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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and their Assemblies Using Mass Spectrometry-based Approaches</title><author><name sortKey="Yu, Eizadora T" sort="Yu, Eizadora T" uniqKey="Yu E" first="Eizadora T." last="Yu">Eizadora T. Yu</name><affiliation><nlm:aff id="A1">Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Hawkins, Arie" sort="Hawkins, Arie" uniqKey="Hawkins A" first="Arie" last="Hawkins">Arie Hawkins</name><affiliation><nlm:aff id="A4">Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA</nlm:aff></affiliation></author><author><name sortKey="Kuntz, Irwin D" sort="Kuntz, Irwin D" uniqKey="Kuntz I" first="Irwin D." last="Kuntz">Irwin D. Kuntz</name><affiliation><nlm:aff id="A5">UCSF Molecular Design Institute, 513 Parnassus Avenue, S926, Box 0046, San Francisco, CA, 94143-0046</nlm:aff></affiliation></author><author><name sortKey="Rahn, Larry A" sort="Rahn, Larry A" uniqKey="Rahn L" first="Larry A." last="Rahn">Larry A. Rahn</name><affiliation><nlm:aff id="A2">Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Rothfuss, Andrew" sort="Rothfuss, Andrew" uniqKey="Rothfuss A" first="Andrew" last="Rothfuss">Andrew Rothfuss</name><affiliation><nlm:aff id="A2">Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Sale, Kenneth" sort="Sale, Kenneth" uniqKey="Sale K" first="Kenneth" last="Sale">Kenneth Sale</name><affiliation><nlm:aff id="A1">Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Young, Malin M" sort="Young, Malin M" uniqKey="Young M" first="Malin M." last="Young">Malin M. Young</name><affiliation><nlm:aff id="A1">Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Yang, Christine L" sort="Yang, Christine L" uniqKey="Yang C" first="Christine L." last="Yang">Christine L. Yang</name><affiliation><nlm:aff id="A3">Exploratory Computer and Software Engineering Department, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Pancerella, Carmen M" sort="Pancerella, Carmen M" uniqKey="Pancerella C" first="Carmen M." last="Pancerella">Carmen M. Pancerella</name><affiliation><nlm:aff id="A2">Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Fabris, Daniele" sort="Fabris, Daniele" uniqKey="Fabris D" first="Daniele" last="Fabris">Daniele Fabris</name><affiliation><nlm:aff id="A4">Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18817429</idno><idno type="pmc">2677910</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677910</idno><idno type="RBID">PMC:2677910</idno><idno type="doi">10.1021/pr800443f</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000285</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and their Assemblies Using Mass Spectrometry-based Approaches</title><author><name sortKey="Yu, Eizadora T" sort="Yu, Eizadora T" uniqKey="Yu E" first="Eizadora T." last="Yu">Eizadora T. Yu</name><affiliation><nlm:aff id="A1">Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Hawkins, Arie" sort="Hawkins, Arie" uniqKey="Hawkins A" first="Arie" last="Hawkins">Arie Hawkins</name><affiliation><nlm:aff id="A4">Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA</nlm:aff></affiliation></author><author><name sortKey="Kuntz, Irwin D" sort="Kuntz, Irwin D" uniqKey="Kuntz I" first="Irwin D." last="Kuntz">Irwin D. Kuntz</name><affiliation><nlm:aff id="A5">UCSF Molecular Design Institute, 513 Parnassus Avenue, S926, Box 0046, San Francisco, CA, 94143-0046</nlm:aff></affiliation></author><author><name sortKey="Rahn, Larry A" sort="Rahn, Larry A" uniqKey="Rahn L" first="Larry A." last="Rahn">Larry A. Rahn</name><affiliation><nlm:aff id="A2">Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Rothfuss, Andrew" sort="Rothfuss, Andrew" uniqKey="Rothfuss A" first="Andrew" last="Rothfuss">Andrew Rothfuss</name><affiliation><nlm:aff id="A2">Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Sale, Kenneth" sort="Sale, Kenneth" uniqKey="Sale K" first="Kenneth" last="Sale">Kenneth Sale</name><affiliation><nlm:aff id="A1">Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Young, Malin M" sort="Young, Malin M" uniqKey="Young M" first="Malin M." last="Young">Malin M. Young</name><affiliation><nlm:aff id="A1">Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Yang, Christine L" sort="Yang, Christine L" uniqKey="Yang C" first="Christine L." last="Yang">Christine L. Yang</name><affiliation><nlm:aff id="A3">Exploratory Computer and Software Engineering Department, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Pancerella, Carmen M" sort="Pancerella, Carmen M" uniqKey="Pancerella C" first="Carmen M." last="Pancerella">Carmen M. Pancerella</name><affiliation><nlm:aff id="A2">Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff></affiliation></author><author><name sortKey="Fabris, Daniele" sort="Fabris, Daniele" uniqKey="Fabris D" first="Daniele" last="Fabris">Daniele Fabris</name><affiliation><nlm:aff id="A4">Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA</nlm:aff></affiliation></author></analytic><series><title level="j">Journal of proteome research</title><idno type="ISSN">1535-3893</idno><idno type="eISSN">1535-3907</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research lab or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application, the shared work environment is a general approach to building collaborative work groups. The goal of which is to not only provide a common data sharing and archiving system but also to assist in the building of new collaborations and to spur the development of new tools and technologies.