The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
Identifieur interne : 000865 ( Main/Exploration ); précédent : 000864; suivant : 000866The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
Auteurs : Morris A. Swertz [Pays-Bas, Royaume-Uni] ; Martijn Dijkstra [Pays-Bas] ; Tomasz Adamusiak [Royaume-Uni] ; Joeri K. Van Der Velde [Pays-Bas] ; Alexandros Kanterakis [Pays-Bas] ; Erik T. Roos [Pays-Bas] ; Joris Lops [Pays-Bas] ; Gudmundur A. Thorisson [Royaume-Uni] ; Danny Arends [Pays-Bas] ; George Byelas [Pays-Bas] ; Juha Muilu [Finlande] ; Anthony J. Brookes [Royaume-Uni] ; Engbert O. De Brock [Pays-Bas] ; Ritsert C. Jansen [Pays-Bas] ; Helen Parkinson [Royaume-Uni]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2010.
Abstract
There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed.
The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS’ generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This ‘model-driven’ method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software.
In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist’s satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the ‘ExtractModel’ procedure.
The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at
Url:
DOI: 10.1186/1471-2105-11-S12-S12
PubMed: 21210979
PubMed Central: 3040526
Affiliations:
- Finlande, Pays-Bas, Royaume-Uni
- Groningue (province), Uusimaa
- Groningue (ville), Helsinki
- Université d'Helsinki, Université de Groningue
Links toward previous steps (curation, corpus...)
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Le document en format XML
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Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation><affiliation><nlm:aff id="I4">EU-PANACEA consortium. http://www.panaceaproject.eu</nlm:aff></affiliation><affiliation><nlm:aff id="I5">EU-EUROTRANS cosortium. http://www.euratrans.eu</nlm:aff></affiliation></author><author><name sortKey="Kanterakis, Alexandros" sort="Kanterakis, Alexandros" uniqKey="Kanterakis A" first="Alexandros" last="Kanterakis">Alexandros Kanterakis</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation></author><author><name sortKey="Roos, Erik T" sort="Roos, Erik T" uniqKey="Roos E" first="Erik T" last="Roos">Erik T. Roos</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. 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Thorisson</name><affiliation><nlm:aff id="I2">EU-GEN2PHEN consortium. http://www.gen2phen.org</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="I10">Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH</wicri:regionArea><wicri:noRegion>Leicester LE1 7RH</wicri:noRegion></affiliation></author><author><name sortKey="Arends, Danny" sort="Arends, Danny" uniqKey="Arends D" first="Danny" last="Arends">Danny Arends</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation></author><author><name sortKey="Byelas, George" sort="Byelas, George" uniqKey="Byelas G" first="George" last="Byelas">George Byelas</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation></author><author><name sortKey="Muilu, Juha" sort="Muilu, Juha" uniqKey="Muilu J" first="Juha" last="Muilu">Juha Muilu</name><affiliation><nlm:aff id="I2">EU-GEN2PHEN consortium. http://www.gen2phen.org</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="I9">Institute for Molecular Medicine Finland, University of Helsinki, Haartmaninkatu 8, FIN-00290, Helsinki, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Institute for Molecular Medicine Finland, University of Helsinki, Haartmaninkatu 8, FIN-00290, Helsinki</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Brookes, Anthony J" sort="Brookes, Anthony J" uniqKey="Brookes A" first="Anthony J" last="Brookes">Anthony J. Brookes</name><affiliation><nlm:aff id="I2">EU-GEN2PHEN consortium. http://www.gen2phen.org</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="I10">Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH</wicri:regionArea><wicri:noRegion>Leicester LE1 7RH</wicri:noRegion></affiliation></author><author><name sortKey="De Brock, Engbert O" sort="De Brock, Engbert O" uniqKey="De Brock E" first="Engbert O" last="De Brock">Engbert O. De Brock</name><affiliation wicri:level="4"><nlm:aff id="I11">Cluster Information Systems, Faculty of Economics and Business, University of Groningen, P.O. Box 800, 9700 AV Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Cluster Information Systems, Faculty of Economics and Business, University of Groningen, P.O. Box 800, 9700 AV Groningen</wicri:regionArea><orgName type="university">Université de Groningue</orgName><placeName><settlement type="city">Groningue (ville)</settlement><region>Groningue (province)</region></placeName></affiliation></author><author><name sortKey="Jansen, Ritsert C" sort="Jansen, Ritsert C" uniqKey="Jansen R" first="Ritsert C" last="Jansen">Ritsert C. Jansen</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation><affiliation><nlm:aff id="I4">EU-PANACEA consortium. http://www.panaceaproject.eu</nlm:aff></affiliation><affiliation><nlm:aff id="I5">EU-EUROTRANS cosortium. http://www.euratrans.eu</nlm:aff></affiliation></author><author><name