Keeping modelling notebooks with TRACE: Good for you and good for environmental research and management support
2021
Ayllón, Daniel | Railsback, Steven | Gallagher, Cara | Augusiak, Jacqueline | Baveco, Hans | Berger, Uta | Charles, Sandrine | Martin, Romina | Focks, Andreas | Galic, Nika | Liu, Chun | van Loon, E. Emiel | Nabe-Nielsen, Jacob | Piou, Cyril | Polhill, J. Gareth | Preuss, Thomas | Radchuk, Viktoriia | Schmolke, Amelie | Stadnicka-Michalak, Julita | Thorbek, Pernille | Grimm, Volker | Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM) | Lang Railsback & Associates | Department of Bioscience [Aarhus] | Charles River Laboratories Den Bosch B.V. (CRIVER) | Wageningen University and Research [Wageningen] (WUR) | Wageningen Environmental Research (Alterra) | Technische Universität Dresden = Dresden University of Technology (TU Dresden) | Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE) ; Université Claude Bernard Lyon 1 (UCBL) ; Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS) | Stockholm University | Syngenta Crop Protection LLC | Jealott’s Hill International Research Centre | Syngenta ; Jealott’s Hill International Research Centre | Institute for Biodiversity and Ecosystem Dynamics (IBED) ; Universiteit van Amsterdam = University of Amsterdam (UvA) | Centre de Biologie pour la Gestion des Populations (UMR CBGP) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [Occitanie])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro) | Département Systèmes Biologiques (Cirad-BIOS) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad) | The James Hutton Institute | Bayer Pharma AG [Berlin] | Leibniz Institute for Zoo and Wildlife Research (IZW) ; Leibniz Association | Waterborne Environmental Inc. | Swiss Federal Institute of Aquatic Science and Technology [Dübendorf] (EAWAG) | BASF SE | Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ) | University of Potsdam = Universität Potsdam | D. Ayllon was financially supported by the Spanish Ministry of Economy, Industry and Competitiveness through the research project CGL 2017-84269-P. S. Charles is participating under the umbrella of the Graduate School H2O'Lyon (ANR-17-EURE-0018) and "Université de Lyon" (UdL), as part of the program "Investissements d'Avenir" run by "Agence Nationale de la Recherche" (ANR). C. Piou participated under the funding from ANR-JCJC PEPPER (ANR-18-CE32-0010). J. G. Polhill receives funding from the Scottish Government Rural Affairs Food and Environment Strategic Research Programme. | ANR-17-EURE-0018,H2O'LYON,School of Integrated Watershed Sciences(2017) | ANR-18-CE32-0010,PEPPER,Etude de l'émergence du polyphénisme de phase et des risques associés(2018)
International audience
Mostrar más [+] Menos [-]Inglés. Highlights: • The quality and reproducibility of modelling would be increased by keeping modelling notebooks. • Simulation modellers have not yet developed a strong culture of keeping notebooks. • We propose a standard format for notebooks based on the TRACE document framework. • We make recommendations about the type of information to be included in the notebooks. • We describe existing tools to keep notebooks.Abstract: The acceptance and usefulness of simulation models are often limited by the efficiency, transparency, reproducibility, and reliability of the modelling process. We address these issues by suggesting that modellers (1) "trace" the iterative modelling process by keeping a modelling notebook corresponding to the laboratory notebooks used by empirical researchers, (2) use a standardized notebook structure and terminology based on the existing TRACE documentation framework, and (3) use their notebooks to compile TRACE documents that supplement publications and reports. These practices have benefits for model developers, users, and stakeholders: improved and efficient model design, analysis, testing, and application; increased model acceptance and reuse; and replicability and reproducibility of the model and the simulation experiments. Using TRACE terminology and structure in modelling notebooks facilitates production of TRACE documents. We explain the rationale of TRACE, provide example TRACE documents, and suggest strategies for keeping "TRACE Modelling Notebooks."
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