2026-04-17T11:47:56Zhttps://recercat.cat/oai/request

oai:recercat.cat:2445/1719552025-11-19T20:40:51Zcom_2072_1057col_2072_478781col_2072_478917

00925njm 22002777a 4500 dc Emami Khoonsari, Payam author Moreno, Pablo author Bergmann, Sven author Burman, Joachim author Capuccini, Marco author Carone, Matteo author Cascante i Serratosa, Marta author Atauri Carulla, Ramón de author Foguet Coll, Carles author Gonzalez-Beltran, Alejandra author Hankemeier, Thomas author Haug, Kenneth author He, Sijin author Herman, Stephanie author Johnson, David author Kale, Namrata author Larsson, Anders author Neumann, Steffen author Peters, Kristian author Pireddu, Luca author Rocca-Serra, Philippe author Roger, Pierrick author Rueedi, Rico author Ruttkies, Cristoph author Sadawi, Noureddin author Salek, Reza M. author Sansone, Susanna-Assunta author Schober, Daniel author Selivanov, Vitaly author Thevenot, Etienne A. author van Vliet, Michael author Zanetti, Gianluigi author Steinbeck, Christoph author Kultima, Kim author Spjuth, Ola author 2020-11-11T11:23:28Z 2020-11-11T11:23:28Z 2019-03-09 2020-11-11T11:23:28Z 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. Espectrometria de masses Interoperabilitat en xarxes d'ordinadors Programari Mass spectrometry Internetworking (Telecommunication) Computer software Interoperable and scalable data analysis with microservices: applications in metabolomics