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paper.bib
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paper.bib
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@MISC{Docker-hub,
title = "Docker Hub",
howpublished = "\url{https://hub.docker.com/}",
note = "Accessed: 2015-11-4"
}
@MISC{noauthor_undated-vt,
title = "{GitHub} Pages",
abstract = "Websites for you and your projects, hosted directly from your
GitHub repository. Just edit, push, and your changes are live.",
institution = "Github"
}
@ARTICLE{Ram2013-km,
title = "Git can facilitate greater reproducibility and increased
transparency in science",
author = "Ram, Karthik",
affiliation = "Environmental Science, Policy, and Management, University of
California, Berkeley, Berkeley, CA 94720, USA.
karthik.ram@berkeley.edu.",
abstract = "BACKGROUND: Reproducibility is the hallmark of good science.
Maintaining a high degree of transparency in scientific
reporting is essential not just for gaining trust and
credibility within the scientific community but also for
facilitating the development of new ideas. Sharing data and
computer code associated with publications is becoming
increasingly common, motivated partly in response to data
deposition requirements from journals and mandates from
funders. Despite this increase in transparency, it is still
difficult to reproduce or build upon the findings of most
scientific publications without access to a more complete
workflow. FINDINGS: Version control systems (VCS), which have
long been used to maintain code repositories in the software
industry, are now finding new applications in science. One
such open source VCS, Git, provides a lightweight yet robust
framework that is ideal for managing the full suite of
research outputs such as datasets, statistical code, figures,
lab notes, and manuscripts. For individual researchers, Git
provides a powerful way to track and compare versions, retrace
errors, explore new approaches in a structured manner, while
maintaining a full audit trail. For larger collaborative
efforts, Git and Git hosting services make it possible for
everyone to work asynchronously and merge their contributions
at any time, all the while maintaining a complete authorship
trail. In this paper I provide an overview of Git along with
use-cases that highlight how this tool can be leveraged to
make science more reproducible and transparent, foster new
collaborations, and support novel uses.",
journal = "Source Code Biol. Med.",
volume = 8,
number = 1,
pages = "7",
month = feb,
year = 2013,
language = "en"
}
@ARTICLE{Sochat2017-ud,
title = "Enhancing reproducibility in scientific computing: Metrics and
registry for Singularity containers",
author = "Sochat, Vanessa V and Prybol, Cameron J and Kurtzer, Gregory M",
abstract = "Here we present Singularity Hub, a framework to build and deploy
Singularity containers for mobility of compute, and the
singularity-python software with novel metrics for assessing
reproducibility of such containers. Singularity containers make
it possible for scientists and developers to package reproducible
software, and Singularity Hub adds automation to this workflow by
building, capturing metadata for, visualizing, and serving
containers programmatically. Our novel metrics, based on custom
filters of content hashes of container contents, allow for
comparison of an entire container, including operating system,
custom software, and metadata. First we will review Singularity
Hub's primary use cases and how the infrastructure has been
designed to support modern, common workflows. Next, we conduct
three analyses to demonstrate build consistency, reproducibility
metric and performance and interpretability, and potential for
discovery. This is the first effort to demonstrate a rigorous
assessment of measurable similarity between containers and
operating systems. We provide these capabilities within
Singularity Hub, as well as the source software
singularity-python that provides the underlying functionality.
Singularity Hub is available at https://singularity-hub.org, and
we are excited to provide it as an openly available platform for
building, and deploying scientific containers.",
journal = "PLoS One",
volume = 12,
number = 11,
pages = "e0188511",
month = nov,
year = 2017,
language = "en"
}
@ARTICLE{Merkel2014-da,
title = "Docker: Lightweight Linux Containers for Consistent Development
and Deployment",
author = "Merkel, Dirk",
journal = "Linux J.",
publisher = "Belltown Media",
volume = 2014,
number = 239,
month = mar,
year = 2014,
address = "Houston, TX"
}
@MISC{noauthor_undated-hl,
title = "container-diff",
abstract = "container-diff: Diff your Docker containers",
institution = "Github"
}
@MISC{noauthor_undated-nt,
title = "Continuous Integration and Deployment",
abstract = "Hosted Continuous Integration for web applications. Set up
your application for testing in one click, on the fastest
testing platform on the internet.",
howpublished = "\url{https://circleci.com/dashboard}",
note = "Accessed: 2018-8-4"
}