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，研究人员，教育工作者和企业家可以在机构和地理边界上访问，从而促进社区参与并加速跨学科研究。使用现有组件并在新泽西州和宾夕法尼亚州现有的网络基础结构和资源上建立联合数据系统。直接参与了七所大学（宾夕法尼亚州立大学的三个罗格斯大学校园，宾夕法尼亚大学，匹兹堡大学，德雷克斯尔大学，坦普尔大学和纽约市）；在新泽西州和宾夕法尼亚州高速网络服务的其他区域学校也间接参加。该系统适用于几个科学和工程领域，例如蛋白质-DNA相互作用和智能城市，并且可能对其他领域可扩展。网络基础设施应纳入几个机构的研究生和本科课程。最终产品是一个完整的研究系统，用于研究和教育社区。数据管理和共享系统是基于商业现成技术的。该存储系统基于Hadoop分布式文件系统（HDFS），该文件系统基于Java的文件系统提供可扩展可靠的数据存储，旨在跨越大量的商品服务器群。使用了Fedora和Vivo基于对象的存储系统，从而实现了链接的数据方法。该系统将与现有的研究数据存储库集成，例如海洋天文台计划和蛋白质数据库存储库。利用了区域高性能计算和网络基础架构，包括新泽西州的区域教育与研究网络（NJEDGE），宾夕法尼亚州的基于网络的教育与研究的基石倡议（KINBER），极端的科学与工程发现环境（XSSEDE环境（XSSEDE）计算能力，开放科学网络，开放科学网络，以及其他NSF Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus Campus camberin。该项目还开发了自定义站点联合和数据服务层；数据服务层为数据链接，搜索和共享提供服务；与计算，分析和可视化耦合；附加独特的数字对象标识符（DOIS），存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，以确保不可变和真实的数据和可重复的研究。

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）

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

DOI：
10.1371/journal.pone.0225382
发表时间：
2019-11-22
期刊：
PLOS ONE
影响因子：
3.7
作者：
Abbas, Mostafa;Matta, John;EL-Manzalawy, Yasser
通讯作者：
EL-Manzalawy, Yasser

iScore: a novel graph kernel-based function for scoring protein-protein docking models

DOI：
10.1093/bioinformatics/btz496
发表时间：
2020-01-01
期刊：
BIOINFORMATICS
影响因子：
5.8
作者：
Geng, Cunliang;Jung, Yong;Xue, Li C.
通讯作者：
Xue, Li C.

Fairness in Algorithmic Decision Making: An Excursion Through the Lens of Causality

DOI：
10.1145/3308558.3313559
发表时间：
2019-01-01
期刊：
WEB CONFERENCE 2019: PROCEEDINGS OF THE WORLD WIDE WEB CONFERENCE (WWW 2019)
影响因子：
0
作者：
Khademi, Aria;Lee, Sanghack;Honavar, Vasant
通讯作者：
Honavar, Vasant

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