PhenoMeNal: processing and analysis of metabolomics data in the cloud

  1. Kristian Peters
  2. James Bradbury
  3. Sven Bergmann
  4. Marco Capuccini
  5. Marta Cascante
  6. Pedro de Atauri
  7. Timothy M D Ebbels
  8. Carles Foguet
  9. Robert Glen
  10. Alejandra Gonzalez-Beltran
  11. Ulrich L Günther
  12. Evangelos Handakas
  13. Thomas Hankemeier
  14. Kenneth Haug
  15. Stephanie Herman
  16. Petr Holub
  17. Massimiliano Izzo
  18. Daniel Jacob
  19. David Johnson
  20. Fabien Jourdan
  21. Namrata Kale
  22. Ibrahim Karaman
  23. Bita Khalili
  24. Payam Emami Khonsari
  25. Kim Kultima
  26. Samuel Lampa
  27. Anders Larsson
  28. Christian Ludwig
  29. Pablo Moreno
  30. Steffen Neumann
  31. Jon Ander Novella
  32. Claire O'Donovan
  33. Jake T M Pearce
  34. Alina Peluso
  35. Marco Enrico Piras
  36. Luca Pireddu
  37. Michelle A C Reed
  38. Philippe Rocca-Serra
  39. Pierrick Roger
  40. Antonio Rosato
  41. Rico Rueedi
  42. Christoph Ruttkies
  43. Noureddin Sadawi
  44. Reza M Salek
  45. Susanna-Assunta Sansone
  46. Vitaly Selivanov
  47. Ola Spjuth
  48. Daniel Schober
  49. Etienne A Thévenot
  50. Mattia Tomasoni
  51. Merlijn van Rijswijk
  52. Michael van Vliet
  53. Mark R Viant
  54. Ralf J M Weber
  55. Gianluigi Zanetti
  56. Christoph Steinbeck

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Abstract

Background

Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution.

Findings

PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm.

Conclusions

PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and ‘omics research domains.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giy149

    Kristian Peters 1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kristian PetersJames Bradbury 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSven Bergmann 3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland4Swiss Institute of Bioinformatics, Lausanne, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMarco Capuccini 5Division of Scientific Computing, Department of Information Technology, Uppsala University, Sweden6Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMarta Cascante 7Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y DigestivasFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Marta CascantePedro de Atauri 8Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Pedro de AtauriTimothy M D Ebbels 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCarles Foguet 8Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Carles FoguetRobert Glen 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom10Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB21EW, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlejandra Gonzalez-Beltran 11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alejandra Gonzalez-BeltranUlrich Guenther 22College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteEvangelos Handakas 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteThomas Hankemeier 12Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands13Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for DrugFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Thomas HankemeierKenneth Haug 14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kenneth HaugStephanie Herman 15Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Stephanie HermanPetr Holub 29BBMRI-ERIC, Graz, AustriaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Petr HolubMassimiliano Izzo 11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Massimiliano IzzoDaniel Jacob 16INRA, University of Bordeaux, Plateforme Métabolome Bordeaux-MetaboHUB, 33140 Villenave d’Ornon, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteDavid Johnson 11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for David JohnsonFabien Jourdan 17INRA - French National Institute for Agricultural Research, UMR1331, Toxalim, Research Centre in Food Toxicology, Toulouse, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteNamrata Kale 14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Namrata KaleIbrahim Karaman 18Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St. Mary’s Campus, Norfolk Place, W2 1PG, London, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ibrahim KaramanBita Khalili 3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland4Swiss Institute of Bioinformatics, Lausanne, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePayam Emami Khonsari 15Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Payam Emami KhonsariKim Kultima 15Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Kim KultimaSamuel Lampa 6Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Samuel LampaAnders Larsson 19National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Anders LarssonChristian Ludwig 22College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePablo Moreno 14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Pablo MorenoSteffen Neumann 1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany20German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Steffen NeumannJon Ander Novella 19National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteClaire O’Donovan 14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UKFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Claire O’DonovanJake TM Pearce 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jake TM PearceAlina Peluso 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Alina PelusoLuca Pireddu 21Distributed Computing Group, CRS4, Pula, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Luca PiredduMichelle AC Reed 22College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michelle AC ReedPhilippe Rocca-Serra 11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Philippe Rocca-SerraPierrick Roger 23CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAntonio Rosato 24Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence and CIRMMP, 50019 Sesto Fiorentino, Florence, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Antonio RosatoRico Rueedi 3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland4Swiss Institute of Bioinformatics, Lausanne, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Rico RueediChristoph Ruttkies 1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christoph RuttkiesNoureddin Sadawi 9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Noureddin SadawiReza M Salek 25European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, U.KFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Reza M SalekSusanna-Assunta Sansone 11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.Find this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Susanna-Assunta SansoneVitaly Selivanov 8Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), SpainFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Vitaly SelivanovOla Spjuth 6Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, SwedenFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ola SpjuthDaniel Schober 1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Daniel SchoberEtienne A. Thévenot 23CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Etienne A. ThévenotMattia Tomasoni 3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland4Swiss Institute of Bioinformatics, Lausanne, SwitzerlandFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteMerlijn van Rijswijk 26ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands27Netherlands Metabolomics Center, Leiden, 2333 CC, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Merlijn van RijswijkMichael van Vliet 28Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, 2333 CC, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Michael van VlietMark R Viant 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mark R ViantRalf J. M. Weber 2School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United KingdomFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteGianluigi Zanetti 21Distributed Computing Group, CRS4, Pula, ItalyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gianluigi ZanettiChristoph Steinbeck 30Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, GermanyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christoph Steinbeck

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy149 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101467 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101468

  2. Version published to 10.1093/gigascience/giy149
  3. Version published to 10.1101/409151v2 on bioRxiv
  4. Version published to 10.1101/409151v1 on bioRxiv