openBIS: a flexible framework for managing and analyzing complex data in biology research
Identifieur interne : 000635 ( Main/Exploration ); précédent : 000634; suivant : 000636openBIS: a flexible framework for managing and analyzing complex data in biology research
Auteurs : Angela Bauch [Suisse] ; Izabela Adamczyk [Suisse] ; Piotr Buczek [Suisse] ; Franz-Josef Elmer [Suisse] ; Kaloyan Enimanev [Suisse] ; Pawel Glyzewski [Suisse] ; Manuel Kohler [Suisse] ; Tomasz Pylak [Suisse] ; Andreas Quandt [Suisse] ; Chandrasekhar Ramakrishnan [Suisse] ; Christian Beisel [Suisse] ; Lars Malmström [Suisse] ; Ruedi Aebersold [Suisse] ; Bernd Rinn [Suisse]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2011.
Abstract
Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.
We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.
openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.
Url:
DOI: 10.1186/1471-2105-12-468
PubMed: 22151573
PubMed Central: 3275639
Affiliations:
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Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Elmer, Franz Josef" sort="Elmer, Franz Josef" uniqKey="Elmer F" first="Franz-Josef" last="Elmer">Franz-Josef Elmer</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Enimanev, Kaloyan" sort="Enimanev, Kaloyan" uniqKey="Enimanev K" first="Kaloyan" last="Enimanev">Kaloyan Enimanev</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country 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Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Kohler, Manuel" sort="Kohler, Manuel" uniqKey="Kohler M" first="Manuel" last="Kohler">Manuel Kohler</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Pylak, Tomasz" sort="Pylak, Tomasz" uniqKey="Pylak T" first="Tomasz" last="Pylak">Tomasz Pylak</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Quandt, Andreas" sort="Quandt, Andreas" uniqKey="Quandt A" first="Andreas" last="Quandt">Andreas Quandt</name><affiliation wicri:level="1"><nlm:aff id="I4">Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Ramakrishnan, Chandrasekhar" sort="Ramakrishnan, Chandrasekhar" uniqKey="Ramakrishnan C" first="Chandrasekhar" last="Ramakrishnan">Chandrasekhar Ramakrishnan</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Beisel, Christian" sort="Beisel, Christian" uniqKey="Beisel C" first="Christian" last="Beisel">Christian Beisel</name><affiliation wicri:level="1"><nlm:aff id="I3">Department of Biosystems Science and Engineering, Quantitative Genomics Facility, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Quantitative Genomics Facility, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Malmstrom, Lars" sort="Malmstrom, Lars" uniqKey="Malmstrom L" first="Lars" last="Malmström">Lars Malmström</name><affiliation wicri:level="1"><nlm:aff id="I4">Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Aebersold, Ruedi" sort="Aebersold, Ruedi" uniqKey="Aebersold R" first="Ruedi" last="Aebersold">Ruedi Aebersold</name><affiliation wicri:level="1"><nlm:aff id="I4">Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:aff id="I5">Faculty of Science, University of Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Faculty of Science, University of Zurich</wicri:regionArea><placeName><settlement type="city">Zurich</settlement><region nuts="3" type="region">Canton de Zurich</region></placeName><orgName type="university">Université de Zurich</orgName></affiliation></author><author><name sortKey="Rinn, Bernd" sort="Rinn, Bernd" uniqKey="Rinn B" first="Bernd" last="Rinn">Bernd Rinn</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22151573</idno><idno type="pmc">3275639</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3275639</idno><idno type="RBID">PMC:3275639</idno><idno