Abstract
BackgroundBiological 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.ResultsWe 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.ConclusionsDeviceEditor 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.
Highlights
Biological Computer Aided Design 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
Despite the growing utility of Biological Computer Aided Design (bioCAD) software, three critical design automation needs within the Synthetic Biology community remain unmet: 1) software integration, 2) combinatorial library design visualization, and 3) user-specifiable design rules
First and foremost, the end-to-end design process is crippled by the lack of integration among individual software tools that specialize in modelling, DNA assembly, or genetic component (e.g., ribosomal-binding site (RBS) [15]) design
Summary
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. BioCAD tools (reviewed in [2,3,4]) make it possible to automatically query parts repositories for putative design components [5] and model the performance of candidate component combinations [6,7,8,9] These software tools can address design workflow bottlenecks by providing canvases for abstractly visualizing and arranging genetic components [10] and automating the design and execution of the DNA assembly process [11,12] (reviewed in [13,14]). Despite the growing utility of bioCAD software, three critical design automation needs within the Synthetic Biology community remain unmet: 1) software integration, 2) combinatorial library design visualization, and 3) user-specifiable design rules. While bioCAD tools have been developed to visualize specification-compliant designs [21] or exploit composition grammars to guide the visual arrangement of parts [10], the underlying specifications and grammars must be defined within a programming-like language [20,22] or remain opaque by being neither viewable nor modifiable by the user [10]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
