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

CZI Workshop Lightning Talk on Manubot: Empowering scholars with a personal preprint server & platform for open scholarly writing.

By Daniel Himmelstein

CZI Workshop Lightning Talk on Manubot: Empowering scholars with a personal preprint server & platform for open scholarly writing.

Presentation by Daniel Himmelstein at the Chan Zuckerberg Biohub on 2019-12-04 for the CZI event titled "Preprints I/O: Strengthening the open science ecosystem by extending preprints". This presentation is released under a CC BY 4.0 License.

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