CIF21 DIBBs: PD: Accelerating Comparative Metagenomics through an Ocean Cloud Commons

CIF21 DIBB：PD：通过海洋云共享加速比较宏基因组学

• 批准号: 1640775
• 负责人: Bonnie Hurwitz
• 金额: $ 49.61万
• 依托单位: University of Arizona
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1640775&HistoricalAwards=false
• 关键词: CIF21; DIBBs; PD; Accelerating; Comparative

The Tara Oceans Expedition has provided the largest publicly available contiguous dataset available in genomics for any scientific project in the world. Using the research schooner Tara and modern sequencing and state-of-the-art imaging technologies, a multinational team of scientists sampled microscopic plankton at hundreds of sites and depths in all the major oceanic regions. The Tara Oceans Expedition data have been released, but it is a challenge for researchers to access, manipulate, and analyze such large-scale resources. This project creates an Ocean Cloud Commons (OCC), a cloud-based resource and repository allowing researchers to query the Tara Oceans Expedition Data in the cloud; it also makes available comparative metagenomic tools through the Ocean Treasure Box (OTB).The Ocean Cloud Commons and Ocean Treasure Box build upon established partnerships with organizations such as CyVerse Cyberinfrastructure, Agave Platform, OpenCloud, and computing facilities at the Texas Advanced Computing Center. The Ocean Cloud Commons uses an algorithm based on MapReduce to create a comparative metagenomics data resource in a Hadoop big data framework. The OCC can be widely accessed by researchers using tools developed in the Ocean Treasure Box and implemented as Apps in the CyVerse Cyberinfrastructure. Specifically, OTB tools deploy and compute on OCC data in OpenCloud via the Agave Platform and Developer API from CyVerse. Taken together, the OTB tools and OCC data resources enable researchers to address global-scale questions about the distribution of microbes across the sea that affect climate and ecosystem function.This award by the Advanced Cyberinfrastructure Division is jointly supported by the NSF Directorate for Biological Sciences (Division of Biological Infrastructure), and the NSF Directorate for Geosciences.

塔拉海洋探险队为世界上任何科学项目提供了基因组学领域最大的公开连续数据集。 一个多国科学家团队利用塔拉号研究船以及现代测序和最先进的成像技术，在所有主要海洋区域的数百个地点和深度对微观浮游生物进行了采样。 塔拉海洋探险数据已经发布，但对研究人员来说，获取、操纵和分析如此大规模的资源是一个挑战。 该项目创建了一个 Ocean Cloud Commons (OCC)，一个基于云的资源和存储库，允许研究人员在云中查询塔拉海洋探险数据；它还通过 Ocean Treasure Box (OTB) 提供比较宏基因组工具。Ocean Cloud Commons 和 Ocean Treasure Box 建立在与 CyVerse Cyber​​infrastruct、Agave Platform、OpenCloud 和德克萨斯高级计算中心的计算设施等组织建立的合作伙伴关系的基础上。 Ocean Cloud Commons使用基于MapReduce的算法在Hadoop大数据框架中创建比较宏基因组数据资源。 研究人员可以使用海洋宝箱中开发的工具广泛访问 OCC，并在 CyVerse 网络基础设施中作为应用程序实施。 具体来说，OTB 工具通过 CyVerse 的 Agave 平台和开发人员 API 在 OpenCloud 中的 OCC 数据上进行部署和计算。 总而言之，OTB 工具和 OCC 数据资源使研究人员能够解决影响气候和生态系统功能的海洋微生物分布的全球范围问题。该奖项由高级网络基础设施部门颁发，并得到 NSF 生物科学理事会的共同支持（生物基础设施司）和 NSF 地球科学理事会。

项目成果

The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes

• DOI: 10.3389/fmicb.2019.00806
• 发表时间: 2019-04-16
• 期刊: FRONTIERS IN MICROBIOLOGY
• 影响因子: 5.2
• 作者: Ponsero, Alise J.;Hurwitz, Bonnie L.
• 通讯作者: Hurwitz, Bonnie L.

Libra: Improved Partitioning Strategies for Massive Comparative Metagenomics Analysis

Libra：改进的大规模比较宏基因组分析的分区策略

• DOI: 10.1145/3217880.3217882
• 发表时间: 2018
• 期刊: Proceedings of the 9th Workshop on Scientific Cloud Computing
• 作者: Choi, Illyoung;Ponsero, Alise J.;Youens-Clark, Ken;Bomhoff, Matthew;Hurwitz, Bonnie L.;Hartman, John H.
• 通讯作者: Hartman, John H.

iMicrobe: Tools and data-driven discovery platform for the microbiome sciences

iMicrobe：微生物组科学的工具和数据驱动的发现平台

• DOI: 10.1093/gigascience/giz083
• 发表时间: 2019
• 期刊: GigaScience
• 影响因子: 9.2
• 作者: Youens-Clark, Ken;Bomhoff, Matt;Ponsero, Alise J;Wood-Charlson, Elisha M;Lynch, Joshua;Choi, Illyoung;Hartman, John H;Hurwitz, Bonnie L
• 通讯作者: Hurwitz, Bonnie L