Cloud-SPAN: Specialised analyses for environmental 'omics with Cloud-based High Performance Computing

Cloud-SPAN:利用基于云的高性能计算对环境组学进行专业分析

基本信息

  • 批准号:
    MR/V038680/1
  • 负责人:
  • 金额:
    $ 89.59万
  • 依托单位:
  • 依托单位国家:
    英国
  • 项目类别:
    Research Grant
  • 财政年份:
    2021
  • 资助国家:
    英国
  • 起止时间:
    2021 至 无数据
  • 项目状态:
    未结题

项目摘要

Environmental Biotechnology (EB) addresses global challenges using engineered microbial systems for environmental protection, bio-remediation and resource recovery. It is a critical and expanding area for the UK and underpins some of the world's most important industries. This is acknowledged by the funding invested in the creation of BBSRC's Networks in Industrial Biotechnology and Bioenergy (NIBBs). A deep mechanistic understanding of the complex microbial communities involved in the biological cycling of global resources is essential to meet global challenges such as Net Zero, waste management and increased demand. The complexity of these microbiomes can be orders of magnitude larger than those found in the human gut, requiring different approaches to experimental design and analysis with High Performance Computing (HPC). However, EB is an interdisciplinary field that attracts researchers from a broad range of disciplines including Mathematics, Engineering, Biology, Social Sciences, Management, Physics and Chemistry and big data 'omics analyses on HPC systems are often not core skills for such researchers.This proposal aims to develop and deliver highly accessible resources that will upskill these interdisciplinary researchers so that they are able to generate and analyze big data relating to EB using Cloud HPC. Although infrastructure and resources exist for microbial 'omics (e.g. JGI's IMG/M, MG-RAST, Galaxy, CLIMB, EBI) there is a lack of systematic training tightly linked to the EB domain and documentation is often focussed on technical proficiency rather than contextualised with a strong understanding of experimental design. We will provide foundational training and develop and deliver new advanced modules covering the specialised skills required to generate and analyse 'omics data using Cloud HPC resources. These will include experimental design and statistical modules to ensure researchers can generate data appropriate to investigate their research question. Modules will deploy cloud-based containerised instances provided by Google Education and Amazon Web Services (AWS) for exemplar workflows free to the learner. They will form a complete training resource with fully articulated prerequisites and learning objectives that can be used for in-person or online tutor-led workshops or self-paced learning. Our proposal offers structured Learning Paths from the statistical skills required for robust experimental design through to the reproducible execution and interpretation of 'omics analyses with HPC to cater to researchers with differing levels of previous experience and which allow self-assessment of training needs. We also provide Diversity Scholarships to enable members of underrepresented groups to participate in online or in-person training.The collaboration between the University of York and the Software Sustainability Institute (SSI) brings together excellence in data science pedagogy and environmental 'omics research with the SSI's UK-leading expertise in research computing and community building. This will ensure the training developed genuinely complements, and aligns with, existing materials to enhance national provision. Sustainability will be fostered by making the resources Findable, Accessible, Interoperable and Reusable (FAIR), providing cross-platform images for deployment and by developing and proactively engaging with a Community of Practice and providing Code Retreats for the supported practice of methods to participants' own data. In addition, "Cloud Administration Guides" will be developed for institutional HPC Teams to run specialised modules with their own resources. These Guides will be supported 1-to-2 day training by Cloud-SPAN systems administrators. The project will be promoted by our partners, the SSI, Google Education, AWSand the N8 Centre of Excellence in Computationally Intensive Research and through delivery of conference talks and seminars.
环境生物技术(EB)利用工程微生物系统解决环境保护,生物修复和资源回收的全球挑战。它是英国的一个关键和不断扩大的领域,并支撑着世界上一些最重要的行业。这一点得到了投资于创建BBSRC工业生物技术和生物能源网络(NIBBs)的资金的认可。深入了解参与全球资源生物循环的复杂微生物群落的机理,对于应对净零排放、废物管理和需求增加等全球挑战至关重要。这些微生物群的复杂性可能比人类肠道中发现的微生物群大几个数量级,需要采用不同的方法来进行实验设计和高性能计算(HPC)分析。然而,电子商务是一个跨学科的领域,吸引了来自广泛学科的研究人员,包括数学,工程,生物学,社会科学,管理,物理和化学以及HPC系统上的大数据组学分析通常不是这些研究人员的核心技能。该提案旨在开发和提供高度可访问的资源,以提高这些跨学科研究人员的技能,使他们能够生成和分析使用云HPC实现与EB相关的大数据。尽管微生物组学的基础设施和资源已经存在(例如JGI的IMG/M、MG-RAST、Galaxy、CLIMB、EBI),但缺乏与EB领域紧密相关的系统性培训,并且文档通常侧重于技术熟练程度,而不是对实验设计有深刻理解的背景。我们将提供基础培训,并开发和提供新的高级模块,涵盖使用云HPC资源生成和分析组学数据所需的专业技能。这些将包括实验设计和统计模块,以确保研究人员可以生成适当的数据来调查他们的研究问题。模块将部署由Google Education和Amazon Web Services(AWS)提供的基于云的容器化实例,用于免费向学习者提供示例工作流。它们将形成一个完整的培训资源,具有充分阐述的先决条件和学习目标,可用于面对面或在线导师主导的研讨会或自定进度的学习。我们的建议提供了结构化的学习路径,从稳健的实验设计所需的统计技能到HPC组学分析的可重复执行和解释,以满足具有不同先前经验水平的研究人员,并允许自我评估培训需求。我们还提供多样性奖学金,使代表性不足的群体的成员能够参加在线或面对面的培训。约克大学和软件可持续发展研究所(SSI)之间的合作将数据科学教学法和环境组学研究方面的卓越成果与SSI在研究计算和社区建设方面的英国领先专业知识结合在一起。这将确保开发的培训真正补充并符合现有材料,以加强国家提供。可持续性将通过使资源可查找、可解释、可互操作和可重用(FAIR)、提供跨平台映像以供部署、开发和积极参与实践社区以及为参与者自己的数据提供方法的支持实践提供代码务虚会来促进。此外,还将为机构HPC团队开发“云管理指南”,以便使用自己的资源运行专门的模块。这些指南将由Cloud-SPAN系统管理员提供1至2天的培训。该项目将由我们的合作伙伴,SSI,Google Education,AW和N8计算密集型研究卓越中心以及通过会议讲座和研讨会进行推广。

