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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology</title><author><name sortKey="Taufer, Michela" sort="Taufer, Michela" uniqKey="Taufer M" first="Michela" last="Taufer">Michela Taufer</name><affiliation><nlm:aff id="A1">Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716, United States</nlm:aff></affiliation></author><author><name sortKey="Leung, Ming Ying" sort="Leung, Ming Ying" uniqKey="Leung M" first="Ming-Ying" last="Leung">Ming-Ying Leung</name><affiliation><nlm:aff id="A2">Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation><affiliation><nlm:aff id="A3">Bioinformatics Program, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation></author><author><name sortKey="Solorio, Thamar" sort="Solorio, Thamar" uniqKey="Solorio T" first="Thamar" last="Solorio">Thamar Solorio</name><affiliation><nlm:aff id="A5">Department of Computer Science, The University of Texas at Dallas, Richardson, TX 75080, United States</nlm:aff></affiliation></author><author><name sortKey="Licon, Abel" sort="Licon, Abel" uniqKey="Licon A" first="Abel" last="Licon">Abel Licon</name><affiliation><nlm:aff id="A1">Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716, United States</nlm:aff></affiliation></author><author><name sortKey="Mireles, David" sort="Mireles, David" uniqKey="Mireles D" first="David" last="Mireles">David Mireles</name><affiliation><nlm:aff id="A6">Department of Computer Science, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation></author><author><name sortKey="Araiza, Roberto" sort="Araiza, Roberto" uniqKey="Araiza R" first="Roberto" last="Araiza">Roberto Araiza</name><affiliation><nlm:aff id="A6">Department of Computer Science, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation></author><author><name sortKey="Johnson, Kyle L" sort="Johnson, Kyle L" uniqKey="Johnson K" first="Kyle L." last="Johnson">Kyle L. Johnson</name><affiliation><nlm:aff id="A7">Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19885376</idno><idno type="pmc">2714649</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2714649</idno><idno type="RBID">PMC:2714649</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000290</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology</title><author><name sortKey="Taufer, Michela" sort="Taufer, Michela" uniqKey="Taufer M" first="Michela" last="Taufer">Michela Taufer</name><affiliation><nlm:aff id="A1">Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716, United States</nlm:aff></affiliation></author><author><name sortKey="Leung, Ming Ying" sort="Leung, Ming Ying" uniqKey="Leung M" first="Ming-Ying" last="Leung">Ming-Ying Leung</name><affiliation><nlm:aff id="A2">Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation><affiliation><nlm:aff id="A3">Bioinformatics Program, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation></author><author><name sortKey="Solorio, Thamar" sort="Solorio, Thamar" uniqKey="Solorio T" first="Thamar" last="Solorio">Thamar Solorio</name><affiliation><nlm:aff id="A5">Department of Computer Science, The University of Texas at Dallas, Richardson, TX 75080, United States</nlm:aff></affiliation></author><author><name sortKey="Licon, Abel" sort="Licon, Abel" uniqKey="Licon A" first="Abel" last="Licon">Abel Licon</name><affiliation><nlm:aff id="A1">Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716, United States</nlm:aff></affiliation></author><author><name sortKey="Mireles, David" sort="Mireles, David" uniqKey="Mireles D" first="David" last="Mireles">David Mireles</name><affiliation><nlm:aff id="A6">Department of Computer Science, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation></author><author><name sortKey="Araiza, Roberto" sort="Araiza, Roberto" uniqKey="Araiza R" first="Roberto" last="Araiza">Roberto Araiza</name><affiliation><nlm:aff id="A6">Department of Computer Science, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation></author><author><name sortKey="Johnson, Kyle L" sort="Johnson, Kyle L" uniqKey="Johnson K" first="Kyle L." last="Johnson">Kyle L. Johnson</name><affiliation><nlm:aff id="A7">Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation><affiliation><nlm:aff id="A4">Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, United States</nlm:aff></affiliation></author></analytic><series><title level="j">Parallel computing</title><idno type="ISSN">0167-8191</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">As ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation, their secondary structures have been the focus of many recent studies. Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. This paper presents RNAVLab (RNA Virtual Laboratory), a virtual laboratory for studying RNA secondary structures including pseudoknots that allows scientists to address this challenge. Two important case studies show the versatility and functionalities of RNAVLab. The first study quantifies its capability to rebuild longer secondary structures from motifs found in systematically sampled nucleotide segments. The extensive sampling and predictions are made feasible in a short turnaround time because of the grid technology used. The second study shows how RNAVLab allows scientists to study the viral RNA genome replication mechanisms used by members of the virus family <italic>Nodaviridae</italic>.</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">101469721</journal-id><journal-id journal-id-type="pubmed-jr-id">34273</journal-id><journal-id journal-id-type="nlm-ta">Parallel Comput</journal-id><journal-title>Parallel computing</journal-title><issn pub-type="ppub">0167-8191</issn></journal-meta><article-meta><article-id pub-id-type="pmid">19885376</article-id><article-id pub-id-type="pmc">2714649</article-id><article-id pub-id-type="manuscript">NIHMS113807</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Taufer</surname><given-names>Michela</given-names></name><xref ref-type="aff" rid="A1">a</xref><xref ref-type="corresp" rid="CR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Leung</surname><given-names>Ming-Ying</given-names></name><xref ref-type="aff" rid="A2">b</xref><xref ref-type="aff" rid="A3">c</xref><xref ref-type="aff" rid="A4">d</xref></contrib><contrib contrib-type="author"><name><surname>Solorio</surname><given-names>Thamar</given-names></name><xref ref-type="aff" rid="A5">e</xref></contrib><contrib contrib-type="author"><name><surname>Licon</surname><given-names>Abel</given-names></name><xref ref-type="aff" rid="A1">a</xref></contrib><contrib contrib-type="author"><name><surname>Mireles</surname><given-names>David</given-names></name><xref ref-type="aff" rid="A6">f</xref></contrib><contrib contrib-type="author"><name><surname>Araiza</surname><given-names>Roberto</given-names></name><xref ref-type="aff" rid="A6">f</xref></contrib><contrib contrib-type="author"><name><surname>Johnson</surname><given-names>Kyle L.</given-names></name><xref ref-type="aff" rid="A7">g</xref><xref ref-type="aff" rid="A4">d</xref></contrib></contrib-group><aff id="A1"><label>a</label>Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716, United States</aff><aff id="A2"><label>b</label>Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX 79968, United States</aff><aff id="A3"><label>c</label>Bioinformatics Program, The University of Texas at El Paso, El Paso, TX 79968, United States</aff><aff id="A4"><label>d</label>Border Biomedical Research Center, The University of Texas at El Paso, El Paso, TX 79968, United States</aff><aff id="A5"><label>e</label>Department of Computer Science, The University of Texas at Dallas, Richardson, TX 75080, United States</aff><aff id="A6"><label>f</label>Department of Computer Science, The University of Texas at El Paso, El Paso, TX 79968, United States</aff><aff id="A7"><label>g</label>Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968, United States</aff><author-notes><corresp id="CR1"><label>*</label>Corresponding author. <italic>E-mail address</italic>: <email>taufer@acm.org</email> (M. Taufer).</corresp></author-notes><pub-date pub-type="nihms-submitted"><day>29</day><month>4</month><year>2009</year></pub-date><pub-date pub-type="ppub"><day>1</day><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>34</volume><issue>11</issue><fpage>661</fpage><lpage>680</lpage><permissions><copyright-statement>© 2008 Elsevier B.V. All rights reserved.</copyright-statement><copyright-year>2008</copyright-year></permissions><abstract><p id="P1">As ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation, their secondary structures have been the focus of many recent studies. Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. This paper presents RNAVLab (RNA Virtual Laboratory), a virtual laboratory for studying RNA secondary structures including pseudoknots that allows scientists to address this challenge. Two important case studies show the versatility and functionalities of RNAVLab. The first study quantifies its capability to rebuild longer secondary structures from motifs found in systematically sampled nucleotide segments. The extensive sampling and predictions are made feasible in a short turnaround time because of the grid technology used. The second study shows how RNAVLab allows scientists to study the viral RNA genome replication mechanisms used by members of the virus family <italic>Nodaviridae</italic>.</p></abstract><kwd-group><kwd>Pseudoknots</kwd><kwd>Condor</kwd><kwd>Family <italic>Nodaviridae</italic></kwd></kwd-group><contract-num rid="GM1">S06 GM008012-380007
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