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Title: DeviceEditor visual biological CAD canvas

Abstract

Background: Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly.Results: We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions: DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse,more » and the minimization of DNA assembly costs.« less

Authors:
 [1];  [2];  [1];  [3];  [1]
  1. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Boston Univ., MA (United States)
  3. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23), Biological Systems Science Division (SC-23.2)
OSTI Identifier:
1511335
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Biological Engineering
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 1754-1611
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Chen, Joanna, Densmore, Douglas, Ham, Timothy S., Keasling, Jay D., and Hillson, Nathan J. DeviceEditor visual biological CAD canvas. United States: N. p., 2012. Web. doi:10.1186/1754-1611-6-1.
Chen, Joanna, Densmore, Douglas, Ham, Timothy S., Keasling, Jay D., & Hillson, Nathan J. DeviceEditor visual biological CAD canvas. United States. doi:10.1186/1754-1611-6-1.
Chen, Joanna, Densmore, Douglas, Ham, Timothy S., Keasling, Jay D., and Hillson, Nathan J. Sat . "DeviceEditor visual biological CAD canvas". United States. doi:10.1186/1754-1611-6-1. https://www.osti.gov/servlets/purl/1511335.
@article{osti_1511335,
title = {DeviceEditor visual biological CAD canvas},
author = {Chen, Joanna and Densmore, Douglas and Ham, Timothy S. and Keasling, Jay D. and Hillson, Nathan J.},
abstractNote = {Background: Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly.Results: We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions: DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.},
doi = {10.1186/1754-1611-6-1},
journal = {Journal of Biological Engineering},
issn = {1754-1611},
number = 1,
volume = 6,
place = {United States},
year = {2012},
month = {12}
}

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Cited by: 40 works
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Works referenced in this record:

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