Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool

Patel, Bhavesh; Soundarajan, Sanjay; Ménager, Hervé; Hu, Zicheng

doi:10.1038/s41597-023-02463-x

Cited by 7 publications

(2 citation statements)

References 79 publications

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“…It may also include a link to the research article, citation instructions and a mention of the software license. A recently described set of recommendations for documenting software describes further measures that data analysts could use to enhance their code documentation [ 136 ].…”

Section: Recommendationsmentioning

confidence: 99%

The five pillars of computational reproducibility: bioinformatics and beyond

Ziemann,

Poulain,

Bora

2023

Briefings in Bioinformatics

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Computational reproducibility is a simple premise in theory, but is difficult to achieve in practice. Building upon past efforts and proposals to maximize reproducibility and rigor in bioinformatics, we present a framework called the five pillars of reproducible computational research. These include (1) literate programming, (2) code version control and sharing, (3) compute environment control, (4) persistent data sharing and (5) documentation. These practices will ensure that computational research work can be reproduced quickly and easily, long into the future. This guide is designed for bioinformatics data analysts and bioinformaticians in training, but should be relevant to other domains of study.

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Section: Recommendationsmentioning

confidence: 99%

The five pillars of computational reproducibility: bioinformatics and beyond

Ziemann,

Poulain,

Bora

2023

Briefings in Bioinformatics

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show abstract

Section: Documentationmentioning

confidence: 99%

The five pillars of computational reproducibility: Bioinformatics and beyond

Ziemann,

Poulain,

Bora

2023

Preprint

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Computational reproducibility is a simple premise in theory, but is difficult to achieve in practice. Building upon past efforts and proposals to maximize reproducibility and rigor in bioinformatics, we present a framework called the five pillars of reproducible computational research. These include (1) code version control and sharing, (2) compute environment control, (3) literate programming, (4) documentation and (5) FAIR data sharing. These best practices will ensure that computational research work can be reproduced quickly and easily, long into the future. This guide is designed for bioinformatic data analysts, but should be relevant for other domains.

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SODA: Software to Support the Curation and Sharing of FAIR Autonomic Nervous System Data

Marroquin,

Clark,

Portillo

et al. 2023

Preprint

Self Cite

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Since 2014, the National Institute of Health (NIH)'s Stimulating Peripheral Activity to Relieve Conditions (SPARC) Program has been supporting research and development of therapeutic devices that modulate electrical activity in the autonomic nervous system (ANS) to improve organ function, also known as bioelectronic medicine. To optimize the reusability of data resulting from ANS-related research, the SPARC Program also supported the development of guidelines for curating and sharing data in line with the FAIR (Findable, Accessible, Interoperable, Reusable) Principles. These guidelines are exhaustive to maximize FAIRness of data but as a result, they are difficult and time-consuming for researchers to implement. To address these challenges, we developed SODA (Software to Organize Data Automatically), an open source and free cross-platform desktop software that guides researchers step-by-step in preparing and sharing their ANS-related data according to the SPARC guidelines. SODA combines intuitive user interfaces with automation to streamline the process and reduce researchers' time, effort, and error in making their data FAIR. We provide in this paper an overview of SODA and results of testing its performance. We also provide an overview of the impact of SODA which is, to our knowledge, the first researcher-oriented tool for making data FAIR.

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Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool

Cited by 7 publications

References 79 publications

The five pillars of computational reproducibility: bioinformatics and beyond

The five pillars of computational reproducibility: bioinformatics and beyond

The five pillars of computational reproducibility: Bioinformatics and beyond

SODA: Software to Support the Curation and Sharing of FAIR Autonomic Nervous System Data

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