Reproducible Bioconductor workflows using browser-based interactive notebooks and containers

Journal of the American Medical Informatics Association : JAMIA
Reem AlmugbelKa Yee Yeung

Abstract

Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, that allows users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server. We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq data and KinomeScan data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified. This is accomplished using Binder, which runs the notebook inside software containers, thus avoiding the need to install any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder. BiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a ...Continue Reading

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Citations

Jul 3, 2019·Briefings in Bioinformatics·Charles VesteghemMartin Bøgsted
Apr 19, 2018·Journal of the American Medical Informatics Association : JAMIA·Enrico CoieraFarah Magrabi
Oct 28, 2018·BMC Bioinformatics·Neha KulkarniRaffaele A Calogero
Dec 12, 2019·BMC Bioinformatics·Benjamin Ulfenborg

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