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.com/dhimmel/czi-preprint-workshop

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)? 

https://manubot.org

inception

https://github.com/greenelab/deep-review

most viewed bioRxiv preprint of 2017

33 affiliations

deep review contribution history

features

citation by persistent identifier

This is a sentence with 5 citations [
  @doi:10.1038/nbt.3780;
  @pmid:29424689;
  @pmcid:PMC5938574;
  @arxiv:1407.3561;
  @url:https://greenelab.github.io/meta-review/
].

References

  1. Reproducibility of computational workflows is automated using continuous analysis
    Brett K Beaulieu-Jones, Casey S Greene
    Nature Biotechnology (2017-03-13) https://doi.org/f9ttx6
    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) https://www.ncbi.nlm.nih.gov/pubmed/29424689
    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) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5938574/
    DOI: 10.1098/rsif.2017.0387 · PMID: 29618526 · PMCID: PMC5938574
     
  4. IPFS - Content Addressed, Versioned, P2P File System
    Juan Benet
    arXiv (2014-07-14) https://arxiv.org/abs/1407.3561v1
     
  5. Open collaborative writing with Manubot
    Daniel S. Himmelstein, David R. Slochower, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
    (2018-08-03) https://greenelab.github.io/meta-review/
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

changelogs, diffs, permalinks

Timestamped on the Bitcoin blockchain via OpenTimestamps

free timestamping for historical integrity

(update slide post this issue)

https://manubot.org/catalog/

Thanks!

@dhimmel

0000-0002-3012-7446

Slides
https://slides.com/dhimmel/czi-preprint-workshop

extras

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