Interoperable and scalable data analysis with microservices: applications in metabolomics.

Emami Khoonsari P, Moreno P, Bergmann S, Burman J, Capuccini M, Carone M, Cascante M, de Atauri P, Foguet C, Gonzalez-Beltran AN, Hankemeier T, Haug K, He S, Herman S, Johnson D, Kale N, Larsson A, Neumann S, Peters K, Pireddu L, Rocca-Serra P, Roger P, Rueedi R, Ruttkies C, Sadawi N, Salek RM, Sansone SA, Schober D, Selivanov V, Thévenot EA, van Vliet M, Zanetti G, Steinbeck C, Kultima K, Spjuth O

Bioinformatics 35 (19) 3752-3760 [2019-10-01; online 2019-03-10]

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. 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 mass-spectrometry-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. The PhenoMeNal consortium maintains a web portal ( providing a GUI for launching the Virtual Research Environment. The GitHub repository hosts the source code of all projects. Supplementary data are available at Bioinformatics online.

Bioinformatics Compute and Storage [Service]

Bioinformatics Support and Infrastructure [Collaborative]

Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed 30851093

DOI 10.1093/bioinformatics/btz160

Crossref 10.1093/bioinformatics/btz160

pii: 5372675
pmc: PMC6761976

Publications 7.1.2