Enabling UK wheat research with the CyVerse UK cyberinfrastructure

利用 CyVerse 英国网络基础设施支持英国小麦研究

• 批准号: BB/R000662/1
• 负责人: Robert Davey
• 金额: $ 36.11万
• 依托单位: Earlham Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FR000662%2F1
• 关键词: Enabling; UK; wheat; research; CyVerse

Bread wheat represents one of the most complex examples of a plant genome, as well as one of the most commercially important in the UK and internationally with over 750 million tonnes harvested annually, 14 million in the UK alone. This juxtaposition creates a range of challenges for biologists and data analysts - how can the balance between needing large amounts of data to answer complex biological questions about wheat genetics and the requirements for analysing this data and be found? Furthermore, the pressing issues of climate change that we face are all too evident. We need to use modern technology to increase productivity and output for our wheat researchers, drive breeding strategies, and benefit the public's nutritional needs.CyVerse represents such a technology, whereby computational resources, data storage, and analytical tools are made available through web-based graphical interfaces for end users or command line interfaces for power users or system administrators. CyVerse UK is the first implementation of the multi-million dollar CyVerse project outside the US, and both systems are interoperable, i.e. able to share their compute and storage services without the user needing to know where their analyses will be taking place. This federation allows a reduction in shared management cost, and an increase in productivity through shared expertise and software development.The use of "the cloud" is commonplace in today's internet era. Users are moving away from storing data on their own devices, but using services hosted by third party providers such as Google, Microsoft, and Amazon. Furthermore, these vendors also supply complete computing environments over the internet, e.g. Amazon Web Services, and Microsoft Azure. However, these resources are not designed for the kinds of scale that are required for wheat researchers to make the most of publicly available and personal datasets, and the costs of running such environments are unclear at best and prohibitive at worst. Therefore, through the deployment of the proposed CyVerse Atmosphere cloud computing platform in the UK, we would be able to supply virtual server resources to users "elastically", i.e. elastic computing resources can be scaled up and down easily by users themselves. In this way, we can provide flexible computing power when and wherever required, to wheat researchers, labs, and breeders. These virtual wheat data analysis labs can be shared with a wider research group, even internationally, promoting collaboration and knowledge transfer.

面包小麦是植物基因组中最复杂的例子之一，也是英国和国际上最重要的商业作物之一，每年收获超过7.5亿吨，仅英国就有1400万吨。这种并列为生物学家和数据分析师带来了一系列挑战-如何在需要大量数据来回答有关小麦遗传学的复杂生物学问题与分析这些数据的要求之间找到平衡？此外，我们面临的紧迫的气候变化问题非常明显。我们需要使用现代技术来提高小麦研究人员的生产力和产量，推动育种策略，并使公众的营养需求受益。CyVerse代表了这样一种技术，通过基于Web的图形界面为最终用户提供计算资源，数据存储和分析工具，或者通过命令行界面为高级用户或系统管理员提供命令行界面。CyVerse UK是在美国以外的数百万美元CyVerse项目的第一个实施，两个系统都是可互操作的，即能够共享他们的计算和存储服务，而用户不需要知道他们的分析将在哪里进行。这种联合可以减少共享管理成本，并通过共享专业知识和软件开发来提高生产率。在当今的互联网时代，“云”的使用是司空见惯的。用户不再将数据存储在自己的设备上，而是使用由谷歌、微软和亚马逊等第三方提供商托管的服务。此外，这些供应商还通过互联网提供完整的计算环境，例如Amazon Web Services和Microsoft Azure。然而，这些资源并不是为小麦研究人员充分利用公共和个人数据集所需的规模而设计的，而且运行这种环境的成本充其量是不清楚的，最坏的情况是令人望而却步。因此，透过在英国部署建议的CyVerse Atmosphere云端计算平台，我们将能够“弹性”地向用户提供虚拟服务器资源，即弹性计算资源可由用户自行轻松地按比例增加和减少。通过这种方式，我们可以随时随地为小麦研究人员、实验室和育种者提供灵活的计算能力。这些虚拟小麦数据分析实验室可以与更广泛的研究小组共享，甚至在国际上，促进合作和知识转移。

项目成果

COPO: a metadata platform for brokering FAIR data in the life sciences

• DOI: 10.1101/782771
• 发表时间: 2019-09
• 期刊: bioRxiv
• 作者: Anthony Etuk;Felix Shaw;Alejandra N. González-Beltrán;David Johnson;Marie-Angélique Laporte;P. Rocca-Serra;E. Arnaud;M. Devare;P. Kersey;Susanna-Assunta Sansone;Robert P. Davey

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems.

• DOI: 10.1016/j.patter.2020.100105
• 发表时间: 2020-10-09
• 期刊: Patterns (New York, N.Y.)
• 作者: Arnaud E;Laporte MA;Kim S;Aubert C;Leonelli S;Miro B;Cooper L;Jaiswal P;Kruseman G;Shrestha R;Buttigieg PL;Mungall CJ;Pietragalla J;Agbona A;Muliro J;Detras J;Hualla V;Rathore A;Das RR;Dieng I;Bauchet G;Menda N;Pommier C;Shaw F;Lyon D;Mwanzia L;Juarez H;Bonaiuti E;Chiputwa B;Obileye O;Auzoux S;Yeumo ED;Mueller LA;Silverstein K;Lafargue A;Antezana E;Devare M;King B
• 通讯作者: King B

Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement.

• DOI: 10.1038/s41587-021-01058-4
• 发表时间: 2022-03
• 期刊: Nature biotechnology
• 影响因子: 46.9
• 作者: Gaurav K;Arora S;Silva P;Sánchez-Martín J;Horsnell R;Gao L;Brar GS;Widrig V;John Raupp W;Singh N;Wu S;Kale SM;Chinoy C;Nicholson P;Quiroz-Chávez J;Simmonds J;Hayta S;Smedley MA;Harwood W;Pearce S;Gilbert D;Kangara N;Gardener C;Forner-Martínez M;Liu J;Yu G;Boden SA;Pascucci A;Ghosh S;Hafeez AN;O'Hara T;Waites J;Cheema J;Steuernagel B;Patpour M;Justesen AF;Liu S;Rudd JC;Avni R;Sharon A;Steiner B;Kirana RP;Buerstmayr H;Mehrabi AA;Nasyrova FY;Chayut N;Matny O;Steffenson BJ;Sandhu N;Chhuneja P;Lagudah E;Elkot AF;Tyrrell S;Bian X;Davey RP;Simonsen M;Schauser L;Tiwari VK;Randy Kutcher H;Hucl P;Li A;Liu DC;Mao L;Xu S;Brown-Guedira G;Faris J;Dvorak J;Luo MC;Krasileva K;Lux T;Artmeier S;Mayer KFX;Uauy C;Mascher M;Bentley AR;Keller B;Poland J;Wulff BBH
• 通讯作者: Wulff BBH

AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids.

AutoCloner：自动同源特异性引物设计，用于多倍体中的全基因克隆。

• DOI: 10.1186/s12859-020-03601-7
• 发表时间: 2020
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Coulton A

Colombia's cyberinfrastructure for biodiversity: Building data infrastructure in emerging countries to foster socioeconomic growth

哥伦比亚的生物多样性网络基础设施：在新兴国家建设数据基础设施以促进社会经济增长

• DOI: 10.1002/ppp3.10086
• 发表时间: 2019
• 期刊: PLANTS, PEOPLE, PLANET
• 作者: De Vega J