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dc.contributor.authorChen, Joannaen_US
dc.contributor.authorDensmore, Douglasen_US
dc.contributor.authorHam, Timothy S.en_US
dc.contributor.authorKeasling, Jay D.en_US
dc.contributor.authorHillson, Nathan J.en_US
dc.coverage.spatialEnglanden_US
dc.date2012-02-28
dc.date.accessioned2018-03-21T15:19:48Z
dc.date.available2018-03-21T15:19:48Z
dc.date.issued2012-02-28
dc.identifierhttps://www.ncbi.nlm.nih.gov/pubmed/22373390
dc.identifier.citationJoanna Chen, Douglas Densmore, Timothy S Ham, Jay D Keasling, Nathan J Hillson. 2012. "DeviceEditor visual biological CAD canvas.." J Biol Eng, Volume 6, Issue 1:1.
dc.identifier.issn1754-1611
dc.identifier.urihttps://hdl.handle.net/2144/27830
dc.description.abstractBACKGROUND: 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.en_US
dc.format.extent1en_US
dc.languageeng
dc.relation.ispartofJ Biol Eng
dc.rights© 2012 Chen et al.. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.rights.urihttp://creativecommons.org/licenses/by/2.0
dc.subjectScience & technologyen_US
dc.subjectLife sciences & biomedicineen_US
dc.subjectBiochemical research methodsen_US
dc.subjectBiotechnology & applied microbiologyen_US
dc.subjectBiochemistry & molecular biologyen_US
dc.subjectbioCADen_US
dc.subjectVisual design abstractionen_US
dc.subjectCorrect-by-construction designen_US
dc.subjectDesign specification rulesen_US
dc.subjectCombinatorial libraryen_US
dc.subjectDNA assemblyen_US
dc.subjectBiotechnologyen_US
dc.titleDeviceEditor visual biological CAD canvasen_US
dc.typeArticleen_US
dc.identifier.doi10.1186/1754-1611-6-1
pubs.elements-sourcepubmeden_US
pubs.notesEmbargo: Not knownen_US
pubs.organisational-groupBoston Universityen_US
pubs.organisational-groupBoston University, College of Engineeringen_US
pubs.organisational-groupBoston University, College of Engineering, Department of Electrical & Computer Engineeringen_US
pubs.publication-statusPublished onlineen_US


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© 2012 Chen et al.. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as © 2012 Chen et al.. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.