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Winder CL, Witting M, Tugizimana F, Dunn WB, Reinke SN. Providing metabolomics education and training: pedagogy and considerations. Metabolomics 2022; 18:106. [PMID: 36512139 PMCID: PMC9746579 DOI: 10.1007/s11306-022-01957-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/11/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Metabolomics is a highly multidisciplinary and non-standardised research field. Metabolomics researchers must possess and apply extensive cross-disciplinary content knowledge, subjective experience-based judgement, and the associated diverse skill sets. Accordingly, appropriate educational and training initiatives are important in developing this knowledge and skills base in the metabolomics community. For these initiatives to be successful, they must consider both pedagogical best practice and metabolomics-specific contextual challenges. AIM OF REVIEW The aim of this review is to provide consolidated pedagogical guidance for educators and trainers in metabolomics educational and training programmes. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, we discuss the principles of pedagogical best practice as they relate to metabolomics. We then discuss the challenges and considerations in developing and delivering education and training in metabolomics. Finally, we present examples from our own teaching practice to illustrate how pedagogical best practice can be integrated into metabolomics education and training programmes.
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Affiliation(s)
- Catherine L Winder
- Analytical & Clinical Metabolomics Group and Liverpool Training Centre for Metabolomics, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa
- International Research and Development Division, Omnia Group Ltd., Bryanston, Johannesburg, 2021, South Africa
| | - Warwick B Dunn
- Analytical & Clinical Metabolomics Group and Liverpool Training Centre for Metabolomics, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB, UK
| | - Stacey N Reinke
- Centre for Integrative Metabolomics & Computational Biology, School of Science, Edith Cowan University, Joondalup, 6027, Australia.
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2
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Harrill JA, Viant MR, Yauk CL, Sachana M, Gant TW, Auerbach SS, Beger RD, Bouhifd M, O'Brien J, Burgoon L, Caiment F, Carpi D, Chen T, Chorley BN, Colbourne J, Corvi R, Debrauwer L, O'Donovan C, Ebbels TMD, Ekman DR, Faulhammer F, Gribaldo L, Hilton GM, Jones SP, Kende A, Lawson TN, Leite SB, Leonards PEG, Luijten M, Martin A, Moussa L, Rudaz S, Schmitz O, Sobanski T, Strauss V, Vaccari M, Vijay V, Weber RJM, Williams AJ, Williams A, Thomas RS, Whelan M. Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology. Regul Toxicol Pharmacol 2021; 125:105020. [PMID: 34333066 DOI: 10.1016/j.yrtph.2021.105020] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022]
Abstract
Omics methodologies are widely used in toxicological research to understand modes and mechanisms of toxicity. Increasingly, these methodologies are being applied to questions of regulatory interest such as molecular point-of-departure derivation and chemical grouping/read-across. Despite its value, widespread regulatory acceptance of omics data has not yet occurred. Barriers to the routine application of omics data in regulatory decision making have been: 1) lack of transparency for data processing methods used to convert raw data into an interpretable list of observations; and 2) lack of standardization in reporting to ensure that omics data, associated metadata and the methodologies used to generate results are available for review by stakeholders, including regulators. Thus, in 2017, the Organisation for Economic Co-operation and Development (OECD) Extended Advisory Group on Molecular Screening and Toxicogenomics (EAGMST) launched a project to develop guidance for the reporting of omics data aimed at fostering further regulatory use. Here, we report on the ongoing development of the first formal reporting framework describing the processing and analysis of both transcriptomic and metabolomic data for regulatory toxicology. We introduce the modular structure, content, harmonization and strategy for trialling this reporting framework prior to its publication by the OECD.
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Affiliation(s)
- Joshua A Harrill
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, United States.
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom; Michabo Health Science, University of Birmingham Enterprise, Birmingham Research Park, Vincent Drive, Birmingham, B15 2SQ, United Kingdom.
