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Bioboxes specifications


Unique identifier OMICS_25951
Name Bioboxes
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Michael Barton

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Publication for Bioboxes

Bioboxes citations


The Dockstore: enabling modular, community focused sharing of Docker based genomics tools and workflows

PMCID: 5333608
PMID: 28344774
DOI: 10.5256/f1000research.10919.r19471

[…] standard, allowing the creation of a tool sharing network of registries. Multiple sites that have different models of how Docker-based tools should be built, shared, and secured, such as BioShaDock, Bioboxes, and BioDocker ( can flourish independently, but benefit from supporting the emerging GA4GH API standard. Such a network stands a good chance of gaining the critical mas […]


Free living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge

PMCID: 3633350
PMID: 23401293
DOI: 10.1002/mbo3.70

[…] were collected from their respective habitats within a distance of 10 m using the remotely-operated vehicle (ROV) remotely operated platform for ocean sciences (ROPOS) and placed in separate, closing bioboxes. Aggregations of the short-fat morphotype were typically found near a black smoker in relatively high temperature and vigorous diffuse fluid flow areas (A). The long-skinny morphotype, which […]


The Discovery of New Deep Sea Hydrothermal Vent Communities in the Southern Ocean and Implications for Biogeography

PLoS Biol
PMCID: 3250512
PMID: 22235194
DOI: 10.1371/journal.pbio.1001234

[…] usly on the carapaces of bythograeid crabs , as well as on the shells of vent molluscs and the tubes of siboglinid worms . Not as visually apparent, but abundant in sediment residue in the ROV sample bioboxes from vent and diffuse flow areas at E2 and E9, is a small species of provannid gastropod. Several unidentified octopi were also observed within hydrothermal vent fields at E9 (). The vent fau […]

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Bioboxes institution(s)
Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany; Computational Biology of Infection Research Helmholtz Centre for Infection Research, Braunschweig, Germany; DOE Joint Genome Institute, Walnut Creek, CA, USA

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