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PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud

View ORCID ProfileKristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, View ORCID ProfileMarta Cascante, View ORCID ProfilePedro de Atauri, Timothy M D Ebbels, View ORCID ProfileCarles Foguet, Robert Glen, View ORCID ProfileAlejandra Gonzalez-Beltran, Ulrich Guenther, Evangelos Handakas, View ORCID ProfileThomas Hankemeier, View ORCID ProfileKenneth Haug, View ORCID ProfileStephanie Herman, View ORCID ProfilePetr Holub, View ORCID ProfileMassimiliano Izzo, Daniel Jacob, View ORCID ProfileDavid Johnson, Fabien Jourdan, View ORCID ProfileNamrata Kale, View ORCID ProfileIbrahim Karaman, Bita Khalili, View ORCID ProfilePayam Emami Khonsari, View ORCID ProfileKim Kultima, View ORCID ProfileSamuel Lampa, View ORCID ProfileAnders Larsson, Christian Ludwig, View ORCID ProfilePablo Moreno, View ORCID ProfileSteffen Neumann, Jon Ander Novella, View ORCID ProfileClaire O’Donovan, View ORCID ProfileJake TM Pearce, View ORCID ProfileAlina Peluso, View ORCID ProfileLuca Pireddu, View ORCID ProfileMarco Enrico Piras, View ORCID ProfileMichelle AC Reed, View ORCID ProfilePhilippe Rocca-Serra, Pierrick Roger, View ORCID ProfileAntonio Rosato, View ORCID ProfileRico Rueedi, View ORCID ProfileChristoph Ruttkies, View ORCID ProfileNoureddin Sadawi, View ORCID ProfileReza M Salek, View ORCID ProfileSusanna-Assunta Sansone, View ORCID ProfileVitaly Selivanov, View ORCID ProfileOla Spjuth, View ORCID ProfileDaniel Schober, View ORCID ProfileEtienne A. Thévenot, Mattia Tomasoni, View ORCID ProfileMerlijn van Rijswijk, View ORCID ProfileMichael van Vliet, View ORCID ProfileMark R Viant, Ralf J. M. Weber, View ORCID ProfileGianluigi Zanetti, View ORCID ProfileChristoph Steinbeck
doi: https://doi.org/10.1101/409151
Kristian Peters
1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
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James Bradbury
2School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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Sven Bergmann
3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
4Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Marco Capuccini
5Division of Scientific Computing, Department of Information Technology, Uppsala University, Sweden
6Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
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Marta Cascante
7Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas
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Pedro 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), Spain
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Timothy M D Ebbels
9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
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Carles 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), Spain
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Robert Glen
9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
10Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB21EW, United Kingdom
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Alejandra Gonzalez-Beltran
11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.
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Ulrich Guenther
22College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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Evangelos Handakas
9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
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Thomas Hankemeier
12Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands
13Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug
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Kenneth Haug
14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Stephanie Herman
15Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
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Petr Holub
29BBMRI-ERIC, Graz, Austria
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Massimiliano Izzo
11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.
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Daniel Jacob
16INRA, University of Bordeaux, Plateforme Métabolome Bordeaux-MetaboHUB, 33140 Villenave d’Ornon, France
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David Johnson
11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.
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Fabien Jourdan
17INRA - French National Institute for Agricultural Research, UMR1331, Toxalim, Research Centre in Food Toxicology, Toulouse, France
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Namrata Kale
14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Ibrahim Karaman
18Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, St. Mary’s Campus, Norfolk Place, W2 1PG, London, United Kingdom
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Bita Khalili
3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
4Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Payam Emami Khonsari
15Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
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Kim Kultima
15Department of Medical Sciences, Clinical Chemistry, Uppsala University, 751 85 Uppsala, Sweden
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Samuel Lampa
6Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
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Anders Larsson
19National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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Christian Ludwig
22College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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Pablo Moreno
14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Steffen Neumann
1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
20German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
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Jon Ander Novella
19National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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Claire O’Donovan
14European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Jake TM Pearce
9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
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Alina Peluso
9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
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Luca Pireddu
21Distributed Computing Group, CRS4, Pula, Italy
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Marco Enrico Piras
21Distributed Computing Group, CRS4, Pula, Italy
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Michelle AC Reed
22College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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Philippe Rocca-Serra
11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.
