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Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

Cohen-Boulakia Sarah, Belhajjame Khalid, Collin Olivier, Chopard Jérôme, Froidevaux Christine, Gaignard Alban, Hinsen Konrad, Larmande Pierre, Le Bras Yvan, Lemoine Frédéric, Mareuil Fabien, Ménager Hervé, Pradal Christophe, Blanchet Christophe. 2017. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Computer Systems, 75 : pp. 284-298.

Journal article ; Article de synthèse ; Article de revue à facteur d'impact
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Quartile : Outlier, Sujet : COMPUTER SCIENCE, THEORY & METHODS

Abstract : With the development of new experimental technologies, biologists are faced with an avalanche of data to be computationally analyzed for scientific advancements and discoveries to emerge. Faced with the complexity of analysis pipelines, the large number of computational tools, and the enormous amount of data to manage, there is compelling evidence that many if not most scientific discoveries will not stand the test of time: increasing the reproducibility of computed results is of paramount importance. The objective we set out in this paper is to place scientific workflows in the context of reproducibility. To do so, we define several kinds of reproducibility that can be reached when scientific workflows are used to perform experiments. We characterize and define the criteria that need to be catered for by reproducibility-friendly scientific workflow systems, and use such criteria to place several representative and widely used workflow systems and companion tools within such a framework. We also discuss the remaining challenges posed by reproducible scientific workflows in the life sciences. Our study was guided by three use cases from the life science domain involving in silico experiments. (Résumé d'auteur)

Mots-clés libres : Reproducibility, Scientific workflows, Provenance, Packaging environments, OpenAlea, Galaxy

Classification Agris : C30 - Documentation and information
U30 - Research methods

Champ stratégique Cirad : Hors axes (2014-2018)

Auteurs et affiliations

  • Cohen-Boulakia Sarah, INRIA (FRA)
  • Belhajjame Khalid, Université Paris-Dauphine (FRA)
  • Collin Olivier, IRISA (FRA)
  • Chopard Jérôme, INRA (FRA)
  • Froidevaux Christine, Université Paris-Sud (FRA)
  • Gaignard Alban, CHU de Nantes (FRA)
  • Hinsen Konrad, CNRS (FRA)
  • Larmande Pierre, IRD (FRA)
  • Le Bras Yvan, INRIA (FRA)
  • Lemoine Frédéric, Institut Pasteur (FRA)
  • Mareuil Fabien, Institut Pasteur (FRA)
  • Ménager Hervé, Institut Pasteur (FRA)
  • Pradal Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-2555-761X
  • Blanchet Christophe, CNRS (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/583255/)

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