Evidence map›Paper›PMID 39555474›Full record

ArticleComputational and structural biotechnology journal2024

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

Panagiotis D Kolokathis, Nikolaos K Sidiropoulos, Dimitrios Zouraris, Dimitra-Danai Varsou, Dimitris G Mintis, Andreas Tsoumanis, Francesco Dondero, Thomas E Exner, Haralambos Sarimveis, Evgenia Chaideftou and 14 more

Abstract read
In one paragraph

Article in Computational and structural biotechnology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
  2. Article
  3. Journal of chemical information and modeling · 2025
    Article
  4. Article
  5. CompSafeNano project: NanoInformatics approaches for safe-by-design nanomaterials.Computational and structural biotechnology journal · 2025
    Article
  6. Article
  7. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

24 authors.

Panagiotis D KolokathisNovaMechanics MIKE, Piraeus 18545, Greece.
Nikolaos K SidiropoulosNovaMechanics MIKE, Piraeus 18545, Greece.
Dimitrios ZourarisEntelos Institute, Larnaca 6059, Cyprus.
Dimitra-Danai VarsouNovaMechanics MIKE, Piraeus 18545, Greece.
Dimitris G MintisEntelos Institute, Larnaca 6059, Cyprus.
Andreas TsoumanisNovaMechanics MIKE, Piraeus 18545, Greece.
Francesco DonderoEntelos Institute, Larnaca 6059, Cyprus.
Thomas E ExnerSevenPastNine GmbH, Rebacker 68, 79650 Schopfheim, Germany.
Haralambos SarimveisSchool of Chemical Engineering, National Technical University of Athens, 15780 Zografou, Greece.
Evgenia ChaideftouDepartment of Medical Biochemistry, Medical University of Innsbruck, Innsbruck, Austria.
Martin PaparellaDepartment of Medical Biochemistry, Medical University of Innsbruck, Innsbruck, Austria.
Fotini NikiforouAristotle University of Thessaloniki, Department of Chemical Engineering, Environmental Engineering Laboratory, University Campus, Thessaloniki 54124, Greece.
Achilleas KarakoltzidisAristotle University of Thessaloniki, Department of Chemical Engineering, Environmental Engineering Laboratory, University Campus, Thessaloniki 54124, Greece.
Spyros KarakitsiosAristotle University of Thessaloniki, Department of Chemical Engineering, Environmental Engineering Laboratory, University Campus, Thessaloniki 54124, Greece.
Dimosthenis SarigiannisAristotle University of Thessaloniki, Department of Chemical Engineering, Environmental Engineering Laboratory, University Campus, Thessaloniki 54124, Greece.
Jesper FriisDepartment of Materials and Nanotechnology, SINTEF Industry, Trondheim N-7465, Norway.
Gerhard GoldbeckEuropean Materials Modelling Council, Brussels 1050, Belgium.
David A WinklerLa Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.
Willie PeijnenburgInstitute of Environmental Sciences (CML), Leiden University, Leiden 2300 RA, The Netherlands.
Angela SerraFHAIVE, Faculty of Medicine and Health Technology, Tampere University, Finland.
Dario GrecoFHAIVE, Faculty of Medicine and Health Technology, Tampere University, Finland.
Georgia MelagrakiDivision of Physical Sciences and Applications, Hellenic Military Academy, Vari 16672, Greece.
Iseult LynchEntelos Institute, Larnaca 6059, Cyprus.
Antreas AfantitisNovaMechanics MIKE, Piraeus 18545, Greece.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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.

Indexed as

CEN Workshop Agreement (CWA 17284:2018)Easy-MODAMODAQMRFScientific simulation workflows

Identifiers

PMID39555474
PMCPMC11566491

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.