Collaborative Research: ABI Sustaining: The National Center for Genome Analysis Support

基因组研究是理解生命变异性、生物功能、种群动态以及生物体如何应对外部影响的关键和快速增长的组成部分。基因组学从质量上提高了我们研究生物动力学的能力，并做出了重要的发现，这些发现是理解环境变化、发展和保护作物以及改善健康结果等主题的基础。然而，基因组分析对实践生物学家来说是一个重大挑战。大多数需要从事基因组科学的生物学家在相关分析工具方面不够专业，或者不了解从测序仪生成的初始数据到具有生物学意义的分析结果所需的复杂工作流程。此外，很少有人能够获得处理和管理基因组学数据所需的超级计算资源和大规模存储。国家基因组分析支持中心（NCGAS）通过提供由专家咨询和教育服务组成的综合服务、通过易于使用的基于web的工作流管理工具、大内存超级计算机以及大规模数据存储和发布设施提供的加固和优化软件来解决这些挑战。这些资源对来自规模较小、服务于少数族裔的机构的研究人员特别有用，这些机构通常无法获得所需的专业知识和网络基础设施，但他们的研究同样重要。自2011年成立以来，NCGAS已经支持了80多个研究项目，研究经费超过6100万美元。它开展了51项培训活动，为691人提供了服务，其中241人来自传统上服务不足的人口。NCGAS （http://ncgas.org）于2011年通过国家科学基金会ABI发展奖成立，旨在帮助国家研究界完成需要大规模数据管理和计算基础设施的基因组学研究。NCGAS是由印第安纳大学普及技术研究所、匹兹堡超级计算中心、德克萨斯高级计算中心和圣地亚哥超级计算中心合作建立的。它通过为基因组分析，特别是基因组和转录组组装，包括研究设计，数据分析和可视化提供优秀的生物信息学咨询服务，满足现代基因组科学的技术挑战。它在国家超级计算系统上优化、支持和提供基因组分析软件，例如由NSF极限数字（XD）计划资助、由极限科学与工程发现环境（XSEDE）和开放科学网格（OSG）协调的超级计算系统。NCGAS维护并支持易于使用的网关，包括Galaxy web门户，用于基因组分析工作流程，降低了科学家创建、执行、记录和共享基因组分析的障碍。它向研究计算设施和一般研究社区分发用于基因组分析的软件工具，以便It经理可以更容易地在他们的系统上安装这些工具。提供长期档案保管服务。NCGAS为数据集、出版物、报告或文件集合的传播提供了一个数字图书馆资源，这将使研究可见，数据在未来几十年内可以重复使用。它为全国的生物学教师和学生提供基因组分析、解释和数据管理方面的教育和推广项目。这些计划将提高执业科学家的技术素养，并帮助发展生物信息学劳动力。这些服务特别适用于全国范围内没有超级计算机、生物信息学专业知识或培训的小型机构。NCGAS将实现没有先进网络基础设施支持就不可能实现的突破。

The study of genomes is a critical and rapidly growing component in understanding the variability of life, biological functions, population dynamics, and how organisms respond to external influences. Genomics has qualitatively improved our ability to investigate biological dynamics and to make important discoveries that are the foundations for understanding topics such as environmental change, developing and protecting crops, and improving health outcomes. Genome analysis, however, is a significant challenge for the practicing biologist. Most biologists who need to undertake genome science are not sufficiently expert in the relevant analytical tools, or understand the complex workflows required to get from the initial data generated by sequencers to a biologically meaningful analyzed result. In addition, few have access to the supercomputing resources and large-scale storage required for processing and managing genomics data. The National Center for Genome Analysis Support (NCGAS) addresses these challenges by providing an integrated service comprised of expert consulting and educational services, hardened and optimized software available through easy to use web-based workflow management tools, large memory supercomputers, and large scale data storage and publishing facilities. These resources are particularly useful for researchers from smaller, and minority serving, institutions that typically do not have access to the required expertise and cyberinfrastructure, yet whose investigations are equally important. Since its inception in 2011, the NCGAS has supported over 80 research projects representing over $61M in funded research. It engaged in 51 training events that served 691 individuals, of which 241 were from traditionally underserved populations.The NCGAS (http://ncgas.org) was established in 2011 through a National Science Foundation ABI development award to help the national research community complete genomics research that requires data management and computational infrastructures at scale. NCGAS is a partnership among the Indiana University Pervasive Technology Institute, the Pittsburgh Supercomputing Center, the Texas Advanced Computing Center, and the San Diego Supercomputing Center. It meets the technology challenges of modern genome science by providing excellent bioinformatics consulting services for genome analysis, particularly genome and transcriptome assembly, including research design, data analysis and visualization. It optimizes, supports, and delivers genome analysis software on national supercomputing systems such as those funded by the NSF eXtreme Digital (XD) program and coordinated by the eXtreme Science and Engineering Discovery Environment (XSEDE) and the Open Science Grid (OSG). The NCGAS maintains and supports easy-to-use gateways, including Galaxy web portals, for genome analysis workflows that lower barriers for scientist to create, execute, document, and share genomics analyses. It distributes software tools for genome analysis to research computing facilities and the general research community so that IT managers can more easily install these tools on their systems. It provides long-term archival storage services. The NCGAS provides a digital library resource for the dissemination of data sets, publications, reports, or collections of files that will allow research to be visible and data to be re-used for decades to come. It delivers education and outreach programs on genome analysis, interpretation, and data management to biology faculty and students nationally. These programs will enhance the technology literacy of practicing scientists and help grow the bioinformatics workforce. These services are particularly available to smaller institutions across the country without access to supercomputers, bioinformatics expertise, or training. The NCGAS will enable breakthroughs that would not be possible without advanced cyberinfrastructure support.