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Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

Sun, Shulei; Chen, Jing; Li, Weizhong; Altintas, Ilkay; Lin, Abel; Peltier, Steve; Stocks, Karen; Allen, Eric E.; Ellisman, Mark; Grethe, Jeffrey; Wooley, John
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
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The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, http://camera.calit2.net/) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets...

The emergence of spatial cyberinfrastructure

Wright, Dawn J.; Wang, Shaowen
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
EN
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Cyberinfrastructure integrates advanced computer, information, and communication technologies to empower computation-based and data-driven scientific practice and improve the synthesis and analysis of scientific data in a collaborative and shared fashion. As such, it now represents a paradigm shift in scientific research that has facilitated easy access to computational utilities and streamlined collaboration across distance and disciplines, thereby enabling scientific breakthroughs to be reached more quickly and efficiently. Spatial cyberinfrastructure seeks to resolve longstanding complex problems of handling and analyzing massive and heterogeneous spatial datasets as well as the necessity and benefits of sharing spatial data flexibly and securely. This article provides an overview and potential future directions of spatial cyberinfrastructure. The remaining four articles of the special feature are introduced and situated in the context of providing empirical examples of how spatial cyberinfrastructure is extending and enhancing scientific practice for improved synthesis and analysis of both physical and social science data. The primary focus of the articles is spatial analyses using distributed and high-performance computing, sensor networks...

Louisiana: a model for advancing regional e-Research through cyberinfrastructure

Katz, Daniel S.; Allen, Gabrielle; Cortez, Ricardo; Cruz-Neira, Carolina; Gottumukkala, Raju; Greenwood, Zeno D.; Guice, Les; Jha, Shantenu; Kolluru, Ramesh; Kosar, Tevfik; Leger, Lonnie; Liu, Honggao; McMahon, Charlie; Nabrzyski, Jarek; Rodriguez-Milla,
Fonte: The Royal Society Publicador: The Royal Society
Tipo: Artigo de Revista Científica
Publicado em 28/06/2009 EN
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Louisiana researchers and universities are leading a concentrated, collaborative effort to advance statewide e-Research through a new cyberinfrastructure: computing systems, data storage systems, advanced instruments and data repositories, visualization environments and people, all linked together by software programs and high-performance networks. This effort has led to a set of interlinked projects that have started making a significant difference in the state, and has created an environment that encourages increased collaboration, leading to new e-Research. This paper describes the overall effort, the new projects and environment and the results to date.

Adapting Federated Cyberinfrastructure for Shared Data Collection Facilities in Structural Biology

Murphy, Frank V.; Deacon, Ashley; Stokes-Rees, Ian; Levesque, Ian; Yang, Wei; Sliz, Piotr
Fonte: International Union of Crystallography Publicador: International Union of Crystallography
Tipo: Artigo de Revista Científica
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Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities.

Final Report of the Indiana University Cyberinfrastructure Research Taskforce

Wheeler, Bradley; McRobbie, Michael
Fonte: The Trustees of Indiana University Publicador: The Trustees of Indiana University
Tipo: Outros Formato: 449318 bytes; application/pdf
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The Cyberinfrastructure Research Taskforce met during the 2004-05 academic year to consider Indiana University???s (IU) needs for shared cyberinfrastructure investments. In particular, the charge to the taskforce asked scholars to focus on needs that could help support a doubling of IU???s externally funded research by 2010-2011. This report to the IU Vice President for Research & Information Technology conveys 10 specific recommendations. It recognizes both current progress in cyberinfrastructure development while also proposing new directions for cyberinfrastructure needs and opportunities. In summary, the recommendations affirm a continuity of investment in the core IT infrastructure that is the foundation for advanced cyberinfrastructure. Developing deep capabilities for serving the complete research data lifecycle emerged as a clear and pervasive theme across many disciplines. The recommendations provide guidance for storage capacity; data movement across networks; collection, annotation and provenance; and data publishing, curation, and custodianship. The taskforce advocated ???continuing without pause??? renewed investment in IU???s High Performance Computing (HPC) systems and visualization facilities and strongly advocated HPC as a competitive necessity for data-intensive scholarship. Beyond the technology investments...

