Adapting federated cyberinfrastructure for shared data collection facilities in structural biology
Identifieur interne : 000556 ( Pmc/Curation ); précédent : 000555; suivant : 000557Adapting federated cyberinfrastructure for shared data collection facilities in structural biology
Auteurs : Ian Stokes-Rees [États-Unis] ; Ian Levesque [États-Unis] ; Frank V. Murphy [États-Unis] ; Wei Yang [États-Unis] ; Ashley Deacon [États-Unis] ; Piotr Sliz [États-Unis]Source :
- Journal of Synchrotron Radiation [ 0909-0495 ] ; 2012.
Abstract
It has been difficult, historically, to manage and maintain early-stage experimental data collected by structural biologists in synchrotron facilities. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to manage collected data at synchrotrons and to facilitate the efficient and secure transfer of data to the owner’s home institution.
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DOI: 10.1107/S0909049512009776
PubMed: 22514186
PubMed Central: 3329960
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Murphy</name><affiliation wicri:level="1"><nlm:aff id="c">Northeast Collaborative Access Team (NE-CAT), Advanced Photon Source,<institution>Argonne National Laboratory</institution>, Argonne, IL 60439,<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="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name><affiliation wicri:level="1"><nlm:aff id="d">Joint Center for Structural Genomics, Stanford Synchrotron Radiation Light Source,<institution>Stanford University</institution>, Menlo Park, CA 94025,<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="Deacon, Ashley" sort="Deacon, Ashley" uniqKey="Deacon A" first="Ashley" last="Deacon">Ashley Deacon</name><affiliation wicri:level="1"><nlm:aff id="d">Joint Center for Structural Genomics, Stanford Synchrotron Radiation Light Source,<institution>Stanford University</institution>, Menlo Park, CA 94025,<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="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22514186</idno><idno type="pmc">3329960</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329960</idno><idno type="RBID">PMC:3329960</idno><idno type="doi">10.1107/S0909049512009776</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000556</idno><idno type="wicri:Area/Pmc/Curation">000556</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Adapting federated cyberinfrastructure for shared data collection facilities in structural biology</title><author><name sortKey="Stokes Rees, Ian" sort="Stokes Rees, Ian" uniqKey="Stokes Rees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<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="Levesque, Ian" sort="Levesque, Ian" uniqKey="Levesque I" first="Ian" last="Levesque">Ian Levesque</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="b">Howard Hughes Medical Institute,<institution>Harvard Medical School</institution>, Boston, MA 02115,<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="Murphy, Frank V" sort="Murphy, Frank V" uniqKey="Murphy F" first="Frank V." last="Murphy">Frank V. Murphy</name><affiliation wicri:level="1"><nlm:aff id="c">Northeast Collaborative Access Team (NE-CAT), Advanced Photon Source,<institution>Argonne National Laboratory</institution>, Argonne, IL 60439,<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="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name><affiliation wicri:level="1"><nlm:aff id="d">Joint Center for Structural Genomics, Stanford Synchrotron Radiation Light Source,<institution>Stanford University</institution>, Menlo Park, CA 94025,<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="Deacon, Ashley" sort="Deacon, Ashley" uniqKey="Deacon A" first="Ashley" last="Deacon">Ashley Deacon</name><affiliation wicri:level="1"><nlm:aff id="d">Joint Center for Structural Genomics, Stanford Synchrotron Radiation Light Source,<institution>Stanford University</institution>, Menlo Park, CA 94025,<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="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<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 Synchrotron Radiation</title><idno type="ISSN">0909-0495</idno><idno type="eISSN">1600-5775</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>It has been difficult, historically, to manage and maintain early-stage experimental data collected by structural biologists in synchrotron facilities. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to manage collected data at synchrotrons and to facilitate the efficient and secure transfer of data to the owner’s home institution.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></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 Synchrotron Radiat</journal-id><journal-id journal-id-type="iso-abbrev">J Synchrotron Radiat</journal-id><journal-id journal-id-type="publisher-id">J. Synchrotron Rad.</journal-id><journal-title-group><journal-title>Journal of Synchrotron Radiation</journal-title></journal-title-group><issn pub-type="ppub">0909-0495</issn><issn pub-type="epub">1600-5775</issn><publisher><publisher-name>International Union of Crystallography</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22514186</article-id><article-id pub-id-type="pmc">3329960</article-id><article-id pub-id-type="publisher-id">ie5073</article-id><article-id pub-id-type="doi">10.1107/S0909049512009776</article-id><article-id pub-id-type="coden">JSYRES</article-id><article-id pub-id-type="pii">S0909049512009776</article-id><article-categories><subj-group subj-group-type="heading"><subject>Computer Programs</subject></subj-group></article-categories><title-group><article-title>Adapting federated cyberinfrastructure for shared data collection facilities in structural biology</article-title><alt-title>Adapting federated cyberinfrastructure</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Stokes-Rees</surname><given-names>Ian</given-names></name><xref ref-type="aff" rid="a">a</xref></contrib><contrib contrib-type="author"><name><surname>Levesque</surname><given-names>Ian</given-names></name><xref ref-type="aff" rid="a">a</xref><xref ref-type="aff" rid="b">b</xref></contrib><contrib contrib-type="author"><name><surname>Murphy</surname><given-names>Frank V.</given-names><suffix>IV</suffix></name><xref ref-type="aff" rid="c">c</xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Wei</given-names></name><xref ref-type="aff" rid="d">d</xref></contrib><contrib contrib-type="author"><name><surname>Deacon</surname><given-names>Ashley</given-names></name><xref ref-type="aff" rid="d">d</xref></contrib><contrib contrib-type="author"><name><surname>Sliz</surname><given-names>Piotr</given-names></name><xref ref-type="aff" rid="a">a</xref><xref ref-type="corresp" rid="cor">*</xref></contrib><aff id="a"><label>a</label>Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></aff><aff id="b"><label>b</label>Howard Hughes Medical Institute,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></aff><aff id="c"><label>c</label>Northeast Collaborative Access Team (NE-CAT), Advanced Photon Source,<institution>Argonne National Laboratory</institution>, Argonne, IL 60439,<country>USA</country></aff><aff id="d"><label>d</label>Joint Center for Structural Genomics, Stanford Synchrotron Radiation Light Source,<institution>Stanford University</institution>, Menlo Park, CA 94025,<country>USA</country></aff></contrib-group><author-notes><corresp id="cor">Correspondence e-mail: <email>piotr_sliz@hms.harvard.edu</email></corresp></author-notes><pub-date pub-type="ppub"><day>01</day><month>5</month><year>2012</year></pub-date><pub-date pub-type="epub"><day>06</day><month>4</month><year>2012</year></pub-date><pub-date pub-type="pmc-release"><day>06</day><month>4</month><year>2012</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>19</volume><issue>Pt 3</issue><issue-id pub-id-type="publisher-id">s120300</issue-id><fpage>462</fpage><lpage>467</lpage><history><date date-type="received"><day>09</day><month>12</month><year>2011</year></date><date date-type="accepted"><day>05</day><month>3</month><year>2012</year></date></history><permissions><copyright-statement>© Ian Stokes-Rees et al. 2012</copyright-statement><copyright-year>2012</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0/uk/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.</license-p></license></permissions><self-uri xlink:type="simple" xlink:href="http://dx.doi.org/10.1107/S0909049512009776">A full version of this article is available from Crystallography Journals Online.</self-uri><abstract abstract-type="toc"><p>It has been difficult, historically, to manage and maintain early-stage experimental data collected by structural biologists in synchrotron facilities. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to manage collected data at synchrotrons and to facilitate the efficient and secure transfer of data to the owner’s home institution.</p></abstract><abstract><p>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 <italic>Virtual Data Toolkit</italic> and <italic>Globus</italic>, 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.</p></abstract><kwd-group><kwd>grid computing</kwd><kwd>data handling and security</kwd><kwd>diffraction images</kwd><kwd>collaborative tools</kwd><kwd>structural biology</kwd></kwd-group></article-meta></front><floats-group><fig id="fig1" position="float"><label>Figure 1</label><caption><p>Geographic distribution of five endpoints participating in the trial of the prototype system. The flags represent, from left to right, Stanford Synchrotron Radiation Lightsource (blue, Stanford Linear Accelerator Center, Palo Alto, CA, USA), Fermi National Accelerator Laboratory (white, Batavia, IL, USA), Northeast Collaborative Access Team (green, Advanced Photon Source, Argonne, IL, USA), National Center for Supercomputing Applications (red, University of Illinois Urbana-Champaign, Champaign, IL, USA) and Harvard Medical School (yellow, Boston, MA, USA).