</p></div></front></TEI><pmc article-type="research-article" xml:lang="EN"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101128775</journal-id><journal-id journal-id-type="pubmed-jr-id">30137</journal-id><journal-id journal-id-type="nlm-ta">J Proteome Res</journal-id><journal-title>Journal of proteome research</journal-title><issn pub-type="ppub">1535-3893</issn><issn pub-type="epub">1535-3907</issn></journal-meta><article-meta><article-id pub-id-type="pmid">18817429</article-id><article-id pub-id-type="pmc">2677910</article-id><article-id pub-id-type="doi">10.1021/pr800443f</article-id><article-id pub-id-type="manuscript">NIHMS91087</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and their Assemblies Using Mass Spectrometry-based Approaches</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Yu</surname><given-names>Eizadora T.</given-names></name><xref rid="A1" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Hawkins</surname><given-names>Arie</given-names></name><xref rid="A4" ref-type="aff">4</xref></contrib><contrib contrib-type="author"><name><surname>Kuntz</surname><given-names>Irwin D.</given-names></name><xref rid="A5" ref-type="aff">5</xref></contrib><contrib contrib-type="author"><name><surname>Rahn</surname><given-names>Larry A.</given-names></name><xref rid="A2" ref-type="aff">2</xref></contrib><contrib contrib-type="author"><name><surname>Rothfuss</surname><given-names>Andrew</given-names></name><xref rid="A2" ref-type="aff">2</xref></contrib><contrib contrib-type="author"><name><surname>Sale</surname><given-names>Kenneth</given-names></name><xref rid="A1" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Young</surname><given-names>Malin M.</given-names></name><xref rid="A1" ref-type="aff">1</xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Christine L.</given-names></name><xref rid="A3" ref-type="aff">3</xref></contrib><contrib contrib-type="author"><name><surname>Pancerella</surname><given-names>Carmen M.</given-names></name><xref rid="A2" ref-type="aff">2</xref></contrib><contrib contrib-type="author"><name><surname>Fabris</surname><given-names>Daniele</given-names></name><xref rid="A4" ref-type="aff">4</xref><xref rid="FN1" ref-type="author-notes">*</xref></contrib></contrib-group><aff id="A1"><label>1</label>Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</aff><aff id="A2"><label>2</label>Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</aff><aff id="A3"><label>3</label>Exploratory Computer and Software Engineering Department, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</aff><aff id="A4"><label>4</label>Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA</aff><aff id="A5"><label>5</label>UCSF Molecular Design Institute, 513 Parnassus Avenue, S926, Box 0046, San Francisco, CA, 94143-0046</aff><author-notes><corresp id="FN1"><label>*</label>Corresponding author <email>fabris@umbc.edu</email></corresp></author-notes><pub-date pub-type="nihms-submitted"><day>17</day><month>2</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>26</day><month>9</month><year>2008</year></pub-date><pub-date pub-type="ppub"><month>11</month><year>2008</year></pub-date><pub-date pub-type="pmc-release"><day>1</day><month>11</month><year>2009</year></pub-date><volume>7</volume><issue>11</issue><fpage>4848</fpage><lpage>4857</lpage><abstract><p id="P1">Modern biomedical research is evolving with the rapid growth of diverse data types, biophysical characterization methods, computational tools and extensive collaboration among researchers spanning various communities and having complementary backgrounds and expertise. Collaborating researchers are increasingly dependent on shared data and tools made available by other investigators with common interests, thus forming communities that transcend the traditional boundaries of the single research lab or institution. Barriers, however, remain to the formation of these virtual communities, usually due to the steep learning curve associated with becoming familiar with new tools, or with the difficulties associated with transferring data between tools. Recognizing the need for shared reference data and analysis tools, we are developing an integrated knowledge environment that supports productive interactions among researchers. Here we report on our current collaborative environment, which focuses on bringing together structural biologists working in the area of mass spectrometric based methods for the analysis of tertiary and quaternary macromolecular structures (MS3D) called the Collaboratory for MS3D (C-MS3D). C-MS3D is a web-portal designed to provide collaborators with a shared work environment that integrates data storage and management with data analysis tools. Files are stored and archived along with pertinent meta data in such a way as to allow file handling to be tracked (data provenance) and data files to be searched using keywords and modification dates. While at this time the portal is designed around a specific application, the shared work environment is a general approach to building collaborative work groups. The goal of which is to not only provide a common data sharing and archiving system but also to assist in the building of new collaborations and to spur the development of new tools and technologies.</p></abstract><kwd-group><kwd>Collaboratory</kwd><kwd>data analysis tools</kwd><kwd>structural biology</kwd><kwd>mass spectrometry</kwd></kwd-group><contract-num rid="RR1">R01 RR019864-05</contract-num><contract-sponsor id="RR1">National Center for Research Resources : NCRR</contract-sponsor></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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