Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jun 14:7:ISCB Comm J-742.
doi: 10.12688/f1000research.15140.2. eCollection 2018.

Recommendations for the packaging and containerizing of bioinformatics software

Bjorn Gruening  1 , Olivier Sallou  2 , Pablo Moreno  3 , Felipe da Veiga Leprevost  4 , Hervé Ménager  5 , Dan Søndergaard  6 , Hannes Röst  7 , Timo Sachsenberg  8 , Brian O'Connor  9 , Fábio Madeira  3 , Victoria Dominguez Del Angel  10 , Michael R Crusoe  11 , Susheel Varma  3 , Daniel Blankenberg  12 , Rafael C Jimenez  13 ; BioContainers Community; Yasset Perez-Riverol  3
Affiliations

Recommendations for the packaging and containerizing of bioinformatics software

Bjorn Gruening et al. F1000Res. .

Abstract

Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily install bioinformatics software, maintain multiple versions of the same software and combine tools into powerful analysis pipelines. However, containers and software packages should be produced under certain rules and standards in order to be reusable, compatible and easy to integrate into pipelines and analysis workflows. Here, we presented a set of recommendations developed by the BioContainers Community to produce standardized bioinformatics packages and containers. These recommendations provide practical guidelines to make bioinformatics software more discoverable, reusable and transparent. They are aimed to guide developers, organisations, journals and funders to increase the quality and sustainability of research software.

Keywords: best practices bioinformatics; containers and packages; reproducibility.

PubMed Disclaimer

Conflict of interest statement

No competing interests were disclosed.

References

    1. Macleod MR, Michie S, Roberts I, et al. : Biomedical research: increasing value, reducing waste. Lancet. 2014;383(9912):101–4. 10.1016/S0140-6736(13)62329-6 - DOI - PubMed
    1. Baker M: 1,500 scientists lift the lid on reproducibility. Nature. 2016;533(7604):452–4. 10.1038/533452a - DOI - PubMed
    1. Sandve GK, Nekrutenko A, Taylor J, et al. : Ten simple rules for reproducible computational research. PLoS Comput Biol. 2013;9(10):e1003285. 10.1371/journal.pcbi.1003285 - DOI - PMC - PubMed
    1. Grüning B, Chilton J, Köster J, et al. : The backbone of research reproducibility-sustainable and flexible tool deployment. F1000Res.In Bioinformatics Open Source Conference 2017;2017. 10.7490/f1000research.1114482.1 - DOI
    1. Perez-Riverol Y, Gatto L, Wang R, et al. : Ten Simple Rules for Taking Advantage of Git and GitHub. PLoS Comput Biol. 2016;12(7):e1004947. 10.1371/journal.pcbi.1004947 - DOI - PMC - PubMed

Publication types

LinkOut - more resources