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Machine Learning-Based Classification to Improve Gas Chromatography-Mass Spectrometry Data Processing

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Machine learning-based classification to improve Gas Chromatography-Mass spectrometry data processing. Yoann Gloaguen, Nico Borgsmüller, Tobias Opialla, Eric Blanc, Emilie Sicard, Anne Lise Royer, Bruno Le Bizec, Stéphanie Durand, Carole Migné, Mélanie Pétéra, et al. To cite this version: Yoann Gloaguen, Nico Borgsmüller, Tobias Opialla, Eric Blanc, Emilie Sicard, et al.. Machine learning-based classification to improve Gas Chromatography-Mass spectrometry data processing.. European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France. 263 p., 2020, Oral and poster abstracts European RFMF Metabomeeting 2020. hal-02505901 HAL Id: hal-02505901 https://hal.archives-ouvertes.fr/hal-02505901 Submitted on 2 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License [Tapez ici] [Tapez- 0 - ici] [Tapez ici] We are very pleased to welcome you to the 2020 European RFMF-Metabomeeting conference in Toulouse. This conference gathers together two metabolomics and fluxomics networks, the RFMF (French- speaking Metabolomics and Fluxomics Network) and the MPF (Metabolic Profiling Forum) with more than 10 years of existence. MPF and RFMF share the same objectives which are to catalyze metabolomics and fluxomics research, organize conferences and promote early career scientists. Both networks also put forward networking and social aspects as strong leverage to achieve cutting edge science. For all these reasons we decided to organize this joint event. With the growing interest in metabolomics, several regional and national networks have been created across Europe (and affiliated islands) within the last years. That is the reason why we decided to also include them in the organization of this event. They were particularly instrumental in creating a high-level scientific program and providing travel grants (a staggering 21 travel grants!). We expect this conference to demonstrate the recent breakthroughs in metabolomics and fluxomics in a wide range of application fields. We made the choice to keep the scope of the conference as broad as possible (in terms of techniques and applications) since we think that interactions between communities is key in creating new paradigms, collaborations and scientific hypothesis. One of our aims in this conference is to promote early career scientist participation. That is the reason why we did our best to keep registration prices as low as possible. As mentioned, networks made a strong effort to offer travel grants. Early careers were also strongly involved in the scientific organization of the conference. In fact, an early career committee was set up, led by Alison Woodward, and selected the early career presentations that you will see during the conference. They also proposed and organized workshops and social events. Finally, they will co-chair sessions with the (less early career) scientists. Good science is generally the outcome of hard work within a friendly and supportive environment. All organisers agreed on the fact that this friendly atmosphere is of upmost importance for the organization of the conference. That is the reason why we did our best to have exciting social and networking events before and during the conference. We also aim at following RFMF mantra of “Good food Good science” with a very local and original gala dinner. Finally, we would like to acknowledge all the academic and industrial sponsors for supporting this event and previous ones. We also thank all the people involved in the scientific and practical organization of this conference. MetaboHub-Metatoul metabolomics and fluxomics facility contribution was outstanding and our warmest thoughts go to Justine Bertrand Michel and Floriant Bellvert for their hard work and unbreakable optimism. We wish you a fruitful scientific, human and enjoyable conference! Jules Griffin (MPF) Fabien Jourdan (RFMF) - 1 - - 2 - - 3 - ACADEMIC PARTNERS - 4 - PLATINIUM SPONSORS - 5 - GOLD SPONSORS SILVER SPONSORS - 6 - BRONZE SPONSORS MEDIA SPONSORS - 7 - EUROPEAN REGIONAL AND NATIONAL NETWORKS AND SOCIETIES - 8 - - 9 - SCIENTIFIC COMMITTEE Floriant Bellvert RFMF CNRS Justine Bertrand RFMF INSERM Michel Lorraine Brennan Ireland University College Dublin The University of Karl Burgess Scottish Metabolomics Network Edinburgh Marta Cascante Spanish Metabolomics Society University Barecelona Frédérique Courant RFMF Université de Montpellier