type="doi">10.1186/1471-2105-12-468</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000279</idno><idno type="wicri:Area/Pmc/Curation">000279</idno><idno type="wicri:Area/Pmc/Checkpoint">000456</idno><idno type="wicri:Area/Ncbi/Merge">000272</idno><idno type="wicri:Area/Ncbi/Curation">000272</idno><idno type="wicri:Area/Ncbi/Checkpoint">000272</idno><idno type="wicri:Area/Main/Merge">000637</idno><idno type="wicri:Area/Main/Curation">000635</idno><idno type="wicri:Area/Main/Exploration">000635</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">openBIS: a flexible framework for managing and analyzing complex data in biology research</title><author><name sortKey="Bauch, Angela" sort="Bauch, Angela" uniqKey="Bauch A" first="Angela" last="Bauch">Angela Bauch</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Adamczyk, Izabela" sort="Adamczyk, Izabela" uniqKey="Adamczyk I" first="Izabela" last="Adamczyk">Izabela Adamczyk</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Buczek, Piotr" sort="Buczek, Piotr" uniqKey="Buczek P" first="Piotr" last="Buczek">Piotr Buczek</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Elmer, Franz Josef" sort="Elmer, Franz Josef" uniqKey="Elmer F" first="Franz-Josef" last="Elmer">Franz-Josef Elmer</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Enimanev, Kaloyan" sort="Enimanev, Kaloyan" uniqKey="Enimanev K" first="Kaloyan" last="Enimanev">Kaloyan Enimanev</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Glyzewski, Pawel" sort="Glyzewski, Pawel" uniqKey="Glyzewski P" first="Pawel" last="Glyzewski">Pawel Glyzewski</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Kohler, Manuel" sort="Kohler, Manuel" uniqKey="Kohler M" first="Manuel" last="Kohler">Manuel Kohler</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Pylak, Tomasz" sort="Pylak, Tomasz" uniqKey="Pylak T" first="Tomasz" last="Pylak">Tomasz Pylak</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Quandt, Andreas" sort="Quandt, Andreas" uniqKey="Quandt A" first="Andreas" last="Quandt">Andreas Quandt</name><affiliation wicri:level="1"><nlm:aff id="I4">Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Ramakrishnan, Chandrasekhar" sort="Ramakrishnan, Chandrasekhar" uniqKey="Ramakrishnan C" first="Chandrasekhar" last="Ramakrishnan">Chandrasekhar Ramakrishnan</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author><author><name sortKey="Beisel, Christian" sort="Beisel, Christian" uniqKey="Beisel C" first="Christian" last="Beisel">Christian Beisel</name><affiliation wicri:level="1"><nlm:aff id="I3">Department of Biosystems Science and Engineering, Quantitative Genomics Facility, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Quantitative Genomics Facility, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Malmstrom, Lars" sort="Malmstrom, Lars" uniqKey="Malmstrom L" first="Lars" last="Malmström">Lars Malmström</name><affiliation wicri:level="1"><nlm:aff id="I4">Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Aebersold, Ruedi" sort="Aebersold, Ruedi" uniqKey="Aebersold R" first="Ruedi" last="Aebersold">Ruedi Aebersold</name><affiliation wicri:level="1"><nlm:aff id="I4">Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:aff id="I5">Faculty of Science, University of Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Faculty of Science, University of Zurich</wicri:regionArea><placeName><settlement type="city">Zurich</settlement><region nuts="3" type="region">Canton de Zurich</region></placeName><orgName type="university">Université de Zurich</orgName></affiliation></author><author><name sortKey="Rinn, Bernd" sort="Rinn, Bernd" uniqKey="Rinn B" first="Bernd" last="Rinn">Bernd Rinn</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Biosystems Science and Engineering, Center for Information Sciences and Databases, Swiss Federal Institute of Technology (ETH) Zurich</wicri:regionArea><wicri:noRegion>Swiss Federal Institute of Technology (ETH) Zurich</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Swiss Institute of Bioinformatics (SIB), Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Swiss Institute of Bioinformatics (SIB)</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.