The future of the TeraGrid and the national advanced cyberinfrastructure: a perspective from the Coalition for Academic Scientific Computation

Stewart, Craig A.; Ahalt, Stan C.; Pritchard, Richard H.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Trabalho em Andamento Formato: 141637 bytes; application/pdf
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What is Cyberinfrastructure?

Stewart, Craig A.; Simms, Stephen; Plale, Beth; Link, Matthew; Hancock, David Y.; Fox, Geoffrey C.
Fonte: ACM Publicador: ACM
Tipo: Trabalho em Andamento
EN_US
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Cyberinfrastructure is a word commonly used but lacking a single, precise definition. One recognizes intuitively the analogy with infrastructure, and the use of cyber to refer to thinking or computing ??? but what exactly is cyberinfrastructure as opposed to information technology infrastructure? Indiana University has developed one of the more widely cited definitions of cyberinfrastructure: "Cyberinfrastructure consists of computing systems, data storage systems, advanced instruments and data repositories, visualization environments, and people, all linked together by software and high performance networks to improve research productivity and enable breakthroughs not otherwise possible." A second definition, more inclusive of scholarship generally and educational activities, has also been published and is useful in describing cyberinfrastructure: "Cyberinfrastructure consists of systems, data and information management, advanced instruments, visualization environments, and people, all linked together by software and advanced networks to improve scholarly productivity and enable knowledge breakthroughs and discoveries not otherwise possible." In this paper, we describe the origin of the term cyberinfrastructure based on the history of the root word infrastructure...

Usage of UITS advanced research cyberinfrastructure for 2011

Link, Matthew R.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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IU has a proud tradition in open access to its research computing and cyberinfrastructure (CI) facilities, going back to the precedents set by Marshall Wrubel (appointed the first permanent director of the IU Research Computing Center in 1955). Starting in 1997 President Myles Brand and then-Vice President Michael McRobbie initiated a tremendous acceleration in growth of IU???s cyberinfrastructure facilities through developing and then executing the first Indiana University Information Technology Strategic Plan. Through a decade and a half of purposeful execution of excellent strategies in support for research and scholarly activities generally, University Information Technology Services (UITS) has provided exceptional support to a group of researchers. This includes usage from disciplines that are among the traditional users of high performance computing ??? physics, chemistry, and astronomy, as well as emerging areas of application of HPC including biology, business, and the arts.

Making Campus Cyberinfrastructure Work for Your Campus

Almes, Guy; Dreher, Patrick; Stewart, Craig A.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Presented at EDUCAUSE 2008 Conference, 28-31 October, Orlando, FL.; This presentation discusses the workshop, "Developing a Coherent Cyberinfrastructure from Local Campus to National Facilities: Challenges and Strategies"; Coalition for Advanced Scientific Computation / EDUCAUSE

Development of an advanced cyberinfrastructure at Indiana University

Stewart, Craig A.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Presented at IBM Watson Research Center.; Funding for projects described in this talk has come from the National Science Foundation, National Institutes of Health, Lilly Endowment, Inc., State of Indiana (particularly through support of I-light Initiative and the 21st Century Fund), IBM (through Shared University Research grants and IU???s relationship with IBM as an IBM Life Sciences Institute of Innovation)

Indiana University???s Response to House Energy and Commerce Committee Request for Suggestions: 21st Century Cures: Leveraging Technology to Accelerate the #Path2Cures

Indiana University; Stewart, Craig A.; Barnett, William K.; Shekar, Anantha; Sheehan, Vincent; Wasitis, Douglas A.; Wheeler, Bradley C.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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Indiana University embraces and supports the goals set out in the House Energy and Commerce Committee white paper ???21st Century Cures: A Call to Action.??? The state of Indiana, through collaborative efforts led by Indiana University, provides a model that can be adopted throughout the US. The combination of willingness to collaborate across public/private boundaries, a high performance network, and a cyberinfrastructure suitable for research using private and protected health records, is enabling the state of Indiana to accelerate new discoveries and their rapid translation into everyday medical practice and improved quality of life. Similar collaborations in other states and between states across the country would accelerate the delivery of medical breakthroughs and improve healthcare delivery and lower costs across the country.

