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PhenoMeNal: processing and analysis of metabolomics data in the cloud

hal.structure.identifierDepartment of Stress and Developmental Biology
dc.contributor.authorPETERS, Kristian
hal.structure.identifierSchool of Biosciences
dc.contributor.authorBRADBURY, James
hal.structure.identifierUniversité de Lausanne = University of Lausanne [UNIL]
hal.structure.identifierSwiss Institute of Bioinformatics [Lausanne] [SIB]
dc.contributor.authorBERGMANN, Sven
hal.structure.identifierUppsala University
hal.structure.identifierDepartment of Pharmaceutical Biosciences
dc.contributor.authorCAPUCCINI, Marco
hal.structure.identifierDepartment of Biochemistry and Molecular Biomedicine
hal.structure.identifierInstituto de Salud Carlos III [Madrid] [ISC]
dc.contributor.authorCASCANTE, Marta
hal.structure.identifierDepartment of Biochemistry and Molecular Biomedicine
hal.structure.identifierInstituto de Salud Carlos III [Madrid] [ISC]
dc.contributor.authorDE ATAURI, Pedro
hal.structure.identifierDepartment of Surgery & Cancer
dc.contributor.authorEBBELS, Timothy M. D.
hal.structure.identifierDepartment of Biochemistry and Molecular Biomedicine
hal.structure.identifierInstituto de Salud Carlos III [Madrid] [ISC]
dc.contributor.authorFOGUET, Carles
hal.structure.identifierDepartment of Surgery & Cancer
hal.structure.identifierUniversity of Cambridge [UK] [CAM]
dc.contributor.authorGLEN, Robert
hal.structure.identifierDepartment of Engineering Science
dc.contributor.authorGONZALEZ-BELTRAN, Alejandra
hal.structure.identifierUniversity of Birmingham
dc.contributor.authorGÜNTHER, Ulrich L.
hal.structure.identifierDepartment of Surgery & Cancer
dc.contributor.authorHANDAKAS, Evangelos
hal.structure.identifierUniversiteit Leiden = Leiden University
dc.contributor.authorHANKEMEIER, Thomas
hal.structure.identifierEuropean Molecular Biology Laboratory European Bioinformatics Institute
dc.contributor.authorHAUG, Kenneth
hal.structure.identifierDepartment of Pharmaceutical Biosciences
hal.structure.identifierDepartment of Medical Sciences, Clinical Chemistry
dc.contributor.authorHERMAN, Stephanie
hal.structure.identifierEuropean research infrastructure for biobanking [BBMRI-ERIC]
dc.contributor.authorHOLUB, Petr
hal.structure.identifierDepartment of Engineering Science
dc.contributor.authorIZZO, Massimiliano
hal.structure.identifierBiologie du fruit et pathologie [BFP]
hal.structure.identifierPlateforme Bordeaux Metabolome
dc.contributor.authorJACOB, Daniel
hal.structure.identifierDepartment of Engineering Science
hal.structure.identifierDepartment of Informatics and Media
dc.contributor.authorJOHNSON, David
hal.structure.identifierMétabolisme et Xénobiotiques [ToxAlim-MeX]
dc.contributor.authorJOURDAN, Fabien
hal.structure.identifierEuropean Molecular Biology Laboratory European Bioinformatics Institute
dc.contributor.authorKALE, Namrata
hal.structure.identifierSchool of Public Health - Department of Epidemiology and Biostatistics
dc.contributor.authorKARAMAN, Ibrahim
hal.structure.identifierUniversité de Lausanne = University of Lausanne [UNIL]
hal.structure.identifierSwiss Institute of Bioinformatics [Lausanne] [SIB]
dc.contributor.authorKHALILI, Bita
hal.structure.identifierDepartment of Medical Sciences, Clinical Chemistry
dc.contributor.authorKHONSARI, Payam Emami
hal.structure.identifierDepartment of Medical Sciences, Clinical Chemistry
dc.contributor.authorKULTIMA, Kim
hal.structure.identifierDepartment of Pharmaceutical Biosciences
dc.contributor.authorLAMPA, Samuel
hal.structure.identifierDepartment of Pharmaceutical Biosciences
hal.structure.identifierUppsala University
dc.contributor.authorLARSSON, Anders
dc.contributor.authorLUDWIG, Christian
hal.structure.identifierEuropean Molecular Biology Laboratory European Bioinformatics Institute
dc.contributor.authorMORENO, Pablo
hal.structure.identifierGerman Centre for Integrative Biodiversity Research [iDiv]
hal.structure.identifierLeibniz Institute of Plant Biochemistry [IPB]
dc.contributor.authorNEUMANN, Steffen
hal.structure.identifierDepartment of Pharmaceutical Biosciences
hal.structure.identifierUppsala University
dc.contributor.authorNOVELLA, Jon Ander
hal.structure.identifierEuropean Molecular Biology Laboratory European Bioinformatics Institute
dc.contributor.authorO'DONOVAN, Claire
hal.structure.identifierDepartment of Surgery & Cancer
dc.contributor.authorPEARCE, Jake T. M.
