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Reproducible Bioconductor workflows using browser-based interactive notebooks and containers.

Reem Almugbel1, Ling-Hong Hung1, Jiaming Hu1

  • 1Institute of Technology, University of Washington, Tacoma, WA, USA.

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Summary
This summary is machine-generated.

Interactive software notebooks simplify documenting complex bioinformatics workflows. BiocImageBuilder enables easy sharing and execution of reproducible bioinformatics research via interactive notebooks.

Keywords:
automatedbioconductor workflowscontainersdata sciencereproducibility

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Scientific Software Development

Background:

  • Bioinformatics publications often struggle to convey complex software workflows.
  • Reproducibility and distribution of bioinformatics research present significant challenges.

Purpose of the Study:

  • To introduce and demonstrate the utility of interactive software notebooks for documenting and distributing bioinformatics research.
  • To present BiocImageBuilder, a user-friendly tool for creating and sharing interactive bioinformatics protocols.

Main Methods:

  • Developed four interactive Jupyter notebooks using R and Bioconductor for diverse bioinformatics analyses (gene expression, cross-platform data, RNA-seq, KinomeScan).
  • Utilized Binder and software containers to ensure execution and reproducibility of notebooks without local software installation.
  • Created custom files with BiocImageBuilder to generate the interactive notebooks.

Main Results:

  • Demonstrated the dissemination of various bioinformatics analyses through interactive notebooks.
  • Confirmed that software containers ensure reproducible results by mirroring the original software environment.
  • Showcased BiocImageBuilder's point-and-click interface for simplifying workflow publication.

Conclusions:

  • Interactive notebooks offer a powerful method for documenting and distributing complex bioinformatics workflows.
  • The use of software containers guarantees reproducibility and facilitates verification of published bioinformatics results.
  • Interactive notebooks are poised to become essential tools in bioinformatics research, akin to laboratory notebooks.