ORCA: a comprehensive bioinformatics container environment for education and research
SUMMARY: The ORCA bioinformatics environment is a Docker image that contains hundreds of bioinformatics tools and their dependencies. The ORCA image and accompanying server infrastructure provide a comprehensive bioinformatics environment for education and research. The ORCA environment on a server...
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ftpubmed:oai:pubmedcentral.nih.gov:6821186 2023-05-15T17:52:55+02:00 ORCA: a comprehensive bioinformatics container environment for education and research Jackman, Shaun D Mozgacheva, Tatyana Chen, Susie O’Huiginn, Brendan Bailey, Lance Birol, Inanc Jones, Steven J M 2019-11-01 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821186/ http://www.ncbi.nlm.nih.gov/pubmed/31004474 https://doi.org/10.1093/bioinformatics/btz278 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821186/ http://www.ncbi.nlm.nih.gov/pubmed/31004474 http://dx.doi.org/10.1093/bioinformatics/btz278 © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. CC-BY Applications Notes Text 2019 ftpubmed https://doi.org/10.1093/bioinformatics/btz278 2019-11-10T01:25:43Z SUMMARY: The ORCA bioinformatics environment is a Docker image that contains hundreds of bioinformatics tools and their dependencies. The ORCA image and accompanying server infrastructure provide a comprehensive bioinformatics environment for education and research. The ORCA environment on a server is implemented using Docker containers, but without requiring users to interact directly with Docker, suitable for novices who may not yet have familiarity with managing containers. ORCA has been used successfully to provide a private bioinformatics environment to external collaborators at a large genome institute, for teaching an undergraduate class on bioinformatics targeted at biologists, and to provide a ready-to-go bioinformatics suite for a hackathon. Using ORCA eliminates time that would be spent debugging software installation issues, so that time may be better spent on education and research. AVAILABILITY AND IMPLEMENTATION: The ORCA Docker image is available at https://hub.docker.com/r/bcgsc/orca/. The source code of ORCA is available at https://github.com/bcgsc/orca under the MIT license. Text Orca PubMed Central (PMC) Bioinformatics 35 21 4448 4450 |
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Applications Notes Jackman, Shaun D Mozgacheva, Tatyana Chen, Susie O’Huiginn, Brendan Bailey, Lance Birol, Inanc Jones, Steven J M ORCA: a comprehensive bioinformatics container environment for education and research |
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Applications Notes |
description |
SUMMARY: The ORCA bioinformatics environment is a Docker image that contains hundreds of bioinformatics tools and their dependencies. The ORCA image and accompanying server infrastructure provide a comprehensive bioinformatics environment for education and research. The ORCA environment on a server is implemented using Docker containers, but without requiring users to interact directly with Docker, suitable for novices who may not yet have familiarity with managing containers. ORCA has been used successfully to provide a private bioinformatics environment to external collaborators at a large genome institute, for teaching an undergraduate class on bioinformatics targeted at biologists, and to provide a ready-to-go bioinformatics suite for a hackathon. Using ORCA eliminates time that would be spent debugging software installation issues, so that time may be better spent on education and research. AVAILABILITY AND IMPLEMENTATION: The ORCA Docker image is available at https://hub.docker.com/r/bcgsc/orca/. The source code of ORCA is available at https://github.com/bcgsc/orca under the MIT license. |
format |
Text |
author |
Jackman, Shaun D Mozgacheva, Tatyana Chen, Susie O’Huiginn, Brendan Bailey, Lance Birol, Inanc Jones, Steven J M |
author_facet |
Jackman, Shaun D Mozgacheva, Tatyana Chen, Susie O’Huiginn, Brendan Bailey, Lance Birol, Inanc Jones, Steven J M |
author_sort |
Jackman, Shaun D |
title |
ORCA: a comprehensive bioinformatics container environment for education and research |
title_short |
ORCA: a comprehensive bioinformatics container environment for education and research |
title_full |
ORCA: a comprehensive bioinformatics container environment for education and research |
title_fullStr |
ORCA: a comprehensive bioinformatics container environment for education and research |
title_full_unstemmed |
ORCA: a comprehensive bioinformatics container environment for education and research |
title_sort |
orca: a comprehensive bioinformatics container environment for education and research |
publisher |
Oxford University Press |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821186/ http://www.ncbi.nlm.nih.gov/pubmed/31004474 https://doi.org/10.1093/bioinformatics/btz278 |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821186/ http://www.ncbi.nlm.nih.gov/pubmed/31004474 http://dx.doi.org/10.1093/bioinformatics/btz278 |
op_rights |
© The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
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CC-BY |
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https://doi.org/10.1093/bioinformatics/btz278 |
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