Conceptualizing a Genomics Software Institute (GSI)
Identifieur interne : 000432 ( Pmc/Checkpoint ); précédent : 000431; suivant : 000433Conceptualizing a Genomics Software Institute (GSI)
Auteurs : Jack A. Gilbert [États-Unis] ; Charlie Catlett [États-Unis] ; Narayan Desai [États-Unis] ; Rob Knight [États-Unis] ; Owen White [États-Unis] ; Robert Robbins [États-Unis] ; Rajesh Sankaran [États-Unis] ; Susanna-Assunta Sansone [Royaume-Uni] ; Dawn Field [Royaume-Uni] ; Folker Meyer [États-Unis]Source :
- Standards in Genomic Sciences [ 1944-3277 ] ; 2012.
Abstract
Microbial ecology has been enhanced greatly by the ongoing ‘omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).
Url:
DOI: 10.4056/sigs.2485911
PubMed: 22675605
PubMed Central: 3359878
Affiliations:
- Royaume-Uni, États-Unis
- Angleterre, Californie, Colorado, Illinois, Maryland, Oxfordshire
- Baltimore, Oxford
- Université d'Oxford
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PMC:3359878Le document en format XML
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<front><div type="abstract" xml:lang="en"><p>Microbial ecology has been enhanced greatly by the ongoing ‘omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).</p>
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<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Whitman, Wb" uniqKey="Whitman W">WB Whitman</name>
</author>
<author><name sortKey="Coleman, Dc" uniqKey="Coleman D">DC Coleman</name>
</author>
<author><name sortKey="Wiebe, Wj" uniqKey="Wiebe W">WJ Wiebe</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gilbert, Ja" uniqKey="Gilbert J">JA Gilbert</name>
</author>
<author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name>
</author>
<author><name sortKey="Antonopoulos, D" uniqKey="Antonopoulos D">D Antonopoulos</name>
</author>
<author><name sortKey="Balaji, P" uniqKey="Balaji P">P Balaji</name>
</author>
<author><name sortKey="Brown, Ct" uniqKey="Brown C">CT Brown</name>
</author>
<author><name sortKey="Brown, Ct" uniqKey="Brown C">CT Brown</name>
</author>
<author><name sortKey="Desai, N" uniqKey="Desai N">N Desai</name>
</author>
<author><name sortKey="Eisen, Ja" uniqKey="Eisen J">JA Eisen</name>
</author>
<author><name sortKey="Evers, D" uniqKey="Evers D">D Evers</name>
</author>
<author><name sortKey="Field, D" uniqKey="Field D">D Field</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Delmont, To" uniqKey="Delmont T">TO Delmont</name>
</author>
<author><name sortKey="Malandain, C" uniqKey="Malandain C">C Malandain</name>
</author>
<author><name sortKey="Prestat, E" uniqKey="Prestat E">E Prestat</name>
</author>
<author><name sortKey="Larose, C" uniqKey="Larose C">C Larose</name>
</author>
<author><name sortKey="Monier, Jm" uniqKey="Monier J">JM Monier</name>
</author>
<author><name sortKey="Simonet, P" uniqKey="Simonet P">P Simonet</name>
</author>
<author><name sortKey="Vogel, Tm" uniqKey="Vogel T">TM Vogel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gilbert, Ja" uniqKey="Gilbert J">JA Gilbert</name>
</author>
<author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name>
</author>
<author><name sortKey="Bailey, Mj" uniqKey="Bailey M">MJ Bailey</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gilbert, Ja" uniqKey="Gilbert J">JA Gilbert</name>
</author>
<author><name sortKey="Steele, Ja" uniqKey="Steele J">JA Steele</name>
</author>
<author><name sortKey="Caporaso, Jg" uniqKey="Caporaso J">JG Caporaso</name>
</author>
<author><name sortKey="Steinbruck, L" uniqKey="Steinbruck L">L Steinbrück</name>
</author>
<author><name sortKey="Reeder, J" uniqKey="Reeder J">J Reeder</name>
</author>
<author><name sortKey="Temperton, B" uniqKey="Temperton B">B Temperton</name>
</author>
<author><name sortKey="Huse, S" uniqKey="Huse S">S Huse</name>
</author>
<author><name sortKey="Mchardy, Ac" uniqKey="Mchardy A">AC McHardy</name>
</author>
<author><name sortKey="Knight, R" uniqKey="Knight R">R Knight</name>
</author>
<author><name sortKey="Joint, I" uniqKey="Joint I">I Joint</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gilbert, Ja" uniqKey="Gilbert J">JA Gilbert</name>
</author>
