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manubot
Does one skip the "biorxiv" submission step with manubot?
Since each manubot build has a DOI, would one "need" to submit a manuscript to Biorxiv? I'd imagine it's not necessary, but maybe a nice advertisement platform once the manuscript is submitted to a journal. What has been people's experiences with the tool and preprint submission?
Many of us do prefer to post the Manubot-generated PDF to a preprint server at the time of submission. As you noted, it helps bring visibility to the manuscript and can be a good way to solicit feedback. In addition, even though Manubot versions the manuscript and creates permalinks, those aren't guaranteed to be persistent and are not DOIs. The manuscript author could delete their GitHub repository and the versioned manuscripts would disappear, unless they had been independently archived.
The downside of posting to a preprint server is that the interactive HTML version of a Manubot manuscript is the best way to view it.
To get a broader overview of what others have done, you can check the Manubot catalog and filter by has preprint. There are now Manubot papers in bioRxiv, arXiv, ChemRxiv, PeerJ Preprints, figshare, and institutional repositories.
For https://greenelab.github.io/meta-review/, we never uploaded the PDF to a preprint server. But in this case, we wanted all readers to interact with the Manubot version because the manuscript was about Manubot. But in other cases, the increased visibility, persistence, and citeability of a preprint server makes sense. So really, it's up to the author.
In the longterm, I would like the Manubot catalog to gain some of the features of preprint servers, such as issuing DOIs and ensuring persistent availability. At this point, bioRxiv or other preprint servers would likely be redundant. But this is far off.
Okay, got it! I think the visibility factor is pretty important to me so I'll still go the Biorxiv route. @agitter didn't know about the Manubot catalog, pretty cool!
Good plan. We encourage you to submit your manuscript to the catalog with a pull request once it's ready: https://github.com/manubot/catalog#contributing
Perhaps it's worth it to mention that we might also integrate with online open source journals such as this in the future: https://joss.theoj.org/
