Open sourceror. 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 released under CC BY 4.0
Manubot: Empowering scholars with a personal preprint server & platform for open scholarly writing.
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
deep review contribution history
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/ ].
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
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
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
IPFS - Content Addressed, Versioned, P2P File System
arXiv (2014-07-14) https://arxiv.org/abs/1407.3561v1
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
changelogs, diffs, permalinks
Timestamped on the Bitcoin blockchain via OpenTimestamps
free timestamping for historical integrity
(update slide post this issue)
Grant G-2018-11163 to DSH
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