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Ten simple rules for writing Dockerfiles for reproducible data science

Daniel Nüst, Vanessa Sochat, Ben Marwick, Stephen J. Eglen, Tim Head, Tony Hirst, Benjamin D. Evans, Scott Markel
2020 PLoS Computational Biology  
In support of this approach, we present a set of rules to help researchers write understandable Dockerfiles for typical data science workflows.  ...  Computational science has been greatly improved by the use of containers for packaging software and data dependencies.  ...  Summary of the 10 simple rules for writing Dockerfiles for reproducible data science. https://doi.org/10.1371/journal.pcbi.1008316.g001 Fig 2 . 2 Fig 2.  ... 
doi:10.1371/journal.pcbi.1008316 pmid:33170857 fatcat:xsc3dr2oejcxhi7plh3arktzny

Opening Reproducible Research: A Research Project Website And Blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  We thank again our guests for their valuable inputs. Having their backgrounds in research as well as scientific publishing, their critical evaluation helps us to shape a clear direction for our work.  ...  We get to know the common language as well as points of contact for the involved parties as we create a closer connection between research, preservation, and publication communities.  ... 
doi:10.5281/zenodo.1485438 fatcat:v6m44mhrvvfmtkz2urjv5grgu4

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  Opening Reproducible Research | doi:10.5281/zenodo.1485438  ...  Opening Reproducible Research | doi:10.5281/zenodo.1485438 We have a good understanding of how far the process of creating research compendia can be automated, and what efforts remain for authors or preservationists  ... 
doi:10.5281/zenodo.2361304 fatcat:gspygrzekjb7jprdwe5l4gf6pi

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  Opening Reproducible Research | doi:10.5281/zenodo.1485438  ...  Opening Reproducible Research | doi:10.5281/zenodo.1485438 We have a good understanding of how far the process of creating research compendia can be automated, and what efforts remain for authors or preservationists  ... 
doi:10.5281/zenodo.2546507 fatcat:dau5hho335boznxi675w6shf6q

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  not be able without the support of Copernicus Publications, the software maintainers most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, R-spatial, Open Science, and Reproducible  ...  Acknowledgements The software updates were contributed by Daniel Nüst from the project Opening Reproducible Research (o2r) at the Institute for Geoinformatics, University of Münster, Germany, but would  ... 
doi:10.5281/zenodo.3264899 fatcat:lvvqfxjtijal7et2gmqlclujeq

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  We thank again our guests for their valuable inputs. Having their backgrounds in research as well as scientific publishing, their critical evaluation helps us to shape a clear direction for our work.  ...  We get to know the common language as well as points of contact for the involved parties as we create a closer connection between research, preservation, and publication communities.  ... 
doi:10.5281/zenodo.2576175 fatcat:izgbl64n4neebbuwct4enci5dm

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  not be able without the support of Copernicus Publications, the software maintainers most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, R-spatial, Open Science, and Reproducible  ...  Acknowledgements The software updates were contributed by Daniel Nüst from the project Opening Reproducible Research (o2r) at the Institute for Geoinformatics, University of Münster, Germany, but would  ... 
doi:10.5281/zenodo.3258365 fatcat:ccn6mak76jhv3fezvzqdufxf3u

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r is funded by the German  ...  not be able without the support of Copernicus Publications, the software maintainers most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, R-spatial, Open Science, and Reproducible  ...  Acknowledgements The software updates were contributed by Daniel Nüst from the project Opening Reproducible Research (o2r) at the Institute for Geoinformatics, University of Münster, Germany, but would  ... 
doi:10.5281/zenodo.2576176 fatcat:o75zoynj7jdebbu7wd3jlobbju

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  not be able without the support of Copernicus Publications, the software maintainers most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, R-spatial, Open Science, and Reproducible  ...  Acknowledgements The software updates were contributed by Daniel Nüst from the project Opening Reproducible Research (o2r) at the Institute for Geoinformatics, University of Münster, Germany, but would  ... 
doi:10.5281/zenodo.2640847 fatcat:mdrorsy5nnhyrazzo5inu347ba

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r is funded by the German  ...  not be able without the support of Copernicus Publications, the software maintainers most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, R-spatial, Open Science, and Reproducible  ...  Acknowledgements The software updates were contributed by Daniel Nüst from the project Opening Reproducible Research (o2r) at the Institute for Geoinformatics, University of Münster, Germany, but would  ... 
doi:10.5281/zenodo.2576313 fatcat:w4vnb4dnfvhgfhcxsu4uwrnfhy

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  Tomi approached reproducibility from the question "How science works?" and connected it to his work on Linked Open Science (see also the original Prezi).  ...  New ways for searching scientific work based on the integrated and linked parts of a research compendium (text, code, data, user interface bindings).  ... 
doi:10.5281/zenodo.3403565 fatcat:tosltkk6srcj7mvymjystfiu7q

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  not be able without the support of Copernicus Publications, the software maintainers most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, Rspatial, Open Science, and Reproducible  ...  Automatic (bordering on magical) creation of executable research compendia based on typical science workspaces for R-based geosciences.  ... 
doi:10.5281/zenodo.4384840 fatcat:obaudbxvwfello2ndjb2nmu3vq

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  New ways for searching scientific work based on the integrated and linked parts of a research compendium (text, code, data, user interface bindings).  ...  Automatic (bordering on magical) creation of executable research compendia based on typical science workspaces for R-based geosciences.  ... 
doi:10.5281/zenodo.3480121 fatcat:vibppm77jrfdhihoo3geek3rf4

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  not be able without the support of Copernicus Publications, the software maintainers most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, R-spatial, Open Science, and Reproducible  ...  Acknowledgements The software updates were contributed by Daniel Nüst from the project Opening Reproducible Research (o2r) at the Institute for Geoinformatics, University of Münster, Germany, but would  ... 
doi:10.5281/zenodo.3335838 fatcat:oigiczctnfhqpajci6nvhpkpey

Opening Reproducible Research: a research project website and blog [article]

Daniel Nüst, Marc Schutzeichel, Markus Konkol
2018 Zenodo  
All blog entries of the blog for the research project Opening Reproducible Research (o2r, see also Offene Reproduzierbare Forschung @ DFG GEPRIS), online at https://o2r.info. o2r was funded by the German  ...  most notably Yihui Xie and Will Pearse, and the general awesomeness of the R, R-spatial, Open Science, and Reproducible Research communities.  ...  Reproducible research manuscripts Sustainable access to supplemental data Main takeaways Acknowledgements References Acknowledgements The software updates were contributed by Daniel Nüst from the project  ... 
doi:10.5281/zenodo.5155998 fatcat:wa77g2ytojfqxgmgxe5iev3nge
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