Adapting federated cyberinfrastructure for shared data collection facilities in structural biology
Identifieur interne : 000300 ( Ncbi/Checkpoint ); précédent : 000299; suivant : 000301Adapting 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.
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
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.
Url:
DOI: 10.1107/S0909049512009776
PubMed: 22514186
PubMed Central: 3329960
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000556
- to stream Pmc, to step Curation: 000556
- to stream Pmc, to step Checkpoint: 000442
- to stream PubMed, to step Corpus: 000031
- to stream PubMed, to step Curation: 000031
- to stream PubMed, to step Checkpoint: 000031
- to stream Ncbi, to step Merge: 000300
- to stream Ncbi, to step Curation: 000300
Links to Exploration step
PMC:3329960Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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>
</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>
<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>
</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><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>
</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>
</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>
<affiliations><list><country><li>États-Unis</li>
</country>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Stokes Rees, Ian" sort="Stokes Rees, Ian" uniqKey="Stokes Rees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name>
</noRegion>
<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="Levesque, Ian" sort="Levesque, Ian" uniqKey="Levesque I" first="Ian" last="Levesque">Ian Levesque</name>
<name sortKey="Murphy, Frank V" sort="Murphy, Frank V" uniqKey="Murphy F" first="Frank V." last="Murphy">Frank V. Murphy</name>
<name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name>
<name sortKey="Yang, Wei" sort="Yang, Wei" uniqKey="Yang W" first="Wei" last="Yang">Wei Yang</name>
</country>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Ncbi/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000300 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd -nk 000300 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Ncbi |étape= Checkpoint |type= RBID |clé= PMC:3329960 |texte= Adapting federated cyberinfrastructure for shared data collection facilities in structural biology }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/RBID.i -Sk "pubmed:22514186" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd \ | NlmPubMed2Wicri -a CyberinfraV1
![]() | This area was generated with Dilib version V0.6.25. | ![]() |