Fuels Synthesis Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA.
J Biol Eng. 2012 Feb 28;6(1):1. doi: 10.1186/1754-1611-6-1.
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.
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.
生物计算机辅助设计（bioCAD）可协助从头设计和选择现有的遗传元件，以实现所需的生物活性，这是集成设计-构建-测试周期的一部分。为了满足合成生物学的新兴需求，bioCAD 工具必须解决组合文库设计、设计规则规范以及无痕多部分 DNA 组装日益普及的问题。
我们报告了基于网络的 bioCAD 软件 DeviceEditor 的开发和部署，该软件提供了一个图形设计环境，模拟了生物实验室中直观的视觉白板设计流程。DeviceEditor 的主要创新包括可视化组合文库设计、与无痕多部分 DNA 组装设计自动化的直接集成，以及用于创建和修改设计规范规则的图形用户界面。我们展示了如何在 DeviceEditor 画布上呈现生物设计，并展示了在复杂设计中基因组件排序和组合变化的有效可视化效果。
DeviceEditor 将研究人员从 DNA 碱基对操作中解放出来，并使用标准化、功能和可视化抽象使用户能够创建成功的原型。开放和记录的软件接口支持进一步将 DeviceEditor 与其他 bioCAD 工具和软件平台集成。通过构造正确的设计、自动化繁琐的任务、设计重用以及最小化 DNA 组装成本，DeviceEditor 为研究人员节省了时间和机构资源。
