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

TL;DR

This review examines 11 software applications that facilitate reproducible and transparent scholarly communication by supporting executable code and data sharing, highlighting features, hosting options, and user interfaces for researchers and readers.

Contribution

It provides a comprehensive comparison of active tools for publishing reproducible computational research, focusing on features, hosting, and user support.

Findings

Eight applications support free self-hosting for publishers.

Most applications support Jupyter Notebooks and R Markdown.

All tools assist readers in studying and manipulating analyses.

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 was actively maintained at the time the data for this paper was collected, supports the publication of executable code and data, is connected to the scholarly publication process. By investigating the software documentation and published articles, we compared the applications across 19 criteria, e.g. 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 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. 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.