sortKey="Parkinson, Helen" sort="Parkinson, Helen" uniqKey="Parkinson H" first="Helen" last="Parkinson">Helen Parkinson</name><affiliation><nlm:aff id="I2">EU-GEN2PHEN consortium. http://www.gen2phen.org</nlm:aff></affiliation><affiliation><nlm:aff id="I3">EU-CASIMIR consortium. http://www.casimir.ac.uk</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="I8">European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SD</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21210979</idno><idno type="pmc">3040526</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040526</idno><idno type="RBID">PMC:3040526</idno><idno type="doi">10.1186/1471-2105-11-S12-S12</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000483</idno><idno type="wicri:Area/Pmc/Curation">000483</idno><idno type="wicri:Area/Pmc/Checkpoint">000546</idno><idno type="wicri:Area/Ncbi/Merge">000187</idno><idno type="wicri:Area/Ncbi/Curation">000187</idno><idno type="wicri:Area/Ncbi/Checkpoint">000187</idno><idno type="wicri:Area/Main/Merge">000867</idno><idno type="wicri:Area/Main/Curation">000865</idno><idno type="wicri:Area/Main/Exploration">000865</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button</title><author><name sortKey="Swertz, Morris A" sort="Swertz, Morris A" uniqKey="Swertz M" first="Morris A" last="Swertz">Morris A. Swertz</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation><affiliation><nlm:aff id="I2">EU-GEN2PHEN consortium. http://www.gen2phen.org</nlm:aff></affiliation><affiliation><nlm:aff id="I3">EU-CASIMIR consortium. http://www.casimir.ac.uk</nlm:aff></affiliation><affiliation><nlm:aff id="I4">EU-PANACEA consortium. http://www.panaceaproject.eu</nlm:aff></affiliation><affiliation><nlm:aff id="I5">EU-EUROTRANS cosortium. http://www.euratrans.eu</nlm:aff></affiliation><affiliation><nlm:aff id="I6">BBMRI-NL, Postzone S4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands http://www.bbmri.nl</nlm:aff><wicri:noCountry code="subfield">The Netherlands http://www.bbmri.nl</wicri:noCountry></affiliation><affiliation><nlm:aff id="I7">Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands http://www.nbic.nl</nlm:aff><wicri:noCountry code="subfield">The Netherlands http://www.nbic.nl</wicri:noCountry></affiliation><affiliation wicri:level="1"><nlm:aff id="I8">European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SD</wicri:noRegion></affiliation></author><author><name sortKey="Dijkstra, Martijn" sort="Dijkstra, Martijn" uniqKey="Dijkstra M" first="Martijn" last="Dijkstra">Martijn Dijkstra</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation><affiliation><nlm:aff id="I7">Netherlands Bioinformatics Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands http://www.nbic.nl</nlm:aff><wicri:noCountry code="subfield">The Netherlands http://www.nbic.nl</wicri:noCountry></affiliation></author><author><name sortKey="Adamusiak, Tomasz" sort="Adamusiak, Tomasz" uniqKey="Adamusiak T" first="Tomasz" last="Adamusiak">Tomasz Adamusiak</name><affiliation><nlm:aff id="I2">EU-GEN2PHEN consortium. http://www.gen2phen.org</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="I8">European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SD</wicri:noRegion></affiliation></author><author><name sortKey="Van Der Velde, Joeri K" sort="Van Der Velde, Joeri K" uniqKey="Van Der Velde J" first="Joeri K" last="Van Der Velde">Joeri K. Van Der Velde</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation><affiliation><nlm:aff id="I4">EU-PANACEA consortium. http://www.panaceaproject.eu</nlm:aff></affiliation><affiliation><nlm:aff id="I5">EU-EUROTRANS cosortium. http://www.euratrans.eu</nlm:aff></affiliation></author><author><name sortKey="Kanterakis, Alexandros" sort="Kanterakis, Alexandros" uniqKey="Kanterakis A" first="Alexandros" last="Kanterakis">Alexandros Kanterakis</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation></author><author><name sortKey="Roos, Erik T" sort="Roos, Erik T" uniqKey="Roos E" first="Erik T" last="Roos">Erik T. Roos</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation></author><author><name sortKey="Lops, Joris" sort="Lops, Joris" uniqKey="Lops J" first="Joris" last="Lops">Joris Lops</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation></author><author><name sortKey="Thorisson, Gudmundur A" sort="Thorisson, Gudmundur A" uniqKey="Thorisson G" first="Gudmundur A" last="Thorisson">Gudmundur A. Thorisson</name><affiliation><nlm:aff id="I2">EU-GEN2PHEN consortium. http://www.gen2phen.org</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="I10">Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH</wicri:regionArea><wicri:noRegion>Leicester LE1 7RH</wicri:noRegion></affiliation></author><author><name sortKey="Arends, Danny" sort="Arends, Danny" uniqKey="Arends D" first="Danny" last="Arends">Danny Arends</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation></author><author><name sortKey="Byelas, George" sort="Byelas, George" uniqKey="Byelas G" first="George" last="Byelas">George Byelas</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation></author><author><name