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Magdalini Sachana
- Organisation for Economic Co-operation and Development (OECD), Environment Health and Safety Division, Paris, France
| | - Timothy W Gant
- Centre for Radiation, Chemical and Environmental Hazards (CRCE), Public Health England (PHE), Harwell Science Campus, Oxfordshire, United Kingdom
| | - Scott S Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Richard D Beger
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | | | - Jason O'Brien
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Ottawa, ON, K1A 0H3, Canada
| | - Lyle Burgoon
- US Army Engineer Research and Development Center, 3909 Halls Ferry Rd, Vicksburg, MS, 39180, USA
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, the Netherlands
| | - Donatella Carpi
- European Commission, Joint Research Centre (JRC), 21027, Ispra, Italy
| | - Tao Chen
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Brian N Chorley
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, United States
| | - John Colbourne
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom; Michabo Health Science, University of Birmingham Enterprise, Birmingham Research Park, Vincent Drive, Birmingham, B15 2SQ, United Kingdom
| | - Raffaella Corvi
- European Commission, Joint Research Centre (JRC), 21027, Ispra, Italy
| | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), INRAE UMR 1331, ENVT, INP-Purpan, Paul Sabatier University (UPS), Toulouse, France; MetaToul-AXIOM Platform, MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, Toulouse, France
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Timothy M D Ebbels
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, SW7 2AZ, United Kingdom
| | - Drew R Ekman
- Center for Environmental Measurement and Modeling, Office of Research and Development, U.S. Environmental Protection Agency, Athens, GA, 30605, United States
| | | | - Laura Gribaldo
- European Commission, Joint Research Centre (JRC), 21027, Ispra, Italy
| | - Gina M Hilton
- PETA Science Consortium International e.V., Friolzheimer Str. 3, 70499, Stuttgart, Germany
| | - Stephanie P Jones
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Ottawa, ON, K1A 0H3, Canada
| | - Aniko Kende
- Syngenta Jealott's Hill International Research Centre, Bracknell, RG42 6EY, United Kingdom
| | - Thomas N Lawson
- Michabo Health Science, University of Birmingham Enterprise, Birmingham Research Park, Vincent Drive, Birmingham, B15 2SQ, United Kingdom
| | - Sofia B Leite
- European Commission, Joint Research Centre (JRC), 21027, Ispra, Italy
| | - Pim E G Leonards
- Department of Environment and Health, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV, Amsterdam, the Netherlands
| | - Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Laura Moussa
- US Food and Drug Administration, Center for Veterinary Medicine, Rockville, MD, United States
| | - Serge Rudaz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland; Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Oliver Schmitz
- BASF Metabolome Solutions, Metabolome Data Science, Tegeler Weg 33, 10589, Berlin, Germany
| | | | - Volker Strauss
- BASF SE, Toxicology and Ecology, 67056, Ludwigshafen, Germany
| | - Monica Vaccari
- Center for Environmental Health and Prevention, Regional Agency for Prevention, Environment and Energy of Emilia-Romagna, Bologna, Italy
| | - Vikrant Vijay
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom; Michabo Health Science, University of Birmingham Enterprise, Birmingham Research Park, Vincent Drive, Birmingham, B15 2SQ, United Kingdom
| | - Antony J Williams
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, United States
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Russell S Thomas
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, United States
| | - Maurice Whelan
- European Commission, Joint Research Centre (JRC), 21027, Ispra, Italy
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Phapale P, Rai V, Mohanty AK, Srivastava S. Untargeted Metabolomics Workshop Report: Quality Control Considerations from Sample Preparation to Data Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2006-2010. [PMID: 32872787 DOI: 10.1021/jasms.0c00224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Proteomics Society, India (PSI), hosted the Metabolomics workshop on experimental and data analysis training for untargeted metabolomics in December 2019. The workshop included six tutorial lectures and hands-on data analysis training sessions presented by seven speakers from across the globe. The tutorials and hands-on data analysis sessions focused on workflows for liquid chromatography-mass spectrometry (LC-MS) based on untargeted metabolomics. We review here three main topics from the workshop, which were uniquely identified as bottlenecks for new researchers: (a) experimental design, (b) quality controls during sample preparation and instrumental analysis, and (c) data quality evaluation using open source tools. Our objective here is to present common challenges faced by novice researchers and present guidelines to address them. We provide resources and good practices for researchers who are at the initial stage of setting up metabolomics workflows in their laboratories.
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Affiliation(s)
- Prasad Phapale
- Metabolomics Core Facility, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Vineeta Rai
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Ashok Kumar Mohanty
- Animal Biotechnology Centre National Dairy Research Institute Karnal, Haryana 132001, India
| | - Sanjeeva Srivastava
- Proteomics Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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4
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Viant MR, Ebbels TMD, Beger RD, Ekman DR, Epps DJT, Kamp H, Leonards PEG, Loizou GD, MacRae JI, van Ravenzwaay B, Rocca-Serra P, Salek RM, Walk T, Weber RJM. Use cases, best practice and reporting standards for metabolomics in regulatory toxicology. Nat Commun 2019; 10:3041. [PMID: 31292445 PMCID: PMC6620295 DOI: 10.1038/s41467-019-10900-y] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 06/07/2019] [Indexed: 12/23/2022] Open
Abstract
Metabolomics is a widely used technology in academic research, yet its application to regulatory science has been limited. The most commonly cited barrier to its translation is lack of performance and reporting standards. The MEtabolomics standaRds Initiative in Toxicology (MERIT) project brings together international experts from multiple sectors to address this need. Here, we identify the most relevant applications for metabolomics in regulatory toxicology and develop best practice guidelines, performance and reporting standards for acquiring and analysing untargeted metabolomics and targeted metabolite data. We recommend that these guidelines are evaluated and implemented for several regulatory use cases.
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Affiliation(s)
- Mark R Viant
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | | | | | | | - David J T Epps
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | | | | | | | | | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, OX1 3QG, UK
| | - Reza M Salek
- International Agency for Research on Cancer, Lyon, France
| | - Tilmann Walk
- BASF Metabolome Solutions, 10589, Berlin, Germany
| | - Ralf J M Weber
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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5
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Broadhurst D, Goodacre R, Reinke SN, Kuligowski J, Wilson ID, Lewis MR, Dunn WB. Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies. Metabolomics 2018; 14:72. [PMID: 29805336 PMCID: PMC5960010 DOI: 10.1007/s11306-018-1367-3] [Citation(s) in RCA: 440] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/03/2018] [Indexed: 12/25/2022]
Abstract
BACKGROUND Quality assurance (QA) and quality control (QC) are two quality management processes that are integral to the success of metabolomics including their application for the acquisition of high quality data in any high-throughput analytical chemistry laboratory. QA defines all the planned and systematic activities implemented before samples are collected, to provide confidence that a subsequent analytical process will fulfil predetermined requirements for quality. QC can be defined as the operational techniques and activities used to measure and report these quality requirements after data acquisition. AIM OF REVIEW This tutorial review will guide the reader through the use of system suitability and QC samples, why these samples should be applied and how the quality of data can be reported. KEY SCIENTIFIC CONCEPTS OF REVIEW System suitability samples are applied to assess the operation and lack of contamination of the analytical platform prior to sample analysis. Isotopically-labelled internal standards are applied to assess system stability for each sample analysed. Pooled QC samples are applied to condition the analytical platform, perform intra-study reproducibility measurements (QC) and to correct mathematically for systematic errors. Standard reference materials and long-term reference QC samples are applied for inter-study and inter-laboratory assessment of data.
