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Japan's RIKEN Hosts Online 'Rational Genome Design' Contest


Japanese research institute RIKEN has kicked off GenoCon, or the International Rational Genome Design Contest, an online challenge in which researchers will computationally redesign the genome of Arabidopsis thaliana so that it can eliminate and detoxify airborne formaldehyde.

GenoCon began May 25 and runs through Sept. 30. Awards will be announced in June 2011.

RIKEN's Bioinformatics and Systems Engineering division is hosting the contest, which makes use of several online tools developed at the institute, including a semantic database-sharing platform called the Scientists’ Networking System, or SciNeS, and a web-based collaborative framework called Open-Optimization Research.

SciNeS is built upon the semantic web and hosts thousands of "virtual laboratories" that enable researchers to create and publish databases without maintaining individual web servers. GenoCon is organized as a virtual lab in the system, and each contestant will establish a workspace in the GenoCon virtual lab, which includes a programming environment, a digital lab notebook, and information resources for biomass engineering research.

Participants in GenoCon will use genomic and protein data contained in SciNeS to design a DNA sequence that confers to A. thaliana the ability to absorb formaldehyde.

Contestants will design the sequence a browser-based programming environment provided by SciNeS and submit input data, a JavaScript program, and their designed DNA sequences. RIKEN and its research partners will then first perform a document review of the submitted sequences and will then experimentally evaluate those that pass the review by synthesizing the designed sequences and inserting them into A. thaliana genomes.

All submitted genome designs and programs will be compiled within SciNeS and shared under a Creative Commons Public License.

RIKEN said that GenoCon differs from the International Genetically Engineered Machine competition, a synthetic biology challenge that is organized by the Massachusetts Institute of Technology, because GenoCon emphasizes computational design while iGEM participants perform their own experimental verification. In addition, RIKEN said that iGEM uses E. coli as its experimental organism, while GenoCon is focused on a model plant, which has "direct application to bio-energy and environmental problems."

Further information about GenoCon is available here.

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