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Pierrick Roger
23CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
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Antonio Rosato
24Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence and CIRMMP, 50019 Sesto Fiorentino, Florence, Italy
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Rico Rueedi
3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
4Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Christoph Ruttkies
1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
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Noureddin Sadawi
9Department of Surgery & Cancer, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
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Reza M Salek
25European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
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Susanna-Assunta Sansone
11Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OX1 3QG, Oxford, UK.
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Vitaly 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), Spain
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Ola Spjuth
6Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24 Uppsala, Sweden
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Daniel Schober
1Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany
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Etienne A. Thévenot
23CEA, LIST, Laboratory for Data Analysis and Systems’ Intelligence, MetaboHUB, Gif-Sur-Yvette F-91191, France
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Mattia Tomasoni
3Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
4Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Merlijn van Rijswijk
26ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands
27Netherlands Metabolomics Center, Leiden, 2333 CC, The Netherlands
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Michael van Vliet
28Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, 2333 CC, The Netherlands
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Mark R Viant
2School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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  • ORCID record for Mark R Viant
Ralf J. M. Weber
2School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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Gianluigi Zanetti
21Distributed Computing Group, CRS4, Pula, Italy
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Christoph Steinbeck
30Cheminformatics and Computational Metabolomics, Institute for Analytical Chemistry, Lessingstr. 8, 07743 Jena, Germany
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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 The PhenoMeNal (Phenome and Metabolome aNalysis) e-infrastructure provides a complete, workflow-oriented, interoperable metabolomics data analysis solution for a modern infrastructure-as-a-service (IaaS) cloud platform. PhenoMeNal seamlessly integrates a wide array of existing open source tools which 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 infrastructures available for metabolomics. It provides scientists with a ready-to-use, workflow-driven, reproducible and shareable data analysis platform harmonizing the software installation and configuration through user-friendly web interfaces. The deployed cloud environments can be dynamically scaled to enable large-scale analyses which are interfaced through standard data formats, versioned, and have been tested for reproducibility and interoperability. The flexible implementation of PhenoMeNal allows easy adaptation of the infrastructure to other application areas and ‘omics research domains.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M D Ebbels, Carles Foguet, Robert Glen, Alejandra Gonzalez-Beltran, Ulrich Guenther, Evangelos Handakas, Thomas Hankemeier, Kenneth Haug, Stephanie Herman, Petr Holub, Massimiliano Izzo, Daniel Jacob, David Johnson, Fabien Jourdan, Namrata Kale, Ibrahim Karaman, Bita Khalili, Payam Emami Khonsari, Kim Kultima, Samuel Lampa, Anders Larsson, Christian Ludwig, Pablo Moreno, Steffen Neumann, Jon Ander Novella, Claire O’Donovan, Jake TM Pearce, Alina Peluso, Luca Pireddu, Marco Enrico Piras, Michelle AC Reed, Philippe Rocca-Serra, Pierrick Roger, Antonio Rosato, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M Salek, Susanna-Assunta Sansone, Vitaly Selivanov, Ola Spjuth, Daniel Schober, Etienne A. Thévenot, Mattia Tomasoni, Merlijn van Rijswijk, Michael van Vliet, Mark R Viant, Ralf J. M. Weber, Gianluigi Zanetti, Christoph Steinbeck
bioRxiv 409151; doi: https://doi.org/10.1101/409151
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PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud
Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M D Ebbels, Carles Foguet, Robert Glen, Alejandra Gonzalez-Beltran, Ulrich Guenther, Evangelos Handakas, Thomas Hankemeier, Kenneth Haug, Stephanie Herman, Petr Holub, Massimiliano Izzo, Daniel Jacob, David Johnson, Fabien Jourdan, Namrata Kale, Ibrahim Karaman, Bita Khalili, Payam Emami Khonsari, Kim Kultima, Samuel Lampa, Anders Larsson, Christian Ludwig, Pablo Moreno, Steffen Neumann, Jon Ander Novella, Claire O’Donovan, Jake TM Pearce, Alina Peluso, Luca Pireddu, Marco Enrico Piras, Michelle AC Reed, Philippe Rocca-Serra, Pierrick Roger, Antonio Rosato, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M Salek, Susanna-Assunta Sansone, Vitaly Selivanov, Ola Spjuth, Daniel Schober, Etienne A. Thévenot, Mattia Tomasoni, Merlijn van Rijswijk, Michael van Vliet, Mark R Viant, Ralf J. M. Weber, Gianluigi Zanetti, Christoph Steinbeck
bioRxiv 409151; doi: https://doi.org/10.1101/409151

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