containerit: Generating Dockerfiles for reproducible research with R

@article{Nst2019containeritGD,
  title={containerit: Generating Dockerfiles for reproducible research with R},
  author={Daniel N{\"u}st and Matthias Hinz},
  journal={J. Open Source Softw.},
  year={2019},
  volume={4},
  pages={1603}
}
Linux containers have become a promising tool to increase transparency, portability, and reproducibility of research in several domains and use cases: data science (Boettiger, 2015), software engineering research (Cito & Gall, 2016), multi-step bioinformatics pipelines (Kim, Ali, Lijeron, Afgan, & Krampis, 2017), standardised environments for exchangeable software (Belmann et al., 2015), computational archaeology (Marwick, 2017), packaging algorithms (Hosny, Vera-Licona, Laubenbacher, & Favre… Expand
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References

SHOWING 1-10 OF 36 REFERENCES
Bio-Docklets: Virtualization Containers for Single-Step Execution of NGS Pipelines
TLDR
The goal of the approach is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts, on any computing environment whether a laboratory workstation, university computer cluster, or a cloud service provider. Expand
Reproducibility and Practical Adoption of GEOBIA with Open-Source Software in Docker Containers
Geographic Object-Based Image Analysis (GEOBIA) mostly uses proprietary software,but the interest in Free and Open-Source Software (FOSS) for GEOBIA is growing. This interest stems not only from costExpand
Bio-Docklets: virtualization containers for single-step execution of NGS pipelines
TLDR
The goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Expand
An introduction to Docker for reproducible research
TLDR
How the popular emerging technology Docker combines several areas from systems research - such as operating system virtualization, cross-platform portability, modular re-usable elements, versioning, and a 'DevOps' philosophy, to address these challenges is examined. Expand
Kliko - The scientific compute container format
TLDR
Two reference implementations based on the Kliko library are discussed: RODRIGUES, a web-based Kliko container scheduler, and output visualizer specifically for astronomical data, and VerMeerKAT, a multi-container workflow data reduction pipeline which is being used as a prototype pipeline for the commissioning of the MeerKat radio telescope. Expand
Reproducibility of computational workflows is automated using continuous analysis
TLDR
The development of continuous analysis is reported, a workflow that enables reproducible computational analyses and allows reviewers, editors or readers to verify reproducibility without manually downloading and rerunning code and can provide an audit trail for analyses of data that cannot be shared. Expand
ReproZip: Computational Reproducibility With Ease
TLDR
ReproZip was designed to simplify the process of making an existing computational experiment reproducible across platforms, even when the experiment was put together without reproducibility in mind. Expand
Using Docker Containers to Improve Reproducibility in Software Engineering Research
  • Jürgen Cito, H. Gall
  • Computer Science
  • 2016 IEEE/ACM 38th International Conference on Software Engineering Companion (ICSE-C)
  • 2016
TLDR
A technical briefing presents how Docker containers can overcome issues and aid the reproducibility of research artifacts in software engineering and discusses their applications in the field. Expand
A Framework for the Preservation of a Docker Container
TLDR
This work provides a simple framework to address the question of the preservation of containers and its environment and captures the processes used and put them into the W3C PROV ontology to provide a complete overview of the workflow. Expand
AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms
TLDR
AlgoRun, a dedicated packaging system for implemented algorithms, using Docker technology, addresses the growing need in bioinformatics for easy-to-use software implementations of algorithms that are usable across platforms. Expand
...
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3
4
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