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CIF21 DIBBs: EI: Virtual Data Collaboratory: A Regional Cyberinfrastructure for Collaborative Data Intensive Science

CIF21 DIBB：EI：虚拟数据协作：协作数据密集型科学的区域网络基础设施

基本信息

批准号：
1640834
负责人：
Ivan Rodero
金额：
$ 400万
依托单位：
Rutgers University New Brunswick
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2016
资助国家：
美国
起止时间：
2016-09-01 至 2022-03-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1640834&HistoricalAwards=false
关键词：
CIF21 DIBBs EI Virtual Data

项目摘要

This project develops a virtual data collaboratory that can be accessed by researchers, educators, and entrepreneurs across institutional and geographic boundaries, fostering community engagement and accelerating interdisciplinary research. A federated data system is created, using existing components and building upon existing cyberinfrastructure and resources in New Jersey and Pennsylvania. Seven universities are directly involved (the three Rutgers University campuses, Pennsylvania State University, the University of Pennsylvania, the University of Pittsburgh, Drexel University, Temple University, and the City University of New York); indirectly, other regional schools served by the New Jersey and Pennsylvania high-speed networks also participate. The system has applicability to a several science and engineering domains, such as protein-DNA interaction and smart cities, and is likely to be extensible to other domains. The cyberinfrastructure is to be integrated into both graduate and undergraduate programs across several institutions. The end product is a fully-developed system for collaborative use by the research and education community. A data management and sharing system is constructed, based largely on commercial off-the-shelf technology. The storage system is based on the Hadoop Distributed File System (HDFS), a Java-based file system providing scalable and reliable data storage, designed to span large clusters of commodity servers. The Fedora and VIVO object-based storage systems are used, enabling linked data approaches. The system will be integrated with existing research data repositories, such as the Ocean Observatories Initiative and Protein Data Bank repositories. Regional high-performance computing and network infrastructure is leveraged, including New Jersey's Regional Education and Research Network (NJEdge), Pennsylvania's Keystone Initiative for Network Based Education and Research (KINBER), the Extreme Science and Engineering Discovery Environment (XSEDE) computing capabilities, Open Science Grid, and other NSF Campus Cyberinfrastructure investments. The project also develops a custom site federation and data services layer; the data services layer provides services for data linking, search, and sharing; coupling to computation, analytics, and visualization; mechanisms to attach unique Digital Object Identifiers (DOIs), archive data, and broadly publish to internal and wider audiences; and manage the long-term data lifecycle, ensuring immutable and authentic data and reproducible research.

该项目开发了一个虚拟数据协作实验室，研究人员，教育工作者和企业家可以跨越机构和地理界限访问，促进社区参与并加速跨学科研究。利用现有组件并在新泽西和宾夕法尼亚州现有网络基础设施和资源的基础上创建联合数据系统。七所大学直接参与（罗格斯大学的三个校区，宾夕法尼亚州立大学，宾夕法尼亚大学，匹兹堡大学，德雷克塞尔大学，坦普尔大学和纽约城市大学）;间接地，新泽西和宾夕法尼亚高速网络服务的其他地区学校也参与其中。该系统适用于多个科学和工程领域，如蛋白质-DNA相互作用和智能城市，并可能扩展到其他领域。网络基础设施将被整合到几个机构的研究生和本科生课程中。最终产品是一个完全开发的系统，供研究和教育界协作使用。建立了一个数据管理和共享系统，主要是基于商业现成的技术。存储系统基于Hadoop分布式文件系统（HDFS），这是一种基于Java的文件系统，提供可扩展和可靠的数据存储，旨在跨越大型商用服务器集群。使用Fedora和VIVO基于对象的存储系统，支持链接数据方法。该系统将与海洋观测站倡议和蛋白质数据库等现有研究数据储存库相结合。利用区域高性能计算和网络基础设施，包括新泽西的区域教育和研究网络（NJEdge），宾夕法尼亚州的基于网络的教育和研究的基石倡议（KINBER），极限科学和工程发现环境（XSEDE）计算能力，开放科学网格和其他NSF校园网络基础设施投资。该项目还开发了一个自定义站点联合和数据服务层;数据服务层提供数据链接，搜索和共享服务;耦合到计算，分析和可视化;附加唯一数字对象标识符（DOI），归档数据并广泛发布给内部和更广泛的受众的机制;并管理长期数据生命周期，确保不可变和真实的数据和可复制的研究。

项目成果

期刊论文数量（28）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Submarine: A subscription‐based data streaming framework for integrating large facilities and advanced cyberinfrastructure

Submarine：基于订阅的数据流框架，用于集成大型设施和先进的网络基础设施

DOI：
10.1002/cpe.5256
发表时间：
2019
期刊：
Concurrency and Computation: Practice and Experience
影响因子：
0
作者：
Zamani, Ali Reza;AbdelBaky, Moustafa;Balouek‐Thomert, Daniel;Villalobos, J. J.;Rodero, Ivan;Parashar, Manish
通讯作者：
Parashar, Manish

Enabling Data Streaming-based Science Gateways through Federated Cyberinfrastructure

通过联合网络基础设施启用基于数据流的科学网关

DOI：
发表时间：
2019
期刊：
Gateways 2019
影响因子：
0
作者：
Rodero, I;Qin, Y;Valls, J;Simonet, A;Villalobos, J.J.;Parashar, M;Youn, C;Wang, C;Thareja, K;Ruth, P
通讯作者：
Ruth, P

iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines

iScore：一款 MPI 支持的软件，用于基于随机游走图内核和支持向量机对蛋白质对接模型进行排名

DOI：
10.1016/j.softx.2020.100462
发表时间：
2020
期刊：
SoftwareX
影响因子：
3.4
作者：
Renaud, Nicolas;Jung, Yong;Honavar, Vasant;Geng, Cunliang;Bonvin, Alexandre M.J.J.;Xue, Li C.
通讯作者：
Xue, Li C.

Biomarker discovery in inflammatory bowel diseases using network-based feature selection