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AutoBioCAD : full biodesign automation of genetic circuits
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Rodrigo, Guillermo and Jaramillo, Alfonso (2013) AutoBioCAD : full biodesign automation of genetic circuits. ACS Synthetic Biology, 2 (5). pp. 230-236. doi:10.1021/sb300084h ISSN 2161-5063.
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Official URL: http://dx.doi.org/10.1021/sb300084h
Abstract
Synthetic regulatory networks with prescribed functions are engineered by assembling a reduced set of functional elements. We could also assemble them computationally if the mathematical models of those functional elements were predictive enough in different genetic contexts. Only after achieving this will we have libraries of models of biological parts able to provide predictive dynamical behaviors for most circuits constructed with them. We thus need tools that can automatically explore different genetic contexts, in addition to being able to use such libraries to design novel circuits with targeted dynamics. We have implemented a new tool, AutoBioCAD, aimed at the automated design of gene regulatory circuits. AutoBioCAD loads a library of models of genetic elements and implements evolutionary design strategies to produce (i) nucleotide sequences encoding circuits with targeted dynamics that can then be tested experimentally and (ii) circuit models for testing regulation principles in natural systems, providing a new tool for synthetic biology. AutoBioCAD can be used to model and design genetic circuits with dynamic behavior, thanks to the incorporation of stochastic effects, robustness, qualitative dynamics, multiobjective optimization, or degenerate nucleotide sequences, all facilitating the link with biological part/circuit engineering.
Item Type: | Journal Article | ||||||||
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Subjects: | T Technology > TA Engineering (General). Civil engineering (General) | ||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||
Library of Congress Subject Headings (LCSH): | Evolutionary computation, Automation | ||||||||
Journal or Publication Title: | ACS Synthetic Biology | ||||||||
Publisher: | American Chemical Society | ||||||||
ISSN: | 2161-5063 | ||||||||
Official Date: | 17 May 2013 | ||||||||
Dates: |
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Volume: | 2 | ||||||||
Number: | 5 | ||||||||
Number of Pages: | 6 | ||||||||
Page Range: | pp. 230-236 | ||||||||
DOI: | 10.1021/sb300084h | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Restricted or Subscription Access | ||||||||
Funder: | Seventh Framework Programme (European Commission) (FP7) | ||||||||
Grant number: | 043338 (FP7), ALTF-1177-2011 |
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