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  1. IPB Halle
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    • Research Mission and Profile
    • Trenner 0
    • Molecular Signal Processing
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Nutrient Sensing
        • Symbiosis Signaling
        • Jasmonate Signaling
    • Bioorganic Chemistry
      • Secretariat & All Staff
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      • Publications
      • Research Groups
        • Bioactives
        • Natural Products & Metabolomics
        • Biotechnology
        • Biofunctional Synthesis
        • Computational Chemistry
        • Data & Resources
    • Biochemistry of Plant Interactions
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Calcium-dependent Protein Kinases
        • Cellular Signaling
        • Metabolite-based Defense Mechanisms
        • Nuclear Processes in Plant Defense
    • Cell and Metabolic Biology
      • Secretariat & All Staff
      • Technical Resources
      • Publications
      • Research Groups
        • Glandular Trichomes and Isoprenoid Biosynthesis
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        • Auxin Signaling
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Emami Khoonsari, P.; Moreno, P.; Bergmann, S.; Burman, J.; Capuccini, M.; Carone, M.; Cascante, M.; de Atauri, P.; Foguet, C.; Gonzalez-Beltran, A.; 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, R.; Sansone, S.-A.; Schober, D.; Selivanov, V.; Thévenot, E. A.; van Vliet, M.; Zanetti, G.; Steinbeck, C.; Kultima, K.; Spjuth, O.; Interoperable and scalable data analysis with microservices: Applications in Metabolomics bioRxiv (2017) DOI: 10.1101/213603
  • Abstract
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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 in parallel using the Kubernetes container orchestrator. The access point is a virtual research environment which can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and established workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry studies, one nuclear magnetic resonance spectroscopy study and one fluxomics study, showing that the method scales dynamically with increasing availability of computational resources. We achieved a complete integration of the major software suites resulting in the first turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, multivariate statistics, and metabolite identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science.

Publications

van Rijswijk, M.; Beirnaert, C.; Caron, C.; Cascante, M.; Dominguez, V.; Dunn, W. B.; Ebbels, T. M. D.; Giacomoni, F.; Gonzalez-Beltran, A.; Hankemeier, T.; Haug, K.; Izquierdo-Garcia, J. L.; Jimenez, R. C.; Jourdan, F.; Kale, N.; Klapa, M. I.; Kohlbacher, O.; Koort, K.; Kultima, K.; Le Corguillé, G.; Moreno, P.; Moschonas, N. K.; Neumann, S.; O’Donovan, C.; Reczko, M.; Rocca-Serra, P.; Rosato, A.; Salek, R. M.; Sansone, S.-A.; Satagopam, V.; Schober, D.; Shimmo, R.; Spicer, R. A.; Spjuth, O.; Thévenot, E. A.; Viant, M. R.; Weber, R. J. M.; Willighagen, E. L.; Zanetti, G.; Steinbeck, C.; The future of metabolomics in ELIXIR F1000Research 6 1649 (2017) DOI: 10.12688/f1000research.12342.2
  • Abstract
  • BibText
  • RIS

Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the “Future of metabolomics in ELIXIR” was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.

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