BioContainers: an open-source and community-driven framework for software standardization
By F. Leprevost, Björn A. Grüning, S. Aflitos, Hannes L. Röst, J. Uszkoreit, Harald Barsnes, M. Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber and 8 more. Bioinform., 2017
759 citations recorded by the source corpus.
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/.
Subfields: Information Systems and Management, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/a7850f6e39ae3881260cc1214f56b7d394f17ee1
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In Information Systems and Management
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In Molecular Biology
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Citations in the corpus
- The PRIDE database and related tools and resources in 2019: improving support for quantification data (2018, methodology): “The main rationale is to make possible the use of that software in cloud infrastructures (using the EMBL-EBI cloud as the starting point), so that in the future the pipelines can be used by the community in the cloud using software container technologies (39,40).”
- Cooler: scalable storage for Hi-C data and other genomically-labeled arrays (2019, methodology): “For docker users, the command line interface is also available through BioContainers (27).”
- The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update (2018, background): “1101/207092) and the BioContainer (36) projects, Galaxy is able to provision and use reproducible tool execution environments ((37); https://doi.”