Dataset Information

Towards Molecular Simulations that are Transparent, Reproducible, Usable By Others, and Extensible (TRUE).

ABSTRACT: Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a "bespoke" fashion, resulting in many published soft matter simulations not being reproducible based on the information provided in the publications. To address the issue of reproducibility and to provide tools for computational screening, we have been developing the open-source Molecular Simulation and Design Framework (MoSDeF) software suite. In this paper, we propose a set of principles to create Transparent, Reproducible, Usable by others, and Extensible (TRUE) molecular simulations. MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in molecular simulation, thus enhancing their reproducibility. We provide several examples of TRUE molecular simulations: All of the steps involved in creating, running and extracting properties from the simulations are distributed on open-source platforms (within MoSDeF and on GitHub), thus meeting the definition of TRUE simulations.

SUBMITTER: Thompson MW

PROVIDER: S-EPMC7576934 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Towards Molecular Simulations that are Transparent, Reproducible, Usable By Others, and Extensible (TRUE).

Thompson Matthew W MW Gilmer Justin B JB Matsumoto Ray A RA Quach Co D CD Shamaprasad Parashara P Yang Alexander H AH Iacovella Christopher R CR Cabe Clare M CM Cummings Peter T PT

Molecular physics 20200408 9-10

Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in ...[more]

PMID: 33100401

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Project description:BackgroundThe use of e-health can lead to several positive outcomes. However, the potential for e-health to improve healthcare is partially dependent on its ease of use. In order to determine the usability for any technology, rigorously developed and appropriate measures must be chosen.ObjectivesTo identify psychometrically tested questionnaires that measure usability of e-health tools, and to appraise their generalizability, attributes coverage, and quality.MethodsWe conducted a systematic review of studies that measured usability of e-health tools using four databases (Scopus, PubMed, CINAHL, and HAPI). Non-primary research, studies that did not report measures, studies with children or people with cognitive limitations, and studies about assistive devices or medical equipment were systematically excluded. Two authors independently extracted information including: questionnaire name, number of questions, scoring method, item generation, and psychometrics using a data extraction tool with pre-established categories and a quality appraisal scoring table.ResultsUsing a broad search strategy, 5,558 potentially relevant papers were identified. After removing duplicates and applying exclusion criteria, 35 articles remained that used 15 unique questionnaires. From the 15 questionnaires, only 5 were general enough to be used across studies. Usability attributes covered by the questionnaires were: learnability (15), efficiency (12), and satisfaction (11). Memorability (1) was the least covered attribute. Quality appraisal showed that face/content (14) and construct (7) validity were the most frequent types of validity assessed. All questionnaires reported reliability measurement. Some questionnaires scored low in the quality appraisal for the following reasons: limited validity testing (7), small sample size (3), no reporting of user centeredness (9) or feasibility estimates of time, effort, and expense (7).ConclusionsExisting questionnaires provide a foundation for research on e-health usability. However, future research is needed to broaden the coverage of the usability attributes and psychometric properties of the available questionnaires.

Dataset Information

Towards Molecular Simulations that are Transparent, Reproducible, Usable By Others, and Extensible (TRUE).

Publications

Towards Molecular Simulations that are Transparent, Reproducible, Usable By Others, and Extensible (TRUE).

Similar Datasets

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