CLIMB-BIG-DATA: A Cloud Infrastructure for Big-Data Microbial Bioinformatics

高通量测序改变了微生物学，带来了基因组和宏基因组大数据的爆炸式增长。然而，许多微生物学家仍然无法利用大型基因组学数据集来解决微生物学中的关键问题，因为他们无法获得相关的计算资源、生物信息学工具或数据分析方面的专业知识。为了解决这个问题，我们在六年前启动了CLIMB，这是一个由MRC资助的开创性的英国云计算基础设施项目，已经支持了900个用户。随着CLIMB项目即将结束，我们提出了一个独特的新合作伙伴关系——CLIMB- Big-Data（大数据微生物生物信息学云基础设施），以满足英国微生物界在21世纪20年代的生物信息学需求。这种新的CLIMB-BIG-DATA合作伙伴关系将在英国占据独特的地位，支持学术部门的研究，以及政府机构和卫生服务的一线工作，同时也支持针对各种国家/UKRI和国际战略优先事项和官方发展援助目标的研究。为响应社区需求（bbbb160个签署国证明了这一点），拟议的伙伴关系将维持现有的CLIMB基础设施，以支持数百个研究项目，包括追踪埃博拉或寨卡病毒传播的高调努力。然而，我们也承诺在我们能为用户提供的服务的规模和范围上实现一个阶段性的改变。我们将采用矩阵模型，将一系列活动映射到我们的研究人员所倡导的具有重要战略意义的主题，包括抗菌素耐药性；新发传染病与全球卫生；微生物基因组学用于公共卫生；微生物群落与宏基因组学；病原生物学与功能基因组学；测序技术。旨在促进社区参与的活动将包括生物信息学研讨会、黑客马拉松和专题讨论会。侧重于工具和集成的活动将包括增强对共享软件和数据、工作流集成和云之间迁移的支持；加强对临床应用的支持和安全；再加上与外部设施（如欧洲核苷酸档案馆）的大型数据集的集成。以基础设施为重点的活动包括：提供图形处理单元和增强存储；维护原有的云计算基础设施，以支持微生物生物信息学；加上冈比亚MRC单位和Quadram研究所的云基础设施的结合。CLIMB-BIG-DATA合作项目将作为英国资助的项目运行五年，预计该项目将通过稳健的可持续性和扩展途径实现自负盈亏。该合作伙伴关系将吸引来自多个研究机构的合作伙伴和来自政府机构的合作者，它将从诺里奇的Quadram研究所运行，该研究所作为UKRI的战略资助研究机构，将为项目的未来提供一流的稳定和弹性环境。

High-throughput sequencing has transformed microbiology, delivering an explosion in genomic and metagenomic big data. However, many microbiologists remain unable to exploit large genomics datasets to address key questions in microbiology, because they lack access to the relevant computational resources, bioinformatics tools or expertise in data analysis. To address this problem, six years ago we launched CLIMB, a pioneering British cloud-computing infrastructure project funded by the MRC that has supported >900 users. As CLIMB comes to an end, we propose a unique new partnership--CLIMB-BIG-DATA (Cloud Infrastructure for Big-Data Microbial Bioinformatics)- to meet the bioinformatic needs of the UK microbiology community as we head into the 2020s. This new CLIMB-BIG-DATA partnership will occupy a distinctive position in the UK, underpinning research in the academic sector alongside the front-line work of government agencies and the health service, while also supporting research that maps on to a wide variety of national/UKRI and international strategic priorities and Official Development Assistance objectives. In response to community needs (as evidenced by >160 signatories), the proposed partnership will maintain the existing CLIMB infrastructure to support hundreds of research projects including high-profile efforts to track the spread of Ebola or Zika virus. However, we also promise to deliver a step-change in the scale and scope of what we can offer to users. We will adopt a matrix model, in which a range of activities will be mapped on to strategically important themes championed by our investigators, including Antimicrobial Resistance; Emerging Infectious Disease and Global Health; Microbial Genomics for Public Health; Microbial communities and metagenomics; Pathogen Biology and Functional Genomics; Sequencing Technologies. Activities aimed at community engagement will include bioinformatics workshops, hackathons and symposia. Activities focused on tools and integration will include enhanced support for sharing software and data, workflow integration and migration between clouds; enhanced support and security for clinical applications; plus integration with large datasets at external facilities, such as the European Nucleotide Archive. Activities focused on infrastructure include: provision of graphics processing units and enhanced storage; maintenance of our original cloud-computing infrastructure to support microbial bioinformatics; plus incorporation of cloud infrastructures from the MRC unit in the Gambia and from the Quadram Institute. The CLIMB-BIG-DATA partnership will run as a UKRI-supported project for five years, with the expectation that the project will become self-financing through robust pathways to sustainability and expansion. The partnership will draw upon a diverse team of partners from multiple research organisations and collaborators from government agencies, and it will be run from the Quadram Institute in Norwich, which as a strategically funded UKRI research institute will provide a first-class stable and resilient environment for the project's future.