slides.com/dhimmel/psb
Manubot is an open source tool for writing manuscripts on GitHub in markdown format. Manubot applies the git-based software workflow to scholarly writing, enabling enhanced transparency, collaboration, automation, and reproducibility.
This working group will go over how to write your next manuscript using Manubot and what features of Manubot can help biomedical researchers document and publish their computational research. For example, Manubot enables citation by persistent identifier to automate bibliographic metadata retrieval and formatting as well as allowing templating so results can be directly inserted from the analyses that produced them. Learn more about Manbuot at https://manubot.org or https://git.io/fxb4C.
Attendees are encouraged to bring a laptop if they would like assistance setting up a manuscript during the last 40 minutes of the workshop. Attendees should also feel free to leave around 4:20 when the personalized tutorials begin.
Organizer: Daniel Himmelstein
Email: daniel dot himmelstein at gmail dot com
Open collaborative writing with Manubot
Daniel S. Himmelstein, David R. Slochower, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
Manubot Preprint (2018) https://greenelab.github.io/meta-review/
Timestamped on the Bitcoin blockchain via OpenTimestamps
https://greenelab.github.io/scihub-manuscript/v/17dd2015ec9396e59cdbc3c2b0abb7d33481bcbf/
Beyond the PDF First Day Notes by De Jongens van de Tekeningen. CC BY 3.0
input
output
manubot process
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/
].
This is a sentence with 5 citations [1,2,3,4,5].
Example from my uBiome SmartGut report
https://github.com/greenelab/manubot
manubot on PyPI
pip install manubot
Prefix | Resource |
---|---|
doi | DOI Content Negotation |
pmcid | NCBI Literature Citation Exporter |
pmid | NCBI E-utilities |
arxiv | arXiv API |
isbn | Zotero translation-server |
wikidata | Zotero translation-server |
url | Zotero translation-server |
raw | user must supply CSL JSON metadata |
[
{
"publisher": "eLife Sciences Publications, Ltd",
"abstract": "<jats:p>The website Sci-Hub enables users to download PDF versions of scholarly articles, including many articles that are paywalled at their journal’s site. Sci-Hub has grown rapidly since its creation in 2011, but the extent of its coverage has been unclear. Here we report that, as of March 2017, Sci-Hub’s database contains 68.9% of the 81.6 million scholarly articles registered with Crossref and 85.1% of articles published in toll access journals. We find that coverage varies by discipline and publisher, and that Sci-Hub preferentially covers popular, paywalled content. For toll access articles, we find that Sci-Hub provides greater coverage than the University of Pennsylvania, a major research university in the United States. Green open access to toll access articles via licit services, on the other hand, remains quite limited. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection, suggesting the toll access business model may become unsustainable.</jats:p>",
"DOI": "10.7554/elife.32822",
"type": "article-journal",
"source": "Crossref",
"title": "Sci-Hub provides access to nearly all scholarly literature",
"volume": "7",
"author": [
{
"given": "Daniel S",
"family": "Himmelstein"
},
{
"given": "Ariel Rodriguez",
"family": "Romero"
},
{
"given": "Jacob G",
"family": "Levernier"
},
{
"given": "Thomas Anthony",
"family": "Munro"
},
{
"given": "Stephen Reid",
"family": "McLaughlin"
},
{
"given": "Bastian",
"family": "Greshake Tzovaras"
},
{
"given": "Casey S",
"family": "Greene"
}
],
"container-title": "eLife",
"language": "en",
"issued": {
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[
2018,
3,
1
]
]
},
"URL": "https://doi.org/ckcj",
"PMCID": "PMC5832410",
"PMID": "29424689",
"id": "IhliSZDo"
}
]
manubot cite doi:10.7554/eLife.32822
manubot cite --allow-invalid-csl-data \ doi:10.7554/eLife.32822
[
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"abstract": "<jats:p>The website Sci-Hub enables users to download PDF versions of scholarly articles, including many articles that are paywalled at their journal’s site. Sci-Hub has grown rapidly since its creation in 2011, but the extent of its coverage has been unclear. Here we report that, as of March 2017, Sci-Hub’s database contains 68.9% of the 81.6 million scholarly articles registered with Crossref and 85.1% of articles published in toll access journals. We find that coverage varies by discipline and publisher, and that Sci-Hub preferentially covers popular, paywalled content. For toll access articles, we find that Sci-Hub provides greater coverage than the University of Pennsylvania, a major research university in the United States. Green open access to toll access articles via licit services, on the other hand, remains quite limited. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection, suggesting the toll access business model may become unsustainable.</jats:p>",
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{
