Managing and Documenting Legacy Scientific Workflows

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doi doi:10.2390/biecoll-jib-2015-277
submission September 08, 2015
last revision September 09, 2015
published October 06, 2015

Ruben Acuña, Jacques Chomilier and Zoé Lacroix

Correspondence should be addressed to:
Zoé Lacroix
Arizona State University


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.


Ruben Acuña, Jacques Chomilier and Zoé Lacroix. Managing and Documenting Legacy Scientific Workflows. Journal of Integrative Bioinformatics, 12(3):277, 2015. Online Journal:
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