Recommendations for the packaging and containerizing of bioinformatics software: [version 2; peer review: 2 approved, 1 approved with reservations]

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

  • Bjorn Gruening, University of Freiburg
  • ,
  • Olivier Sallou, Universite de Rennes 1
  • ,
  • Pablo Moreno, European Bioinformatics Institute
  • ,
  • Felipe da Veiga Leprevost, University of Michigan, Ann Arbor, Michigan.
  • ,
  • Hervé Ménager, Institut Pasteur Paris
  • ,
  • Dan Søndergaard
  • Hannes Röst, University of Toronto
  • ,
  • Timo Sachsenberg, University of Tübingen
  • ,
  • Brian O'connor, University of California, Santa Cruz
  • ,
  • Fábio Madeira, European Bioinformatics Institute
  • ,
  • Victoria Dominguez Del Angel, Universite Paris-Saclay
  • ,
  • Michael R. Crusoe, Michigan State University
  • ,
  • Susheel Varma, European Bioinformatics Institute
  • ,
  • Daniel Blankenberg, The Cleveland Clinic Foundation
  • ,
  • Rafael C. Jimenez, ELIXIR Hub
  • ,
  • BioContainers Community
  • ,
  • Yasset Perez-Riverol, European Bioinformatics Institute

Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. However, containers and software packages should be produced under certain rules and standards in order to be reusable, compatible and easy to integrate into pipelines and analysis workflows. Here, we presented a set of recommendations developed by the BioContainers Community to produce standardized bioinformatics packages and containers. These recommendations provide practical guidelines to make bioinformatics software more discoverable, reusable and transparent. They are aimed to guide developers, organisations, journals and funders to increase the quality and sustainability of research software.

Original languageEnglish
Article number742
JournalF1000Research
Volume7
Number of pages16
ISSN2046-1402
DOIs
Publication statusPublished - 2019

    Research areas

  • Best practices bioinformatics, Containers and packages, Reproducibility

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