Writing bio-computational manuscripts with Manubot

🌴 next generation publishing 🌴

slides.com/dhimmel/psb

#PSB19

January 4, 2019 · 3:45–5:00 PM

Salon 2 & 3

Fairmont Orcid, Big Island, Hawaii

Abstract

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

what is Manubot?

system for writing papers via GitHub

powering the next generation of scholarly manuscript

  • transparent & reproducible
  • immediate & permissionless
  • versioned & automated
  • collaborative
  • open & free of charge

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/

Manubot mechanics

1. modify the manuscript source

2. continuous integration rebuilds the manuscript

Timestamped on the Bitcoin blockchain via OpenTimestamps

3. continuous deployment back to GitHub

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

open source software workflow

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/
].

citation by persistent identifier

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].

versus

  1. B. Durmaz, M. Dalgalar, R. Durmaz, Anaerobe 11 (2005) 318-321.
  2. J.I. Keenan, A. Aitchison, R.V. Purcell, R. Greenlees, J.F. Pearson, F.A. Frizelle, Anaerobe 40 (2016) 50-53.
  3. J. Silva, D. Leite, M. Fernandes, C. Mena, P.A. Gibbs, P. Teixeira, Front. Microbiol. 2 (2011) 200.

Example from my uBiome SmartGut report

References

  1. 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

manubot cite

https://github.com/greenelab/manubot

manubot on PyPI

python command line utility

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

Technical details of citation metadata retrieval

[
  {
    "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": {
      "date-parts": [
        [
          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
[
  {
    "indexed": {
      "date-parts": [
        [
          2018,
          10,
          11
        ]
      ],
      "date-time": "2018-10-11T04:22:36Z",
      "timestamp": 1539231756463
    },
    "reference-count": 126,
    "publisher": "eLife Sciences Publications, Ltd",
    "license": [
      {
        "URL": "http://creativecommons.org/licenses/by/4.0/",
        "start": {
          "date-parts": [
            [
              2018,
              3,
              1
            ]
          ],
          "date-time": "2018-03-01T00:00:00Z",
          "timestamp": 1519862400000
        },
        "delay-in-days": 0,
        "content-version": "vor"
      },
      {
        "URL": "http://creativecommons.org/licenses/by/4.0/",
        "start": {
          "date-parts": [
            [
              2018,
              3,
              1
            ]
          ],
          "date-time": "2018-03-01T00:00:00Z",
          "timestamp": 1519862400000
        },
        "delay-in-days": 0,
        "content-version": "am"
      },
      {
        "URL": "http://creativecommons.org/licenses/by/4.0/",
        "start": {
          "date-parts": [
            [
              2018,
              3,
              1
            ]
          ],
          "date-time": "2018-03-01T00:00:00Z",
          "timestamp": 1519862400000
        },
        "delay-in-days": 0,
        "content-version": "tdm"
      }
    ],
    "funder": [
      {
        "DOI": "10.13039/100000936",
        "name": "Gordon and Betty Moore Foundation",
        "doi-asserted-by": "publisher",
        "award": [
          "GBMF 4552"
        ]
      }
    ],
    "content-domain": {
      "domain": [],
      "crossmark-restriction": false
    },
    "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",
    "created": {
      "date-parts": [
        [
          2018,
          2,
          9
        ]
      ],
      "date-time": "2018-02-09T13:00:23Z",
      "timestamp": 1518181223000
    },
    "source": "Crossref",
    "is-referenced-by-count": 3,
    "title": "Sci-Hub provides access to nearly all scholarly literature",
    "prefix": "10.7554",
    "volume": "7",
    "author": [
      {
        "ORCID": "http://orcid.org/0000-0002-3012-7446",
        "authenticated-orcid": true,
        "given": "Daniel S",
        "family": "Himmelstein",
        "sequence": "first",
        "affiliation": [
          {
            "name": "Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, United States"
          }
        ]
      },
      {
        "ORCID": "http://orcid.org/0000-0003-2290-4927",
        "authenticated-orcid": true,
        "given": "Ariel Rodriguez",
        "family": "Romero",
        "sequence": "additional",
        "affiliation": [
          {
            "name": "Bidwise, Inc, Miami, United States"
          }
        ]
      },
      {
        "ORCID": "http://orcid.org/0000-0003-1563-7314",
        "authenticated-orcid": true,
        "given": "Jacob G",
        "family": "Levernier",
        "sequence": "additional",
        "affiliation": [
          {
            "name": "Library Technology Services and Strategic Initiatives, University of Pennsylvania, Philadelphia, United States"
          }
        ]
      },
      {
        "ORCID": "http://orcid.org/0000-0002-3366-7149",
        "authenticated-orcid": true,
        "given": "Thomas Anthony",
        "family": "Munro",
        "sequence": "additional",
        "affiliation": [
          {
            "name": "School of Life and Environmental Sciences, Deakin University, Melbourne, Australia"
          }
        ]
      },
      {
        "ORCID": "http://orcid.org/0000-0002-9888-3168",
