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Bioinformatics pipeline using JUDI: Just Do It!

Soumitra Pal1, Teresa M Przytycka1

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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Summary
This summary is machine-generated.

JUDI simplifies bioinformatics pipelines by managing software parameters using a database approach. This reduces scripting needs and enhances research reproducibility and exploration of new parameter settings.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Software Engineering

Background:

  • Large-scale bioinformatics data analysis relies on complex software pipelines.
  • Existing workflow management systems (WMS) require extensive scripting for parameter adjustments.
  • Efficient execution and parameter management are crucial for reproducibility and exploration.

Purpose of the Study:

  • To develop a novel system, JUDI, for systematic handling of parameter settings in bioinformatics pipelines.
  • To simplify the plug-and-play of pipeline stages through a modular approach.
  • To reduce scripting effort and improve research reproducibility and parameter exploration.

Main Methods:

  • Developed JUDI, a system built on the Python-based workflow management system DoIt.
  • Implemented a modular approach encapsulating parameter databases within each task and associated files.
  • Leveraged principles from database management systems for parameter handling.

Main Results:

  • JUDI significantly reduces scripting requirements for parameter management, by a factor of O(n) for n parameters.
  • The system simplifies the integration and modification of pipeline stages.
  • Facilitates reproducible research by managing specific parameter values.

Conclusions:

  • JUDI offers a streamlined approach to managing parameters in bioinformatics pipelines.
  • The system enhances the ability to reproduce research and explore novel parameter settings.
  • JUDI represents a significant improvement in workflow management for complex data analysis.