Página 1 dos resultados de 36 itens digitais encontrados em 0.000 segundos

Experiences with a large-memory HP cluster ??? performance on benchmarks and genome codes

Stewart, Craig A.; Henschel, Robert; Barnett, William K.; Doak, Thomas
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Presented at: HP-CAST 17 - HP Consortium for Advanced Scientific and Technical Computing World-Wide User Group Meeting. Renaissance Hotel, 515 Madison Street, Seattle WA, USA, November 12th 2011.; This presentation discusses the new National Center for Genome Analysis Support (NCGAS) and benchmarking of an HP ProLiant DL580 G7 supercomputer.

Technical Report: Benchmarking an HP DL580 cluster at Indiana University (Mason)

Stewart, Craig A.; Link, Matthew R.; Henschel, Robert; Hancock, David; Li, Huian
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the funding agencies that supported this work.; Detailed system description and benchmark performance of Mason, an HP DL580 system installed in 2011.

A Nation-Wide Area Networked File System for Very Large Scientific Data

Barnett, William K.; LeDuc, Richard
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Presented at Bio-IT World Conference and Expo ???12.; Sequencing is creating analytical problems that cannot be solved at sequencing centers or labs. Bioinformatics support, storage, data transfer, and computation all needed to do the science. NCGAS provides a model of a scaled infrastructure for biologists who cannot become bioinformaticians to accomplish their research.; This document was developed with support from National Science Foundation (NSF) grant OCI-1053575. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.

National Center for Genome Analysis Support (Poster)

Doak, Thomas G.; Wu, Le-Shin; Stewart, Craig A.; Henschel, Robert; Barnett, William K.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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This document was developed with support from National Science Foundation (NSF) grant OCI-1053575. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.

High Performance Data Management and Computational Architectures for Genomics Research at National and International Scales

Barnett, William K.; LeDuc, Richard
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Presented at Bio-IT World Asia.; Summary: Changing genomics analytical needs; NCGAS and its mission; NCGAS cyberinfrastructure; the 100 Gigabit demonstration; scaling genomics analysis; the NCGAS research model; and outcomes for life sciences research; This document was developed with support from National Science Foundation (NSF) grant OCI-1053575. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF.

The National Center for Genome Analysis Support and Galaxy

LeDuc, Richard D.; Barnett, William K.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Presented in Chicago Illinois at the Galaxy Community Conference, 2012; The National Center for Genome Analysis Support is an NSF funded resource designed to supply bioinformatic support and computational infrastructure to genomics projects requiring large RAM computational resources ??? specifically de novo sequence assembly. We are developing a national scale infrastructure to support biological researchers that will use Galaxy to interface between the biologists and the cyberinfrastructure. The ability of NCGAS to assist with bioinformatic software optimization was recently demonstrated by our assistance in optimizing the runtime performance of Trinity resulting in over 3x speed improvement.; This material is based upon work supported by the National Science Foundation under Grants No. ABI-1062432. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Empowering Bioinformatics Workflows Using the Lustre Wide Area File System across a 100 Gigabit Network

Simms, Stephen; Seiffert, Kurt
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Presented at BioITWorld Cloud Summit September 11-13, 2012.; Managing the profusion and accumulated volumes of life-science data is cumbersome; transferring them can require anything from shipping a hard drive to paying a graduate student to babysit transfers. Indiana University???s Data Capacitor solves this problem by exporting a high-performance Lustre file system across wide area networks to multiple locations. A mounted file system lets researchers run simple and familiar commands without having to contend with special tools for data transfer. Moreover, multiple mounts let researchers compute against their data from anywhere. To meet the insatiable bandwidth demands of life scientists, network infrastructure providers are increasingly offering 100 Gigabit circuits. IU recently used Lustre across a 100 Gigabit network spanning 2,300 miles to demonstrate application performance across a great distance. This presentation will describe the Data Capacitor cyber infrastructure and associated work, explore future use cases applicable to bioinformatics, and explain how the National Center for Genome Analysis Support (NCGAS) at Indiana University intends to integrate the Data Capacitor into their workflows.

