Kolokathis Panagiotis D, Sidiropoulos Nikolaos K, Zouraris Dimitrios, Varsou Dimitra-Danai, Mintis Dimitris G, Tsoumanis Andreas, Dondero Francesco, Exner Thomas E, Sarimveis Haralambos, Chaideftou Evgenia, Paparella Martin, Nikiforou Fotini, Karakoltzidis Achilleas, Karakitsios Spyros, Sarigiannis Dimosthenis, Friis Jesper, Goldbeck Gerhard, Winkler David A, Peijnenburg Willie, Serra Angela, Greco Dario, Melagraki Georgia, Lynch Iseult, Afantitis Antreas
NovaMechanics MIKE, Piraeus 18545, Greece.
Entelos Institute, Larnaca 6059, Cyprus.
Comput Struct Biotechnol J. 2024 Oct 18;25:256-268. doi: 10.1016/j.csbj.2024.10.018. eCollection 2024 Dec.
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.
已在欧洲标准化委员会研讨会协议(CWA 17284:2018)中提出了建模数据(MODA)报告指南,用于通用术语以及记录基于物理的材料建模和模拟的元数据。其目的与定量构效关系(QSAR)模型报告表(QMRF)类似,后者旨在增强行业和监管机构对QSAR模型的信心,但适用于更广泛的模型类型。最近,世界公平信息资源项目(WorldFAIR)的纳米材料案例研究表明,QMRF和MODA模板都是提高纳米信息学模型及其基础数据集符合FAIR原则(可查找、可访问、可互操作、可重用)的重要手段。尽管材料特性和现象的计算建模取得了进展,但预测模型在监管方面的应用进展缓慢。部分原因在于对复杂模型缺乏验证以及科学模拟缺乏文档记录。这些模型通常很复杂,输出可能依赖于硬件和软件,并且缺乏共享标准。尽管通过其模板倡导对模拟协议进行标准化和透明的文档记录,但由于缺乏用于自动创建、共享和存储的工具,MODA指南在建模人员的实际操作中很少被使用。它们还缺乏关于如何使用以记录不同类型模型和系统的用户指导。对于更为成熟的QMRF存在这样的工具,并且这些工具有助于QMRF的广泛实施。为了弥补这一差距,已开发了一个简化程序和在线工具Easy-MODA,以指导用户为基于物理和基于数据的模型及其各种组合创建MODA。Easy-MODA作为一个网络工具可在Enalos云平台(https://www.enaloscloud.novamechanics.com/insight/moda/)上获取。该工具简化了详细MODA文档的创建,即使对于复杂的多模型工作流程也是如此,并促进了MODA工作流程和文档在数据库中的注册,从而提高了它们的可查找性,进而提高了可重用性。这增强了多尺度材料建模中的沟通、互操作性和可重复性,并通过改进文档记录提高了对模型的信任。通过一个涉及相互关联模型和数据转换的纳米毒性评估案例研究,举例说明了Easy-MODA工具的使用,以展示该工具在整合复杂计算方法方面的有效性及其在提高科学模拟的FAIR性方面的重要作用。