The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and their Assemblies Using Mass Spectrometry-based Approaches
Identifieur interne : 000D58 ( Main/Exploration ); précédent : 000D57; suivant : 000D59The Collaboratory for MS3D: A New Cyberinfrastructure for the Structural Elucidation of Biological Macromolecules and their Assemblies Using Mass Spectrometry-based Approaches
Auteurs : Eizadora T. Yu [États-Unis] ; Arie Hawkins [États-Unis] ; Irwin D. Kuntz ; Larry A. Rahn [États-Unis] ; Andrew Rothfuss [États-Unis] ; Kenneth Sale [États-Unis] ; Malin M. Young [États-Unis] ; Christine L. Yang [États-Unis] ; Carmen M. Pancerella [États-Unis] ; Daniele Fabris [États-Unis]Source :
- Journal of proteome research [ 1535-3893 ] ; 2008.
English descriptors
- KwdEn :
- Amino Acid Sequence, Base Sequence, Computational Biology (methods), Cooperative Behavior, Database Management Systems, Information Storage and Retrieval, Internet, Mass Spectrometry, Molecular Sequence Data, Nucleic Acids (chemistry), Nucleic Acids (metabolism), Protein Structure, Quaternary, Protein Structure, Tertiary, Proteins (chemistry), Proteins (metabolism), Research Personnel, Software, Systems Integration.
- MESH :
- chemical , chemistry : Nucleic Acids, Proteins.
- chemical , metabolism : Nucleic Acids, Proteins.
- methods : Computational Biology.
- Amino Acid Sequence, Base Sequence, Cooperative Behavior, Database Management Systems, Information Storage and Retrieval, Internet, Mass Spectrometry, Molecular Sequence Data, Protein Structure, Quaternary, Protein Structure, Tertiary, Research Personnel, Software, Systems Integration.
Abstract
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.
Url:
DOI: 10.1021/pr800443f
PubMed: 18817429
PubMed Central: 2677910
Affiliations:
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Le document en format XML
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Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></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 wicri:level="2"><nlm:aff id="A1">Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></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 wicri:level="2"><nlm:aff id="A3">Exploratory Computer and Software Engineering Department, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Exploratory Computer and Software Engineering Department, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></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 wicri:level="2"><nlm:aff id="A2">Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Fabris, Daniele" sort="Fabris, Daniele" uniqKey="Fabris D" first="Daniele" last="Fabris">Daniele Fabris</name><affiliation wicri:level="4"><nlm:aff id="A4">Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></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><idno type="wicri:Area/Pmc/Curation">000285</idno><idno type="wicri:Area/Pmc/Checkpoint">000662</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000073</idno><idno type="wicri:Area/PubMed/Curation">000073</idno><idno type="wicri:Area/PubMed/Checkpoint">000073</idno><idno type="wicri:Area/Ncbi/Merge">000064</idno><idno type="wicri:Area/Ncbi/Curation">000064</idno><idno type="wicri:Area/Ncbi/Checkpoint">000064</idno><idno type="wicri:doubleKey">1535-3893:2008:Yu E:the:collaboratory:for</idno><idno type="wicri:Area/Main/Merge">000D65</idno><idno type="wicri:Area/Main/Curation">000D58</idno><idno type="wicri:Area/Main/Exploration">000D58</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 wicri:level="2"><nlm:aff id="A1">Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Hawkins, Arie" sort="Hawkins, Arie" uniqKey="Hawkins A" first="Arie" last="Hawkins">Arie Hawkins</name><affiliation wicri:level="4"><nlm:aff id="A4">Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></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><wicri:noCountry code="subfield">94143-0046</wicri:noCountry></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 wicri:level="2"><nlm:aff id="A2">Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Rothfuss, Andrew" sort="Rothfuss, Andrew" uniqKey="Rothfuss A" first="Andrew" last="Rothfuss">Andrew Rothfuss</name><affiliation wicri:level="2"><nlm:aff