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Author Oberortner, Ernst ♦ Bhatia, Swapnil ♦ Lindgren, Erik ♦ Densmore, Douglas
Source ACM Digital Library
Content type Text
Publisher Association for Computing Machinery (ACM)
File Format PDF
Copyright Year ©2014
Language English
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Synthetic biology ♦ Design ♦ Language ♦ Rule ♦ Specification ♦ Template
Abstract Synthetic Biology is an engineering discipline where parts of DNA sequences are composed into novel, complex systems that execute a desired biological function. Functioning and well-behaving biological systems adhere to a certain set of biological “rules”. Data exchange standards and Bio-Design Automation (BDA) tools support the organization of part libraries and the exploration of rule-compliant compositions. In this work, we formally define a design specification language, enabling the integration of biological rules into the Synthetic Biology engineering process. The supported rules are divided into five categories: $\textit{Counting},$ $\textit{Pairing},$ $\textit{Positioning},$ $\textit{Orientation},$ and $\textit{Interactions}.$ We formally define the semantics of each rule, characterize the language's expressive power, and perform a case study in that we iteratively design a genetic Priority Encoder circuit following two alternative paradigms—rule-based and template-driven. Ultimately, we touch a method to approximate the complexity and time to computationally enumerate all rule-compliant designs. Our specification language may or may not be expressive enough to capture all designs that a Synthetic Biologist might want to describe, or the complexity one might find through experiments. However, computational support for the acquisition, specification, management, and application of biological rules is inevitable to understand the functioning of biology.
ISSN 15504832
Age Range 18 to 22 years ♦ above 22 year
Educational Use Research
Education Level UG and PG
Learning Resource Type Article
Publisher Date 2014-12-01
Publisher Place New York
e-ISSN 15504840
Journal ACM Journal on Emerging Technologies in Computing Systems (JETC)
Volume Number 11
Issue Number 3
Page Count 19
Starting Page 1
Ending Page 19

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Source: ACM Digital Library