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Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192.

BioContainers: an open-source and community-driven framework for software standardization.

Author information

1
Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
2
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany.
3
Albert-Ludwigs-University, Department of Computer Science, Bioinformatics Group, Freiburg, Baden-Württemberg, 79110 Freiburg, Freiburg.
4
Wageningen Plant Research, Cluster Bioinformatics, Wageningen, 6700 AD, Gelderland, Netherlands.
5
Department of Genetics, Stanford University, USA.
6
Medizinisches Proteom-Center, Ruhr-University Bochum, Germany, 44801.
7
Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Bergen, Norway.
8
Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Bergen, Norway.
9
KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway.
10
(I) KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway, 5020; (II) Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway, 5020.
11
EMBL Outstation, European Bioinformatics Institute, Proteomics Services, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
12
Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
13
Universität Tübingen, Wilhelm Schickard Institut für Informatik, Applied Bioinformatics Group,D-72076 Tübingen, Germany.
14
Eberhard-Karls-Universität Tübingen, Department of Computer Science, Applied bioinformatics, 72076 Tübingen.
15
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
16
Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria.
17
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

Abstract

Motivation:

BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. BioContainers is based on popular open-source projects Docker and rkt frameworks, that allow software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics technologies. These containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (local desktop, cloud environments or HPC clusters).

Availability and Implementation:

The software is freely available at github.com/BioContainers/.

Contact:

yperez@ebi.ac.uk.

PMID:
28379341
PMCID:
PMC5870671
DOI:
10.1093/bioinformatics/btx192
[Indexed for MEDLINE]
Free PMC Article

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