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A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease
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BioShake: a Haskell EDSL for bioinformatics workflows.

Justin Bedő1,2

  • 1Bioinformatics Division, The Walter and Eliza Hall Institute, Parkville, VIC, Australia.

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BioShake is a Haskell-based workflow system for bioinformatics that enhances reproducible research. It statically checks workflows during compilation, minimizing errors before execution and supporting cluster job submission.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Software Engineering

Background:

  • Bioinformatics analyses often involve complex, long-running computational workflows.
  • Ensuring reproducibility and minimizing errors in these workflows is crucial for scientific research.
  • Existing workflow frameworks may not adequately address static error detection.

Purpose of the Study:

  • To introduce BioShake, a novel domain-specific language for specifying and executing bioinformatics workflows.
  • To enhance the robustness and reproducibility of computational workflows in bioinformatics.
  • To leverage type-level properties for static error checking.

Main Methods:

  • BioShake is implemented as an embedded domain-specific language in Haskell.
  • It utilizes the Shake build tool for dependency tracking, parallel execution, and reporting.
  • Workflow correctness is statically verified at compile time by raising properties to the type level.
  • Execution is abstracted to allow direct execution or submission to compute clusters.

Main Results:

  • BioShake significantly reduces the occurrence of errors by enabling static verification.
  • It catches workflow errors during compilation, preventing lengthy execution of incorrect pipelines.
  • The system provides robust dependency tracking, parallel execution, and resumption capabilities.
  • BioShake offers flexible job execution, supporting both direct execution and cluster submission.

Conclusions:

  • BioShake provides a powerful and safe approach to managing and executing bioinformatics workflows.
  • Its type-level static checking enhances reproducibility and minimizes errors in computational biology.
  • The framework offers a robust, efficient, and flexible solution for modern bioinformatics research.