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Journal articles
Recommendations for the packaging and containerizing of bioinformatics software
Bjorn Gruening
1
Olivier Sallou
2
Pablo Moreno
3
Felipe da Veiga Leprevost
4
Hervé Ménager
5
Dan Søndergaard
6
Hannes Röst
7
Timo Sachsenberg
8
Brian O'Connor
9
Fábio Madeira
3
Victoria Dominguez del Angel
10, 11
Michael Crusoe
12
Susheel Varma
3
Daniel Blankenberg
13
Rafael Jimenez
14
Yasset Perez-Riverol
3, *
Biocontainers Community
*
Corresponding author
Bjorn Gruening 1
Author
Olivier Sallou 2
Author IdHAL : osallou
Pablo Moreno 3
Author
Felipe da Veiga Leprevost 4
Author
Hervé Ménager 5
Author IdHAL : herve-menager ORCID : https://orcid.org/0000-0002-7552-1009
Dan Søndergaard 6
Author
Hannes Röst 7
Author
Timo Sachsenberg 8
Author
Brian O'Connor 9
Author
Fábio Madeira 3
Author
Victoria Dominguez del Angel 10, 11
Author
Michael Crusoe 12
Author
Susheel Varma 3
Author
Daniel Blankenberg 13
Author
Rafael Jimenez 14
Author
Yasset Perez-Riverol 3
Correspondent author
Biocontainers Community
Author
1
Department of Computer Science [Freiburg] (Georges-Kohler-Allee 79, 79108 Freiburg, Germany - Germany)
- University of Freiburg [Freiburg] (Friedrichstr. 39 79098 Freiburg - Germany)
2
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires (Avenue du général Leclerc
Campus de Beaulieu
35042 RENNES CEDEX - France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- INSA Rennes - Institut National des Sciences Appliquées - Rennes (20, avenue des Buttes de Coësmes - CS 70839 - 35708 Rennes cedex 7 - France)
- UBS - Université de Bretagne Sud (BP 92116 - 56321 Lorient cedex - France)
- ENS Rennes - École normale supérieure - Rennes (Campus de Ker Lann - avenue Robert Schuman - 35170 Bruz - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- CentraleSupélec (3, rue Joliot Curie, Plateau de Moulon, 91192 GIF-SUR-YVETTE Cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR6074 (France)
- IMT Atlantique - IMT Atlantique Bretagne-Pays de la Loire (Campus Brest : Technopôle Brest-Iroise CS 8381829238 BREST Cedex 3 -
Campus Nantes : 4, rue Alfred Kastler- La chantrerie 44300 NANTES -
Campus Rennes : 2 Rue de la Châtaigneraie, 35510 CESSON SEVIGNE - France)
- IMT - Institut Mines-Télécom [Paris] (37-39 Rue Dareau, 75014 Paris - France)
3
EMBL-EBI - European Bioinformatics Institute [Hinxton] (EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK - United Kingdom)
- EMBL Heidelberg (Meyerhofstraße 1 69117 Heidelberg - Germany)
4
Department of Pathology [Ann Arbor, USA] (Medical Science Unit I, 1301 Catherine St, Ann Arbor, MI 48109, États-Unis - United States)
- University of Michigan [Ann Arbor] (500 Church Street Ann Arbor, MI 48109-1090 - United States)
- University of Michigan System (Michigan - United States)
5
Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB (Département de biologie computationnelle (ex C3BI), 25-28 rue du Docteur Roux, 75724 Paris cedex 15 - France)
- Institut Pasteur [Paris] (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
- CNRS - Centre National de la Recherche Scientifique : USR3756 (France)
6
Bioinformatics Research Centre (Denmark)
- Aarhus University [Aarhus] (Nordre Ringgade 1 DK-8000 Aarhus C - Denmark)
7
Donnelly Centre [Toronto, ON, Canada] (Canada)
- University of Toronto (27 King's College Circle, Toronto M5S 1A1 - Canada)
8
Wilhelm-Schickard-Institut für Informatik [Tübingen] (Eberhard Karls Universität Tübingen Geschwister-Scholl-Platz 72074 Tübingen - Germany)
- Eberhard Karls Universität Tübingen ( Geschwister-Scholl-Platz 72074 Tübingen - Germany)
9
Santa Cruz Genomics Institute (MS CBSE, University of California
1156 High Street, Santa Cruz, CA, 95064 - United States)
- UCSC - University of California [Santa Cruz] (1156 High Street, Santa Cruz, Ca 95064 - United States)
- University of California (United States)
10
Université Paris-Saclay (Espace Technologique, Bat. Discovery - RD 128 - 2e ét., 91190 Saint-Aubin - France)
11
IFB-CORE - Institut Français de Bioinformatique - UMS CNRS 3601 (Institut Français de Bioinformatique - UMS CNRS 3601
F- Gif-sur-Yvette - France)
- INRA - Institut National de la Recherche Agronomique : UMS1385 (France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- CEA - Commissariat à l'énergie atomique et aux énergies alternatives : DSV (Centre de Saclay Centre de Grenoble Centre de Cadarache etc - France)
- CNRS - Centre National de la Recherche Scientifique : UMS 3601 (France)
- INSERM - Institut National de la Santé et de la Recherche Médicale (101, rue de Tolbiac, 75013 Paris - France)
12
Department of Microbiology and Molecular Genetics (Michigan State University East Lansing Michigan 48824 - United States)
- Michigan State University [East Lansing] (220 Trowbridge Rd
East Lansing, MI 48824 - United States)
- Michigan State University System (Michigan - United States)
13
Genomic Medicine Institute [Cleveland] (Cleveland Clinic, Ohio - United States)
- Cleveland Clinic (9500 Euclid Avenue, Cleveland, Ohio 44195 - United States)
14
ELIXIR Hub [Cambridge] (Wellcome Trust Genome Campus, Hinxton,
Cambridge
CB10 1SD - United Kingdom)
Abstract : 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.
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Journal articles
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https://hal-pasteur.archives-ouvertes.fr/pasteur-02769991
Contributor : Hervé Ménager <>
Submitted on : Thursday, June 4, 2020 - 11:29:23 AM
Last modification on : Tuesday, September 7, 2021 - 3:36:27 PM
Long-term archiving on: : Thursday, December 3, 2020 - 12:35:26 PM
Contributor : Hervé Ménager <>
Submitted on : Thursday, June 4, 2020 - 11:29:23 AM
Last modification on : Tuesday, September 7, 2021 - 3:36:27 PM
Long-term archiving on: : Thursday, December 3, 2020 - 12:35:26 PM
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Recommendations for the packag...
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Distributed under a Creative Commons Attribution 4.0 International License
Identifiers
- HAL Id : pasteur-02769991, version 1
- DOI : 10.12688/f1000research.15140.2
- PUBMED : 31543945
- PUBMEDCENTRAL : PMC6738188
Collections
PASTEUR | UNIV-RENNES1 | CEA | INRIA | CEA-UPSAY | UNIV-RENNES | INSA-GROUPE | IRISA | CNRS | INRAE | CENTRALESUPELEC | INSERM | INSTITUT-TELECOM | UR1-UFR-ISTIC | INSA-RENNES | INRA
Citation
Bjorn Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, et al.. Recommendations for the packaging and containerizing of bioinformatics software. F1000Research, Faculty of 1000, 2018, 7, pp.742. ⟨10.12688/f1000research.15140.2⟩. ⟨pasteur-02769991⟩
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