UITS Research Technologies Cyberinfrastucture for IU Research and Academics

Ping, Robert
Fonte: Indiana University Digital Collections Services Publicador: Indiana University Digital Collections Services
Tipo: Conferência ou Objeto de Conferência
EN_US
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UITS Research Technologies develops, delivers, and supports advanced technology to improve the productivity of and enable new possibilities in research, scholarly endeavors, and creative activity at IU. Join Robert Ping, RT Manager of Education and Outreach, as he introduces the nine service areas available to all IU faculty, staff, and students: Science Gateways, Computation, Data Storage, Visualization, Analysis and Software delivery and support, Services for biomedical biological and health-related research, Campus birding: connecting to local and national cyberinfrastructure, Education and outreach, and Grant support and custom for-fee services. http://researchtech.iu.edu

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...

Results of 2013 Survey of Parallel Computing Needs Focusing on NSF-funded Researchers

Stewart, Craig A.; Arenson, Andrew; Fischer, Jeremy; Link, Matthew R.; Michael, Scott A.; Wernert, Julie A
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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The field of supercomputing is experiencing a rapid change in system structure, programming models, and software environments in response to advances in application requirements and in underlying enabling technologies. Traditional parallel programming approaches have relied on static resource allocation and task scheduling through programming interfaces such as MPI and OpenMP. These methods are reaching their efficiency and scalability limits on the new emerging classes of systems, spurring the creation of innovative dynamic strategies and software tools, including advanced runtime system software and programming interfaces that use them. To accelerate adoption of these next-generation methods, Indiana University is investigating the creation of a single supported Reconfigurable Execution Framework Testbed (REFT) to be used by parallel application algorithm developers as well as researchers in advanced tools for parallel computing. These investigations are funded by the National Science Foundation Award Number 1205518 to Indiana University with Thomas Sterling as Principal Investigator, and Maciej Brodowicz, Matthew R. Link, Andrew Lumsdaine, and Craig Stewart as Co-Principal Investigators. As a starting point in this research we proposed to assess needs in parallel computing in general and needs for software tools and testbeds in particular within the NSF-funded research community. As one set of data toward understanding these needs...

XSEDE Value Added, Cost Avoidance, and Return on Investment - Preprint; To appear in Proceedings of XSEDE 15 Conference

Stewart, Craig A.; Roskies, Ralph; Knepper, Richard; Moore, Richard L.; Whitt, Justin; Cockerill, Timothy M.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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In science and engineering discovery often lags years behind research, whose full potential may not be known for decades. Large research facilities struggle to quantify a return on the substantial federal investments that fund their often-broad scopes of operations. This paper presents a three-part methodology that shows the value from the investment in XSEDE: 1) a qualitative examination of the primary areas where XSEDE adds value to the open research community, 2) a “thought model” examining the savings realized by the National Science Foundation (NSF) through the centralization and coordination XSEDE provides, and 3) an assessment of the value provided to Service Providers in the XSEDE ecosystem. XSEDE adds significantly to the US research community because it functions as a unified interface to the XD ecosystem and because of its scale. We cannot yet put a figure on this value but according to anecdotal evidence it is significant – perhaps greater than the entire cost of XSEDE over five years. We can qualitatively assess return on investment (ROI) for XSEDE’s delivery of essential core functions for a national advanced cyberinfrastructure center. A partly quantitative, partly qualitative analysis suggests ROI for XSEDE’s delivery of essential core functions to the nation is greater than 1.0. Qualitative arguments considering anecdotal evidence of XSEDE’s value added suggest XSEDE has an ROI of greater than 1.0 in terms of return to the nation on the NSF investment in XSEDE.; This report was based on research funded in part by the National Science Foundation through grant number ACI-1053575...

