Establishment of iBioFoundry for synthetic biology applications

LU Hui; ZHANG Fangli; HUANG Lei

doi:10.12211/2096-8280.2023-027

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Establishment of iBioFoundry for synthetic biology applications

Invited Review | 更新时间：2025-03-20

- Establishment of iBioFoundry for synthetic biology applications
- Synthetic Biology Journal Vol. 4, Issue 5, Pages: 877-891(2023)
- 作者机构：
  
  1.浙江大学杭州国际科创中心，杭州浙江 311215
  2.浙江大学生物工程研究所，化学工程与生物工程学院，浙江杭州 310058
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2023-027
  CLC： Q819
- Received：31 March 2023，
  
  Revised：2023-05-24，
  
  Published：31 October 2023
- 稿件说明：
移动端阅览
卢挥，张芳丽，黄磊. 合成生物学自动化装置iBioFoundry的构建与应用［J］. 合成生物学， 2023， 4（5）： 877-891

LU Hui， ZHANG Fangli， HUANG Lei. Establishment of iBioFoundry for synthetic biology applications［J］. Synthetic Biology Journal， 2023， 4（5）： 877-891
卢挥，张芳丽，黄磊. 合成生物学自动化装置iBioFoundry的构建与应用［J］. 合成生物学， 2023， 4（5）： 877-891 DOI： 10.12211/2096-8280.2023-027.

LU Hui， ZHANG Fangli， HUANG Lei. Establishment of iBioFoundry for synthetic biology applications［J］. Synthetic Biology Journal， 2023， 4（5）： 877-891 DOI： 10.12211/2096-8280.2023-027.

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。

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 per

ipheral 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.

关键词

Keywords

references

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