Recommendations for the packaging and containerizing of bioinformatics software

Autor: Fábio Madeira, Dan Søndergaard, Victoria Dominguez Del Angel, Daniel Blankenberg, Susheel Varma, Hannes L. Röst, Yasset Perez-Riverol, BioContainers Community, Olivier Sallou, Hervé Ménager, Bjorn Gruening, Michael R. Crusoe, Rafael C. Jimenez, Brian O'Connor, Timo Sachsenberg, Felipe da Veiga Leprevost, Pablo Moreno
Přispěvatelé: Department of Computer Science [Freiburg], University of Freiburg [Freiburg], Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Department of Pathology [Ann Arbor, USA], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Bioinformatics Research Centre, Aarhus University [Aarhus], Donnelly Centre [Toronto, ON, Canada], University of Toronto, Wilhelm-Schickard-Institut für Informatik [Tübingen], Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Santa Cruz Genomics Institute, University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), Université Paris-Saclay, Institut Français de Bioinformatique - UMS CNRS 3601 (IFB-CORE), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Microbiology and Molecular Genetics, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Genomic Medicine Institute [Cleveland], Cleveland Clinic, ELIXIR Hub [Cambridge], This work was partially supported by ELIXIR-EXCELERATE. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement numbers 676559. The BioContainers workshop (Paris 2017) and the BioContainers community that developed these recommendations are supported by the ELIXIR Tools platform. FVL is supported by NIH grants R01GM94231 and U24CA210967., BioContainers Community, European Project: 676559,H2020,H2020-INFRADEV-1-2015-1,ELIXIR-EXCELERATE(2015), Ménager, Hervé, ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences. - ELIXIR-EXCELERATE - - H20202015-09-01 - 2019-08-31 - 676559 - VALID, Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of California [Santa Cruz] (UCSC), University of California-University of California, Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)
Rok vydání: 2018
Předmět:
0301 basic medicine
best practices bioinformatics
Computer science
media_common.quotation_subject
General Biochemistry
Genetics and Molecular Biology
Scientific software
Workflow
Set (abstract data type)
03 medical and health sciences
Software
0302 clinical medicine
Bioinformatics software
11. Sustainability
Humans
Quality (business)
General Pharmacology
Toxicology and Pharmaceutics
reproducibility
media_common
[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
General Immunology and Microbiology
containers and packages
business.industry
Computational Biology
Articles
General Medicine
Opinion Article
Research Personnel
030104 developmental biology
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Software engineering
business
030217 neurology & neurosurgery
Research software
Zdroj: F1000Research
F1000Research, 2018, 7, pp.742. ⟨10.12688/f1000research.15140.2⟩
F1000Research, Faculty of 1000, 2018, 7, pp.742. ⟨10.12688/f1000research.15140.2⟩
ISSN: 2046-1402
DOI: 10.12688/f1000research.15140.2⟩
Popis: International audience; 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.
Databáze: OpenAIRE
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