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

Konkol M, Nüst D, Goulier L

Research article (journal) | Peer reviewed

Details about the publication

Volume5
Issue10
StatusPublished
Release year2020 (14/07/2020)
Language in which the publication is writtenEnglish
DOI10.1186/s41073-020-00095-y
Link to the full texthttps://doi.org/10.1186/s41073-020-00095-y
KeywordsBackground; 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; Methods; 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; Results; 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 applications support these formats); All approaches provide features to assist readers in studying the materials; e.g; one-click reproducible results or tools for manipulating the analysis parameters; Six applications allow for modifying materials after publication; Conclusions; The applications support authors to publish reproducible research predominantly with literate programming; Concerning readers; most applications provide user interfaces to inspect and manipulate the computational analysis; The next step is to investigate the gaps identified in this review; such as the costs publishers have to expect when hosting an application; the consideration of sensitive data; and impacts on the review process

Authors from the University of Münster

Goulier, Laura
Professur für Geoinformatik (Prof. Kray)
Konkol, Markus
Professur für Geoinformatik (Prof. Kray)
Nüst, Daniel
Professur für Geoinformatik (Prof. Pebesma)

Projects the publication originates from

Duration: 01/03/2019 - 31/07/2021 | 2nd Funding period
Funded by: DFG - Scientific Library Services and Information Systems
Type of project: Individual project

Promotionen, aus denen die Publikation resultiert

Infrastructures and Practices for Reproducible Research in Geography, Geosciences, and GIScience
Candidate: Nüst, Daniel | Supervisors: Pebesma, Edzer
Period of time: 04/01/2016 - 14/02/2022
Doctoral examination procedure finished at: Doctoral examination procedure at University of Münster