        "authenticated-orcid": true,
        "given": "Stephen Reid",
        "family": "McLaughlin",
        "sequence": "additional",
        "affiliation": [
          {
            "name": "School of Information, University of Texas at Austin, Austin, United States"
          }
        ]
      },
      {
        "ORCID": "http://orcid.org/0000-0002-9925-9623",
        "authenticated-orcid": true,
        "given": "Bastian",
        "family": "Greshake Tzovaras",
        "sequence": "additional",
        "affiliation": [
          {
            "name": "Department of Applied Bioinformatics, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany"
          }
        ]
      },
      {
        "ORCID": "http://orcid.org/0000-0001-8713-9213",
        "authenticated-orcid": true,
        "given": "Casey S",
        "family": "Greene",
        "sequence": "additional",
        "affiliation": [
          {
            "name": "Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, United States"
          }
        ]
      }
    ],
    "member": "4374",
    "published-online": {
      "date-parts": [
        [
          2018,
          3,
          1
        ]
      ]
    },
    "reference": [
      {
        "key": "bib1",
        "author": "Archambault",
        "year": "2014",
        "unstructured": "Archambault É, Amyot D, Deschamps P, Nicol A, Provencher F, Rebout L, Roberge G. 2014. Proportion of Open Access Papers Published in Peer-Reviewed Journals at the European and World Levels: 1996–2013. University of Nebraska-Lincoln. http://digitalcommons.unl.edu/scholcom/8 [Accessed February 7, 2018].",
        "article-title": "Proportion of Open Access Papers Published in Peer-Reviewed Journals at the European and World Levels: 1996–2013",
        "volume-title": "University of Nebraska-Lincoln"
      },
      {
        "key": "bib2",
        "author": "Association of Research Libraries",
        "year": "2017",
        "unstructured": "Association of Research Libraries. 2017. Graph 4: Expenditure Trends in ARL Libraries, 1986-2015. ARL Statistics 2014–2015. http://www.arl.org/storage/documents/expenditure-trends.pdf [Accessed February 7, 2018].",
        "article-title": "Graph 4: Expenditure Trends in ARL Libraries, 1986-2015",
        "volume-title": "ARL Statistics 2014–2015"
      },
      {
        "key": "bib3",
        "author": "Barnes A",
        "year": "2017",
        "unstructured": "Barnes A L, Weslow D E, Gardner M J. 2017. Complaint – Document #1 of American Chemical Society v. Does – Case 1:17-cv-00726-LMB-JFA. Eastern District Court of Virginia. https://www.courtlistener.com/docket/6146630/1/american-chemical-society-v-does-1-99/ [Accessed February 7, 2018].",
        "article-title": "Complaint – Document #1 of American Chemical Society v. Does – Case 1:17-cv-00726-LMB-JFA",
        "volume-title": "Eastern District Court of Virginia"
      },
      {
        "key": "bib4",
        "doi-asserted-by": "publisher",
        "first-page": "342",
        "DOI": "10.1038/nbt.3780",
        "article-title": "Reproducibility of computational workflows is automated using continuous analysis",
        "volume": "35",
        "author": "Beaulieu-Jones",
        "year": "2017",
        "journal-title": "Nature Biotechnology"
      },
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        "first-page": "11",
        "DOI": "10.1038/535011f",
        "article-title": "Publisher under fire for fake article webpages",
        "volume": "535",
        "author": "Becker",
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      },
      {
        "key": "bib6",
        "doi-asserted-by": "publisher",
        "first-page": "e608",
        "DOI": "10.1016/S2214-109X(16)30188-7",
        "article-title": "Sci-Hub and medical practice: an ethical dilemma in Peru",
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      {
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        "unstructured": "Benet J. 2014. IPFS - Content Addressed, Versioned, P2P File System. arXiv. https://arxiv.org/abs/1407.3561v1 [Accessed February 7, 2018].",
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      },
      {
        "key": "bib8",
        "doi-asserted-by": "publisher",
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        "volume": "111",
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      },
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      {
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        "DOI": "10.2139/ssrn.2616636",
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      },
      {
        "key": "bib11",
        "author": "Bodó",
        "year": "2016",
        "unstructured": "Bodó B. 2016. Pirates in the Library An Inquiry into the Guerilla Open Access Movement. 8th Annual Workshop of the International Society for the History and Theory of Intellectual Property.",
        "article-title": "Pirates in the Library An Inquiry into the Guerilla Open Access Movement",
        "DOI": "10.2139/ssrn.2816925",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib12",
        "doi-asserted-by": "publisher",
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        "DOI": "10.1126/science.352.6285.511",
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      },
      {
        "key": "bib13",
        "doi-asserted-by": "publisher",
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        "DOI": "10.1126/science.352.6285.508",
