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

Felipe da Veiga Leprevost¹, Björn A Grüning^{2

3}, Saulo Alves Aflitos⁴, Hannes L Röst⁵, Julian Uszkoreit⁶, Harald Barsnes^{7

8}, Marc Vaudel^{9

10}, Pablo Moreno¹¹, Laurent Gatto¹², Jonas Weber², Mingze Bai¹¹, Rafael C Jimenez¹¹, Timo Sachsenberg¹³, Julianus Pfeuffer¹⁴, Roberto Vera Alvarez¹⁵, Johannes Griss^{11

16}, Alexey I Nesvizhskii^{1

17}, Yasset Perez-Riverol¹¹

Affiliations

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.

PMID: 28379341
PMCID: PMC5870671
DOI: 10.1093/bioinformatics/btx192

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

Felipe da Veiga Leprevost et al. Bioinformatics. 2017.

. 2017 Aug 15;33(16):2580-2582.

doi: 10.1093/bioinformatics/btx192.

Authors

Affiliations

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.

PMID: 28379341
PMCID: PMC5870671
DOI: 10.1093/bioinformatics/btx192

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.

PubMed Disclaimer

Figures

**Fig. 1**
Overview of the BioContainers architecture: Users and developers can use the BioContainers infrastructure by interacting via GitHub account page. All container Dockerfiles are freely available and people are encouraged to participate submitting pull requests or asking for new containerized software. Containers can be acquired via Docker command line interface, or by downloading the Dockerfile directly from the GitHub organization

See this image and copyright information in PMC

References

1. Afgan E. et al. (2016) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res., 44, W3–W10. - PMC - PubMed
1. Belmann P. et al. (2015) Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience, 4. - PMC - PubMed
1. Leprevost F. d V. et al. (2014) On best practices in the development of bioinformatics software. Bioinf. Comput. Biol., 5, 199. - PMC - PubMed
1. Moreews F. et al. (2015) BioShaDock: a community driven bioinformatics shared Docker-based tools registry. F1000Research, 4, 1443. - PMC - PubMed
1. Perez-Riverol Y. et al. (2014) Open source libraries and frameworks for mass spectrometry based proteomics: a developer’s perspective. Biochim. Biophys. Acta (BBA) Proteins Proteomics, 1844, 63–76. - PMC - PubMed

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

Affiliations

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

Authors

Affiliations

Abstract

Figures

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

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