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SciPipe - A workflow library for agile development of complex and dynamic bioinformatics pipelines

Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
doi: https://doi.org/10.1101/380808
Samuel Lampa
1Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
2Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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Martin Dahlö
1Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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Jonathan Alvarsson
1Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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Ola Spjuth
1Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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Abstract

Background The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines and assist with job automation and aids reproducibility of analyses. Many contemporary workflow tools are specialized and not designed for highly complex workflows, such as with nested loops, dynamic scheduling and parametrization, which is common in e.g. machine learning.

Findings SciPipe is a workflow programming library implemented in the programming language Go, for managing complex and dynamic pipelines in bioinformatics, cheminformatics and other fields. SciPipe helps in particular with workflow constructs common in machine learning, such as extensive branching, parameter sweeps and dynamic scheduling and parametrization of downstream tasks. SciPipe builds on Flow-based programming principles to support agile development of workflows based on a library of self-contained, re-usable components. It supports running subsets of workflows for improved iterative development, and provides a data-centric audit logging feature that saves a full audit trace for every output file of a workflow, which can be converted to other formats such as HTML, TeX and PDF on-demand. The utility of SciPipe is demonstrated with a machine learning pipeline, a genomics, and a transcriptomics pipeline.

Conclusions SciPipe provides a solution for agile development of complex and dynamic pipelines, especially in machine leaning, through a flexible programming API suitable for scientists used to programming or scripting.

  • List of abbreviations

    API
    Application programming interface
    CPU
    Central processing unit (the core part of every computer)
    DSL
    Domain-specific language
    FBP
    Flow-based programming
    HPC
    High-performance computing
    RAM
    Random access memory
    SVM
    Support vector machine
  • 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 4.0 International license.
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    Posted August 01, 2018.
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    SciPipe - A workflow library for agile development of complex and dynamic bioinformatics pipelines
    Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
    bioRxiv 380808; doi: https://doi.org/10.1101/380808
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    SciPipe - A workflow library for agile development of complex and dynamic bioinformatics pipelines
    Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
    bioRxiv 380808; doi: https://doi.org/10.1101/380808

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