ODF: Support infrastructure for NextGen sequence storage analysis and mgt

ODF：下一代序列存储分析和管理的支持基础设施

• 批准号: 9270754
• 负责人: Owen R White
• 金额: $ 12.35万
• 依托单位: UNIVERSITY OF MARYLAND BALTIMORE
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-05-15 至 2017-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9270754
• 关键词: Architecture; Archives; Bioinformatics; Client; Communities; Complex; Computer software; Computers; Consultations; Controlled Vocabulary; DDBJ; Data; Data Analyses; Data Display; Data Set; Data Storage and Retrieval; Databases; Detection; Development; Documentation; Effectiveness; Ensure; Environment; Epigenetic Process; Genbank; Genetic Variation; Genome; Genomics; Goals; Human; Human Genetics; Human Microbiome; Individual; Institutes; Internet; Medical Research; Metadata; Metagenomics; Online Systems; Procedures; Process; Production; Research; Research Infrastructure; Research Personnel; Resources; Retrieval; Services; Site; Software Framework; Strategic Planning; System; Time; Training; Translational Research; Variant; Work; application programming interface; base; cloud based; computerized data processing; computing resources; cost; cost effective; data access; data exchange; data modeling; data sharing; design; distributed data; file format; genome analysis; genome sequencing; genomic data; laptop; meetings; microbiome; next generation sequencing; open data; open source; repository; success; technological innovation; tool; transcriptome; transcriptomics; usability; virtual; working group

DESCRIPTION (provided by applicant): The Open Science Data Framework (OSDF) will provide the architecture and software necessary for conducting bioinformatics analyses in a federated cloud-enabled data and computational environment. The OSDF consists of a data store and data exchange procedures with an Application Program Interface (API) to support data submissions, retrievals and analysis for the user community. OSDF will support a diverse set of users, including (1) sequence generators that need to store and process raw data (2) tool and pipeline developers that need access to reference data sets, and (3) web-based resources that need real-time querying of reference data. The genomics community will be able to use this resource to process human genomic, transcriptomics, and metagenomic data to conduct analyses that include human variation detection, transcriptome analysis, epigenetic analysis, and microbiome analysis. To accomplish these goals we propose to: 1) establish the OSDF software stack and; 2) ensure the usability of this data by integrating OSDF with established community supported pipelines in Cloud-enabled virtual machines; 3) create two OSDF Instances where we will host publicly available genomic, transcriptomics, and metagenomic data from the 1000 Genomes Project, MG-RAST, and Human Microbiome Project and some of the intermediate and final analysis results; 4) provide adequate documentation and training to the user community to use the system.

描述（由申请人提供）：开放科学数据框架（OSDF）将提供在联邦云数据和计算环境中进行生物信息学分析所需的架构和软件。OSDF由一个数据存储和数据交换过程组成，并带有一个应用程序接口（API）来支持用户社区的数据提交、检索和分析。OSDF将支持多种用户，包括(1)需要存储和处理原始数据的序列生成器；(2)需要访问参考数据集的工具和管道开发人员；(3)需要实时查询参考数据的基于web的资源。基因组学社区将能够利用该资源处理人类基因组学、转录组学和宏基因组学数据，以进行包括人类变异检测、转录组分析、表观遗传分析和微生物组分析在内的分析。为了实现这些目标，我们建议：1)建立OSDF软件栈和；2)通过将OSDF与已建立的社区支持的管道集成到支持云的虚拟机中，确保这些数据的可用性；3)创建两个OSDF实例，其中我们将托管来自1000基因组计划，MG-RAST和人类微生物组计划的公开基因组，转录组学和宏基因组学数据以及一些中间和最终分析结果；4)为使用系统的用户群体提供充分的文档和培训。

项目成果

The MG-RAST metagenomics database and portal in 2015.

• DOI: 10.1093/nar/gkv1322
• 发表时间: 2016-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Wilke A;Bischof J;Gerlach W;Glass E;Harrison T;Keegan KP;Paczian T;Trimble WL;Bagchi S;Grama A;Chaterji S;Meyer F
• 通讯作者: Meyer F