Software systems for Imperial College DNA Foundry (LIMS/automation/interfaces)

帝国理工学院 DNA 铸造厂软件系统（LIMS/自动化/接口）

• 批准号: BB/M025632/1
• 负责人: Richard Kitney
• 金额: $ 165.16万
• 依托单位: Imperial College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM025632%2F1
• 关键词: Software; systems; Imperial; College; DNA

Synthetic biology has the tremendous potential for enabling the design and implementation of sophisticated biochemical mechanisms for sensing, computing, control, production, and activation. This approach is anticipated to lead to many breakthrough applications in biotherapeutics, bioremediation, biomaterials, and in vivo-sensing and activation and self-assembly. The hardware available to exploit synthetic biology has evolved to deliver the many protocols for synthesizing DNA and verifying its assembly. Advances in liquid handling, automation, miniaturization, microfluidics and spectroscopy have collectively combined to make possible the rapid construction of synthetic genes, engineered pathways and synthetic genomes. The initial capital funding of this technology at the Centres of DNA Synthesis (The Foundries) has made possible the development of automated workstations organized to synthesize DNA components and assemblies designed to meet defined biofunctional performance parameters. As a direct consequence of the automation of DNA synthesis and assembly there has been a massive increase in throughput, size and complexity of experimental space covered. The research challenge now faced is the lack of an integrated suite of software tools to support DNA synthesis at the Foundry scale. This is part logistical, in the management of the process and data, and part statistical in the interpretation and modeling of the massive amounts of data generated by the Foundry. Similar to the automation of DNA sequencing, automation of synthetic biology in the Foundry will result in the generation and processing of huge amounts of data.The aims of this proposal:- Maximize the efficiencies of the Foundry by developing an open source operating system to support an integrated engineering design workflow allowing seamless inter-tool communication for hardware and software.- Develop a 'Knowledge Centre' capable of providing storage, processing, analysis and predictive modeling of the data coming from DNA design, sequencing, characterization and process metrics generated by the Foundry. - Build the computational infrastructure to comply with the International Gene Synthesis Consortium (IGSC) to prevent the misuse of synthetic genes. Sequences of DNA synthesized will be screened and users vetted to ensure vigilance and biosecurity of the Foundry.

合成生物学具有巨大的潜力，可以设计和实现用于传感，计算，控制，生产和激活的复杂生化机制。这种方法有望在生物治疗、生物修复、生物材料以及体内传感、活化和自组装等方面带来许多突破性的应用。可用于开发合成生物学的硬件已经发展到提供用于合成DNA和验证其组装的许多协议。液体处理、自动化、微型化、微流体和光谱学的进步共同使合成基因、工程途径和合成基因组的快速构建成为可能。DNA合成中心（The Foundries）对这项技术的初始资本资助使得有可能开发自动化工作站，这些工作站被组织起来合成DNA组分和组装，以满足定义的生物功能性能参数。作为DNA合成和组装自动化的直接结果，所覆盖的实验空间的吞吐量、大小和复杂性都有了巨大的增加。现在面临的研究挑战是缺乏一套集成的软件工具来支持Foundry规模的DNA合成。这是流程和数据管理中的部分后勤工作，也是对铸造厂生成的大量数据进行解释和建模的部分统计工作。与DNA测序的自动化类似，Foundry中合成生物学的自动化将导致大量数据的生成和处理。该提案的目的是：-通过开发开源操作系统来支持集成的工程设计工作流程，从而实现硬件和软件的无缝工具间通信，从而最大限度地提高Foundry的效率。-开发一个“知识中心”，能够对来自DNA设计、测序、表征和Foundry生成的工艺指标的数据进行存储、处理、分析和预测建模。- 建立符合国际基因合成联盟（IGSC）的计算基础设施，以防止滥用合成基因。将对合成的DNA序列进行筛选，并对用户进行审查，以确保铸造厂的警惕性和生物安全性。

项目成果

The Foundry: the DNA synthesis and construction Foundry at Imperial College.

• DOI: 10.1042/bst20160007
• 发表时间: 2016-06-15
• 期刊: Biochemical Society transactions
• 影响因子: 3.9
• 作者: Chambers S;Kitney R;Freemont P
• 通讯作者: Freemont P

SARS-CoV-2 infection, clinical features and outcome of COVID-19 in United Kingdom nursing homes

英国疗养院中 SARS-CoV-2 感染、COVID-19 的临床特征和结果

• DOI: 10.1101/2020.05.19.20105460
• 发表时间: 2020
• 作者: Graham N

SARS-CoV-2 infection, clinical features and outcome of COVID-19 in United Kingdom nursing homes.

• DOI: 10.1016/j.jinf.2020.05.073
• 发表时间: 2020-09
• 期刊: The Journal of infection
• 作者: Graham NSN;Junghans C;Downes R;Sendall C;Lai H;McKirdy A;Elliott P;Howard R;Wingfield D;Priestman M;Ciechonska M;Cameron L;Storch M;Crone MA;Freemont PS;Randell P;McLaren R;Lang N;Ladhani S;Sanderson F;Sharp DJ
• 通讯作者: Sharp DJ

Biofoundries are a nucleating hub for industrial translation.

• DOI: 10.1093/synbio/ysab013
• 发表时间: 2021
• 期刊: Synthetic biology (Oxford, England)
• 作者: Farzaneh T;Freemont PS
• 通讯作者: Freemont PS