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:

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

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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

The Deep Review

  • review article on deep learning in precision medicine
  • 27 authors from 20 different institutions
  • readers appreciate the breadth of perspectives

Manubot: the manuscript bot

By Daniel Himmelstein

Manubot: the manuscript bot

Powering the next generation of scholarly manuscript. See https://github.com/greenelab/manubot-rootstock. Released under CC BY 4.0.

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