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Bioboxes specifications

Information


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
Requirements
Docker
Maintained Yes

Versioning


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Maintainer


  • person_outline Michael Barton <>

Additional information


http://bioboxes.org/docs/

Publication for Bioboxes

Bioboxes in publications

 (11)
PMCID: 5139451
PMID: 27994937
DOI: 10.4103/2153-3539.194835

[…] are a few examples of contemporary tools that take advantage of docker to help manage associated pipelines. there are also at least two projects aimed at sharing bioinformatics based docker images: bioboxes (http://bioboxes.org) and biodocker (http://biodocker.org). both contain explicit examples on how to containerize, locally-developed bioinformatics tools, and associated repositories […]

PMCID: 5043174
PMID: 27687574
DOI: 10.1038/srep33997

[…] the study of plastic contamination. by using rovs the exact location and habitat is known, as the collections are made using a suction hose or manipulator arm and deposited into sample containers (bioboxes – made of plastic but not of the type and colour found). these sampling methods limit the potential for contamination by surrounding sediments and reduce trauma, maintaining the structural […]

PMCID: 4688349
PMID: 26779122
DOI: 10.3389/fmicb.2015.01470

[…] temperature of fluids venting from cracks in the outcrop was measured using the “high temperature” thermocouple available from the rov jason ii. using the rov, all samples were placed in plastic “bioboxes” that were sealed at depth to maintain them in seawater from where they were collected. once onboard the ship, samples were immediately photographed and processed in a flame-sterilized steel […]

PMCID: 4561358
PMID: 26441854
DOI: 10.3389/fmicb.2015.00904

[…] veins; w. bach, personal communication)., upon retrieval of the samples on board the research vessel, all seafloor-exposed rocks and surrounding water from the plastic sampling containers (“bioboxes”) were immediately transferred to glass jars and placed at 4°c until processing, as described elsewhere (). basalts were then transferred to ethanol- and flame-sterilized steel processing […]

PMCID: 4316637
PMID: 25539723
DOI: 10.1093/gbe/evu286

[…] in the northwestern hawaiian islands). samples from hawaii and necker were collected using the pisces iv or v submersible, and from derickson using the rov jason ii. corals were placed in insulated bioboxes for return to the surface and subsamples were frozen at −80 °c. the remainder of each specimen was deposited at the smithsonian. united states national museum (usnm)#s for each specimen […]


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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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