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"unstructured": "Elbakyan A. 2015. Letter – Document #50 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS. Southern District Court of New York. https://www.courtlistener.com/docket/4355308/50/elsevier-inc-v-sci-hub/ [Accessed February 7, 2018].",
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"article-title": "Sci-Hub is a goal, changing the system is a method",
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"author": "Elbakyan",
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"volume-title": "Engineuring"
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"author": "Elbakyan",
"year": "2017",
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"article-title": "Some facts on Sci-Hub that Wikipedia gets wrong",
"volume-title": "Engineuring"
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"volume-title": "Times Higher Education"
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"author": "Esposito",
"year": "2016",
"unstructured": "Esposito JJ. 2016. Sci-Hub and the four horsemen of the internet. The Scholarly Kitchen. https://scholarlykitchen.sspnet.org/2016/03/02/sci-hub-and-the-four-horsemen-of-the-internet/ [Accessed February 7, 2018].",
"article-title": "Sci-Hub and the four horsemen of the internet",
"volume-title": "The Scholarly Kitchen"
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"author": "Esposito",
"year": "2017",
"unstructured": "Esposito JJ. 2017. Sci-Hub moves to the center of the ecosystem. The Scholarly Kitchen. https://scholarlykitchen.sspnet.org/2017/09/05/sci-hub-moves-center-ecosystem/ [Accessed February 7, 2018].",
"article-title": "Sci-Hub moves to the center of the ecosystem",
"volume-title": "The Scholarly Kitchen"
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},
{
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"author": "Tzovaras",
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"volume-title": "Zenodo",
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},
{
"key": "bib110",
"author": "Van der Sar",
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"unstructured": "Van der Sar E. 2015a. Elsevier Cracks Down on Pirated Scientific Articles. TorrentFreak. https://torrentfreak.com/elsevier-cracks-down-on-pirated-scientific-articles-150609/ [Accessed February 7, 2018].",
"article-title": "Elsevier Cracks Down on Pirated Scientific Articles",
"volume-title": "TorrentFreak"
},
{
"key": "bib111",
"author": "Van der Sar",
"year": "2015",
"unstructured": "Van der Sar E. 2015b. Court Orders Shutdown of Libgen, Bookfi and Sci-Hub. TorrentFreak. https://torrentfreak.com/court-orders-shutdown-of-libgen-bookfi-and-sci-hub-151102/ [Accessed February 7, 2018].",
"article-title": "Court Orders Shutdown of Libgen, Bookfi and Sci-Hub",
"volume-title": "TorrentFreak"
},
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"key": "bib112",
"author": "Van der Sar",
"year": "2015",
"unstructured": "Van der Sar E. 2015c. Sci-Hub, BookFi and LibGen Resurface After Being Shut Down. TorrentFreak. https://torrentfreak.com/sci-hub-and-libgen-resurface-after-being-shut-down-151121/ [Accessed February 7, 2018].",
"article-title": "Sci-Hub, BookFi and LibGen Resurface After Being Shut Down",
"volume-title": "TorrentFreak"
},
{
"key": "bib113",
"author": "Van der Sar",
"year": "2017",
"unstructured": "Van der Sar E. 2017a. Sci-Hub Ordered to Pay $15 Million in Piracy Damages. TorrentFreak. https://torrentfreak.com/sci-hub-ordered-to-pay-15-million-in-piracy-damages-170623/ [Accessed February 7, 2018].",
"article-title": "Sci-Hub Ordered to Pay $15 Million in Piracy Damages",
"volume-title": "TorrentFreak"
},
{
"key": "bib114",
"author": "Van der Sar",
"year": "2017",
"unstructured": "Van der Sar E. 2017b. New Lawsuit Demands ISP Blockades Against “Pirate” Site Sci-Hub. TorrentFreak. https://torrentfreak.com/new-lawsuit-demands-isp-blockades-against-pirate-site-sci-hub-170629/ [Accessed February 7, 2018].",
"article-title": "New Lawsuit Demands ISP Blockades Against “Pirate” Site Sci-Hub",
"volume-title": "TorrentFreak"
},
{
"key": "bib115",
"doi-asserted-by": "publisher",
"first-page": "821",
"DOI": "10.1098/rstl.1677.0003",
"article-title": "Observations, communicated to the publisher by Mr. Antony van Leewenhoeck, in a dutch Letter of the 9th Octob. 1676. here English'd: concerning little animals by him observed in rain-well-sea- and snow water; as also in water wherein pepper had lain infused",
"volume": "12",
"author": "van Leewenhoeck",
"year": "1677",
"journal-title": "Philosophical Transactions of the Royal Society of London"
},
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"DOI": "10.1038/483134a",
"article-title": "Trouble at the text mine",
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"year": "2012",
"journal-title": "Nature"
},
{
"key": "bib117",
"doi-asserted-by": "publisher",
"first-page": "386",
"DOI": "10.1038/500386a",
"article-title": "Half of 2011 papers now free to read",
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"year": "2013",
"journal-title": "Nature"
},
{
"key": "bib118",
"doi-asserted-by": "publisher",
"first-page": "426",
"DOI": "10.1038/495426a",
