Leveraging the national cyberinfrastructure for biomedical research
Identifieur interne : 000331 ( Main/Exploration ); précédent : 000330; suivant : 000332Leveraging the national cyberinfrastructure for biomedical research
Auteurs : Richard Leduc [États-Unis] ; Matthew Vaughn [États-Unis] ; John M. Fonner [États-Unis] ; Michael Sullivan [États-Unis] ; James G. Williams [États-Unis] ; Philip D. Blood [États-Unis] ; James Taylor [États-Unis] ; William Barnett [États-Unis]Source :
- Journal of the American Medical Informatics Association : JAMIA [ 1067-5027 ] ; 2013.
English descriptors
- KwdEn :
- MESH :
- methods : Information Dissemination.
- organization & administration : Biomedical Research.
- Computer Systems, Genomics, Internet, Medical Informatics.
Abstract
In the USA, the national cyberinfrastructure refers to a system of research supercomputer and other IT facilities and the high speed networks that connect them. These resources have been heavily leveraged by scientists in disciplines such as high energy physics, astronomy, and climatology, but until recently they have been little used by biomedical researchers. We suggest that many of the ‘
Url:
DOI: 10.1136/amiajnl-2013-002059
PubMed: 23964072
PubMed Central: 3932465
Affiliations:
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Fonner</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>Life Sciences Computing</addr-line>,<institution>Texas Advanced Computing Center</institution>,<addr-line>Austin, Texas</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sullivan, Michael" sort="Sullivan, Michael" uniqKey="Sullivan M" first="Michael" last="Sullivan">Michael Sullivan</name><affiliation wicri:level="1"><nlm:aff id="af3"><addr-line>Health Sciences</addr-line>,<institution>Internet2</institution>,<addr-line>Washington, DC</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Williams, James G" sort="Williams, James G" uniqKey="Williams J" first="James G" last="Williams">James G. 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Fonner</name><affiliation wicri:level="1"><nlm:aff id="af2"><addr-line>Life Sciences Computing</addr-line>,<institution>Texas Advanced Computing Center</institution>,<addr-line>Austin, Texas</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sullivan, Michael" sort="Sullivan, Michael" uniqKey="Sullivan M" first="Michael" last="Sullivan">Michael Sullivan</name><affiliation wicri:level="1"><nlm:aff id="af3"><addr-line>Health Sciences</addr-line>,<institution>Internet2</institution>,<addr-line>Washington, DC</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Williams, James G" sort="Williams, James G" uniqKey="Williams J" first="James G" last="Williams">James G. Williams</name><affiliation wicri:level="1"><nlm:aff id="af4"><addr-line>International Networking</addr-line>,<institution>Indiana University</institution>,<addr-line>Bloomington, Indiana</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Blood, Philip D" sort="Blood, Philip D" uniqKey="Blood P" first="Philip D" last="Blood">Philip D. Blood</name><affiliation wicri:level="1"><nlm:aff id="af5"><institution>Pittsburgh Supercomputing Center</institution>,<addr-line>Carnegie Mellon University, Pittsburgh, Pennsylvania</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Taylor, James" sort="Taylor, James" uniqKey="Taylor J" first="James" last="Taylor">James Taylor</name><affiliation wicri:level="1"><nlm:aff id="af6"><addr-line>Department of Biology and Department of Mathematics and Computer Science</addr-line>,<institution>Emory University</institution>,<addr-line>Atlanta, Georgia</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Barnett, William" sort="Barnett, William" uniqKey="Barnett W" first="William" last="Barnett">William Barnett</name><affiliation wicri:level="1"><nlm:aff id="af7"><institution>National Center for Genome Analysis Support, Open Science Grid, Grid Operations Center, Indiana University</institution>,<addr-line>Bloomington, Indiana</addr-line>,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Journal of the American Medical Informatics Association : JAMIA</title><idno type="ISSN">1067-5027</idno><idno type="eISSN">1527-974X</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biomedical Research (organization & administration)</term><term>Computer Systems</term><term>Genomics</term><term>Information Dissemination (methods)</term><term>Internet</term><term>Medical Informatics</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Information Dissemination</term></keywords><keywords scheme="MESH" qualifier="organization & administration" xml:lang="en"><term>Biomedical