hal.structure.identifierDepartment of Surgery & Cancer
dc.contributor.authorPELUSO, Alina
hal.structure.identifierCRS4 Bioinformat
dc.contributor.authorPIRAS, Marco Enrico
hal.structure.identifierCRS4 Bioinformat
dc.contributor.authorPIREDDU, Luca
hal.structure.identifierUniversity of Birmingham
dc.contributor.authorREED, Michelle A. C.
hal.structure.identifierDepartment of Engineering Science
dc.contributor.authorROCCA-SERRA, Philippe
hal.structure.identifierLaboratoire Sciences des Données et de la Décision (CEA, LIST) [LS2D (CEA, LIST)]
dc.contributor.authorROGER, Pierrick
hal.structure.identifierUniversità degli Studi di Firenze = University of Florence = Université de Florence [UniFI]
hal.structure.identifierConsorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine [CIRMMP]
hal.structure.identifierUniversità degli Studi di Firenze = University of Florence = Université de Florence [UniFI]
dc.contributor.authorROSATO, Antonio
hal.structure.identifierUniversité de Lausanne = University of Lausanne [UNIL]
hal.structure.identifierSwiss Institute of Bioinformatics [Lausanne] [SIB]
dc.contributor.authorRUEEDI, Rico
hal.structure.identifierLeibniz Institute of Plant Biochemistry [IPB]
dc.contributor.authorRUTTKIES, Christoph
hal.structure.identifierDepartment of Surgery & Cancer
hal.structure.identifierBrunel University London [Uxbridge]
dc.contributor.authorSADAWI, Noureddin
hal.structure.identifierEuropean Molecular Biology Laboratory European Bioinformatics Institute
dc.contributor.authorSALEK, Reza M.
hal.structure.identifierDepartment of Engineering Science
dc.contributor.authorSANSONE, Susanna-Assunta
hal.structure.identifierDepartment of Biochemistry and Molecular Biomedicine
hal.structure.identifierInstituto de Salud Carlos III [Madrid] [ISC]
dc.contributor.authorSELIVANOV, Vitaly
hal.structure.identifierDepartment of Pharmaceutical Biosciences
dc.contributor.authorSPJUTH, Ola
hal.structure.identifierLeibniz Institute of Plant Biochemistry [IPB]
dc.contributor.authorSCHOBER, Daniel
hal.structure.identifierLaboratoire Sciences des Données et de la Décision (CEA, LIST) [LS2D (CEA, LIST)]
dc.contributor.authorTHEVENOT, Etienne A.
hal.structure.identifierUniversité de Lausanne = University of Lausanne [UNIL]
hal.structure.identifierSwiss Institute of Bioinformatics [Lausanne] [SIB]
dc.contributor.authorTOMASONI, Mattia
hal.structure.identifierNetherlands Metabolomics Centre
hal.structure.identifierLife Sciences
dc.contributor.authorVAN RIJSWIJK, Merlijn
hal.structure.identifierUniversiteit Leiden = Leiden University
dc.contributor.authorVAN VLIET, Michael
hal.structure.identifierSchool of Biosciences
hal.structure.identifierUniversity of Birmingham
dc.contributor.authorVIANT, Mark R.
hal.structure.identifierSchool of Biosciences
hal.structure.identifierUniversity of Birmingham
dc.contributor.authorWEBER, Ralf J. M.
hal.structure.identifierCRS4 Bioinformat
dc.contributor.authorZANETTI, Gianluigi
hal.structure.identifierInstitute of Analytical Chemistry
dc.contributor.authorSTEINBECK, Christoph
dc.date.issued2019-02
dc.description.abstractEnBackground Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution. Findings PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm. Conclusions PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and omics research domains.
dc.description.sponsorshipDéveloppement d'une infrastructure française distribuée pour la métabolomique dédiée à l'innovation
dc.language.isoen
dc.publisherOxford Univ Press
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subjectmetabolomics
dc.subjecte-infrastructures
dc.subjectgalaxy
dc.subjectstatistics
dc.subject.endata analysis
dc.subject.ensignal processing
dc.subject.enSpectrum analysis
dc.subject.enStatistical analysis
dc.subject.enNMR
dc.subject.enmass spectrometry
dc.subject.encomputational workflows
dc.subject.encloud computing
dc.subject.enstandardization
dc.title.enPhenoMeNal: processing and analysis of metabolomics data in the cloud
dc.typeArticle de revue
dc.identifier.doi10.1093/gigascience/giy149
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halSciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire/Génomique, Transcriptomique et Protéomique [q-bio.GN]
dc.subject.halSciences de l'environnement
dc.subject.halSciences du Vivant [q-bio]/Biologie végétale
dc.description.sponsorshipEuropePhenoMeNal: A comprehensive and standardised e-infrastructure for analysing medical metabolic phenotype data
bordeaux.journalGigaScience
bordeaux.pagegiy149
bordeaux.volume8
bordeaux.issue2
bordeaux.peerReviewedoui
hal.identifierhal-02627233
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02627233v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=GigaScience&rft.date=2019-02&rft.volume=8&rft.issue=2&rft.spage=giy149&rft.epage=giy149&rft.au=PETERS,%20Kristian&BRADBURY,%20James&BERGMANN,%20Sven&CAPUCCINI,%20Marco&CASCANTE,%20Marta&rft.genre=article


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