (Harvard)
* Pamela Silver (Harvard)
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* David Sprinzak (Caltech/Tel-Aviv University)
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* David Sprinzak (Tel-Aviv University)
|}
|}

Revision as of 11:03, 24 April 2011

The Critical Assessment for Genetically Engineered Networks (CAGEN) competition is intended to drive new approaches to designing robust, synthetic biological circuits. The competition is targeted at 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).

Contents

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 3-5 best performing designs will be selected as finalists and results will be reviewed and verified by the CAGEN steering committee, who will then select the overall winner based on a set of quantitative 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 2012 CAGEN competition

  • July 2010: first steering committee meeting; selection of draft competition specifications
  • October 2010: internal distribution of draft proposals to steering committee
  • January April 2011: candidate proposals posted for comment
  • April May 2011: selection of 2011 CAGEN challenged announced
  • May 2012: submission deadline
  • June 2012: selection of finalists

CAGEN steering committee

  • 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 (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
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