Preprints I/O: Strengthening the open science ecosystem by extending preprints

Daniel Himmelstein (@dhimmel)

CZI Preprints Workshop

Chan Zuckerberg Biohub

December 4-5, 2019

slides released under CC BY 4.0

Manubot: Empowering scholars with a personal preprint server & platform for open scholarly writing.

event information

Presenting at the workshop

We’re adding to the agenda 3 rounds of lightning talks and would like to ask all invitees to prepare a 3-minute presentation (with or without slides) focused on the following questions:

  • What social/technical integration are you working on (or interested in exploring with this audience), that would enable preprints to accelerate the broader adoption of open science practices in the community?
  • What problem does this integration solve for researchers and why are preprints a good vehicle to address it?
  • What’s standing in the way of implementing it (e.g. policy, technology, incentives)?


most viewed bioRxiv preprint of 2017

33 affiliations

deep review contribution history


citation by persistent identifier

This is a sentence with 5 citations [


  1. Reproducibility of computational workflows is automated using continuous analysis
    Brett K Beaulieu-Jones, Casey S Greene
    Nature Biotechnology (2017-03-13)
    DOI: 10.1038/nbt.3780 · PMID: 28288103 · PMCID: PMC6103790
  2. Sci-Hub provides access to nearly all scholarly literature.
    Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene
    eLife (2018-03-01)
    DOI: 10.7554/elife.32822 · PMID: 29424689 · PMCID: PMC5832410
  3. 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, Michael Zietz, Michael M. Hoffman, … Casey S. Greene
    Journal of the Royal Society Interface (2018-04)
    DOI: 10.1098/rsif.2017.0387 · PMID: 29618526 · PMCID: PMC5938574
  4. IPFS - Content Addressed, Versioned, P2P File System
    Juan Benet
    arXiv (2014-07-14)
  5. Open collaborative writing with Manubot
    Daniel S. Himmelstein, David R. Slochower, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
This is a sentence with 5 citations [1,2,3,4,5].

the future: continuous 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

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Grant G-2018-11163 to DSH

Beyond the PDF First Day Notes

By De Jongens van de Tekeningen

Licensed under CC BY 3.0

Modified to invert colors

the questions begin