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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




No version available


  • person_outline Yasset Perez-Riverol

Publication for BioContainers

BioContainers citations


Using to generate and annotate workbench tool descriptions

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

[…] nt 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 . […]


Navigating freely available software tools for metabolomics analysis

PMCID: 5550549
PMID: 28890673
DOI: 10.1007/s11306-017-1242-7

[…] atible tools, the database could help users with this issue.Tool harmonisation is also being improved by efforts to containerise tools, such as those by the PhenoMeNal consortium (PhenoMeNal) and the BioContainers initiative (Leprevost et al. ). Creating containers for tools (or Dockerising (Docker)) isolates them and their dependencies in terms of installation, which removes incompatibility betwe […]


The Effect of Spaceflight on Growth of Ulocladium chartarum Colonies on the International Space Station

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

[…] nce on the morphology, the extended development of submerged mycelium, the enhancement of exudate drops formation, and the rate of growth. Thanks to the three different growth stages inside the three biocontainers, it could be shown that the longer the colony is grown in space conditions the bigger is the difference with the ground grown colony. As similar observations have been made on samples gr […]


Laccase‐catalysed oxidations of naturally occurring phenols: from in vivo biosynthetic pathways to green synthetic applications

PMCID: 3821676
PMID: 21791030
DOI: 10.1111/j.1751-7915.2011.00273.x

[…] larly useful in the food processing industries (the biopolymers can be used as stabilizing or thickening agents) and in medical applications (the polymers are useful for drug encapsulation or to form biocontainers for controlled release of active molecules).Chromophore formation by oxidative coupling of natural phenols is also of particular interest owing to the need for green processes in dye syn […]

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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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