2010 Best Practices Competition IT & Informatics HPC

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Published Resources for the Life Sciences 250 First Avenue, Suite 300, Needham, MA 02494 | phone: 781‐972‐5400 | fax: 781‐972‐5425 • Maintaining a shared intranet portal for collaboration and document sharing between the OCICB and NIAID laboratories • Documenting minimum requirements for software applications that will be hosted on the NIAID Linux High Performance Computing Cluster (in order to aid OEB in the determination of hardware specifications for the cluster) • Working with the NIAID laboratories to analyze and document workflows/pipelines for downstream data analysis • Installing, maintaining, upgrading, and supporting software applications on the NIAID Linux High Performance Computing Cluster • Providing user‐friendly, web‐based interfaces to software applications hosted on the NIAID Linux High Performance Computing Cluster • Evaluating and selecting a Laboratory Information Management System (LIMS) to assist with end‐to‐end processing and analysis of Next Generation Sequencing data C. RESULTS (highlight major R&D/IT tools deployed; innovative uses of technology). The OCICB’s Operations and Engineering Branch (OEB) has made several significant investments to support Next Generation Sequencing research, including improvements in the NIAID network, in data storage and processing hardware, and in the personnel required to build and maintain this infrastructure. Specific upgrades include the following: • Expansion of network bandwidth from 1 to 10 gigabits per second to support increased network traffic between NIAID research labs and the NIAID Data Center • Construction of a high‐speed and highly‐dense enterprise storage system, originally built at 300‐ terabyte capacity but rapidly scalable to up to 1.2 petabytes • Creation of a high‐performance Linux computing cluster hosting many third‐party applications that enables efficient data processing on a scalable and high‐memory pool of resources • Deployment of a localized mirror of the UCSC Genome Browser for rapid data visualization and sharing In addition to these upgrades, the OCICB’s Bioinformatics and Computational Biosciences Branch (BCBB) will provide bioinformatics collaboration and support to researchers. Specific resources that will be provided include the following: • End‐to‐end laboratory information management system (LIMS) to support sample preparation and tracking; task assignment; interaction with the instrument; downstream analysis and custom pipelines between applications; data sharing; and data publication/visualization • Training on the use of bioinformatics applications and development of custom workflows and application pipelines to streamline data analysis • Collaboration on the data integration, analysis, and annotation/publication processes Some policy decisions for using the centralized infrastructure have yet to be made, including formalizing procedures for long‐term data retention as well as balancing data privacy/security requirements while concurrently facilitating data sharing and publication. Nevertheless, NIAID’s centralized approach highlights the need for a cooperative partnership between bench researchers, computational scientists, and IT professionals in order to advance modern scientific exploration and discovery.
Published Resources for the Life Sciences 250 First Avenue, Suite 300, Needham, MA 02494 | phone: 781‐972‐5400 | fax: 781‐972‐5425 D. ROI achieved or expected (200 words max.): Expected returns on this investment are many and include the tangible and intangible benefits and cost avoidance measures listed below: Tangible Benefits: • Cost savings through reduction of people‐hours for IT development, application deployment, system maintenance, and customer support for centralized implementation (versus distributed implementations to support labs separately) Intangible Benefits: • Improved security/reduced risk by managing a single, centralized pool of infrastructure resources (includes enterprise‐level security, storage, and back‐up; dedicated virtual LAN; failover/load‐sharing file services cluster and scheduler; and a single, formal disaster recovery and continuity of operations plan) • Increased awareness of bioinformatics resources available to labs at NIAID and other NIH Institutes • Elevated access to single, integrated team of subject matter experts including system administrators, infrastructure analysts, bioinformatics developers, and sequence analysis experts • Enhanced collaboration with research organizations external to NIAID that will take advantage of high‐performance computing environment • Improved research productivity to work toward combating/eradicating critical diseases Cost Avoidance: • Efficient use of centralized storage and computing resources used at higher capacity • Leveraged energy efficiency of data center power and cooling systems • Estimated 5‐fold savings in software licensing fees for shared deployment on cluster • Limited consolidation and migration costs for systems/data in centralized implementation E. CONCLUSIONS/implications for the field. Genomic research is a rapidly growing field with broad implications at the NIAID and in the global research community in general. Rather than having laboratory staff attempt to develop the requisite storage, network, and computing capacity themselves, NIAID’s Chief Information Officer has made a significant investment to centralize infrastructure resources in order to maximize efficiency and minimize cost and risk. Major network and storage upgrades, in addition to the construction of a powerful and scalable Linux computing cluster, are the most visible parts of this investment. However, additional personnel – including an experienced Linux Systems Administrator and bioinformatics support staff – have also been acquired. By utilizing the centralized infrastructure and resources, researchers doing important and influential work in immunology, vaccinology, and many other research areas that are immensely beneficial to the public will be better able to conduct their research. Large datasets and powerful multi‐core computers are not unique to Next Generation Sequencing. Other research areas of interest at the NIAID will also benefit from the new high‐performance computing resources. The NIAID has been able to reuse many of its successful development, procurement, and
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