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Affiliation(s)
- David Broadhurst
- School of Science, Centre for Integrative Metabolomics and Computational Biology, Edith Cowan University, Joondalup, Perth, Australia
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Stacey N Reinke
- School of Science, Centre for Integrative Metabolomics and Computational Biology, Edith Cowan University, Joondalup, Perth, Australia
- Separation Sciences and Metabolomics Laboratory, Murdoch University, Perth, WA, Australia
| | - Julia Kuligowski
- Neonatal Research Unit, Health Research Institute La Fe, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Ian D Wilson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London, SW7 2AZ, UK
| | - Matthew R Lewis
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London, SW7 2AZ, UK
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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6
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Guitton Y, Tremblay-Franco M, Le Corguillé G, Martin JF, Pétéra M, Roger-Mele P, Delabrière A, Goulitquer S, Monsoor M, Duperier C, Canlet C, Servien R, Tardivel P, Caron C, Giacomoni F, Thévenot EA. Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics. Int J Biochem Cell Biol 2017; 93:89-101. [DOI: 10.1016/j.biocel.2017.07.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 06/14/2017] [Accepted: 07/10/2017] [Indexed: 12/11/2022]
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7
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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; 6. [PMID: 29043062 PMCID: PMC5627583 DOI: 10.12688/f1000research.12342.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/31/2017] [Indexed: 01/11/2023] Open
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 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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Affiliation(s)
- Merlijn van Rijswijk
- ELIXIR-NL, Dutch Techcentre for Life Sciences, Utrecht, 3503 RM, Netherlands.,Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands
| | - Charlie Beirnaert
- ADReM, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, 2020, Belgium
| | - Christophe Caron
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Victoria Dominguez
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France
| | - Warwick B Dunn
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy M D Ebbels
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Franck Giacomoni
- INRA, UNH, Human Nutrition Unit, PFEM, Metabolism Exploration Platform, MetaboHUB-Clermont, Clermont Auvergne University, Clermont-Ferrand, F-63000, France
| | | | - Thomas Hankemeier
- Netherlands Metabolomics Center, Leiden, 2333 CC, Netherlands.,Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2300 RA, Netherlands
| | - Kenneth Haug
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Jose L Izquierdo-Garcia
- Centro Nacional Investigaciones Cardiovasculares, Madrid, 28029, Spain.,CIBER de Enfermedades Respiratorias, Madrid, 28029 , Spain
| | | | - Fabien Jourdan
- Toxalim, UMR 1331, Université de Toulouse, Toulouse, F-31300, France
| | - Namrata Kale
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, GR-26504, Greece
| | - Oliver Kohlbacher
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany.,Department of Computer Science, University of Tübingen, Tübingen, 72076, Germany.,Center for Bioinformatics, University of Tübingen, Tübingen, 72076, Germany
| | - Kairi Koort
- The Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, Estonia.,School of Natural Sciences and Health, Tallinn University, 10120, 10120, Estonia
| | - Kim Kultima
- Department of Medical Sciences, Uppsala University, Uppsala, 752 36, Sweden
| | - Gildas Le Corguillé
- ELIXIR-FR, French Institute of Bioinformatics, Gif-sur-Yvette, F-91198, France.,UPMC, CNRS, FR2424, ABiMS, Station Biologique, Roscoff, F-29680, France
| | - Pablo Moreno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Nicholas K Moschonas
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology - Hellas (FORTH/ICE-HT), Patras, GR-26504, Greece.,Department of General Biology, School of Medicine, University of Patras, Patras, GR-26504, Greece
| | - Steffen Neumann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | | | - Philippe Rocca-Serra
- Oxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UK
| | - Antonio Rosato
- Magnetic Resonance Center, Interuniversity Consortium for Magnetic Resonance on MetalloProteins, University of Florence, Florence, 50121, Italy
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Engineering Science Department, University of Oxford, Oxford, OX1 3QG, UK
| | - Venkata Satagopam
- Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, L-4367, Luxembourg
| | - Daniel Schober
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
| | - Ruth Shimmo
- The Centre of Excellence in Neural and Behavioural Sciences, Tallinn, Tallinn, 10120, Estonia.,School of Natural Sciences and Health, Tallinn University, 10120, 10120, Estonia
| | - Rachel A Spicer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, 752 36, Sweden
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Analysis and Systems' Intelligence, MetaboHUB, Gif-sur-Yvette, F-91191, France
| | - Mark R Viant
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ralf J M Weber
- School of Biosciences, Phenome Centre Birmingham and Birmingham Metabolomics Training Centre, University of Birmingham, Birmingham, B15 2TT, UK
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, NL-6200, Netherlands
| | - Gianluigi Zanetti
- CRS4, Data Intensive Computing Group, Ed.1 POLARIS, Pula, 09010, Italy
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8
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Larcombe L, Hendricusdottir R, Attwood TK, Bacall F, Beard N, Bellis LJ, Dunn WB, Hancock JM, Nenadic A, Orengo C, Overduin B, Sansone SA, Thurston M, Viant MR, Winder CL, Goble CA, Ponting CP, Rustici G. ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR. F1000Res 2017; 6. [PMID: 28781748 PMCID: PMC5521157 DOI: 10.12688/f1000research.11837.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/19/2017] [Indexed: 11/20/2022] Open
Abstract
ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data. Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ELIXIR-UK contributes to the Training Platform’s coordination and supports the development of training to address key skill gaps amongst UK scientists. As part of this work it acts as a conduit for nationally-important bioinformatics training resources to promote their activities to the ELIXIR community. ELIXIR-UK also leads ELIXIR’s flagship Training Portal, TeSS, which collects information about a diverse range of training and makes it easily accessible to the community. ELIXIR-UK also works with others to provide key digital skills training, partnering with the Software Sustainability Institute to provide Software Carpentry training to the ELIXIR community and to establish the Data Carpentry initiative, and taking a lead role amongst national stakeholders to deliver the StaTS project – a coordinated effort to drive engagement with training in statistics.
