Building national hardware and software infrastructure for UK DNA Foundries

为英国 DNA 铸造厂建设国家硬件和软件基础设施

• 批准号: BB/M025640/1
• 负责人: Yizhi Cai
• 金额: $ 253.92万
• 依托单位: University of Edinburgh
• 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%2FM025640%2F1
• 关键词: Building; national; hardware; software; infrastructure

To date, the BBSRC has invested over £50M towards establishing Synthetic Biology Research Centres (SBRCs) and building DNA synthesis facilities in the UK. This application seeks to build on this investment through establishing a collaboration between Edinburgh, Cambridge and TGAC to develop software infrastructure to improve efficiency and automation and to consolidate and further enhance the services offered at the national DNA foundries based in Edinburgh and Norwich. The software infrastructure will be developed by teams at Edinburgh, TGAC and Cambridge with well-established track records in high quality software engineering. The software will be made freely available under an open source license to all members of the SB community via software repositories. This proposal also complements EPSRC-funded SB work at Edinburgh and Cambridge as part of the nationwide Flowers Consortium thus providing a natural route to dissemination.The infrastructure proposed will significantly enhance the Edinburgh and TGAC DNA synthesis facilities, and the implementation of the software infrastructure will establish a new collaboration between three strong software teams across the UK, with the intention that these collaborations will grow with time. Both hardware and software infrastructure will enhance the speed and efficiency with which DNA can be designed, synthesized, assembled and verified, increasing the capability to generate synthetic DNA sequences. Finally, we will also implement sequence screening protocols to safeguard synthetic biotechnology.

迄今为止，BBSRC已投资超过5000万英镑，用于在英国建立合成生物学研究中心（SBRC）和DNA合成设施。该申请旨在通过建立爱丁堡，剑桥和TGAC之间的合作来建立这项投资，以开发软件基础设施，提高效率和自动化，并巩固和进一步加强爱丁堡和诺维奇国家DNA代工厂提供的服务。软件基础设施将由爱丁堡、TGAC和剑桥的团队开发，这些团队在高质量软件工程方面有着良好的记录。该软件将在开源许可证下通过软件存储库免费提供给SB社区的所有成员。该提案还补充了EPSRC资助的SB在爱丁堡和剑桥的工作，作为全国花卉联盟的一部分，从而提供了一个自然的传播途径。拟议的基础设施将显着增强爱丁堡和TGAC DNA合成设施，软件基础设施的实施将在英国三个强大的软件团队之间建立新的合作，希望这些合作能随着时间的推移而发展。硬件和软件基础设施将提高DNA设计、合成、组装和验证的速度和效率，提高生成合成DNA序列的能力。最后，我们还将实施序列筛选协议，以保障合成生物技术。

项目成果

Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows

Galaxy-SynBioCAD：Galaxy 工作流程中的合成生物学设计自动化工具

• DOI: 10.1101/2020.06.14.145730
• 发表时间: 2020
• 作者: Du Lac M

3D organization of synthetic and scrambled chromosomes.

• DOI: 10.1126/science.aaf4597
• 发表时间: 2017-03-10
• 期刊: Science (New York, N.Y.)
• 作者: Mercy G;Mozziconacci J;Scolari VF;Yang K;Zhao G;Thierry A;Luo Y;Mitchell LA;Shen M;Shen Y;Walker R;Zhang W;Wu Y;Xie ZX;Luo Z;Cai Y;Dai J;Yang H;Yuan YJ;Boeke JD;Bader JS;Muller H;Koszul R
• 通讯作者: Koszul R

Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods.

使用体外和体内合成基因组 SCRaMbLE-in 方法进行快速途径原型设计和工程设计

• DOI: 10.1038/s41467-018-04254-0
• 发表时间: 2018-05-22
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Liu W;Luo Z;Wang Y;Pham NT;Tuck L;Pérez-Pi I;Liu L;Shen Y;French C;Auer M;Marles-Wright J;Dai J;Cai Y
• 通讯作者: Cai Y

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

Leaf LIMS：以合成生物学为重点的灵活实验室信息管理系统。

• DOI: 10.1021/acssynbio.7b00212
• 发表时间: 2017
• 期刊: ACS synthetic biology
• 影响因子: 4.7
• 作者: Craig T

The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering.

• DOI: 10.1038/s41467-022-32661-x
• 发表时间: 2022-08-29
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Herisson, Joan;Duigou, Thomas;du Lac, Melchior;Bazi-Kabbaj, Kenza;Azad, Mahnaz Sabeti;Buldum, Gizem;Telle, Olivier;El Moubayed, Yorgo;Carbonell, Pablo;Swainston, Neil;Zulkower, Valentin;Kushwaha, Manish;Baldwin, Geoff S.;Faulon, Jean-Loup
• 通讯作者: Faulon, Jean-Loup