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Reproducible Bioconductor Workflows Using Browser-based Interactive Notebooks and Containers

Reem Almugbel, Ling-Hong Hung, Jiaming Hu, Abeer Almutairy, Nicole Ortogero, Yashaswi Tamta, Ka Yee Yeung
doi: https://doi.org/10.1101/144816
Reem Almugbel
1Institute of Technology, University of Washington, Tacoma, WA, USA
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Ling-Hong Hung
1Institute of Technology, University of Washington, Tacoma, WA, USA
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Jiaming Hu
1Institute of Technology, University of Washington, Tacoma, WA, USA
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Abeer Almutairy
1Institute of Technology, University of Washington, Tacoma, WA, USA
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Nicole Ortogero
2Department of Clinical Investigation, Madigan Army Medical Center, Tacoma, WA, USA
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Yashaswi Tamta
1Institute of Technology, University of Washington, Tacoma, WA, USA
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Ka Yee Yeung
1Institute of Technology, University of Washington, Tacoma, WA, USA
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  • For correspondence: kayee@uw.edu
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ABSTRACT

Objective 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, to allow users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server.

Materials and methods We present three different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets and process RNA-seq 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 for installation of any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder.

Results BiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a wide range of bioinformatics analyses. The use of software containers to mirror the original software environment ensures reproducibility of results. Parameters and code can be dynamically modified, allowing for robust verification of published results and encouraging rapid adoption of new methods.

Conclusion Given the increasing complexity of bioinformatics workflows, we anticipate that these interactive software notebooks will become as ubiquitous and necessary for documenting software methods as traditional laboratory notebooks have been for documenting bench protocols.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 01, 2017.
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Reproducible Bioconductor Workflows Using Browser-based Interactive Notebooks and Containers
Reem Almugbel, Ling-Hong Hung, Jiaming Hu, Abeer Almutairy, Nicole Ortogero, Yashaswi Tamta, Ka Yee Yeung
bioRxiv 144816; doi: https://doi.org/10.1101/144816
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Reproducible Bioconductor Workflows Using Browser-based Interactive Notebooks and Containers
Reem Almugbel, Ling-Hong Hung, Jiaming Hu, Abeer Almutairy, Nicole Ortogero, Yashaswi Tamta, Ka Yee Yeung
bioRxiv 144816; doi: https://doi.org/10.1101/144816

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