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Related Experiment Video

Updated: Jan 19, 2026

A Workflow for the Quantitative Assessment of the Endophytic and Epiphytic Bacterial Microbiomes of the Bark of Populus trichocarpa
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Building Containerized Workflows Using the BioDepot-Workflow-Builder.

Ling-Hong Hung1, Jiaming Hu1, Trevor Meiss1

  • 1School of Engineering and Technology, University of Washington, Tacoma, WA 98402, USA.

Cell Systems
|September 16, 2019
PubMed
Summary
This summary is machine-generated.

The BioDepot-workflow-builder (Bwb) enables reproducible bioinformatics workflows via a drag-and-drop interface. This tool simplifies creating and sharing complex computational pipelines for diverse platforms.

Keywords:
DockerRNA sequencingbioinformatics workflowsreproducibility of researchsoftware development

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Area of Science:

  • Computational Biology
  • Bioinformatics Software Development

Background:

  • Developing reproducible bioinformatics workflows is crucial for scientific validity.
  • Existing tools may lack user-friendly interfaces or cross-platform compatibility.

Purpose of the Study:

  • To introduce the BioDepot-workflow-builder (Bwb), a novel software tool for creating and executing reproducible bioinformatics workflows.
  • To provide a user-friendly, graphical interface for building and deploying complex computational pipelines.

Main Methods:

  • Utilized a drag-and-drop graphical interface where widgets represent Docker containers for modular tasks.
  • Implemented form-based interfaces within widgets for parameter entry and result display.
  • Enabled workflow customization, sharing via native format, and export as shell scripts.

Main Results:

  • Successfully developed the BioDepot-workflow-builder (Bwb) software.
  • Demonstrated the creation and execution of reproducible bioinformatics workflows.
  • Facilitated deployment across local and cloud platforms.

Conclusions:

  • Bwb offers an intuitive and efficient solution for building reproducible bioinformatics workflows.
  • The tool enhances usability and accessibility for researchers in computational biology.
  • Bwb supports seamless workflow sharing and deployment across various computational environments.