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van Rijswijk M, Beirnaert C, Caron C, et al. The future of metabolomics in ELIXIR. F1000Res. 2017;6doi: 10.12688/f1000research.12342.2.
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. (2017). The future of metabolomics in ELIXIR. F1000Research, 6. https://doi.org/10.12688/f1000research.12342.2
van Rijswijk, Merlijn, et al. "The future of metabolomics in ELIXIR." F1000Research vol. 6 (2017). doi: https://doi.org/10.12688/f1000research.12342.2
van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Le Corguillé G, Moreno P, Moschonas NK, Neumann S, O'Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone SA, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Thévenot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C. The future of metabolomics in ELIXIR. F1000Res. 2017 Sep 06;6. doi: 10.12688/f1000research.12342.2. eCollection 2017. PMID: 29043062; PMCID: PMC5627583.
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F1000Res. 2017 Sep 06;6. doi: 10.12688/f1000research.12342.2. eCollection 2017.

The future of metabolomics in ELIXIR.

F1000Research

Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez, Warwick B Dunn, Timothy M D Ebbels, Franck Giacomoni, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Jose L Izquierdo-Garcia, Rafael C Jimenez, Fabien Jourdan, Namrata Kale, Maria I Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Pablo Moreno, Nicholas K Moschonas, Steffen Neumann, Claire O'Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M Salek, Susanna-Assunta Sansone, Venkata Satagopam, Daniel Schober, Ruth Shimmo, Rachel A Spicer, Ola Spjuth, Etienne A Thévenot, Mark R Viant, Ralf J M Weber, Egon L Willighagen, Gianluigi Zanetti, Christoph Steinbeck

Affiliations

  1. ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands.
  2. Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands.
  3. ADReM, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium.
  4. ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France.
  5. Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain.
  6. School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK.
  7. Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK.
  8. INRA, UNH, Human Nutrition Unit, PFEM, Metabolism Exploration Platform, MetaboHUB-Clermont, Clermont Auvergne University, Clermont-Ferrand, F-63000, France.
  9. Oxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UK.
  10. Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2300 RA, Netherlands.
  11. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK.
  12. Centro Nacional Investigaciones Cardiovasculares, Madrid, 28029, Spain.
  13. CIBER de Enfermedades Respiratorias, Madrid, 28029 , Spain.
  14. ELIXIR Hub, Cambridge, CB10 1SD, UK.
  15. Toxalim, UMR 1331, Université de Toulouse, Toulouse, F-31300, France.
  16. Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, GR-26504, Greece.
  17. Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.
  18. Department of Computer Science, University of Tübingen, Tübingen, 72076, Germany.
  19. Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany.
  20. The Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, Estonia.
  21. School of Natural Sciences and Health, Tallinn University, 10120, 10120, Estonia.
  22. Department of Medical Sciences, Uppsala University, Uppsala, 752 36, Sweden.
  23. UPMC, CNRS, FR2424, ABiMS, Station Biologique, Roscoff, F-29680, France.
  24. Department of General Biology, School of Medicine, University of Patras, Patras, GR-26504, Greece.
  25. Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany.
  26. BSRC "Alexander Fleming", Athens, GR-16672, Greece.
  27. Magnetic Resonance Center, Interuniversity Consortium for Magnetic Resonance on MetalloProteins, University of Florence, Florence, 50121, Italy.
  28. Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg.
  29. Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, 752 36, Sweden.
  30. CEA, LIST, Laboratory for Data Analysis and Systems' Intelligence, MetaboHUB, Gif-sur-Yvette, F-91191, France.
  31. Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, NL-6200, Netherlands.
  32. CRS4, Data Intensive Computing Group, Ed.1 POLARIS, Pula, 09010, Italy.
  33. Friedrich-Schiller-University, Jena, 07743, Germany.

PMID: 29043062 PMCID: PMC5627583 DOI: 10.12688/f1000research.12342.2

Abstract

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

Keywords: bioinformatics infrastructure; cloud computing; computational workflows; data standards; databases; metabolomics; multi-omics approaches; training

Conflict of interest statement

Competing interests: No competing interests were disclosed.

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