Daniel Himmelstein
Head of Data Integration at Related Sciences. Digital craftsman of the biodata revolution.
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
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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
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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
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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
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IPFS - Content Addressed, Versioned, P2P File System
Juan Benet
arXiv (2014-07-14) https://arxiv.org/abs/1407.3561v1
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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.