National Center for Genome Analysis Program Year 1 Report ??? September 15, 2011 ??? September 14, 2012

Barnett, William; Ganote, Carrie; Vaughn, Matthew; LeDuc, Richard D.; Stewart, Craig A.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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Relevância na Pesquisa
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On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support (NCGAS). This technical report describes the activities of the first 12 months of NCGAS, during which time NCGAS brought online a large-RAM computational cluster, recruited 25 NSF-funded genomics projects to use the resource, responded to 502 requests for support, and processed 28,523 computational jobs representing a total of 136.83 core years of computing. NCGAS also laid the framework for creating a truly national-scale center supporting genomics research. By coordinating effort between multiple supercomputing centers, NCGAS is creating a service-oriented computational infrastructure ??? one that is designed to be approachable by end-users unaccustomed to using traditional supercomputing resources. The benefits of such inter-institutional coordination can be seen from events such as the NCGAS co-hosted Daphnia Genomics Jamboree. At this gathering, dozens of scientists from across the US and Europe spent five days accelerating the completion of the Daphnia manga genome. NCGAS-supported staff from both Texas Advanced Computing Center (TACC) and IU gave presentations early in the Jamboree before participants broke into small teams and used NCGAS clusters to perform their analyses. NCGAS also established a Galaxy web portal to allow researchers to use our large-RAM cluster with a familiar web interface...

NCGAS (Poster at AMIA Translational Bioinformatics Summit)

Barnett, William K.; LeDuc, Richard D.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Presented at AMIA Translational Bioinformatics Summit, San Francisco, CA; “This material is based upon work supported by the National Science Foundation under Grants No. ABI-1062432.” “This work was supported in part by the Lilly Endowment, Inc. and the Indiana University Pervasive Technology Institute.” Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation or any other funding agencies.”

Cyberinfrastructure Resources for Bioinformatics Research

Hallock, Barbara L.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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16.76%
Poster presented at the Bio-IT World Expo in Boston, MA, April 2013.; A basic description of cyberinfrastructure resources provided by XSEDE, IU, and NCGAS for bioinformatics researchers.

Optimizing the National Cyberinfrastructure for Lower Bioinformatic Costs: Making the Most of Resources for Publicly Funded Research

Barnett, William K.; LeDuc, Richard D.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Relevância na Pesquisa
27.42%
Presented at the RNA-Seq Conference, June 18-20, 2013 in Boston Massachusetts.; Overviews of NCGAS mission, cyberinfrastructure, and server-on-demand resources and of XSEDE for larger-scale resources.; This material is based upon work supported by the National Science Foundation under Grant No. ABI-1062432, Craig Stewart, PI. William Barnett, Matthew Hahn, and Michael Lynch, co-PIs. This work was supported in part by the Lilly Endowment, Inc. and the Indiana University Pervasive Technology Institute. Any opinions presented here are those of the presenter(s) and do not necessarily represent the opinions of the National Science Foundation or any other funding agencies

National Center for Genome Analysis Program Year 2 Report ??? September 15, 2012 ??? September 14, 2013

Barnett, William K.; LeDuc, Richard D.; Stewart, Craig A.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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Relevância na Pesquisa
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On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support (NCGAS). This technical report describes the activities of the second 12 months of NCGAS; The facilities supported by the Research Technologies division at Indiana University are supported by a number of grants. The authors would like to acknowledge that although the National Center for Genome Analysis Support is funded by NSF 1062432, our work would not be possible without the generous support of the following awards received by our parent organization, the Pervasive Technology Institute at Indiana University. ??? The Indiana University Pervasive Technology Institute was supported in part by two grants from the Lilly Endowment, Inc. ??? NCGAS has also been supported directly by the Indiana METACyt Initiative. The Indiana METACyt Initiative of Indiana University is supported in part by the Lilly Endowment, Inc. ??? This material is based in part upon work supported by the National Science Foundation under Grant No. CNS-0521433. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation (NSF).

Galaxy Deployment on Heterogenous Hardware

Ganote, Carrie; Hayashi, Soichi
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Talk presented at Galaxy Community Conference 2014, June 30 - July 2, 2014. Video is available at URL: https://wiki.galaxyproject.org/Events/GCC2014/Abstracts/Talks#Galaxy_Deployment_on_Heterogenous_Hardware; Indiana University, like many institutions, houses a heterogenous mixture of compute resources. In addition to university resources, the National Center for Genome Analysis Support, the Extreme Science and Engineering Discovery Environment, and the Open Science Grid all provide resources to biologists with NSF affiliations. Such a diverse mixture of compute power and services could be applied to address the equally diverse set of problems and needs in the bioinformatics field. Many software suites are well suited for large numbers of fast CPUS, such as phylogenetic tree building algorithms. De novo assembly problems really crave a machine with lots of RAM to spare. Alignment and mapping problems where each input is a separate invocation lend themselves perfectly to high-throughput, heavily distributed compute systems. Galaxy is a web interface that acts as a mediator between the biologist and the underlying hardware and software - in an ideal setup, Galaxy would be able to delegate work to the best suited underlying infrastructure. We present an instance of Galaxy at Indiana University...

National Center for Genome Analysis Program Year 3 Report – September 15, 2013 – September 14, 2014

Barnett, William K.; Stewart, Craig A.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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Relevância na Pesquisa
27.98%
On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support (NCGAS). This technical report describes the activities of the third 12 months of NCGAS; The facilities supported by the Research Technologies division at Indiana University are supported by a number of grants. The authors would like to acknowledge that although the National Center for Genome Analysis Support is funded by NSF 1062432, our work would not be possible without the generous support of the following awards received by our parent organization, the Pervasive Technology Institute at Indiana University. • The Indiana University Pervasive Technology Institute was supported in part by two grants from the Lilly Endowment, Inc. • NCGAS has also been supported directly by the Indiana METACyt Initiative. The Indiana METACyt Initiative of Indiana University is supported in part by the Lilly Endowment, Inc. • This material is based in part upon work supported by the National Science Foundation under Grant No. CNS-0521433. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation (NSF).

Genome Analysis: Birds of a Feather

Stewart, Craig A.; Blood, Philip; Knepper, Richard D.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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This Birds-of-a-Feather session presents the national infrastructure serving genome science, including NCGAS, iPlant, XSEDE, and networks, detailing goals, resources, and projects.; This research is supported by NSF Award 1062432 ??? ABI Development: National Center for Genome Analysis Support (NCGAS). ??This research was also supported by a generous grant from the Lilly Endowment, Inc. to the Indiana University Pervasive Technology Institute.

Indiana University’s advanced cyberinfrastructure in service of IU strategic goals: Activities of the Research Technologies Division of UITS and National Center for Genome Analysis Support – two Pervasive Technology Institute cyberinfrastructure and service centers - during FY2014

Stewart, Craig A.; Barnett, William K.; Hancock, David Y.; Henschel, Robert; Link, Matthew R.; Miller, Therese; Wernert, Eric A.
Fonte: Indiana University Publicador: Indiana University
Tipo: Relatório
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This report presents information on the activities of the Research Technologies Division of UITS and the National Center for Genome Analysis Support, two cyberinfrastructure and service centers of the Pervasive Technology Institute. Research Technologies (RT) is a subunit of University Information Technology Services (UITS) and it operates and supports the largest computational, data, and visualization systems at IU. The National Center for Genome Analysis Support (NCGAS) is primarily federally funded, serving the national community of genome scientists. NCGAS leadership is drawn from the Office of the Vice President for Information Technology, UITS, the College, and the School of Informatics and Computing. This report focuses on contributions of RT and NCGAS to accomplishment of IU’s bicentennial goals, and is organized according to those goals. Together the activities of NCGAS and RT represent a large share of the activities of PTI in support of the IU community. PTI’s Research Centers (Data to Insight Center, Digital Science Center, and the Center for Applies Cybersecurity Research) also provide support to the IU community in various forms but the primary focus of these research centers is informatics, information technology...

