Initial steps towards a production platform for DNA sequence analysis on the grid
Identifieur interne : 000575 ( Pmc/Checkpoint ); précédent : 000574; suivant : 000576Initial steps towards a production platform for DNA sequence analysis on the grid
Auteurs : Angela Cm Luyf [Pays-Bas] ; Barbera Dc Van Schaik [Pays-Bas] ; Michel De Vries [Pays-Bas] ; Frank Baas [Pays-Bas] ; Antoine Hc Van Kampen [Pays-Bas] ; Silvia D. Olabarriaga [Pays-Bas]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2010.
Abstract
Bioinformatics is confronted with a new data explosion due to the availability of high throughput DNA sequencers. Data storage and analysis becomes a problem on local servers, and therefore it is needed to switch to other IT infrastructures. Grid and workflow technology can help to handle the data more efficiently, as well as facilitate collaborations. However, interfaces to grids are often unfriendly to novice users.
In this study we reused a platform that was developed in the VL-e project for the analysis of medical images. Data transfer, workflow execution and job monitoring are operated from one graphical interface. We developed workflows for two sequence alignment tools (BLAST and BLAT) as a proof of concept. The analysis time was significantly reduced. All workflows and executables are available for the members of the Dutch Life Science Grid and the VL-e Medical virtual organizations All components are open source and can be transported to other grid infrastructures.
The availability of in-house expertise and tools facilitates the usage of grid resources by new users. Our first results indicate that this is a practical, powerful and scalable solution to address the capacity and collaboration issues raised by the deployment of next generation sequencers. We currently adopt this methodology on a daily basis for DNA sequencing and other applications. More information and source code is available via
Url:
DOI: 10.1186/1471-2105-11-598
PubMed: 21156038
PubMed Central: 3018473
Affiliations:
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PMC:3018473Le document en format XML
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Bioinformatics is confronted with a new data explosion due to the availability of high throughput DNA sequencers. Data storage and analysis becomes a problem on local servers, and therefore it is needed to switch to other IT infrastructures. Grid and workflow technology can help to handle the data more efficiently, as well as facilitate collaborations. However, interfaces to grids are often unfriendly to novice users.</p>
</sec>
<sec><title>Results</title>
<p>In this study we reused a platform that was developed in the VL-e project for the analysis of medical images. Data transfer, workflow execution and job monitoring are operated from one graphical interface. We developed workflows for two sequence alignment tools (BLAST and BLAT) as a proof of concept. The analysis time was significantly reduced. All workflows and executables are available for the members of the Dutch Life Science Grid and the VL-e Medical virtual organizations All components are open source and can be transported to other grid infrastructures.</p>
</sec>
<sec><title>Conclusions</title>
<p>The availability of in-house expertise and tools facilitates the usage of grid resources by new users. Our first results indicate that this is a practical, powerful and scalable solution to address the capacity and collaboration issues raised by the deployment of next generation sequencers. We currently adopt this methodology on a daily basis for DNA sequencing and other applications. More information and source code is available via <ext-link ext-link-type="uri" xlink:href="http://www.bioinformaticslaboratory.nl/">http://www.bioinformaticslaboratory.nl/</ext-link>
</p>
</sec>
</div>
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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">BMC Bioinformatics</journal-id>
<journal-title-group><journal-title>BMC Bioinformatics</journal-title>
</journal-title-group>
<issn pub-type="epub">1471-2105</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">21156038</article-id>
<article-id pub-id-type="pmc">3018473</article-id>
<article-id pub-id-type="publisher-id">1471-2105-11-598</article-id>
<article-id pub-id-type="doi">10.1186/1471-2105-11-598</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Initial steps towards a production platform for DNA sequence analysis on the grid</article-title>
</title-group>
<contrib-group><contrib contrib-type="author" equal-contrib="yes" id="A1"><name><surname>Luyf</surname>
<given-names>Angela CM</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>a.c.luyf@amc.uva.nl</email>
</contrib>
<contrib contrib-type="author" corresp="yes" equal-contrib="yes" id="A2"><name><surname>van Schaik</surname>
<given-names>Barbera DC</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>b.d.vanschaik@amc.uva.nl</email>
</contrib>
<contrib contrib-type="author" id="A3"><name><surname>de Vries</surname>