<author><name sortKey="Field, D" uniqKey="Field D">D Field</name>
</author>
<author><name sortKey="Swift, P" uniqKey="Swift P">P Swift</name>
</author>
<author><name sortKey="Thomas, S" uniqKey="Thomas S">S Thomas</name>
</author>
<author><name sortKey="Cummings, D" uniqKey="Cummings D">D Cummings</name>
</author>
<author><name sortKey="Temperton, B" uniqKey="Temperton B">B Temperton</name>
</author>
<author><name sortKey="Weynberg, K" uniqKey="Weynberg K">K Weynberg</name>
</author>
<author><name sortKey="Huse, S" uniqKey="Huse S">S Huse</name>
</author>
<author><name sortKey="Hughes, M" uniqKey="Hughes M">M Hughes</name>
</author>
<author><name sortKey="Joint, I" uniqKey="Joint I">I Joint</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Delmont, To" uniqKey="Delmont T">TO Delmont</name>
</author>
<author><name sortKey="Robe, P" uniqKey="Robe P">P Robe</name>
</author>
<author><name sortKey="Cecillon, S" uniqKey="Cecillon S">S Cecillon</name>
</author>
<author><name sortKey="Clark, Im" uniqKey="Clark I">IM Clark</name>
</author>
<author><name sortKey="Constancias, F" uniqKey="Constancias F">F Constancias</name>
</author>
<author><name sortKey="Simonet, P" uniqKey="Simonet P">P Simonet</name>
</author>
<author><name sortKey="Hirsch, Pr" uniqKey="Hirsch P">PR Hirsch</name>
</author>
<author><name sortKey="Vogel, Tm" uniqKey="Vogel T">TM Vogel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hugenholtz, P" uniqKey="Hugenholtz P">P Hugenholtz</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Field, D" uniqKey="Field D">D Field</name>
</author>
<author><name sortKey="Amaral Zettler, L" uniqKey="Amaral Zettler L">L Amaral-Zettler</name>
</author>
<author><name sortKey="Cochrane, G" uniqKey="Cochrane G">G Cochrane</name>
</author>
<author><name sortKey="Cole, Jr" uniqKey="Cole J">JR Cole</name>
</author>
<author><name sortKey="Dawyndt, P" uniqKey="Dawyndt P">P Dawyndt</name>
</author>
<author><name sortKey="Garrity, Gm" uniqKey="Garrity G">GM Garrity</name>
</author>
<author><name sortKey="Gilbert, J" uniqKey="Gilbert J">J Gilbert</name>
</author>
<author><name sortKey="Glockner, Fo" uniqKey="Glockner F">FO Glöckner</name>
</author>
<author><name sortKey="Hirschman, L" uniqKey="Hirschman L">L Hirschman</name>
</author>
<author><name sortKey="Karsch Mizrachi, I" uniqKey="Karsch Mizrachi I">I Karsch-Mizrachi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rocca Serra, P" uniqKey="Rocca Serra P">P Rocca-Serra</name>
</author>
<author><name sortKey="Brandizi, M" uniqKey="Brandizi M">M Brandizi</name>
</author>
<author><name sortKey="Maguire, E" uniqKey="Maguire E">E Maguire</name>
</author>
<author><name sortKey="Sklyar, N" uniqKey="Sklyar N">N Sklyar</name>
</author>
<author><name sortKey="Taylor, C" uniqKey="Taylor C">C Taylor</name>
</author>
<author><name sortKey="Begley, K" uniqKey="Begley K">K Begley</name>
</author>
<author><name sortKey="Field, D" uniqKey="Field D">D Field</name>
</author>
<author><name sortKey="Harris, S" uniqKey="Harris S">S Harris</name>
</author>
<author><name sortKey="Hide, W" uniqKey="Hide W">W Hide</name>
</author>
<author><name sortKey="Hofmann, O" uniqKey="Hofmann O">O Hofmann</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name>
</author>
<author><name sortKey="Paarmann, D" uniqKey="Paarmann D">D Paarmann</name>
</author>
<author><name sortKey="D Souza, M" uniqKey="D Souza M">M D'Souza</name>
</author>
<author><name sortKey="Olson, R" uniqKey="Olson R">R Olson</name>
</author>
<author><name sortKey="Glass, Em" uniqKey="Glass E">EM Glass</name>
</author>
<author><name sortKey="Kubal, M" uniqKey="Kubal M">M Kubal</name>
</author>
<author><name sortKey="Paczian, T" uniqKey="Paczian T">T Paczian</name>
</author>
<author><name sortKey="Rodriguez, A" uniqKey="Rodriguez A">A Rodriguez</name>
</author>
<author><name sortKey="Stevens, R" uniqKey="Stevens R">R Stevens</name>
</author>
<author><name sortKey="Wilke, A" uniqKey="Wilke A">A Wilke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sansone, S" uniqKey="Sansone S">S Sansone</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Butte, Aj" uniqKey="Butte A">AJ Butte</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Aziz, Rk" uniqKey="Aziz R">RK Aziz</name>
