Leveraging the national cyberinfrastructure for biomedical research
Identifieur interne : 000310 ( Pmc/Checkpoint ); précédent : 000309; suivant : 000311Leveraging 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.
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 ‘
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DOI: 10.1136/amiajnl-2013-002059
PubMed: 23964072
PubMed Central: 3932465
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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. 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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></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><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Am Med Inform Assoc</journal-id><journal-id journal-id-type="iso-abbrev">J Am Med Inform Assoc</journal-id><journal-id journal-id-type="hwp">amiajnl</journal-id><journal-id journal-id-type="publisher-id">jamia</journal-id><journal-title-group><journal-title>Journal of the American Medical Informatics Association : JAMIA</journal-title></journal-title-group><issn pub-type="ppub">1067-5027</issn><issn pub-type="epub">1527-974X</issn><publisher><publisher-name>BMJ Publishing Group</publisher-name><publisher-loc>BMA House, Tavistock Square, London, WC1H 9JR</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23964072</article-id><article-id pub-id-type="pmc">3932465</article-id><article-id pub-id-type="publisher-id">amiajnl-2013-002059</article-id><article-id pub-id-type="doi">10.1136/amiajnl-2013-002059</article-id><article-categories><subj-group subj-group-type="hwp-journal-coll"><subject>1506</subject></subj-group><subj-group subj-group-type="heading"><subject>Perspective</subject></subj-group></article-categories><title-group><article-title>Leveraging the national cyberinfrastructure for biomedical research</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>LeDuc</surname><given-names>Richard</given-names></name><xref ref-type="aff" rid="af1">1</xref><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-6951-2923</contrib-id></contrib><contrib contrib-type="author"><name><surname>Vaughn</surname><given-names>Matthew</given-names></name><xref ref-type="aff" rid="af2">2</xref></contrib><contrib contrib-type="author"><name><surname>Fonner</surname><given-names>John M</given-names></name><xref ref-type="aff" rid="af2">2</xref></contrib><contrib contrib-type="author"><name><surname>Sullivan</surname><given-names>Michael</given-names></name><xref ref-type="aff" rid="af3">3</xref></contrib><contrib contrib-type="author"><name><surname>Williams</surname><given-names>James G</given-names></name><xref ref-type="aff" rid="af4">4</xref></contrib><contrib contrib-type="author"><name><surname>Blood</surname><given-names>Philip D</given-names></name><xref ref-type="aff" rid="af5">5</xref></contrib><contrib contrib-type="author"><name><surname>Taylor</surname><given-names>James</given-names></name><xref ref-type="aff" rid="af6">6</xref></contrib><contrib contrib-type="author"><name><surname>Barnett</surname><given-names>William</given-names></name><xref ref-type="aff" rid="af7">7</xref></contrib></contrib-group><aff id="af1"><label>1</label><institution>National Center for Genome Analysis Support</institution>,<addr-line>Indiana University, Bloomington, Indiana</addr-line>,<country>USA</country></aff><aff id="af2"><label>2</label><addr-line>Life Sciences Computing</addr-line>,<institution>Texas Advanced Computing Center</institution>,<addr-line>Austin, Texas</addr-line>,<country>USA</country></aff><aff id="af3"><label>3</label><addr-line>Health Sciences</addr-line>,<institution>Internet2</institution>,<addr-line>Washington, DC</addr-line>,<country>USA</country></aff><aff id="af4"><label>4</label><addr-line>International Networking</addr-line>,<institution>Indiana University</institution>,<addr-line>Bloomington, Indiana</addr-line>,<country>USA</country></aff><aff id="af5"><label>5</label><institution>Pittsburgh Supercomputing Center</institution>,<addr-line>Carnegie Mellon University, Pittsburgh, Pennsylvania</addr-line>,<country>USA</country></aff><aff id="af6"><label>6</label><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></aff><aff id="af7"><label>7</label><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></aff><author-notes><corresp><label>Correspondence to</label> Dr Richard LeDuc, National Center for Genome Analysis Support, 2709 E. 10th Street, Bloomington, IN 47408, USA; <email>rleduc@iu.edu</email></corresp></author-notes><pub-date pub-type="ppub"><month>3</month><year>2014</year></pub-date><pub-date pub-type="epub"><day>20</day><month>8</month><year>2013</year></pub-date><pub-date pub-type="pmc-release"><day>20</day><month>8</month><year>2013</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>21</volume><issue>2</issue><fpage>195</fpage><lpage>199</lpage><history><date date-type="received"><day>31</day><month>5</month><year>2013</year></date><date date-type="rev-recd"><day>15</day><month>7</month><year>2013</year></date><date date-type="accepted"><day>3</day><month>8</month><year>2013</year></date></history><permissions><copyright-statement>Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions</copyright-statement><copyright-year>2014</copyright-year><license license-type="open-access"><license-p>This is an Open Access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 3.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0/">http://creativecommons.org/licenses/by-nc/3.0/</ext-link></license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="amiajnl-2013-002059.pdf"></self-uri><abstract><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></abstract><kwd-group><kwd>National Cyberinfrastructure</kwd><kwd>Big Data</kwd><kwd>Genomics</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>special-feature</meta-name><meta-value>unlocked</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><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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