"article-title": "Open access: The true cost of science publishing",
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"year": "2013",
"journal-title": "Nature"
},
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"article-title": "Funders punish open-access dodgers",
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"year": "2014",
"journal-title": "Nature"
},
{
"key": "bib120",
"author": "Van Noorden",
"year": "2015",
"article-title": "Nature owner merges with publishing giant",
"journal-title": "Nature",
"DOI": "10.1038/nature.2015.16731",
"doi-asserted-by": "publisher"
},
{
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"author": "Van Noorden",
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"DOI": "10.1038/540507a",
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},
{
"key": "bib122",
"author": "Vogel",
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"article-title": "A bold open-access push in Germany could change the future of academic publishing",
"journal-title": "Science",
"DOI": "10.1126/science.aap7562",
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},
{
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"article-title": "Digital Object Identifiers and Their Use in Libraries",
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"author": "Wang",
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"journal-title": "Serials Review"
},
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"first-page": "e1005962",
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"article-title": "A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts",
"volume": "14",
"author": "Westergaard",
"year": "2017",
"journal-title": "PLoS Computational Biology"
},
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"key": "bib125",
"author": "Woltermann",
"year": "2015",
"unstructured": "Woltermann A. 2015. Declaration in Support of Motion – Document #8 Attachment #23 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS. Southern District Court of New York. https://www.courtlistener.com/docket/4355308/8/23/elsevier-inc-v-sci-hub/ [Accessed February 7, 2018].",
"article-title": "Declaration in Support of Motion – Document #8 Attachment #23 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS",
"volume-title": "Southern District Court of New York"
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],
"container-title": "eLife",
"original-title": [],
"language": "en",
"link": [
{
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"content-type": "application/xml",
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}
],
"deposited": {
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[
2018,
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24
]
],
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"timestamp": 1535123298000
},
"score": 1.0,
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]
},
"references-count": 126,
"alternative-id": [
"10.7554/eLife.32822"
],
"URL": "https://doi.org/ckcj",
"relation": {
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{
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"General Neuroscience",
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CSL Schema Pruning
The provenance of every statement, measure, and figure can be traced to its origin.
![**Downloads per day on Sci-Hub for months with access logs.**](https://raw.githubusercontent.com/greenelab/scihub/e35cc7b0d3b6dd65bf8ce18945007d2b44a6be1e/download/scihub-logs-2017/scihub-log-downloads.svg?sanitize=true)
{
"creation_time_utc": "2018-06-15T14:25:26.787993",
"commit": "63d2468883ea69ad7ad638c39efab0fcbe026298",
"total_commits": 755,
"manuscript_commits": 349,
"deep_review_authors": 36,
"deep_review_post_submission_authors": 14,
"github_stars": 616,
"github_forks": 165,
"merged_pull_requests": 315,
"declined_pull_requests": 22,
"open_pull_requests": 0,
"open_issues": 322,
"closed_issues": 215
}
the Deep Review repository accumulated {{total_commits}} git commits, {{merged_pull_requests}} merged pull requests, {{open_issues + closed_issues}} issues, and {{github_stars}} GitHub stars.
“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
See blog post at https://rhodesmill.org/brandon/2012/one-sentence-per-line/
Manubot is an ideal authoring protocol for real-time open science, especially for projects that are already using an open source software workflow to manage their research. While Manubot does require technical expertise, the benefits are manyfold. Specifically, Manubot demonstrates a system for publishing that is transparent, reproducible, immediate, permissionless, versioned, automated, collaborative, open, linked, provenanced, decentralized, hackable, interactive, annotated, and free of charge. These attributes empower integrating Manubot with an ecosystem of other community-driven tools to make science as open and collaborative as possible.
Manubot is an ideal authoring protocol for real-time open science, especially for projects that are already using an open source software workflow to manage their research.
While Manubot does require technical expertise, the benefits are manyfold.
