xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud[OPEN]
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Auteurs : Jon Duvick [États-Unis] ; Daniel S. Standage [États-Unis] ; Nirav Merchant [États-Unis] ; Volker P. Brendel [États-Unis]Source :
- The Plant Cell [ 1040-4651 ] ; 2016.
Abstract
xGDBvm is a novel tool for scalable, reproducible, and expandable genome annotation via Web-based interfaces that seamlessly integrate background cloud-based data storage and high-performance computer resources.
Url:
DOI: 10.1105/tpc.15.00933
PubMed: 27020957
PubMed Central: 4863385
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud<xref ref-type="fn" rid="fn1"><sup>[OPEN]</sup></xref></title><author><name sortKey="Duvick, Jon" sort="Duvick, Jon" uniqKey="Duvick J" first="Jon" last="Duvick">Jon Duvick</name><affiliation wicri:level="2"><nlm:aff id="aff1">Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Iowa</region></placeName><wicri:cityArea>Department of Genetics, Development and Cell Biology, Iowa State University, Ames</wicri:cityArea></affiliation></author><author><name sortKey="Standage, Daniel S" sort="Standage, Daniel S" uniqKey="Standage D" first="Daniel S." last="Standage">Daniel S. Standage</name><affiliation wicri:level="2"><nlm:aff id="aff2">Department of Biology, Indiana University, Bloomington, Indiana 47405</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Indiana</region></placeName><wicri:cityArea>Department of Biology, Indiana University, Bloomington</wicri:cityArea></affiliation></author><author><name sortKey="Merchant, Nirav" sort="Merchant, Nirav" uniqKey="Merchant N" first="Nirav" last="Merchant">Nirav Merchant</name><affiliation wicri:level="2"><nlm:aff id="aff3">Bio Computing Facility, University of Arizona, Tucson, Arizona 85721</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arizona</region></placeName><wicri:cityArea>Bio Computing Facility, University of Arizona, Tucson</wicri:cityArea></affiliation></author><author><name sortKey="Brendel, Volker P" sort="Brendel, Volker P" uniqKey="Brendel V" first="Volker P." last="Brendel">Volker P. Brendel</name><affiliation wicri:level="2"><nlm:aff id="aff4">Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Indiana</region></placeName><wicri:cityArea>Department of Biology and School of Informatics and Computing, Indiana University, Bloomington</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27020957</idno><idno type="pmc">4863385</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4863385</idno><idno type="RBID">PMC:4863385</idno><idno type="doi">10.1105/tpc.15.00933</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000102</idno><idno type="wicri:Area/Pmc/Curation">000102</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud<xref ref-type="fn" rid="fn1"><sup>[OPEN]</sup></xref></title><author><name sortKey="Duvick, Jon" sort="Duvick, Jon" uniqKey="Duvick J" first="Jon" last="Duvick">Jon Duvick</name><affiliation wicri:level="2"><nlm:aff id="aff1">Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Iowa</region></placeName><wicri:cityArea>Department of Genetics, Development and Cell Biology, Iowa State University, Ames</wicri:cityArea></affiliation></author><author><name sortKey="Standage, Daniel S" sort="Standage, Daniel S" uniqKey="Standage D" first="Daniel S." last="Standage">Daniel S. Standage</name><affiliation wicri:level="2"><nlm:aff id="aff2">Department of Biology, Indiana University, Bloomington, Indiana 47405</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Indiana</region></placeName><wicri:cityArea>Department of Biology, Indiana University, Bloomington</wicri:cityArea></affiliation></author><author><name sortKey="Merchant, Nirav" sort="Merchant, Nirav" uniqKey="Merchant N" first="Nirav" last="Merchant">Nirav Merchant</name><affiliation wicri:level="2"><nlm:aff id="aff3">Bio Computing Facility, University of Arizona, Tucson, Arizona 85721</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Arizona</region></placeName><wicri:cityArea>Bio Computing Facility, University of Arizona, Tucson</wicri:cityArea></affiliation></author><author><name sortKey="Brendel, Volker P" sort="Brendel, Volker P" uniqKey="Brendel V" first="Volker P." last="Brendel">Volker P. Brendel</name><affiliation wicri:level="2"><nlm:aff id="aff4">Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Indiana</region></placeName><wicri:cityArea>Department of Biology and School of Informatics and Computing, Indiana University, Bloomington</wicri:cityArea></affiliation></author></analytic><series><title level="j">The Plant Cell</title><idno type="ISSN">1040-4651</idno><idno type="eISSN">1532-298X</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>xGDBvm is a novel tool for scalable, reproducible, and expandable genome annotation via Web-based interfaces that seamlessly integrate background cloud-based data storage and high-performance computer resources.