id="A2">Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Sale, Kenneth" sort="Sale, Kenneth" uniqKey="Sale K" first="Kenneth" last="Sale">Kenneth Sale</name><affiliation wicri:level="2"><nlm:aff id="A1">Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></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 wicri:level="2"><nlm:aff id="A1">Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosystems Research, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></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 wicri:level="2"><nlm:aff id="A3">Exploratory Computer and Software Engineering Department, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Exploratory Computer and Software Engineering Department, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></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 wicri:level="2"><nlm:aff id="A2">Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Advanced Software R&D, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94551-0969</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Fabris, Daniele" sort="Fabris, Daniele" uniqKey="Fabris D" first="Daniele" last="Fabris">Daniele Fabris</name><affiliation wicri:level="4"><nlm:aff id="A4">Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></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><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Base Sequence</term><term>Computational Biology (methods)</term><term>Cooperative Behavior</term><term>Database Management Systems</term><term>Information Storage and Retrieval</term><term>Internet</term><term>Mass Spectrometry</term><term>Molecular Sequence Data</term><term>Nucleic Acids (chemistry)</term><term>Nucleic Acids (metabolism)</term><term>Protein Structure, Quaternary</term><term>Protein Structure, Tertiary</term><term>Proteins (chemistry)</term><term>Proteins (metabolism)</term><term>Research Personnel</term><term>Software</term><term>Systems Integration</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Nucleic Acids</term><term>Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Nucleic Acids</term><term>Proteins</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Base Sequence</term><term>Cooperative Behavior</term><term>Database Management Systems</term><term>Information Storage and Retrieval</term><term>Internet</term><term>Mass Spectrometry</term><term>Molecular Sequence Data</term><term>Protein Structure, Quaternary</term><term>Protein Structure, Tertiary</term><term>Research Personnel</term><term>Software</term><term>Systems Integration</term></keywords></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><affiliations><list><country><li>États-Unis</li></country><region><li>Californie</li><li>Maryland</li></region><settlement><li>College Park (Maryland)</li></settlement><orgName><li>Université du Maryland</li></orgName></list><tree><noCountry><name sortKey="Kuntz, Irwin D" sort="Kuntz, Irwin D" uniqKey="Kuntz I" first="Irwin D." last="Kuntz">Irwin D. Kuntz</name></noCountry><country name="États-Unis"><region name="Californie"><name sortKey="Yu, Eizadora T" sort="Yu, Eizadora T" uniqKey="Yu E" first="Eizadora T." last="Yu">Eizadora T. Yu</name></region><name sortKey="Fabris, Daniele" sort="Fabris, Daniele" uniqKey="Fabris D" first="Daniele" last="Fabris">Daniele Fabris</name><name sortKey="Hawkins, Arie" sort="Hawkins, Arie" uniqKey="Hawkins A" first="Arie" last="Hawkins">Arie Hawkins</name><name sortKey="Pancerella, Carmen M" sort="Pancerella, Carmen M" uniqKey="Pancerella C" first="Carmen M." last="Pancerella">Carmen M. Pancerella</name><name sortKey="Rahn, Larry A" sort="Rahn, Larry A" uniqKey="Rahn L" first="Larry A." last="Rahn">Larry A. Rahn</name><name sortKey="Rothfuss, Andrew" sort="Rothfuss, Andrew" uniqKey="Rothfuss A" first="Andrew" last="Rothfuss">Andrew Rothfuss</name><name sortKey="Sale, Kenneth" sort="Sale, Kenneth" uniqKey="Sale K" first="Kenneth" last="Sale">Kenneth Sale</name><name sortKey="Yang, Christine L" sort="Yang, Christine L" uniqKey="Yang C" first="Christine L." last="Yang">Christine L. Yang</name><name sortKey="Young, Malin M" sort="Young, Malin M" uniqKey="Young M" first="Malin M." last="Young">Malin M. Young</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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