Managing and Documenting Legacy Scientific Workflows

J Integr Bioinform. 2015 Oct 6;12(3):277. doi: 10.2390/biecoll-jib-2015-277.


Scientific legacy workflows are often developed over many years, poorly documented and implemented with scripting languages. In the context of our cross-disciplinary projects we face the problem of maintaining such scientific workflows. This paper presents the Workflow Instrumentation for Structure Extraction (WISE) method used to process several ad-hoc legacy workflows written in Python and automatically produce their workflow structural skeleton. Unlike many existing methods, WISE does not assume input workflows to be preprocessed in a known workflow formalism. It is also able to identify and analyze calls to external tools. We present the method and report its results on several scientific workflows.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Data Mining / methods*
  • Electronic Data Processing / methods*
  • Programming Languages*