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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan

4 Issues per year


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 12, Issue 3

Issues

Managing and Documenting Legacy Scientific Workflows

Ruben Acuña
  • Scientific Data Management Laboratory, Arizona State University, Tempe, AZ 85287, http://bioinformatics.engineering.asu.edu/, United States of America
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Jacques Chomilier
  • Institut de Minéralogie, de Physique des Milieux Condensés et de Cosmochimie (IMPMC), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Muséum National d’Histoire Naturelle (MNHN), Université Pierre et Marie Curie, Sorbonne Universités, 4 Place Jussieu, Paris, France
  • Ressource Parisienne de Bioinformatique Structurale (RPBS), Université Paris Diderot, 35 Rue Hélène Brion, Paris, France
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Zoé Lacroix
  • Corresponding author
  • Scientific Data Management Laboratory, Arizona State University, Tempe, AZ 85287, http://bioinformatics.engineering.asu.edu/ France
  • Institut de Minéralogie, de Physique des Milieux Condensés et de Cosmochimie (IMPMC), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Muséum National d’Histoire Naturelle (MNHN), Université Pierre et Marie Curie, Sorbonne Universités, 4 Place Jussieu, Paris, France
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  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2015-277

Summary

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.

About the article

Published Online: 2016-10-18

Published in Print: 2015-09-01


Citation Information: Journal of Integrative Bioinformatics, Volume 12, Issue 3, Pages 65–87, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2015-277.

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© 2015 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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