View source for CAGEN: Critical Assessment of Genetically Engineered Networks

[[Image:nakfi-logo.gif|right]]
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 [http://www.keckfutures.org/conferences/synthetic-biology.html 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.

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.

=== Timeline for 2012 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 ===
<center>
{| width=80%
|- valign=top
| width=50% |
* Adam Arkin (UC Berkeley)
* Barry Canton (Ginkgo BioWorks)
* Peter Carr (MIT Media Lab)
* James Collins (Boston University)
* Drew Endy (Stanford)
| width=50% |
* Eric Klavins (U. Washington)
* Richard Murray (Caltech; PI)
* Georg Seelig (U. Washington)
* Pamela Silver (Harvard)
* David Sprinzak (Caltech/Tel-Aviv University)
|}
</center>

== How to Participate ==

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

== External Resources ==

=== More information ===
* [[Media:nakfi-proposal.pdf|NAKFI proposal for CAGEN]]

=== Other critical assessment experiments and competitions ===
* [http://en.wikipedia.org/wiki/CASP CASP] - Critical Assessment of Techniques for Protein Structure Prediction
* [http://en.wikipedia.org/wiki/Critical_Assessment_of_Prediction_of_Interactions CAPRI] - Critical Assessment of Prediction of Interactions