Specifically, Manubot demonstrates a system for publishing that is transparent, reproducible, immediate, permissionless, versioned, automated, collaborative, open, linked, provenanced, decentralized, hackable, interactive, annotated, and free of charge.
These attributes empower integrating Manubot with an ecosystem of other community-driven tools to make science as open and collaborative as possible.
Manubot is an ideal
authoring protocol for
real-time open science,
especially for projects
that are already using
an open source software
workflow to manage their
research. While Manubot
does require technical
expertise, the benefits
are manyfold.
Specifically, Manubot
demonstrates a system
for publishing that is
transparent,
reproducible, immediate,
permissionless,
versioned, automated,
collaborative, open,
linked, provenanced,
decentralized, hackable,
interactive, annotated,
and free of charge.
These attributes empower
integrating Manubot with
an ecosystem of other
community-driven tools
to make science as open
and collaborative as
possible.
As of January 2019, there are about 50 public Manubot manuscripts. https://git.io/fx4g9
The Deep Review
most viewed bioRxiv preprint of 2017
real-time open science
Sci-Hub Coverage Study was most viewed PeerJ Preprint of 2017!
undergraduate progress reports
grant progress reports
climate dataset publications
dataviz OSS manuscripts
personal literature reviews
genomics research papers
historical reproductions
github.com/dhimmel/psb-manuscript
https://git.dhimmel.com/psb-manuscript/
the one time self-citations are officially encouraged!
goal: create a pull request to add your section
use the same indentation as other uncommented authors!
(spaces not tabs)
Greetings, I'm in the [Greene Lab](http://www.greenelab.com/) at the University of Pennsylvania and am the lead developer of the Manubot project.
2019 is my first PSB and I'm exciting to backpack around the Big Island following the conference.
My main area of research is integrating biomedical knowledge using hetnets [@pmid:26158728; @doi:10.7554/eLife.26726].
However, I've also studied Sci-Hub, finding that it provides access to nearly all paywalled scholarly literature [@pmcid:PMC5832410].
Perhaps my biggest discovery was observing an epidemiological association that higher elevation counties have lower rates of lung cancer, suggesting that oxygen is an inhaled carcinogen (Figure @fig:elevcan) [@doi:10.7717/peerj.705; @url:https://nyti.ms/1NuB0WJ].
![
The association between elevation and lung cancer across Western U.S. counties.
](https://github.com/dhimmel/elevcan/raw/7aed9f29d2371eb4918f337a138608e6b6d9e311/manual/figures/peerj/Figure_4.png){#fig:elevcan width="100%"}
I haven't done much text mining, but I did enjoy extracting attendee names for PSB from the online PDF.
Converting the PDF to text in Python was [as easy as](https://github.com/dhimmel/psb-manuscript/blob/15babecdf2a915f88088703e23a61e34e1294b1f/attendees/attendees.ipynb):
```python
# https://stackoverflow.com/a/48673754
import tika.parser
parsed = tika.parser.from_file('attendees.pdf')
text = parsed["content"]
```
markdown: see existing sections for examples
Go to 02.author-sections.md:
git.io/fh3Ty
Click edit pencil, add section about self, create pull request.
Uncomment author info at:
github.com/{username}/psb-manuscript/edit/patch-1/content/metadata.yaml
github.com/dhimmel/psb-manuscript
USAGE: git.io/fh3I8
G-2018-11163
GBMF4552
Open collaborative writing with Manubot
Daniel S. Himmelstein, David R. Slochower, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
Manubot Preprint (2018) https://greenelab.github.io/meta-review/
Deep Review Authors:
Paul-Michael Agapow, Amr M. Alexandari, Brett K. Beaulieu-Jones, Anne E. Carpenter, Travers Ching, Evan M. Cofer, Dave DeCaprio, Brian T. Do, Enrico Ferrero, David J. Harris, Michael M. Hoffman, Alexandr A. Kalinin, Anshul Kundaje, Jack Lanchantin, Christopher A. Lavender, Benjamin J. Lengerich, Zhiyong Lu, Yifan Peng, Yanjun Qi, Gail L. Rosen, Avanti Shrikumar, Srinivas C. Turaga, Gregory P. Way, Laura K. Wiley, Stephen Woloszynek, Wei Xie, Jinbo Xu, and Michael Zietz
Manubot contributors & users:
Ogun Adebali, Evan M. Cofer, Robert Gieseke, Alexander Dunkel, Ansel Halliburton, Achintya Rao, and other GitHub users.
@dhimmel
0000-0002-3012-7446
Getting started
https://manubot.org
Slides
https://slides.com/dhimmel/psb
Big Island Adventure Map
https://goo.gl/R8EpcA