Providing National Cyberinfrastructure to Biologists, esp. genomicists

Barnett, William K.; Doak, Thomas G.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Presented at 2015 Open Science Grid (OSG) All-Hands Meeting; The presentation outlines the science and research addressed by NCGAS, the resources NCGAS provides, and the near- to-mid-term future of bioinformatics research.

Cyberinfrastructure for Research: New Trends and Tools (Part 2 of 2)

Stewart, Craig A,
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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The presentation discusses CI tools and resources for research, including XSEDE, Jetstream, Bridges, NCGAS, XSEDE ECSS, campus bridging, Wrangler, and Comet; Bridges is supported by NSF award 1445606. Comet is supported by NSF award 1341698. Wrangler is supported by NSF award 1341711. Jetstream is supported by NSF award 144560. XSEDE is supported by NSF award 1053575. This work was also supported by the Indiana University Pervasive Technology Institute, which was initiated with major funding from the Lilly Endowment, Inc.

Galaxy based BLAST submission to distributed national high throughput computing resources

Hayashi, Soichi; Gesing, Sandra; Quick, Rob; Teige, Scott; Ganote, Carrie; Wu, Le-shin; Prout, Elizabeth
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Relevância na Pesquisa
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To assist the bioinformatic community in leveraging the national cyberinfrastructure, the National Center for Genomic Analysis Support (NCGAS) along with Indiana University's High Throughput Computing (HTC) group have engineered a method to use the Galaxy to submit BLAST jobs to the Open Science Grid (OSG). OSG is a collaboration of resource providers that utilize opportunistic cycles at more than 100 universities and research centers in the US. BLAST jobs make a significant portion of the research conducted on NCGAS resources, moving jobs that are conducive to an HTC environment to the national cyberinfrastructure would alleviate load on resources at NCGAS and provide a cost effective solution for getting more cycles to reduce the unmet needs of bioinformatic researchers. To this point researchers have tackled this issue by purchasing additional resources or enlisting collaborators doing the same type of research, while HTC experts have focused on expanding the number of resources available to historically HTC friendly science workflows. In this paper, we bring together expertise from both areas to address how a bioinformatics researcher using their normal interface, Galaxy, can seamlessly access the OSG which routinely supplies researchers with millions of compute hours daily. Efficient use of these results will supply additional compute time to researcher and help provide a yet unmet need for BLAST computing cycles.; This material is based upon work supported by the National Science Foundation under Grant No. ABI-1062432...

Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome

Wu, Le-Shin; Ganote, Carrie; Doak, Thomas; Barnett, William K.; Mockaitis, Keithanne; Stewart, Craig A.
Fonte: ACM, New York, NY Publicador: ACM, New York, NY
Tipo: Artigo de Revista Científica
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This paper was presented at XSEDE 15 conference.; Today's genomics technologies generate more sequence data than ever before possible, and at substantially lower costs, serving researchers across biological disciplines in transformative ways. Building transcriptome assemblies from RNA sequencing reads is one application of next-generation sequencing (NGS) that has held a central role in biological discovery in both model and non- model organisms, with and without whole genome sequence references. A major limitation in effective building of transcriptome references is no longer the sequencing data generation itself, but the computing infrastructure and expertise needed to assemble, analyze and manage the data. Here we describe a currently available resource dedicated to achieving such goals, and its use for extensive RNA assembly of up to 1.3 billion reads representing the massive transcriptome of loblolly pine, using four major assembly software installations. The Mason cluster, an XSEDE second tier resource at Indiana University, provides the necessary fast CPU cycles, large memory, and high I/O throughput for conducting large-scale genomics research. The National Center for Genome Analysis Support, or NCGAS, provides technical support in using HPC systems...