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

基因组的研究是理解生命的变异性，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，并取得了重要发现，这些发现是理解环境变化，开发和保护作物以及改善健康状况等主题的基础。然而，基因组分析对执业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来解决这些挑战，通过易于使用的基于Web的工作流程管理工具，大型内存超级计算机和大规模数据存储和发布设施提供强化和优化的软件。 这些资源对于来自较小和少数民族服务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，但他们的调查同样重要。自2011年成立以来，NCGAS已经支持了80多个研究项目，代表了超过6100万美元的资助研究。 NCGAS（ncgas.org）成立于2011年，通过国家科学基金会ABI发展奖，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是印第安纳州大学普适技术研究所、匹兹堡超级计算中心、德克萨斯州高级计算中心和圣地亚哥超级计算中心之间的合作伙伴关系。它通过为基因组分析，特别是基因组和转录组组装提供卓越的生物信息学咨询服务，包括研究设计，数据分析和可视化，来应对现代基因组科学的技术挑战。它优化，支持和提供国家超级计算系统上的基因组分析软件，例如由NSF eXtreme Digital（XD）计划资助并由eXtreme Science and Engineering Discovery Environment（XSEDE）和Open Science Grid（OSG）协调的系统。NCGAS维护和支持易于使用的网关，包括Galaxy门户网站，用于基因组分析工作流程，降低科学家创建，执行，记录和共享基因组学分析的障碍。它将用于基因组分析的软件工具分发给研究计算设施和一般研究社区，以便IT管理人员可以更容易地在其系统上安装这些工具。它提供长期的档案存储服务。NCGAS提供了一个数字图书馆资源，用于传播数据集、出版物、报告或文件集，这将使研究可见，并使数据在未来几十年内重新使用。它为全国的生物学教师和学生提供关于基因组分析，解释和数据管理的教育和推广计划。这些计划将提高实践科学家的技术素养，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.