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Affiliation(s)
- L Larcombe
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - R Hendricusdottir
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - T K Attwood
- School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
| | - F Bacall
- School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
| | - N Beard
- School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
| | - L J Bellis
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - W B Dunn
- Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - A Nenadic
- The Software Sustainability Institute, University of Manchester, Manchester, M13 9PL, UK
| | - C Orengo
- University College London, London, WC1E 6BT, UK
| | - B Overduin
- Edinburgh Genomics, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - S-A Sansone
- Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK
| | - M Thurston
- Oxford e-Research Centre, University of Oxford, Oxford, OX1 3QG, UK
| | - M R Viant
- Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - C L Winder
- Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - C A Goble
- School of Computer Science, University of Manchester, Manchester, M13 9PL, UK
| | - C P Ponting
- MRC Human Genetics Unit, The Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - G Rustici
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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Weber RJM, Lawson TN, Salek RM, Ebbels TMD, Glen RC, Goodacre R, Griffin JL, Haug K, Koulman A, Moreno P, Ralser M, Steinbeck C, Dunn WB, Viant MR. Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy. Metabolomics 2017; 13:12. [PMID: 28090198 PMCID: PMC5192046 DOI: 10.1007/s11306-016-1147-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/30/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Ralf J. M. Weber
- 0000 0004 1936 7486grid.6572.6School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
- 0000 0004 1936 7486grid.6572.6Phenome Centre Birmingham, University of Birmingham, Birmingham, B15 2TT UK
| | - Thomas N. Lawson
- 0000 0004 1936 7486grid.6572.6School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Reza M. Salek
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD UK
| | - Timothy M. D. Ebbels
- 0000 0001 2113 8111grid.7445.2Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ UK
| | - Robert C. Glen
- 0000 0001 2113 8111grid.7445.2Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, SW7 2AZ UK
- Centre for Molecular Informatics, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW UK
| | - Royston Goodacre
- 0000000121662407grid.5379.8Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M1 7DN UK
| | - Julian L. Griffin
- 0000 0004 0606 2472grid.415055.0MRC Human Nutrition Research Unit, Cambridge, CB1 9NL UK
- 0000000121885934grid.5335.0The Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK
| | - Kenneth Haug
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD UK
| | - Albert Koulman
- 0000 0004 0606 2472grid.415055.0MRC Human Nutrition Research Unit, Cambridge, CB1 9NL UK
| | - Pablo Moreno
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD UK
| | - Markus Ralser
- 0000000121885934grid.5335.0The Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK
- 0000 0004 1795 1830grid.451388.3The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Christoph Steinbeck
- 0000 0000 9709 7726grid.225360.0European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD UK
| | - Warwick B. Dunn
- 0000 0004 1936 7486grid.6572.6School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
- 0000 0004 1936 7486grid.6572.6Phenome Centre Birmingham, University of Birmingham, Birmingham, B15 2TT UK
| | - Mark R. Viant
- 0000 0004 1936 7486grid.6572.6School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
- 0000 0004 1936 7486grid.6572.6Phenome Centre Birmingham, University of Birmingham, Birmingham, B15 2TT UK
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