Pietro Franceschi Italian Metabolomics Network Fondazione Edmund Mach Patrick Giraudeau RFMF Université de Nantes Roy Goodacre MPF University of Liverpool Jules Griffin MPF Imperial College Robert Hall Netherlands Metabolomics Centre Wageningen University Anne-Emmanuelle Hay RFMF Université de Lyon 1 Fabien Jourdan RFMF INRA Christophe Junot RFMF CEA Dong-Hyun Kim MPF University of Nottingham Leibniz Institute for Plant Steffen Neumann German Society for Metabolomics Research Biochemistry MateJ Oresic Nordic Metabolomics Society Orebro University Jean-Charles Portais RFMF Université Paul Sabatier Serge Rudaz Swiss Metabolomics Society Université de Genève Andrew Southam MPF University of Birmingham Alison Woodward MPF University of Nottingham - 10 - EARLY CAREER SCIENTIFIC COMMITTEE Jordi Capellades Spanish Metabolomics Society Sylvain Dechaumet RFMF junior Yoric Gagnebin Swiss Metabolomics Society Kate Gallagher MPF Natasa Giallourou MPF Corentine Goossens RFMF junior Katharina Herzog Nordic Metabolomics Society Justine Leenders RFMF junior Youzhong Liu YoungNMC Clément Regnault Scottish Metabolomics Network Sara Tortorella Italian Metabolomics Network Alison Woodward MPF - 11 - LOCAL ORGANISING COMMITTEE Floriant Bellvert MetaboHub-Metatoul Cécilia Berges MetaboHub-Metatoul Justine Bertrand Michel MetaboHub-Metatoul Maxime Chazalviel MedDay Pharmaceuticals Frédérique Courant Université de Montpellier Sandrine Ellero-Simatos INRA-Toxalim Yoann Gloaguen Berlin Institute of Health Anne-Emmanuelle Hay Université de Lyon Fabien Jourdan MetaboHub-Metatoul Hanna Kulyk Barbier MetaboHub-Metatoul Loïc Mervant MetaboHub-Metatoul Jean-Charles Portais MetaboHub-Metatoul Pablo Rodriguez Mier INRA-Toxalim - 12 - - 13 - Workshop 1: W1 Meet the editor (January 21st 8:30pm-10pm) Purpose of the workshop: Attendees will meet editors and reviewers to discuss the following points: • Scientific inspiration versus literary perspiration: What makes a good (Metabolomics) paper? • What you should never do in papers. • Refereeing process: what happens once I have submitted my paper to the abyss... • Scientific ethics: objectivity versus subjectivity Skills acquired at the end of the workshop: • A general understanding of the publication process. • How to be a good reviewer and how to respond to reviewers (good and bad!) • Some further ideas to make your paper better. Intended audience and prerequisites: • Public: priority to early career but can go beyond • Prerequisites: did publish or plan to Organisers: Katharina Herzog, Kate Gallagher, Natasa Giallourou, Roy Goodacre and Jules Griffin. - 14 - Workshop 2: W2 Interactive tutorial, How to process LC-MS data with workflow4metabolomics.org (January 21st, 9am-12am) Purpose of the workshop: Metabolomics data analysis is a complex, multistep process, which is constantly evolving with the development of new analytical technologies, mathematical methods, and bioinformatics tools and databases. The Workflow4Metabolomics(W4M) project aims at developing full LC/MS,GC/MS,FIA/MS and NMR pipelines using Galaxy framework for data analysis including preprocessing, normalization, quality control, statistical analysis and annotation steps. https://workflow4metabolomics.org Intended audience and prerequisites: • Public: Researchers or students involved in metabolomics by LC-MS • Prerequisites: basic knowledge’s of the usual data processing steps for LC-MS metabolomics Skills acquired at the end of the workshop: • What is Galaxy? • Comprehend the diversity of LC-MS metabolomic data analysis. • Get familiar with the main steps constituting a metabolomic workflow for untargeted LC-MS analysis. • Evaluate the potential of a workflow approach when dealing with LC-MS metabolomic data. Organisers: Franck Giacomoni, Yann Guitton and Marie Tremblay Franco References: https://workflow4metabolomics.org Guitton et al (2017) 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 - 15 - Workshop 3: W3 metaRbolomics hackathon plus (January 21st 2020, 1pm-3:45pm.) Purpose of the workshop: The idea of this hackathon is to have a quiet space where active developers and advanced users can work on integrating their packages in R, adding new data to wikidata or wikipathways, mapping identifiers with BridgeDb, tailor-making MetFrag databases to answer identification questions. The hackathon will start with Jo Rainer presenting the new R packages at https://RforMassSpectrometry.org and then we will just hack away! With the new packages it will be relatively easy to implement
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