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Interoperable and scalable data analysis with microservices: applications in metabolomics

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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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cc-by (c) Emami Khoonsari, Payam et al., 2019

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Articles publicats en revistes (Bioquímica i Biomedicina Molecular)

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Interoperable and scalable data analysis with microservices: applications in metabolomics