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Title: Interoperable and scalable data analysis with microservices: applications in metabolomics
Author: Emami Khoonsari, Payam
Moreno, Pablo
Bergmann, Sven
Burman, Joachim
Capuccini, Marco
Carone, Matteo
Cascante i Serratosa, Marta
Atauri Carulla, Ramón de
Foguet Coll, Carles
Gonzalez-Beltran, Alejandra N.
Hankemeier, Thomas
Haug, Kenneth
He, Sijin
Herman, Stephanie
Johnson, David
Kale, Namrata
Larsson, Anders
Neumann, Steffen
Peters, Kristian
Pireddu, Luca
Rocca-Serra, Philippe
Roger, Pierrick
Rueedi, Rico
Ruttkies, Cristoph
Sadawi, Noureddin
Salek, Reza M.
Sansone, Susanna-Assunta
Schober, Daniel
Selivanov, Vitaly
Thevenot, Etienne A.
van Vliet, Michael
Zanetti, Gianluigi
Steinbeck, Christoph
Kultima, Kim
Spjuth, Ola
Keywords: Espectrometria de masses
Interoperabilitat en xarxes d'ordinadors
Mass spectrometry
Internetworking (Telecommunication)
Computer software
Issue Date: 9-Mar-2019
Publisher: Oxford University Press
Abstract: Motivation: Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator. Results: We developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for massspectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science. Availability and implementation: The PhenoMeNal consortium maintains a web portal (https://por providing a GUI for launching the Virtual Research Environment. The GitHub repository hosts the source code of all projects.
Note: Reproducció del document publicat a:
It is part of: Bioinformatics, 2019, vol. 35, num. 19, p. 3752-3760
Related resource:
ISSN: 1367-4803
Appears in Collections:Articles publicats en revistes (Bioquímica i Biomedicina Molecular)

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