The five pillars of computational reproducibility: bioinformatics and beyond

Abstract 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. Thes...

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Bibliographic Details
Published in:Briefings in bioinformatics Vol. 24; no. 6; pp. 1 - 13
Main Authors: Ziemann, Mark, Poulain, Pierre, Bora, Anusuiya
Format: Journal Article
Language:English
Published: England Oxford University Press 22.09.2023
Oxford Publishing Limited (England)
Oxford University Press (OUP)
Subjects:
Bioinformatics
Computational Biology
Computer applications
Computer Science
Information Dissemination
Reproducibility
Reproducibility of Results
Review
Software
Version control
research best practices
reproducibility
bioinformatics
computational research
ISSN:1467-5463, 1477-4054, 1477-4054
Online Access:Get full text
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Summary:Abstract 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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ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbad375