Interoperable and scalable data analysis with microservices: applications in metabolomics

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 encapsulate...

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Detalhes bibliográficos
Autores: 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, 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
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2019
País:España
Recursos:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/171955
Acesso em linha:https://hdl.handle.net/2445/171955
Access Level:acceso abierto
Palavra-chave:Espectrometria de masses
Interoperabilitat en xarxes d'ordinadors
Programari
Mass spectrometry
Internetworking (Telecommunication)
Computer software
Descrição
Resumo: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 tal.phenomenal-h2020.eu) providing a GUI for launching the Virtual Research Environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects.

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