BioContainers specifications


Unique identifier OMICS_17539
Name BioContainers
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Python, Shell (Bash), Other
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Yasset Perez-Riverol <>

Publication for BioContainers

BioContainers in publications

PMCID: 5747335
PMID: 29333231
DOI: 10.5256/f1000research.14069.r28566

[…] references to tools, for example future work will make use of these identifiers to improve the generation of tool descriptions. for instance, linking of the bioconda and biocontainers repositories to will enable tooldog to generate software requirements compatible with workbench platforms ., during the last years, integration of various tools has been eased […]

PMCID: 3634740
PMID: 23637980
DOI: 10.1371/journal.pone.0062130

[…] culture plates (2 of 60 mm and 4 of 30 mm on each side; ) were placed into one biocontainer and sealed. bc#1 contained 3 days old, bc#2 1 day old and bc#3, 5 days old colonies. each of the three biocontainers was equipped with a small programmable miniature-sized temperature data logger (smartbutton from acr systems inc.) as well as passive radiation data loggers (sck cen) to monitor […]

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BioContainers institution(s)
EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Germany; Center for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University Freiburg, Germany; Applied Bioinformatics, Wageningen University, Wageningen, Netherlands; Department of Genetics, Stanford University, USA; Medizinisches Proteom-Center, Ruhr-Universität Bochum, Germany; Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Norway; Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Norway; KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway; Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK; Center for Bioinformatics, University of Tübingen, Germany; Algorithmic Bioinformatics group, Freie Universität Berlin, Germany; Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; Division of Immunology, Allergy and Infectious Diseases, Department of Dermatology, Medical University of Vienna, Austria
BioContainers funding source(s)
This work was supported by NIH grant numbers R01-GM-094231 and U24-CA0-210967, the Swiss National Science Foundation (SNSF grant P2EZP3 162268) and EMBO (ALTF 854-2015) the Bergen Research Foundation and the Research Council of Norway, BMBF (grant nos. FKZ 031 A 535A and FKZ 031 A 534A), US NIH BD2K grant [U54 GM114833], the BBSRC Strategic Longer and Larger grant (Award BB/L002817/1), EC Horizon 2020 grant agreement 654241.

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