Manubot

powering the next generation of scholarly manuscript

The Manubot project began with the [Deep Review](https://github.com/greenelab/deep-review),
where it was used to compose a highly-collaborative review article [@doi:10.1101/142760].
Other manuscripts that were created with Manubot include:

+ The Sci-Hub Coverage Study
  ([GitHub](https://github.com/greenelab/scihub-manuscript), [HTML manuscript](https://greenelab.github.io/scihub-manuscript/)) 
  [@doi:10.7287/peerj.preprints.3100]
+ Michael Zietz's Report for the Vagelos Scholars Program
  ([GitHub](https://github.com/zietzm/Vagelos2017), [HTML manuscript](https://zietzm.github.io/Vagelos2017/)) 
  [@doi:10.6084/m9.figshare.5346577]

The Manubot project began with the Deep Review, where it was used to compose a highly-collaborative review article [1]. Other manuscripts that were created with Manubot include:

The Sci-Hub Coverage Study (GitHub, HTML manuscript) [2]
Michael Zietz’s Report for the Vagelos Scholars Program (GitHub, HTML manuscript) [3]

1. Opportunities And Obstacles For Deep Learning In Biology And Medicine
Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Wei Xie, Gail L. Rosen, … Casey S. Greene
Cold Spring Harbor Laboratory (2017-05-28) https://doi.org/10.1101/142760

2. Sci-Hub provides access to nearly all scholarly literature
Daniel S Himmelstein, Ariel R Romero, Stephen R McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
PeerJ Preprints (2017-07-20) https://doi.org/10.7287/peerj.preprints.3100

3. Vagelos Report Summer 2017
Michael Zietz
Figshare (2017) https://doi.org/10.6084/m9.figshare.5346577

Write markdown

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Automatic bibliographic metadata

[@doi:10.7287/peerj.preprints.3100]

[@arxiv:1407.3561v1]
[@pmid:24159271]
[@url:http://blog.dhimmel.com/biorxiv-licenses/]

1. Modify the manuscript source

2. Continuous integration rebuilds the manuscript

Timestamped on the Bitcoin blockchain via OpenTimestamps

3. Continuous deployment back to GitHub

Pull requests for manuscript collaboration

Get started at tiny.cc/manubot

https://github.com/greenelab/manubot-rootstock

Impact

end-to-end reproducibility
transparent
- contribution record is public
open
- immediate availability
- default CC BY 4.0 license
collaborative
permissionless & gratis self-publication

Technicalities

hackable
markdown source
git for version control
GitHub for collaboration
CSL (citeproc) citations
automated citations and reference metadata
HTML-first output hosted on GitHub pages
continuous integration for testing pull requests and continuous deployment
customizable (especially if you code)
blockchain timestamping
uses Pandoc, so many output types possible
templating for provenance-preserving documents
open source in Python with conda for environment management

the future: living but versioned

“Finally, we estimate that over a six-month period in 2015–2016, Sci-Hub provided access for 99.3% of valid incoming requests.”

— DOI: 10.7287/peerj.preprints.3100v1

“In the first version of this study, we mistakenly treated the log events as requests rather than downloads. Fortunately, Sci-Hub reviewed the preprint in a series of tweets, and pointed out the error…”

— DOI: 10.7287/peerj.preprints.3100v2