BioContainers: an Open-source and Community-driven Framework for Software Standardization

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2017 Apr 6

PMID 28379341

Citations 220

Authors

Felipe da Veiga Leprevost

Bjorn A Gruning

Saulo Alves Aflitos

Hannes L Rost

Julian Uszkoreit

Harald Barsnes

Marc Vaudel

Pablo Moreno

Laurent Gatto

Jonas Weber

Mingze Bai

Rafael C Jimenez

Timo Sachsenberg

Julianus Pfeuffer

Roberto Vera Alvarez

Johannes Griss

Alexey I Nesvizhskii

Yasset Perez-Riverol

Affiliations

Soon will be listed here.

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.

Citing Articles

The genome sequence of the Coppice Mining Bee, (Linnaeus, 1758).

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The genome sequence of the Dotted Footman moth, (Hufnagel, 1767).

Fletcher C, Lees D Wellcome Open Res. 2025; 10:106.

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The genome sequence of the Alder Moth, (Linnaeus, 1767).

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The genome sequence of the Marsh Click-beetle, (Müller, O.F., 1764).

Sivell O, Mitchell R, Geiser M Wellcome Open Res. 2025; 10:81.

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The genome sequence of a pallopterid fly, (Harris, 1780).

Barclay M, Broad G, Sivell O Wellcome Open Res. 2025; 10:55.

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References

Rost H, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F . OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods. 2016; 13(9):741-8. DOI: 10.1038/nmeth.3959. View

Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S . The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res. 2013; 41(Web Server issue):W557-61. PMC: 3692062. DOI: 10.1093/nar/gkt328. View

Perez-Riverol Y, Wang R, Hermjakob H, Muller M, Vesada V, Vizcaino J . Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochim Biophys Acta. 2013; 1844(1 Pt A):63-76. PMC: 3898926. DOI: 10.1016/j.bbapap.2013.02.032. View

Belmann P, Droge J, Bremges A, McHardy A, Sczyrba A, Barton M . Bioboxes: standardised containers for interchangeable bioinformatics software. Gigascience. 2015; 4:47. PMC: 4607242. DOI: 10.1186/s13742-015-0087-0. View

Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, cech M . The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016; 44(W1):W3-W10. PMC: 4987906. DOI: 10.1093/nar/gkw343. View