</author>
<author><name sortKey="Bartels, D" uniqKey="Bartels D">D Bartels</name>
</author>
<author><name sortKey="Best, Aa" uniqKey="Best A">AA Best</name>
</author>
<author><name sortKey="Dejongh, M" uniqKey="Dejongh M">M DeJongh</name>
</author>
<author><name sortKey="Disz, T" uniqKey="Disz T">T Disz</name>
</author>
<author><name sortKey="Edwards, Ra" uniqKey="Edwards R">RA Edwards</name>
</author>
<author><name sortKey="Formsma, K" uniqKey="Formsma K">K Formsma</name>
</author>
<author><name sortKey="Gerdes, S" uniqKey="Gerdes S">S Gerdes</name>
</author>
<author><name sortKey="Glass, Em" uniqKey="Glass E">EM Glass</name>
</author>
<author><name sortKey="Kubal, M" uniqKey="Kubal M">M Kubal</name>
</author>
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</author>
</analytic>
</biblStruct>
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</author>
<author><name sortKey="Ivanova, Nn" uniqKey="Ivanova N">NN Ivanova</name>
</author>
<author><name sortKey="Szeto, E" uniqKey="Szeto E">E Szeto</name>
</author>
<author><name sortKey="Palaniappan, K" uniqKey="Palaniappan K">K Palaniappan</name>
</author>
<author><name sortKey="Chu, K" uniqKey="Chu K">K Chu</name>
</author>
<author><name sortKey="Dalevi, D" uniqKey="Dalevi D">D Dalevi</name>
</author>
<author><name sortKey="Chen, Im" uniqKey="Chen I">IM Chen</name>
</author>
<author><name sortKey="Grechkin, Y" uniqKey="Grechkin Y">Y Grechkin</name>
</author>
<author><name sortKey="Dubchak, I" uniqKey="Dubchak I">I Dubchak</name>
</author>
<author><name sortKey="Anderson, I" uniqKey="Anderson I">I Anderson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gilbert, Ja" uniqKey="Gilbert J">JA Gilbert</name>
</author>
<author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name>
</author>
<author><name sortKey="Knight, R" uniqKey="Knight R">R Knight</name>
</author>
<author><name sortKey="Field, D" uniqKey="Field D">D Field</name>
</author>
<author><name sortKey="Kyrpides, N" uniqKey="Kyrpides N">N Kyrpides</name>
</author>
<author><name sortKey="Yilmaz, P" uniqKey="Yilmaz P">P Yilmaz</name>
</author>
<author><name sortKey="Wooley, J" uniqKey="Wooley J">J Wooley</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vogels, W" uniqKey="Vogels W">W Vogels</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct></biblStruct>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Stand Genomic Sci</journal-id>
<journal-id journal-id-type="iso-abbrev">Stand Genomic Sci</journal-id>
<journal-id journal-id-type="publisher-id">SIGS</journal-id>
<journal-title-group><journal-title>Standards in Genomic Sciences</journal-title>
</journal-title-group>
<issn pub-type="epub">1944-3277</issn>
<publisher><publisher-name>Michigan State University</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22675605</article-id>
<article-id pub-id-type="pmc">3359878</article-id>
<article-id pub-id-type="publisher-id">sigs.2485911</article-id>
<article-id pub-id-type="doi">10.4056/sigs.2485911</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>White Papers</subject>
</subj-group>
</article-categories>
<title-group><article-title>Conceptualizing a Genomics Software Institute (GSI)</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Gilbert</surname>
<given-names>Jack A.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="corresp" rid="cor1"><sup>*</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Catlett</surname>
<given-names>Charlie</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Desai</surname>
<given-names>Narayan</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Knight</surname>
<given-names>Rob</given-names>
</name>
<xref ref-type="aff" rid="aff4"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>White</surname>
<given-names>Owen</given-names>
</name>
<xref ref-type="aff" rid="aff5"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Robbins</surname>
<given-names>Robert</given-names>
</name>
<xref ref-type="aff" rid="aff6"><sup>6</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sankaran</surname>
