A platform-based design environment for synthetic biological systems

Authors:
Douglas Densmore;Anne Van Devender;Matthew Johnson;Nade Sritanyaratana
Affiliations:
University of California, Berkeley;Washington and Lee University;University of California, Berkeley;University of California, Berkeley
Venue:
The Fifth Richard Tapia Celebration of Diversity in Computing Conference: Intellect, Initiatives, Insight, and Innovations
Year:
2009

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A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts

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Hardware that produces bounded rather than exact results

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Abstract

Genomics has reached the stage at which the amount of DNA sequence information in existing databases is quite large. Synthetic biology is now using these databases to catalog sequences according to their functionality thus creating a system of standard biological parts. Flexible tools are needed which both permit access and modification to that data and also allow one to perform meaningful, intelligent manipulation. A Platform-Based Design approach views genetic information as having a particular functionality and assembles platforms (collections of DNA elements) to perform this functionality. Specifically this paper presents the Clotho toolset which uses these concepts to create a complete design environment for standardized biological parts.