Abstract:

Synthetic biology is an interdisciplinary field that focuses on designing, modifying, and synthesizing biosystems. It uses engineering principles to design and modify biosystems and even create novel "artificial life" to provide biological functions that meet human needs. Due to the high complexity of biosystems, extensive trial and error experiments are often required to gradually realize the desired engineering goals, resulting in high research costs and slow progress. With the continuous development of automated synthetic biology technology, multiple automated synthetic biology facilities have been established or are under construction worldwide. Biofoundry is an integrated automated scientific facility that combines the principles of intelligent manufacturing with the theoretical foundation of synthetic biology. It enables fast construction and testing of reprogrammed living organisms through the integration of intelligent and automated high-throughput devices. This article introduces the background, design, operation, and application aspects of iBioFoundry, an automated synthetic biology facility established at ZJU-Hangzhou Global Scientific and Technological Innovation Center. The iBioFoundry adopts a modular design concept and integrates various peripheral devices with three track-mounted robotic arms to build four functional modules: sample library, DNA assembly, cell screening and cultivation, and analysis. To meet the requirements of different research tasks and maximize the utilization of the device, iBioFoundry has a multi-task process management function, which is able to track and record all the process handling information of the entire experimental process and achieve traceability of all samples. Through a brief description and analysis of the high throughput construction of engineered E. coli strains and the enzyme directed evolution and screening, the article discusses the formulation of experimental automation schemes, programming of experimental processes, and on-machine operation. The article also shares some thoughts on the allocation of consumable storage space, parallel execution of multiple experimental tasks, and standardization of experimental processes. Automated synthetic biology facilities can help researchers significantly improve experimental efficiency. By combining the large amount of high-quality data generated by the facility with information technology, the automated "design-build-test-learn (DBTL)" engineering cycle in synthetic biology research can be achieved in a high-throughput, low-cost, and multi-cycle manner, accelerating the research efficiency of synthetic biology in both fundamental and many biotechnological application fields.

Key words: synthetic biology, biofoundry, automation platform, standardized experimental process

摘要：

合成生物学是一门关于设计、改造和重新合成生命的交叉融合性学科。它以工程化理念对生物体进行有目标的设计、改造，使其拥有满足人类需求的生物功能，甚至创造新的“人造生命”。由于生命体的高度复杂性，为达预定目标往往需要进行大量人工试错性实验，导致研究成本高、进展缓慢。随着自动化合成生物技术的不断发展，目前全球各地有多个合成生物自动化设施已建成或在建中。本文从建设背景、设计构建、科研项目运行和应用前景等方面对浙江大学杭州国际科创中心建设的合成生物学自动化装置iBioFoundry进行介绍，通过大肠杆菌工程菌的批量构建和酶的定向进化及筛选案例对实验自动化方案制定、实验流程程序编写和上机运行的过程做简要描述和分析，并就装置耗材存储空间的分配、多实验任务并行和实验流程标准化建设等装置建设过程的一些思考做经验分享。合成生物学自动化装置可以帮助研究人员大幅提高实验效率，装置产生的大量高质量数据结合信息技术，有望高通量、低成本、多循环地实现合成生物学研究中“设计-构建-测试-学习”的自动化运行，加速合成生物学在基础及诸多应用领域的研究效率。

关键词: 合成生物学, 生物铸造厂, 自动化平台, 标准化实验流程