Table 1.
Collaborative writing platforms.
A summary of features that differentiate Manubot from existing collaborative writing platforms. We assessed features in June 2018 using the free version of each platform and updated our assessment in April 2019 to add the features in the bottom three rows and re-evaluate Authorea and Overleaf. Some platforms offer additional features through a paid subscription or software. 1) Additional functionality, such as bibliography management and tracking changes, is available by editing the Word document stored in OneDrive with the paid Word desktop application. 2) Conversations about modifications take place on the document as comments, annotations, or unsaved chats. There is no integrated forum for discussing and editing revisions. 3) In some circumstances, Overleaf Git commits are not modular. Edits made by distinct authors may be attributed to a single author. The GitHub Sync feature attributes all edits to the project owner.
Fig 1.
Any reader can contribute to a Manubot manuscript by proposing a change through a pull request. This example involves three people: a manuscript Maintainer, an existing project Contributor, and an additional Participant in the discussion. Manuscript text is shown in solid lines on the left of the timeline and discussion on GitHub is shown by squiggly lines to the right of the timeline. The Contributor opens a GitHub issue to discuss a manuscript modification. The Maintainer and the Participant provide feedback in the issue, and the Maintainer recommends creating a GitHub pull request to update the text. The Contributor creates the pull request. It is reviewed by the Maintainer and the Participant, and the Contributor updates the pull request in response. Once the pull request is approved, the Maintainer merges the changes into the official version of the manuscript.
Fig 2.
Deep Review contributions by author over time.
The total words added to the Deep Review by each author is plotted over time (final values in parentheses). These statistics were extracted from Git commit diffs of the manuscript’s Markdown source. This figure reveals the composition of written contributions to the manuscript at every point in its history. The Deep Review was initiated in August 2016, and the first complete manuscript was released as a preprint [10] in May 2017. While the article was under review, we continued to maintain the project and accepted new contributions. The preprint was updated in January 2018, and the article was accepted by the journal in March 2018 [5]. As of March 06, 2019, the Deep Review repository accumulated 755 Git commits, 317 merged pull requests, 609 issues, and 819 GitHub stars. The notebook to generate this figure can be interactively launched (https://mybinder.org/v2/gh/greenelab/meta-review/binder?filepath=analyses/deep-review-contrib/02.contrib-viz.ipynb) using Binder [11], enabling users to explore alternative visualizations or analyses of the source data.
Table 2.
Citation types supported by Manubot.
Manubot allows users to cite different types of persistent identifiers. Metadata source indicates the primary resource used to retrieve bibliographic metadata. For certain identifier types, additional metadata sources are queried should the primary fail. For example, when translation-server ISBN lookup fails, Manubot tries Wikipedia’s Citoid (https://www.mediawiki.org/wiki/Citoid) service followed by the isbnlib (https://github.com/xlcnd/isbnlib) Python package. When translation-server URL lookup fails, Manubot then tries Greycite (http://greycite.knowledgeblog.org/) [15]. Raw citations enable citing works when no supported persistent identifiers exist, but require that the user specifies the metadata. Finally, authors may optionally map a named tag to any of the supported identifier types. In this example, the tag avasthi-preprints represents the DOI identifier 10.7554/eLife.38532. API: application programming interface.
Fig 3.
Examples of the various Manubot plugins, illustrating their functionality and usefulness.
Screenshots were taken from existing manuscripts made with Manubot: Sci-Hub Coverage Study (https://greenelab.github.io/scihub-manuscript/v/fd7acb7ed0108c920da56f84819ce13f02f68aa8/) and TPOT-FSS (https://trang1618.github.io/tpot-fss-ms/), available under the CC BY 4.0 License. Clarifying markups are overlaid in purple.