Biological Design Center, Boston University, Boston, MA, USA.
Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA.
Nat Protoc. 2022 Apr;17(4):1097-1113. doi: 10.1038/s41596-021-00675-2. Epub 2022 Feb 23.
Cells interact with their environment, communicate among themselves, track time and make decisions through functions controlled by natural regulatory genetic circuits consisting of interacting biological components. Synthetic programmable circuits used in therapeutics and other applications can be automatically designed by computer-aided tools. The Cello software designs the DNA sequences for programmable circuits based on a high-level software description and a library of characterized DNA parts representing Boolean logic gates. This process allows for design specification reuse, modular DNA part library curation and formalized circuit transformations based on experimental data. This protocol describes Cello 2.0, a freely available cross-platform software written in Java. Cello 2.0 enables flexible descriptions of the logic gates' structure and their mathematical models representing dynamic behavior, new formal rules for describing the placement of gates in a genome, a new graphical user interface, support for Verilog 2005 syntax and a connection to the SynBioHub parts repository software environment. Collectively, these features expand Cello's capabilities beyond Escherichia coli plasmids to new organisms and broader genetic contexts, including the genome. Designing circuits with Cello 2.0 produces an abstract Boolean network from a Verilog file, assigns biological parts to each node in the Boolean network, constructs a DNA sequence and generates highly structured and annotated sequence representations suitable for downstream processing and fabrication, respectively. The result is a sequence implementing the specified Boolean function in the organism and predictions of circuit performance. Depending on the size of the design space and users' expertise, jobs may take minutes or hours to complete.
细胞与环境相互作用，通过由相互作用的生物成分组成的自然调控遗传电路控制的功能在它们之间进行通信，跟踪时间并做出决策。用于治疗和其他应用的合成可编程电路可以通过计算机辅助工具自动设计。Cello 软件根据高级软件描述和代表布尔逻辑门的经过特征描述的 DNA 部件库，为可编程电路设计 DNA 序列。这个过程允许设计规范重用、模块化 DNA 部件库管理以及基于实验数据的正式化电路转换。本协议描述了 Cello 2.0，这是一款免费的跨平台 Java 编写的软件。Cello 2.0 能够灵活描述逻辑门的结构及其代表动态行为的数学模型，用于描述基因组中门放置的新形式规则，新的图形用户界面，对 Verilog 2005 语法的支持，以及与 SynBioHub 部件库软件环境的连接。这些功能共同将 Cello 的能力扩展到了新的生物体和更广泛的遗传背景，包括基因组，超出了大肠杆菌质粒。使用 Cello 2.0 设计电路时，会从 Verilog 文件生成一个抽象的布尔网络，为布尔网络中的每个节点分配生物部件，构建 DNA 序列，并生成高度结构化和注释的序列表示，分别适用于下游处理和制造。结果是在生物体中实现指定布尔函数的序列以及电路性能的预测。根据设计空间的大小和用户的专业知识，作业可能需要几分钟到几个小时才能完成。
