%0 Journal Article
%T DeviceEditor visual biological CAD canvas
%A Joanna Chen
%A Douglas Densmore
%A Timothy S Ham
%A Jay D Keasling
%A Nathan J Hillson
%J Journal of Biological Engineering
%D 2012
%I BioMed Central
%R 10.1186/1754-1611-6-1
%X 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.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.The development of bioCAD software is paramount to our future capacity to rapidly design increasingly complex biological systems for the predictable and reproducible production of biofuels and bio-based chemicals [1]. When considering a DNA construction task, researchers must choose from a rapidly expanding list of candidate gene orthologs and expression systems. BioCAD tools (reviewed in [2-4]) make it possible to automatically query parts repositories for putative design components [5] and model the performance of candidate component combinations [6-9]. These software tools can also 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]).Howe
%K bioCAD
%K Visual design abstraction
%K Correct-by-construction design
%K Design specification rules
%K Combinatorial library
%K DNA assembly
%U http://www.jbioleng.org/content/6/1/1