项目成果

期刊论文数量(3)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes
MAGqual:评估宏基因组组装基因组质量的独立管道
  • DOI:
    10.1101/2023.12.13.571510
  • 发表时间:
    2023
  • 期刊:
  • 影响因子:
    0
  • 作者:
    Cansdale A
  • 通讯作者:
    Cansdale A
Facilitating peer-led group research through virtual collaboration spaces: an exploratory research study
通过虚拟协作空间促进同行主导的小组研究:一项探索性研究
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James Chong其他文献

Differential brain functioning profiles among adolescent mathematics achievers
青少年数学成就者的大脑功能差异
  • DOI:
  • 发表时间:
    1998
  • 期刊:
  • 影响因子:
    0
  • 作者:
    L. L. Yeap;T. Chong;James Chong;Guat Tin Low
  • 通讯作者:
    Guat Tin Low
Tactical Asset Allocation with Macroeconomic Factors
考虑宏观经济因素的战术资产配置
  • DOI:
    10.3905/jwm.2014.17.1.058
  • 发表时间:
    2014
  • 期刊:
  • 影响因子:
    0
  • 作者:
    James Chong;G. Phillips
  • 通讯作者:
    G. Phillips
EVA: The bubble years, meltdown and beyond
EVA:泡沫时期、崩溃及以后
  • DOI:
    10.1057/jam.2009.4
  • 发表时间:
    2009
  • 期刊:
  • 影响因子:
    0
  • 作者:
    James Chong;Drew Fountaine;Monica Her;Michael Phillips
  • 通讯作者:
    Michael Phillips
TRANSCATHETER MICROWAVE ABLATION CAN PRODUCE DEEP CIRCUMFERENTIAL PERIVASCULAR ABLATION AND EFFECTIVE RENAL DENERVATION WITHOUT SIGNIFICANT ARTERIAL INJURY
  • DOI:
    10.1016/s0735-1097(18)31770-4
  • 发表时间:
    2018-03-10
  • 期刊:
  • 影响因子:
  • 作者:
    Pierre Cheng Qian;Michael Barry;Juntang Lu;Ashraf Mina;Joshua Ryan;Sushil Bandodkar;Shirley Alvarez;Virginia James;John Ronquillo;Winny Varikatt;Zoe Clayton;James Chong;Sara Al Raisi;Pramesh Kovoor;Jim Pouliopoulos;Alistair McEwan;Aravinda Thiagalingam;Stuart Thomas
  • 通讯作者:
    Stuart Thomas
Sca1+/CD31−/PDGFRa+ Cardiac Stem Cells are from an Epicardial/Mesodermal but not Neural-crest, Cardiomyocyte or Bone-marrow Origin
  • DOI:
    10.1016/j.hlc.2009.05.005
  • 发表时间:
    2009-01-01
  • 期刊:
  • 影响因子:
  • 作者:
    James Chong;Owen Prall;Vashe Chandrakanthan;Munira Xaymardan;Ishtiaq Ahmed;Chris Scarlett;Emily Colvin;Mark Pinese;Andrew Biankin;Richard Harvey
  • 通讯作者:
    Richard Harvey

James Chong的其他文献

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{{ truncateString('James Chong', 18)}}的其他基金

Understanding how microbial communities respond to design and process engineering in wastewater treatment
了解微生物群落如何响应废水处理中的设计和工艺工程
  • 批准号:
    BB/Y003314/1
  • 财政年份:
    2023
  • 资助金额:
    $ 89.59万
  • 项目类别:
    Research Grant
Rational design of microbial community mixtures for biogas production
沼气生产微生物群落混合物的合理设计
  • 批准号:
    BB/T000740/1
  • 财政年份:
    2020
  • 资助金额:
    $ 89.59万
  • 项目类别:
    Research Grant
Biochemical and genetic characterisation of DNA polymerase D, a novel archaeal replicative polymerase
DNA 聚合酶 D(一种新型古菌复制聚合酶)的生化和遗传特征
  • 批准号:
    BB/K006630/1
  • 财政年份:
    2013
  • 资助金额:
    $ 89.59万
  • 项目类别:
    Research Grant
Functional in vivo and in vitro analysis of the archaeal chaperonin complex
古菌伴侣蛋白复合物的功能体内和体外分析
  • 批准号:
    BB/F003099/1
  • 财政年份:
    2008
  • 资助金额:
    $ 89.59万
  • 项目类别:
    Research Grant
Fluorescence mediated particle analysis of large populations of prokaryotic cells and viruses
对大量原核细胞和病毒进行荧光介导的颗粒分析
  • 批准号:
    BB/D525056/1
  • 财政年份:
    2006
  • 资助金额:
    $ 89.59万
  • 项目类别:
    Research Grant

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Hierarchy and intersection of hallmarks of aging using genetic, pharmacologic, and dietary life span extending interventions in flies and mice.
使用遗传、药理学和饮食延长果蝇和小鼠寿命的干预措施,研究衰老标志的层次结构和交叉点。
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