</p></sec><sec><title>Results</title><p>We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.</p></sec><sec><title>Conclusions</title><p>openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Stein, Ld" uniqKey="Stein L">LD Stein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chaussabel, D" uniqKey="Chaussabel D">D Chaussabel</name></author><author><name sortKey="Ueno, H" uniqKey="Ueno H">H Ueno</name></author><author><name sortKey="Banchereau, J" uniqKey="Banchereau J">J Banchereau</name></author><author><name sortKey="Quinn, C" uniqKey="Quinn C">C Quinn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rauwerda, H" uniqKey="Rauwerda H">H Rauwerda</name></author><author><name sortKey="Roos, M" uniqKey="Roos M">M 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Christian" sort="Beisel, Christian" uniqKey="Beisel C" first="Christian" last="Beisel">Christian Beisel</name><name sortKey="Buczek, Piotr" sort="Buczek, Piotr" uniqKey="Buczek P" first="Piotr" last="Buczek">Piotr Buczek</name><name sortKey="Elmer, Franz Josef" sort="Elmer, Franz Josef" uniqKey="Elmer F" first="Franz-Josef" last="Elmer">Franz-Josef Elmer</name><name sortKey="Elmer, Franz Josef" sort="Elmer, Franz Josef" uniqKey="Elmer F" first="Franz-Josef" last="Elmer">Franz-Josef Elmer</name><name sortKey="Enimanev, Kaloyan" sort="Enimanev, Kaloyan" uniqKey="Enimanev K" first="Kaloyan" last="Enimanev">Kaloyan Enimanev</name><name sortKey="Enimanev, Kaloyan" sort="Enimanev, Kaloyan" uniqKey="Enimanev K" first="Kaloyan" last="Enimanev">Kaloyan Enimanev</name><name sortKey="Glyzewski, Pawel" sort="Glyzewski, Pawel" uniqKey="Glyzewski P" first="Pawel" last="Glyzewski">Pawel Glyzewski</name><name sortKey="Glyzewski, Pawel" sort="Glyzewski, Pawel" uniqKey="Glyzewski P" first="Pawel" last="Glyzewski">Pawel Glyzewski</name><name sortKey="Kohler, Manuel" sort="Kohler, Manuel" uniqKey="Kohler M" first="Manuel" last="Kohler">Manuel Kohler</name><name sortKey="Kohler, Manuel" sort="Kohler, Manuel" uniqKey="Kohler M" first="Manuel" last="Kohler">Manuel Kohler</name><name sortKey="Malmstrom, Lars" sort="Malmstrom, Lars" uniqKey="Malmstrom L" first="Lars" last="Malmström">Lars Malmström</name><name sortKey="Pylak, Tomasz" sort="Pylak, Tomasz" uniqKey="Pylak T" first="Tomasz" last="Pylak">Tomasz Pylak</name><name sortKey="Pylak, Tomasz" sort="Pylak, Tomasz" uniqKey="Pylak T" first="Tomasz" last="Pylak">Tomasz Pylak</name><name sortKey="Quandt, Andreas" sort="Quandt, Andreas" uniqKey="Quandt A" first="Andreas" last="Quandt">Andreas Quandt</name><name sortKey="Ramakrishnan, Chandrasekhar" sort="Ramakrishnan, Chandrasekhar" uniqKey="Ramakrishnan C" first="Chandrasekhar" last="Ramakrishnan">Chandrasekhar Ramakrishnan</name><name sortKey="Ramakrishnan, Chandrasekhar" sort="Ramakrishnan, Chandrasekhar" uniqKey="Ramakrishnan C" first="Chandrasekhar" last="Ramakrishnan">Chandrasekhar Ramakrishnan</name><name sortKey="Rinn, Bernd" sort="Rinn, Bernd" uniqKey="Rinn B" first="Bernd" last="Rinn">Bernd Rinn</name><name sortKey="Rinn, Bernd" sort="Rinn, Bernd" uniqKey="Rinn B" first="Bernd" last="Rinn">Bernd Rinn</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:3275639
|texte= openBIS: a flexible framework for managing and analyzing complex data in biology research
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:22151573" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |