Initial steps towards a production platform for DNA sequence analysis on the grid
Identifieur interne : 000890 ( Main/Exploration ); précédent : 000889; suivant : 000891Initial 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:
Links toward previous steps (curation, corpus...)
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Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Initial steps towards a production platform for DNA sequence analysis on the grid</title><author><name sortKey="Luyf, Angela Cm" sort="Luyf, Angela Cm" uniqKey="Luyf A" first="Angela Cm" last="Luyf">Angela Cm Luyf</name><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation></author><author><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><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation></author><author><name sortKey="De Vries, Michel" sort="De Vries, Michel" uniqKey="De Vries M" first="Michel" last="De Vries">Michel De Vries</name><affiliation wicri:level="1"><nlm:aff id="I2">Virus Discovery Unit, Department of Medical Microbiology, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Virus Discovery Unit, Department of Medical Microbiology, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation></author><author><name sortKey="Baas, Frank" sort="Baas, Frank" uniqKey="Baas F" first="Frank" last="Baas">Frank Baas</name><affiliation wicri:level="1"><nlm:aff id="I3">Department of Neurogenetics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Department of Neurogenetics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation></author><author><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><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I4">Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam</wicri:regionArea><wicri:noRegion>1018 WV Amsterdam</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I5">Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen</wicri:regionArea><wicri:noRegion>6525 GA Nijmegen</wicri:noRegion></affiliation></author><author><name sortKey="Olabarriaga, Silvia D" sort="Olabarriaga, Silvia D" uniqKey="Olabarriaga S" first="Silvia D" last="Olabarriaga">Silvia D. Olabarriaga</name><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21156038</idno><idno type="pmc">3018473</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018473</idno><idno type="RBID">PMC:3018473</idno><idno type="doi">10.1186/1471-2105-11-598</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000482</idno><idno type="wicri:Area/Pmc/Curation">000482</idno><idno 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Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation></author><author><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><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation></author><author><name sortKey="De Vries, Michel" sort="De Vries, Michel" uniqKey="De Vries M" first="Michel" last="De Vries">Michel De Vries</name><affiliation wicri:level="1"><nlm:aff id="I2">Virus Discovery Unit, Department of Medical Microbiology, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Virus Discovery Unit, Department of Medical Microbiology, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation></author><author><name sortKey="Baas, Frank" sort="Baas, Frank" uniqKey="Baas F" first="Frank" last="Baas">Frank Baas</name><affiliation wicri:level="1"><nlm:aff id="I3">Department of Neurogenetics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Department of Neurogenetics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation></author><author><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><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I4">Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam</wicri:regionArea><wicri:noRegion>1018 WV Amsterdam</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I5">Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen</wicri:regionArea><wicri:noRegion>6525 GA Nijmegen</wicri:noRegion></affiliation></author><author><name sortKey="Olabarriaga, Silvia D" sort="Olabarriaga, Silvia D" uniqKey="Olabarriaga S" first="Silvia D" last="Olabarriaga">Silvia D. Olabarriaga</name><affiliation wicri:level="1"><nlm:aff id="I1">Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam, the Netherlands</nlm:aff><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, PO Box 22700, 1100 DE Amsterdam</wicri:regionArea><wicri:noRegion>1100 DE Amsterdam</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Margulies, M" uniqKey="Margulies M">M Margulies</name></author><author><name sortKey="Egholm, M" uniqKey="Egholm M">M Egholm</name></author><author><name sortKey="Altman, We" uniqKey="Altman W">WE Altman</name></author><author><name sortKey="Attiya, S" uniqKey="Attiya S">S Attiya</name></author><author><name sortKey="Bader, Js" uniqKey="Bader J">JS Bader</name></author><author><name sortKey="Bemben, La" uniqKey="Bemben L">LA Bemben</name></author><author><name sortKey="Berka, J" uniqKey="Berka J">J Berka</name></author><author><name sortKey="Braverman, Ms" uniqKey="Braverman M">MS Braverman</name></author><author><name sortKey="Chen, Yj" uniqKey="Chen Y">YJ Chen</name></author><author><name 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uniqKey="Milner K">K Milner</name></author><author><name sortKey="Graves, R" uniqKey="Graves R">R Graves</name></author><author><name sortKey="Field, E" uniqKey="Field E">E Field</name></author><author><name sortKey="Okaya, D" uniqKey="Okaya D">D Okaya</name></author><author><name sortKey="Jordan, T" uniqKey="Jordan T">T Jordan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Glatard, T" uniqKey="Glatard T">T Glatard</name></author><author><name sortKey="Soleman, Rs" uniqKey="Soleman R">RS Soleman</name></author><author><name sortKey="Veltman, Dj" uniqKey="Veltman D">DJ Veltman</name></author><author><name sortKey="Nederveen, A" uniqKey="Nederveen A">A Nederveen</name></author><author><name sortKey="Olabarriaga, Sd" uniqKey="Olabarriaga S">SD Olabarriaga</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><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></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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