Adapting federated cyberinfrastructure for shared data collection facilities in structural biology
Identifieur interne : 000620 ( Main/Exploration ); précédent : 000619; suivant : 000621Adapting federated cyberinfrastructure for shared data collection facilities in structural biology
Auteurs : Ian Stokes-Rees ; Ian Levesque ; Frank V. Murphy Iv ; Wei Yang ; Ashley Deacon ; Piotr SlizSource :
- Journal of Synchrotron Radiation [ 1600-5775 ] ; 2012-05-01.
Descripteurs français
- Wicri :
- geographic : États-Unis.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Proteins.
- geographic : United States.
- Information Dissemination, Information Storage and Retrieval, Software, Synchrotrons.
Abstract
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.
Url:
- https://api.istex.fr/document/05DF845905FEBAA4D37002FDB06BEC0F56BB3980/fulltext/pdf
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329960
DOI: 10.1107/S0909049512009776
Affiliations:
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Le document en format XML
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Murphy Iv</name></author><author><name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name></author><author><name sortKey="Deacon, Ashley" sort="Deacon, Ashley" uniqKey="Deacon A" first="Ashley" last="Deacon">Ashley Deacon</name></author><author><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:05DF845905FEBAA4D37002FDB06BEC0F56BB3980</idno><date when="2012" year="2012">2012</date><idno type="doi">10.1107/S0909049512009776</idno><idno type="url">https://api.istex.fr/document/05DF845905FEBAA4D37002FDB06BEC0F56BB3980/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">000045</idno><idno type="wicri:Area/Istex/Curation">000045</idno><idno type="wicri:Area/Istex/Checkpoint">000139</idno><idno type="wicri:doubleKey">1600-5775:2012:Stokes Ees I:adapting:federated:cyberinfrastructure</idno><idno type="wicri:source">PMC</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329960</idno><idno type="RBID">PMC:3329960</idno><idno type="wicri:Area/Pmc/Corpus">000556</idno><idno type="wicri:Area/Pmc/Curation">000556</idno><idno type="wicri:Area/Pmc/Checkpoint">000442</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000031</idno><idno type="wicri:Area/PubMed/Curation">000031</idno><idno type="wicri:Area/PubMed/Checkpoint">000031</idno><idno type="wicri:Area/Ncbi/Merge">000300</idno><idno type="wicri:Area/Ncbi/Curation">000300</idno><idno type="wicri:Area/Ncbi/Checkpoint">000300</idno><idno type="wicri:doubleKey">0909-0495:2012:Stokes Rees I:adapting:federated:cyberinfrastructure</idno><idno type="wicri:Area/Main/Merge">000621</idno><idno type="wicri:Area/Main/Curation">000620</idno><idno type="wicri:Area/Main/Exploration">000620</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Adapting federated cyberinfrastructure for shared data collection facilities in structural biology</title><author><name sortKey="Stokes Ees, Ian" sort="Stokes Ees, Ian" uniqKey="Stokes Ees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name></author><author><name sortKey="Levesque, Ian" sort="Levesque, Ian" uniqKey="Levesque I" first="Ian" last="Levesque">Ian Levesque</name></author><author><name sortKey="Murphy Iv, Frank V" sort="Murphy Iv, Frank V" uniqKey="Murphy Iv F" first="Frank V." last="Murphy Iv">Frank V. Murphy Iv</name></author><author><name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name></author><author><name sortKey="Deacon, Ashley" sort="Deacon, Ashley" uniqKey="Deacon A" first="Ashley" last="Deacon">Ashley Deacon</name></author><author><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name></author></analytic><monogr></monogr><series><title level="j">Journal of Synchrotron Radiation</title><title level="j" type="abbrev">J. Synchrotron Rad.</title><idno type="ISSN">1600-5775</idno><idno type="eISSN">1600-5775</idno><imprint><publisher>International Union of Crystallography</publisher><pubPlace>5 Abbey Square, Chester, Cheshire CH1 2HU, England</pubPlace><date type="published" when="2012-05-01">2012-05-01</date><biblScope unit="volume">19</biblScope><biblScope unit="issue">3</biblScope><biblScope unit="page" from="462">462</biblScope><biblScope unit="page" to="467">467</biblScope></imprint><idno type="ISSN">1600-5775</idno></series><idno type="istex">05DF845905FEBAA4D37002FDB06BEC0F56BB3980</idno><idno type="DOI">10.1107/S0909049512009776</idno><idno type="ArticleID">JSYIE5073</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1600-5775</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Information Dissemination</term><term>Information Storage and Retrieval</term><term>Proteins (chemistry)</term><term>Software</term><term>Synchrotrons</term><term>United States</term><term>collaborative tools</term><term>data handling and security</term><term>diffraction images</term><term>grid computing</term><term>structural biology</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" type="geographic" xml:lang="en"><term>United States</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Information Dissemination</term><term>Information Storage and Retrieval</term><term>Software</term><term>Synchrotrons</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>États-Unis</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><affiliations><list></list><tree><noCountry><name sortKey="Deacon, Ashley" sort="Deacon, Ashley" uniqKey="Deacon A" first="Ashley" last="Deacon">Ashley Deacon</name><name sortKey="Levesque, Ian" sort="Levesque, Ian" uniqKey="Levesque I" first="Ian" last="Levesque">Ian Levesque</name><name sortKey="Murphy Iv, Frank V" sort="Murphy Iv, Frank V" uniqKey="Murphy Iv F" first="Frank V." last="Murphy Iv">Frank V. Murphy Iv</name><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name><name sortKey="Stokes Ees, Ian" sort="Stokes Ees, Ian" uniqKey="Stokes Ees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name><name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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