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Why not a MS Word file?

Preparing manuscripts with hundreds of coauthors is challenging, time-consuming, and often, frustrating. Sharing MS Word files per email is clearly inefficient and leads to versioning problems. Using Google docs is slightly better, but often results in unreadable manuscripts clogged with comments, where it is difficult to keep track of the different points of view in a transparent manner. Furthermore, Google docs do not handle references, which is obviously inconvenient.

To overcome these problems, we decide to test an alternative workflow, i.e., Manubot
In a nutshell, the manuscript is created and maintained similarly to programming code, whose versions (=edits) are handled using Git – the popular version control software. The code is stored in an online repository (https://github.com/), and each user can access it and suggest changes. Suggested changes are then revised by the maintainer (@fmsabatini in this case) and, if accepted, implemented in the manuscript. Each time a change is done, a hidden workflow (i.e., Manubot) will render the code-like manuscript into a pdf file, as well as an html webpage. An additional benefit of using Github is that co-authors can discuss problems and ideas in dedicated forum threads, i.e., issues. This workflow is clearly different from what most people are used to, so it requires a bit of adaptability, and a GitHub account.

Table of contents

1. Accessing the manuscript
2. Edit the manuscript using GitHub’s browser interface
3. Edit the ms - Alternative to GitHub (not recommended)
4. Editing personal and affiliation information
5. How to open issues, suggest ideas and discuss problems
6. Approve Submission