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant Cell</journal-id><journal-id journal-id-type="iso-abbrev">Plant Cell</journal-id><journal-id journal-id-type="hwp">plantcell</journal-id><journal-id journal-id-type="publisher-id">aspb</journal-id><journal-title-group><journal-title>The Plant Cell</journal-title></journal-title-group><issn pub-type="ppub">1040-4651</issn><issn pub-type="epub">1532-298X</issn><publisher><publisher-name>American Society of Plant Biologists</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27020957</article-id><article-id pub-id-type="pmc">4863385</article-id><article-id pub-id-type="publisher-id">TPC201500933LSBR1</article-id><article-id pub-id-type="doi">10.1105/tpc.15.00933</article-id><article-categories><subj-group subj-group-type="heading"><subject>Large-Scale Biology Article</subject></subj-group></article-categories><title-group><article-title>xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud<xref ref-type="fn" rid="fn1"><sup>[OPEN]</sup></xref></article-title></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0003-4329-2712</contrib-id><name><surname>Duvick</surname><given-names>Jon</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0003-0342-8531</contrib-id><name><surname>Standage</surname><given-names>Daniel S.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Merchant</surname><given-names>Nirav</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0002-8055-7508</contrib-id><name><surname>Brendel</surname><given-names>Volker P.</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref><xref ref-type="corresp" rid="cor1"><sup>1</sup></xref></contrib><aff id="aff1"><label>a</label>Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011</aff><aff id="aff2"><label>b</label>Department of Biology, Indiana University, Bloomington, Indiana 47405</aff><aff id="aff3"><label>c</label>Bio Computing Facility, University of Arizona, Tucson, Arizona 85721</aff><aff id="aff4"><label>d</label>Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405</aff></contrib-group><author-notes><fn><p><ext-link ext-link-type="uri" xlink:href="http://www.plantcell.org/cgi/doi/10.1105/tpc.15.00933">www.plantcell.org/cgi/doi/10.1105/tpc.15.00933</ext-link></p></fn><corresp id="cor1"><label>1</label>Address correspondence to <email>vbrendel@indiana.edu</email>.</corresp><fn id="afn1"><p>The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (<ext-link ext-link-type="uri" xlink:href="http://www.plantcell.org">www.plantcell.org</ext-link>) is: Volker P. Brendel (<email>vbrendel@indiana.edu</email>).</p></fn></author-notes><pmc-comment>Fake ppub date generated by PMC from publisher
pub-date/@pub-type='epub-ppub' </pmc-comment>
<pub-date pub-type="ppub"><month>4</month><year>2016</year></pub-date><pub-date pub-type="epub"><day>28</day><month>3</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>28</day><month>3</month><year>2016</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>28</volume><issue>4</issue><fpage>840</fpage><lpage>854</lpage><history><date date-type="received"><day>02</day><month>11</month><year>2015</year></date><date date-type="rev-recd"><day>29</day><month>2</month><year>2016</year></date><date date-type="accepted"><day>25</day><month>3</month><year>2016</year></date></history><permissions><copyright-statement>© 2016 American Society of Plant Biologists. All rights reserved.</copyright-statement><copyright-year>2016</copyright-year></permissions><self-uri xlink:role="icon" xlink:href="PC_TPC201500933LSBR1_ic1.gif"></self-uri><abstract abstract-type="precis"><p>xGDBvm is a novel tool for scalable, reproducible, and expandable genome annotation via Web-based interfaces that seamlessly integrate background cloud-based data storage and high-performance computer resources.</p></abstract><abstract><p>Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today’s pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant’s Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (<xref ref-type="def" rid="def3">HPC</xref>) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote <xref ref-type="def" rid="def3">HPC</xref> cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching.</p></abstract><counts><page-count count="15"></page-count></counts><custom-meta-group><custom-meta><meta-name> DJS Export </meta-name><meta-value>v1</meta-value></custom-meta></custom-meta-group></article-meta><notes><glossary><title>Glossary</title><def-list><def-item><term id="term1">VM</term><def id="def1"><p>virtual machine</p></def></def-item><def-item><term id="term2">GUI</term><def id="def2"><p>graphical user interface</p></def></def-item><def-item><term id="term3">HPC</term><def id="def3"><p>high-performance computing</p></def></def-item><def-item><term id="term4">TSA</term><def id="def4"><p>transcript sequence assembly</p></def></def-item><def-item><term id="term5">VNC</term><def id="def5"><p>virtual network computing</p></def></def-item></def-list></glossary></notes></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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