Research</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Systems</term><term>Genomics</term><term>Internet</term><term>Medical Informatics</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In the USA, the national cyberinfrastructure refers to a system of research supercomputer and other IT facilities and the high speed networks that connect them. These resources have been heavily leveraged by scientists in disciplines such as high energy physics, astronomy, and climatology, but until recently they have been little used by biomedical researchers. We suggest that many of the ‘<italic>Big Data</italic>’ challenges facing the medical informatics community can be efficiently handled using national-scale cyberinfrastructure. Resources such as the Extreme Science and Discovery Environment, the Open Science Grid, and Internet2 provide economical and proven infrastructures for <italic>Big Data</italic> challenges, but these resources can be difficult to approach. Specialized web portals, support centers, and virtual organizations can be constructed on these resources to meet defined computational challenges, specifically for genomics. We provide examples of how this has been done in basic biology as an illustration for the biomedical informatics community.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Stewart, Ca" uniqKey="Stewart C">CA Stewart</name></author><author><name sortKey="Simms, S" uniqKey="Simms S">S Simms</name></author><author><name sortKey="Plale, B" uniqKey="Plale B">B Plale</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Goff, Ss" uniqKey="Goff S">SS Goff</name></author><author><name sortKey="Vaughn, M" uniqKey="Vaughn M">M Vaughn</name></author><author><name sortKey="Mckay, S" uniqKey="Mckay S">S McKay</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leduc, R" uniqKey="Leduc R">R LeDuc</name></author><author><name sortKey="Wu, L S" uniqKey="Wu L">L-S Wu</name></author><author><name sortKey="Ganote, C" uniqKey="Ganote C">C Ganote</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lenards, A" uniqKey="Lenards A">A Lenards</name></author><author><name sortKey="Merchant, N" uniqKey="Merchant N">N Merchant</name></author><author><name sortKey="Stanzione, D" uniqKey="Stanzione D">D Stanzione</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Skidmore, E" uniqKey="Skidmore E">E Skidmore</name></author><author><name sortKey="Kim, S J" uniqKey="Kim S">S-J Kim</name></author><author><name sortKey="Kuchimanchi, S" uniqKey="Kuchimanchi S">S Kuchimanchi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goecks, J" uniqKey="Goecks J">J Goecks</name></author><author><name sortKey="Nekrutenko, A" uniqKey="Nekrutenko A">A Nekrutenko</name></author><author><name sortKey="Taylor, J" uniqKey="Taylor J">J Taylor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Blankenberg, D" uniqKey="Blankenberg D">D Blankenberg</name></author><author><name sortKey="Kuster, G" uniqKey="Kuster G">G Kuster</name></author><author><name sortKey="Coraor, N" uniqKey="Coraor N">N Coraor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giardine, B" uniqKey="Giardine B">B Giardine</name></author><author><name sortKey="Riemer, C" uniqKey="Riemer C">C Riemer</name></author><author><name sortKey="Hardison, R" uniqKey="Hardison R">R Hardison</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nowoczynski, P" uniqKey="Nowoczynski P">P Nowoczynski</name></author><author><name sortKey="Sommerfield, J" uniqKey="Sommerfield J">J Sommerfield</name></author><author><name sortKey="Yanovich, J" uniqKey="Yanovich J">J Yanovich</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Leduc, Richard" sort="Leduc, Richard" uniqKey="Leduc R" first="Richard" last="Leduc">Richard Leduc</name></noRegion><name sortKey="Barnett, William" sort="Barnett, William" uniqKey="Barnett W" first="William" last="Barnett">William Barnett</name><name sortKey="Blood, Philip D" sort="Blood, Philip D" uniqKey="Blood P" first="Philip D" last="Blood">Philip D. Blood</name><name sortKey="Fonner, John M" sort="Fonner, John M" uniqKey="Fonner J" first="John M" last="Fonner">John M. Fonner</name><name sortKey="Sullivan, Michael" sort="Sullivan, Michael" uniqKey="Sullivan M" first="Michael" last="Sullivan">Michael Sullivan</name><name sortKey="Taylor, James" sort="Taylor, James" uniqKey="Taylor J" first="James" last="Taylor">James Taylor</name><name sortKey="Vaughn, Matthew" sort="Vaughn, Matthew" uniqKey="Vaughn M" first="Matthew" last="Vaughn">Matthew Vaughn</name><name sortKey="Williams, James G" sort="Williams, James G" uniqKey="Williams J" first="James G" last="Williams">James G. Williams</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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