sortKey="Muilu, Juha" sort="Muilu, Juha" uniqKey="Muilu J" first="Juha" last="Muilu">Juha Muilu</name><affiliation><nlm:aff id="I2">EU-GEN2PHEN consortium. http://www.gen2phen.org</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="I9">Institute for Molecular Medicine Finland, University of Helsinki, Haartmaninkatu 8, FIN-00290, Helsinki, Finland</nlm:aff><country xml:lang="fr">Finlande</country><wicri:regionArea>Institute for Molecular Medicine Finland, University of Helsinki, Haartmaninkatu 8, FIN-00290, Helsinki</wicri:regionArea><orgName type="university">Université d'Helsinki</orgName><placeName><settlement type="city">Helsinki</settlement><region type="région" nuts="2">Uusimaa</region></placeName></affiliation></author><author><name sortKey="Brookes, Anthony J" sort="Brookes, Anthony J" uniqKey="Brookes A" first="Anthony J" last="Brookes">Anthony J. Brookes</name><affiliation><nlm:aff id="I2">EU-GEN2PHEN consortium. http://www.gen2phen.org</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="I10">Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH</wicri:regionArea><wicri:noRegion>Leicester LE1 7RH</wicri:noRegion></affiliation></author><author><name sortKey="De Brock, Engbert O" sort="De Brock, Engbert O" uniqKey="De Brock E" first="Engbert O" last="De Brock">Engbert O. De Brock</name><affiliation wicri:level="4"><nlm:aff id="I11">Cluster Information Systems, Faculty of Economics and Business, University of Groningen, P.O. Box 800, 9700 AV Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Cluster Information Systems, Faculty of Economics and Business, University of Groningen, P.O. Box 800, 9700 AV Groningen</wicri:regionArea><orgName type="university">Université de Groningue</orgName><placeName><settlement type="city">Groningue (ville)</settlement><region>Groningue (province)</region></placeName></affiliation></author><author><name sortKey="Jansen, Ritsert C" sort="Jansen, Ritsert C" uniqKey="Jansen R" first="Ritsert C" last="Jansen">Ritsert C. Jansen</name><affiliation wicri:level="1"><nlm:aff id="I1">Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Genomics Coordination Center, Groningen Bioinformatics Center, University of Groningen & Dept. of Genetics, University Medical Center Groningen, P.O. Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation><affiliation><nlm:aff id="I4">EU-PANACEA consortium. http://www.panaceaproject.eu</nlm:aff></affiliation><affiliation><nlm:aff id="I5">EU-EUROTRANS cosortium. http://www.euratrans.eu</nlm:aff></affiliation></author><author><name sortKey="Parkinson, Helen" sort="Parkinson, Helen" uniqKey="Parkinson H" first="Helen" last="Parkinson">Helen Parkinson</name><affiliation><nlm:aff id="I2">EU-GEN2PHEN consortium. http://www.gen2phen.org</nlm:aff></affiliation><affiliation><nlm:aff id="I3">EU-CASIMIR consortium. http://www.casimir.ac.uk</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="I8">European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD</wicri:regionArea><wicri:noRegion>Cambridge CB10 1SD</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>There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed.</p></sec><sec><title>Methods</title><p>The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS’ generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This ‘model-driven’ method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software.</p></sec><sec><title>Results</title><p>In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist’s satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the ‘ExtractModel’ procedure.</p></sec><sec><title>Conclusions</title><p>The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at <ext-link ext-link-type="uri" xlink:href="http://www.molgenis.org">http://www.molgenis.org</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Swertz, Ma" uniqKey="Swertz M">MA Swertz</name></author><author><name sortKey="Jansen, Rc" uniqKey="Jansen R">RC Jansen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stein, Ld" uniqKey="Stein L">LD Stein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thorisson, Ga" uniqKey="Thorisson G">GA Thorisson</name></author><author><name sortKey="Muilu, J" uniqKey="Muilu J">J Muilu</name></author><author><name sortKey="Brookes, Aj" uniqKey="Brookes A">AJ Brookes</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Oinn, T" uniqKey="Oinn T">T 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Brookes</name><name sortKey="Parkinson, Helen" sort="Parkinson, Helen" uniqKey="Parkinson H" first="Helen" last="Parkinson">Helen Parkinson</name><name sortKey="Thorisson, Gudmundur A" sort="Thorisson, Gudmundur A" uniqKey="Thorisson G" first="Gudmundur A" last="Thorisson">Gudmundur A. Thorisson</name></country><country name="Finlande"><region name="Uusimaa"><name sortKey="Muilu, Juha" sort="Muilu, Juha" uniqKey="Muilu J" first="Juha" last="Muilu">Juha Muilu</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|area= CyberinfraV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:3040526
|texte= The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:21210979" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |