Department of Computer Science, University of Bradford, Bradford, BD7 1DP, U.K.
Interdisciplinary Computing and Complex Biosystems Research Group, Newcastle University, Newcastle, NE1 7RU, U.K.
ACS Synth Biol. 2021 Aug 20;10(8):1931-1945. doi: 10.1021/acssynbio.1c00143. Epub 2021 Aug 2.
We present the Infobiotics Workbench (IBW), a user-friendly, scalable, and integrated computational environment for the computer-aided design of synthetic biological systems. It supports an iterative workflow that begins with specification of the desired synthetic system, followed by simulation and verification of the system in high-performance environments and ending with the eventual compilation of the system specification into suitable genetic constructs. IBW integrates , , , and features into a single software suite. This integration is achieved through a new domain-specific biological programming language, the Infobiotics Language (IBL), which tightly combines these different aspects of synthetic biology into a full-stack integrated development environment. Unlike existing synthetic biology modeling or specification languages, IBL uniquely blends modeling, verification, and biocompilation statements into a single file. This allows biologists to incorporate design constraints within the specification file rather than using decoupled and independent formalisms for different analyses. This novel approach offers seamless interoperability across different tools as well as compatibility with SBOL and SBML frameworks and removes the burden of doing manual translations for standalone applications. We demonstrate the features, usability, and effectiveness of IBW and IBL using well-established synthetic biological circuits.
我们提出了 Infobiotics Workbench（IBW），这是一个用户友好、可扩展且集成的计算环境，用于辅助设计合成生物系统。它支持迭代工作流程，从指定所需的合成系统开始，接着在高性能环境中对系统进行模拟和验证，最终将系统规范编译为合适的遗传构建体。IBW 将、、、和 功能集成到一个单一的软件套件中。这种集成是通过一种新的特定于领域的生物编程语言——Infobiotics 语言（IBL）实现的，它将合成生物学的这些不同方面紧密地结合到一个全栈集成开发环境中。与现有的合成生物学建模或规范语言不同，IBL 独特地将建模、验证和生物编译语句融合到单个文件中。这使得生物学家能够在规范文件中包含设计约束，而不是使用不同的分析方法来使用分离和独立的形式主义。这种新方法提供了不同工具之间的无缝互操作性，以及与 SBOL 和 SBML 框架的兼容性，并消除了为独立应用程序进行手动翻译的负担。我们使用成熟的合成生物电路演示了 IBW 和 IBL 的功能、可用性和有效性。