XSEDE Value Added, Cost Avoidance, and Return on Investment (Full Talk)

Stewart, Craig A.; Roskies, Ralph; Knepper, Rich; Moore, Richard; Whitt, Justin; Cockerill, Timothy
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Conferência ou Objeto de Conferência
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Talk describes value XSEDE adds to national cyberinfrastructure and return on investment.; XSEDE is supported by NSF award 1053575 (John Towns, UIUC, PI)

University Information Technology Services' Advanced IT Facilities: The least every researcher needs to know

Cruise, Robert; Hart, David; Papakhian, Mary; Repasky, Richard; Samuel, John; Shankar, Anurag; Stewart, Craig A.; Wernert, Eric
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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This is an archived document containing instructions for using IU's advanced IT facilities ca. 2003. A version of this document updated in 2011 is available from http://hdl.handle.net/2022/13620. Further versions are forthcoming.; This document is designed to be read as a printed document, and designed to permit anyone at all familiar with computers and the Internet to start at the beginning, get a general overview of UITS' advanced IT facilities and what they offer, and then read the detailed portions of the document that are of interest. In many cases, examples are provided, as well as directions on how to download sample files. And in some cases there is information that one is best off really not learning – for example the process of logging into IU's IBM supercomputer the first time involves setup steps that should be followed, keystroke by keystroke, from the directions presented herein, and then promptly forgotten. This document is intended to be a starting point, not a comprehensive guide. As such it should get any reader off to a good start, but then point the reader in the direction of consulting staff and online resources that will permit the reader to get additional help and information as needed. Most of all, this document is provided for the convenience of researchers...

Indiana University's Advanced Cyberinfrastructure

Arenson, Andrew; Boyles, Michael; Cruise, Robert; Gopu, Arvind; Hart, David; Lindenlaub, Peg; Papakhian, Mary; Samuel, John; Seiffert, Kurt; Shankar, Anurag; Stewart, Craig A.; Wernert, Eric
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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This is an archived document. The most current version may be found at http://pti.iu.edu/ci; The purpose of this document is to introduce researchers to Indiana University’s cyberinfrastructure – to clarify what these facilities make possible, to discuss how to use them and the professional staff available to work with you. The resources described here are complex and varied, among the most advanced in the world. The intended audience is anyone unfamiliar with IU’s cyberinfrastructure.

Information technology in support of research, scholarship, and creative activities: A strategic plan for Research Technologies – a division of UITS and a PTI Service and Cyberinfrastructure Center

Stewart, Craig A.; Link, Matthew R.; Wernert, Eric; Barnett, William K.; Miller, Therese M.
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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Stewart, C.A., M.R. Link, E. Wernert, W.K. Barnett, T.M. Miller. 2012. Information technology in support of research, scholarship, and creative activities: A strategic plan for Research Technologies – a division of UITS and a PTI Service and Cyberinfrastructure Center. Indiana University, Bloomington, IN. PTI Technical Report PTI-TR12-007.; IU is currently executing its second information technology strategic plan – Empowering People: Indiana University's Strategic Plan for Information Technology 2009 (hereafter referred to as Empowering People). In this document, we set out long-term goals for the Research Technologies (RT) division of UITS, reaffirm specific goals set for RT for 2019, describe Actions within Empowering People for which RT is responsible, and describe the new internal structure of Research Technologies. The mission of the Research Technologies division of UITS is to develop, deliver, and support advanced technology solutions that improve productivity of and enable new possibilities in research, scholarly endeavors, and creative activity at Indiana University and beyond; and to complement this with education and technology translation activities to improve the quality of life of people in Indiana, the nation, and the world.

Indiana University’s advanced cyberinfrastructure in service of IU strategic goals: Activities of PTI during FY2015

Stewart, Craig A.; Plale, Beth; Welch, Von; Link, Matthew R.; Miller, Therese; Wernert, Eric A.; Boyles, Michael J.; Fulton, Ben; Hancock, David Y.; Henschel, Robert; Michael, Scott A.; Pierce, Marlon; Ping, Robert J.; Gniady, Tassie
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Relatório
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