Open Lab

notebooks

and

workflow systems

26 September 2014

PLOS

Workflow systems


  • The provenance of the research
    • how did the conclusions come about?
    • what iterations did the data go through?
  • System (local or cloud) to keep track of experiments
    • including protocols, documentation, analysis
  • Both high-level and code-based systems
  • Very popular in some fields, non-existent in others

Types

High-Level

  • most popular
  • express computations in higher-level components
  • each component performs a small, well-defined task
  • code is underlying, but written  by someone else
  • researcher connects pre-existing components


Command-Line

If there is no pre-existing component
or tool, the researcher can build his/ her own,
which requires writing the code to create it. Often used in tandem with other  programs that offer a GUI.

Outcome of use

  • Currently:
    • specific fields of study
  • Goal:
    • used across many fields & published
  • How does this fit into scholarly article?
  • Methods section
  • Shows the entire provenance of research
    • text, raw data, code, workflow system
  • replication would be possible
  • peer review of
    • data? code? experiments performed?

    Fields

    • Most documented in computer and information sciences
    • In specific fields, researchers can use already established workflows
      • Bioinformatics is popular
        • Energy Biosciences Institute (EBI)  
        • National Center for Biotechnology Information (NCBI)
          • provide resources in REST or WDSL formats
          • can easily be incorporated into workflow systems

    Galaxy

    Kepler Project

    taverna

    wings

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