Publishing computational research - a review of infrastructures for reproducible and transparent scholarly communication

Research Integrity and Peer Review
Markus KonkolLaura Goulier

Abstract

The trend toward open science increases the pressure on authors to provide access to the source code and data they used to compute the results reported in their scientific papers. Since sharing materials reproducibly is challenging, several projects have developed solutions to support the release of executable analyses alongside articles. We reviewed 11 applications that can assist researchers in adhering to reproducibility principles. The applications were found through a literature search and interactions with the reproducible research community. An application was included in our analysis if it (i) was actively maintained at the time the data for this paper was collected, (ii) supports the publication of executable code and data, (iii) is connected to the scholarly publication process. By investigating the software documentation and published articles, we compared the applications across 19 criteria, such as deployment options and features that support authors in creating and readers in studying executable papers. From the 11 applications, eight allow publishers to self-host the system for free, whereas three provide paid services. Authors can submit an executable analysis using Jupyter Notebooks or R Markdown documents (10 ...Continue Reading

References

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Citations

Jun 12, 2021··Dan GunterGilberto Pastorello

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Software Mentioned

Zenodo
Galaxy
Docker
eLife
Taverna
Code Ocean
JupyterLab
Binder
MATLAB
Ocean Code Ocean

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