Easy-MODA: Simplifying standardised registration of scientific simulation workflows through MODA template guidelines powered by the Enalos Cloud Platform.

Autor:	Kolokathis PD; NovaMechanics MIKE, Piraeus 18545, Greece.; Entelos Institute, Larnaca 6059, Cyprus., Sidiropoulos NK; NovaMechanics MIKE, Piraeus 18545, Greece.; Entelos Institute, Larnaca 6059, Cyprus., Zouraris D; Entelos Institute, Larnaca 6059, Cyprus.; NovaMechanics Ltd, Nicosia 1070, Cyprus., Varsou DD; NovaMechanics MIKE, Piraeus 18545, Greece.; Entelos Institute, Larnaca 6059, Cyprus., Mintis DG; Entelos Institute, Larnaca 6059, Cyprus.; NovaMechanics Ltd, Nicosia 1070, Cyprus., Tsoumanis A; NovaMechanics MIKE, Piraeus 18545, Greece.; NovaMechanics Ltd, Nicosia 1070, Cyprus., Dondero F; Entelos Institute, Larnaca 6059, Cyprus.; Department of Science and Technological Innovation, Università del Piemonte Orientale, 15121 Alessandria, Italy., Exner TE; SevenPastNine GmbH, Rebacker 68, 79650 Schopfheim, Germany., Sarimveis H; School of Chemical Engineering, National Technical University of Athens, 15780 Zografou, Greece., Chaideftou E; Department of Medical Biochemistry, Medical University of Innsbruck, Innsbruck, Austria., Paparella M; Department of Medical Biochemistry, Medical University of Innsbruck, Innsbruck, Austria., Nikiforou F; Aristotle University of Thessaloniki, Department of Chemical Engineering, Environmental Engineering Laboratory, University Campus, Thessaloniki 54124, Greece., Karakoltzidis A; Aristotle University of Thessaloniki, Department of Chemical Engineering, Environmental Engineering Laboratory, University Campus, Thessaloniki 54124, Greece., Karakitsios S; Aristotle University of Thessaloniki, Department of Chemical Engineering, Environmental Engineering Laboratory, University Campus, Thessaloniki 54124, Greece., Sarigiannis D; Aristotle University of Thessaloniki, Department of Chemical Engineering, Environmental Engineering Laboratory, University Campus, Thessaloniki 54124, Greece., Friis J; Department of Materials and Nanotechnology, SINTEF Industry, Trondheim N-7465, Norway.; European Materials Modelling Council, Brussels 1050, Belgium., Goldbeck G; European Materials Modelling Council, Brussels 1050, Belgium.; Goldbeck Consulting Limited, Cambridge CB4 0WS, UK., Winkler DA; La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.; Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia.; School of Pharmacy, University of Nottingham, Nottingham, UK., Peijnenburg W; Institute of Environmental Sciences (CML), Leiden University, Leiden 2300 RA, The Netherlands.; Centre for Safety of Substances and Products, National Institute of Public Health and the Environment (RIVM), Bilthoven 3720, The Netherlands., Serra A; FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Finland., Greco D; FHAIVE, Faculty of Medicine and Health Technology, Tampere University, Finland., Melagraki G; Division of Physical Sciences and Applications, Hellenic Military Academy, Vari 16672, Greece., Lynch I; Entelos Institute, Larnaca 6059, Cyprus.; School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK., Afantitis A; NovaMechanics MIKE, Piraeus 18545, Greece.; Entelos Institute, Larnaca 6059, Cyprus.; NovaMechanics Ltd, Nicosia 1070, Cyprus.
Jazyk:	angličtina
Zdroj:	Computational and structural biotechnology journal [Comput Struct Biotechnol J] 2024 Oct 18; Vol. 25, pp. 256-268. Date of Electronic Publication: 2024 Oct 18 (Print Publication: 2024).
DOI:	10.1016/j.csbj.2024.10.018
Abstrakt:	Modelling Data (MODA) reporting guidelines have been proposed for common terminology and for recording metadata for physics-based materials modelling and simulations in a CEN Workshop Agreement (CWA 17284:2018). Their purpose is similar to that of the Quantitative Structure-Activity Relationship (QSAR) model report form (QMRF) that aims to increase industry and regulatory confidence in QSAR models, but for a wider range of model types. Recently, the WorldFAIR project's nanomaterials case study suggested that both QMRF and MODA templates are an important means to enhance compliance of nanoinformatics models, and their underpinning datasets, with the FAIR principles (Findable, Accessible, Interoperable, Reusable). Despite the advances in computational modelling of materials properties and phenomena, regulatory uptake of predictive models has been slow. This is, in part, due to concerns about lack of validation of complex models and lack of documentation of scientific simulations. The models are often complex, output can be hardware- and software-dependent, and there is a lack of shared standards. Despite advocating for standardised and transparent documentation of simulation protocols through its templates, the MODA guidelines are rarely used in practice by modellers because of a lack of tools for automating their creation, sharing, and storage. They also suffer from a paucity of user guidance on their use to document different types of models and systems. Such tools exist for the more well-established QMRF and have aided widespread implementation of QMRFs. To address this gap, a simplified procedure and online tool, Easy-MODA, has been developed to guide users through MODA creation for physics-based and data-based models, and their various combinations. Easy-MODA is available as a web-tool on the Enalos Cloud Platform (https://www.enaloscloud.novamechanics.com/insight/moda/). The tool streamlines the creation of detailed MODA documentation, even for complex multi-model workflows, and facilitates the registration of MODA workflows and documentation in a database, thereby increasing their Findability and thus Re-usability. This enhances communication, interoperability, and reproducibility in multiscale materials modelling and improves trust in the models through improved documentation. The use of the Easy-MODA tool is exemplified by a case study for nanotoxicity evaluation, involving interlinked models and data transformation, to demonstrate the effectiveness of the tool in integrating complex computational methodologies and its significant role in improving the FAIRness of scientific simulations. Competing Interests: PDK, NS, DZ, DDV, DM, AT, AA are affiliated with NovaMechanics, a cheminformatics and materials informatics company. (© 2024 The Authors.)
Databáze:	MEDLINE
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