<given-names>Michel</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>micheldevries@amc.uva.nl</email>
</contrib>
<contrib contrib-type="author" id="A4"><name><surname>Baas</surname>
<given-names>Frank</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>f.baas@amc.uva.nl</email>
</contrib>
<contrib contrib-type="author" id="A5"><name><surname>van Kampen</surname>
<given-names>Antoine HC</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I4">4</xref>
<xref ref-type="aff" rid="I5">5</xref>
<email>a.h.vankampen@amc.uva.nl</email>
</contrib>
<contrib contrib-type="author" id="A6"><name><surname>Olabarriaga</surname>
<given-names>Silvia D</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>s.d.olabarriaga@amc.uva.nl</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</aff>
<aff id="I2"><label>2</label>
Virus Discovery Unit, Department of Medical Microbiology, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</aff>
<aff id="I3"><label>3</label>
Department of Neurogenetics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</aff>
<aff id="I4"><label>4</label>
Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands</aff>
<aff id="I5"><label>5</label>
Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands</aff>
<pub-date pub-type="collection"><year>2010</year>
</pub-date>
<pub-date pub-type="epub"><day>14</day>
<month>12</month>
<year>2010</year>
</pub-date>
<volume>11</volume>
<fpage>598</fpage>
<lpage>598</lpage>
<history><date date-type="received"><day>26</day>
<month>5</month>
<year>2010</year>
</date>
<date date-type="accepted"><day>14</day>
<month>12</month>
<year>2010</year>
</date>
</history>
<permissions><copyright-statement>Copyright ©2010 Luyf et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2010</copyright-year>
<copyright-holder>Luyf et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2105/11/598"></self-uri>
<abstract><sec><title>Background</title>
<p>Bioinformatics is confronted with a new data explosion due to the availability of high throughput DNA sequencers. Data storage and analysis becomes a problem on local servers, and therefore it is needed to switch to other IT infrastructures. Grid and workflow technology can help to handle the data more efficiently, as well as facilitate collaborations. However, interfaces to grids are often unfriendly to novice users.</p>
</sec>
<sec><title>Results</title>
<p>In this study we reused a platform that was developed in the VL-e project for the analysis of medical images. Data transfer, workflow execution and job monitoring are operated from one graphical interface. We developed workflows for two sequence alignment tools (BLAST and BLAT) as a proof of concept. The analysis time was significantly reduced. All workflows and executables are available for the members of the Dutch Life Science Grid and the VL-e Medical virtual organizations All components are open source and can be transported to other grid infrastructures.</p>
</sec>
<sec><title>Conclusions</title>
<p>The availability of in-house expertise and tools facilitates the usage of grid resources by new users. Our first results indicate that this is a practical, powerful and scalable solution to address the capacity and collaboration issues raised by the deployment of next generation sequencers. We currently adopt this methodology on a daily basis for DNA sequencing and other applications. More information and source code is available via <ext-link ext-link-type="uri" xlink:href="http://www.bioinformaticslaboratory.nl/">http://www.bioinformaticslaboratory.nl/</ext-link>
</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Pays-Bas</li>
</country>
</list>
<tree><country name="Pays-Bas"><noRegion><name sortKey="Luyf, Angela Cm" sort="Luyf, Angela Cm" uniqKey="Luyf A" first="Angela Cm" last="Luyf">Angela Cm Luyf</name>
</noRegion>
<name sortKey="Baas, Frank" sort="Baas, Frank" uniqKey="Baas F" first="Frank" last="Baas">Frank Baas</name>
<name sortKey="De Vries, Michel" sort="De Vries, Michel" uniqKey="De Vries M" first="Michel" last="De Vries">Michel De Vries</name>
<name sortKey="Olabarriaga, Silvia D" sort="Olabarriaga, Silvia D" uniqKey="Olabarriaga S" first="Silvia D" last="Olabarriaga">Silvia D. Olabarriaga</name>
<name sortKey="Van Kampen, Antoine Hc" sort="Van Kampen, Antoine Hc" uniqKey="Van Kampen A" first="Antoine Hc" last="Van Kampen">Antoine Hc Van Kampen</name>
<name sortKey="Van Kampen, Antoine Hc" sort="Van Kampen, Antoine Hc" uniqKey="Van Kampen A" first="Antoine Hc" last="Van Kampen">Antoine Hc Van Kampen</name>
<name sortKey="Van Kampen, Antoine Hc" sort="Van Kampen, Antoine Hc" uniqKey="Van Kampen A" first="Antoine Hc" last="Van Kampen">Antoine Hc Van Kampen</name>
<name sortKey="Van Schaik, Barbera Dc" sort="Van Schaik, Barbera Dc" uniqKey="Van Schaik B" first="Barbera Dc" last="Van Schaik">Barbera Dc Van Schaik</name>
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</tree>
</affiliations>
</record>
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