</p></caption><graphic xlink:href="s-19-00462-fig1"></graphic></fig><fig id="fig2" position="float"><label>Figure 2</label><caption><p>Example usage scenario. User ‘Scott’ from the Sliz Laboratory at Harvard collects data at the NE-CAT beamline. It is stored temporarily to a tier 1 staging server in sliz@necat.aps.argonne.gov:/stage/sliz before being archived to tier 2 storage in sliz@necat.aps.argonne.gov:/data/sliz. Scott can use Globus Online to access his data at NE-CAT and transfer it to his personal space on the laboratory file server scott@sliz.harvard.edu:/home/scott or to his own laptop. Other laboratory members can access his data at NE-CAT owing to the mapping of all Sliz Laboratory members to the same system identity. The general public can access public archived data from 2009 in the tier 3 archival storage through a web interface. More recent archived data from 2010 and 2011 is embargoed and not available to the public.</p></caption><graphic xlink:href="s-19-00462-fig2"></graphic></fig><table-wrap id="table1" position="float"><label>Table 1</label><caption><title>Transfer rates between participating sites</title></caption><table frame="hsides" rules="groups"><thead valign="top"><tr><th style="" rowspan="1" colspan="1" align="left" charoff="50" valign="bottom"> </th><th style="border-bottom:1px solid black;" rowspan="1" colspan="5" align="left" charoff="50" valign="bottom">Transfer rate (MB s<sup>−1</sup>)</th></tr><tr><th style="border-bottom:1px solid black;" rowspan="1" colspan="1" align="left" charoff="50" valign="bottom"> </th><th style="border-bottom:1px solid black;" rowspan="1" colspan="1" align="left" charoff="50" valign="bottom">To HMS</th><th style="border-bottom:1px solid black;" rowspan="1" colspan="1" align="left" charoff="50" valign="bottom">To SSRL</th><th style="border-bottom:1px solid black;" rowspan="1" colspan="1" align="left" charoff="50" valign="bottom">To NE-CAT</th><th style="border-bottom:1px solid black;" rowspan="1" colspan="1" align="left" charoff="50" valign="bottom">To NCSA</th><th style="border-bottom:1px solid black;" rowspan="1" colspan="1" align="left" charoff="50" valign="bottom">To FNAL</th></tr></thead><tbody valign="top"><tr><td style="" rowspan="1" colspan="1" align="left" valign="top">From HMS</td><td style="" rowspan="1" colspan="1" align="left" valign="top"> </td><td style="" rowspan="1" colspan="1" align="left" valign="top">47</td><td style="" rowspan="1" colspan="1" align="left" valign="top">29</td><td style="" rowspan="1" colspan="1" align="left" valign="top">53</td><td style="" rowspan="1" colspan="1" align="left" valign="top">45</td></tr><tr><td style="" rowspan="1" colspan="1" align="left" valign="top">From SSRL</td><td style="" rowspan="1" colspan="1" align="left" valign="top">23</td><td style="" rowspan="1" colspan="1" align="left" valign="top"> </td><td style="" rowspan="1" colspan="1" align="left" valign="top">N/A</td><td style="" rowspan="1" colspan="1" align="left" valign="top">26</td><td style="" rowspan="1" colspan="1" align="left" valign="top">22</td></tr><tr><td style="" rowspan="1" colspan="1" align="left" valign="top">From NE-CAT</td><td style="" rowspan="1" colspan="1" align="left" valign="top">29</td><td style="" rowspan="1" colspan="1" align="left" valign="top">N/A</td><td style="" rowspan="1" colspan="1" align="left" valign="top"> </td><td style="" rowspan="1" colspan="1" align="left" valign="top">N/A</td><td style="" rowspan="1" colspan="1" align="left" valign="top">N/A</td></tr><tr><td style="" rowspan="1" colspan="1" align="left" valign="top">From NCSA</td><td style="" rowspan="1" colspan="1" align="left" valign="top">19</td><td style="" rowspan="1" colspan="1" align="left" valign="top">20</td><td style="" rowspan="1" colspan="1" align="left" valign="top">N/A</td><td style="" rowspan="1" colspan="1" align="left" valign="top"> </td><td style="" rowspan="1" colspan="1" align="left" valign="top">N/A</td></tr><tr><td style="" rowspan="1" colspan="1" align="left" valign="top">From FNAL</td><td style="" rowspan="1" colspan="1" align="left" valign="top">36</td><td style="" rowspan="1" colspan="1" align="left" valign="top">39</td><td style="" rowspan="1" colspan="1" align="left" valign="top">N/A</td><td style="" rowspan="1" colspan="1" align="left" valign="top">N/A</td><td style="" rowspan="1" colspan="1" align="left" valign="top"> </td></tr></tbody></table></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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