<given-names>Rajesh</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sansone</surname>
<given-names>Susanna-Assunta</given-names>
</name>
<xref ref-type="aff" rid="aff7"><sup>7</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Field</surname>
<given-names>Dawn</given-names>
</name>
<xref ref-type="aff" rid="aff7"><sup>7</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Meyer</surname>
<given-names>Folker</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
</contrib>
<aff id="aff1"><label>1</label>
Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA</aff>
<aff id="aff2"><label>2</label>
Argonne National Laboratory, Argonne, IL, USA</aff>
<aff id="aff3"><label>3</label>
Computation Institute, University of Chicago, Chicago, IL USA</aff>
<aff id="aff4"><label>4</label>
Howard Hughes Medical Institute, Boulder, CO, USA</aff>
<aff id="aff5"><label>5</label>
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA</aff>
<aff id="aff6"><label>6</label>
University of California, San Diego, La Jolla, California, USA</aff>
<aff id="aff7"><label>7</label>
Oxford e-Research Centre, University of Oxford, Oxford, UK</aff>
<aff id="aff8"><label>8</label>
Centre for Ecology & Hydrology, Natural Environment Research Council, Crowmarsh Gifford, Wallingford, Oxon, UK</aff>
</contrib-group>
<author-notes><corresp id="cor1"><label>*</label>
Corresponding author: Jack A. Gilbert (<email xlink:href="gilberjack@gmail.com">gilberjack@gmail.com</email>
)</corresp>
</author-notes>
<pub-date pub-type="epub"><day>05</day>
<month>3</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="collection"><day>19</day>
<month>3</month>
<year>2012</year>
</pub-date>
<volume>6</volume>
<issue>1</issue>
<fpage>136</fpage>
<lpage>144</lpage>
<permissions><copyright-year>2012</copyright-year>
<copyright-holder>Gilbert et al.</copyright-holder>
</permissions>
<abstract><p>Microbial ecology has been enhanced greatly by the ongoing ‘omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).</p>
</abstract>
<funding-group><award-group><funding-source id="sp1">Dept. of Energy</funding-source>
<award-id rid="sp1">DE-AC02-06CH11357</award-id>
</award-group>
<award-group><funding-source id="sp2">National Science Foundation</funding-source>
<award-id rid="sp2">DBI-0840989</award-id>
</award-group>
</funding-group>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Royaume-Uni</li>
<li>États-Unis</li>
</country>
<region><li>Angleterre</li>
<li>Californie</li>
<li>Colorado</li>
<li>Illinois</li>
<li>Maryland</li>
<li>Oxfordshire</li>
</region>
<settlement><li>Baltimore</li>
<li>Oxford</li>
</settlement>
<orgName><li>Université d'Oxford</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Illinois"><name sortKey="Gilbert, Jack A" sort="Gilbert, Jack A" uniqKey="Gilbert J" first="Jack A." last="Gilbert">Jack A. Gilbert</name>
</region>
<name sortKey="Catlett, Charlie" sort="Catlett, Charlie" uniqKey="Catlett C" first="Charlie" last="Catlett">Charlie Catlett</name>
<name sortKey="Desai, Narayan" sort="Desai, Narayan" uniqKey="Desai N" first="Narayan" last="Desai">Narayan Desai</name>
<name sortKey="Knight, Rob" sort="Knight, Rob" uniqKey="Knight R" first="Rob" last="Knight">Rob Knight</name>
<name sortKey="Meyer, Folker" sort="Meyer, Folker" uniqKey="Meyer F" first="Folker" last="Meyer">Folker Meyer</name>
<name sortKey="Robbins, Robert" sort="Robbins, Robert" uniqKey="Robbins R" first="Robert" last="Robbins">Robert Robbins</name>
<name sortKey="Sankaran, Rajesh" sort="Sankaran, Rajesh" uniqKey="Sankaran R" first="Rajesh" last="Sankaran">Rajesh Sankaran</name>
<name sortKey="White, Owen" sort="White, Owen" uniqKey="White O" first="Owen" last="White">Owen White</name>
</country>
<country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Sansone, Susanna Assunta" sort="Sansone, Susanna Assunta" uniqKey="Sansone S" first="Susanna-Assunta" last="Sansone">Susanna-Assunta Sansone</name>
</region>
<name sortKey="Field, Dawn" sort="Field, Dawn" uniqKey="Field D" first="Dawn" last="Field">Dawn Field</name>
</country>
</tree>
</affiliations>
</record>
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