        "article-title": "Who's downloading pirated papers? Everyone",
        "volume": "352",
        "author": "Bohannon",
        "year": "2016",
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      },
      {
        "key": "bib14",
        "author": "Bosch",
        "year": "2017",
        "unstructured": "Bosch S, Henderson K. 2017. New World, Same Model | Periodicals Price Survey 2017. Library Journal. http://lj.libraryjournal.com/2017/04/publishing/new-world-same-model-periodicals-price-survey-2017/ [Accessed February 7, 2018].",
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        "volume-title": "Library Journal"
      },
      {
        "key": "bib15",
        "author": "Bosman",
        "year": "2018",
        "article-title": "Open access levels: a quantitative exploration using Web of Science and oaDOI data",
        "volume-title": "PeerJ Preprints",
        "DOI": "10.7287/peerj.preprints.3520v1",
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      },
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        "doi-asserted-by": "publisher",
        "first-page": "1453",
        "DOI": "10.1007/s11192-016-2225-6",
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        "volume": "110",
        "author": "Boudry",
        "year": "2017",
        "journal-title": "Scientometrics"
      },
      {
        "key": "bib17",
        "author": "Brinkema L",
        "year": "2017",
        "unstructured": "Brinkema L M. 2017. Order – Document #37 of American Chemical Society v. Sci-Hub – Case 1:17-cv-00726-LMB-JFA. Eastern District Court of Virginia. https://regmedia.co.uk/2017/11/07/sci_hub_block_order_short.pdf [Accessed February 7, 2018].",
        "article-title": "Order – Document #37 of American Chemical Society v. Sci-Hub – Case 1:17-cv-00726-LMB-JFA",
        "volume-title": "Eastern District Court of Virginia"
      },
      {
        "key": "bib18",
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        "year": "2012",
        "unstructured": "British Standards Institute. 2012. BS ISO 26324:2012 Information and Documentation. Digital Object Identifier System.",
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        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib19",
        "author": "Brook",
        "volume": "20",
        "year": "2014",
        "article-title": "The social, political and legal aspects of text and data mining (TDM)",
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        "DOI": "10.1045/november14-brook",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib20",
        "author": "Buranyi",
        "year": "2017",
        "unstructured": "Buranyi S. 2017. Is the staggeringly profitable business of scientific publishing bad for science?. The Guardian. https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science [Accessed February 7, 2018].",
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      },
      {
        "key": "bib21",
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      },
      {
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        "year": "2017",
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        "unstructured": "ConsenSys. 2016. Decentralized Storage: The Backbone of the Third Web. ConsenSys Media. https://media.consensys.net/decentralized-storage-the-backbone-of-the-third-web-d4bc54e79700 [Accessed February 7, 2018].",
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      {
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        "year": "2015",
        "unstructured": "DeMarco JV, Hirschberg DM, Sen U. 2015a. Complaint – Document #1 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS. Southern District Court of New York. https://www.courtlistener.com/docket/4355308/1/elsevier-inc-v-sci-hub/ [Accessed February 7, 2018].",
        "article-title": "Complaint – Document #1 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS",
        "volume-title": "Southern District Court of New York"
      },
      {
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        "year": "2015",
        "unstructured": "DeMarco JV, Hirschberg DM, Sen U. 2015b. Memorandum of Law in Support of Motion – Document #6 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS. Southern District Court of New York. https://www.courtlistener.com/docket/4355308/6/elsevier-inc-v-sci-hub/ [Accessed February 7, 2018].",
        "article-title": "Memorandum of Law in Support of Motion – Document #6 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS",
        "volume-title": "Southern District Court of New York"
      },
      {
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      },
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        "key": "bib91",
        "author": "Schiermeier",
        "year": "2015",
        "article-title": "Pirate research-paper sites play hide-and-seek with publishers",
        "journal-title": "Nature",
        "DOI": "10.1038/nature.2015.18876",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib92",
        "author": "Schiermeier",
        "year": "2017",
        "article-title": "US court grants Elsevier millions in damages from Sci-Hub",
        "journal-title": "Nature",
        "DOI": "10.1038/nature.2017.22196",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib93",
        "author": "Schiermeier",
        "year": "2017",
        "article-title": "Pirate paper website Sci-Hub dealt another blow by US courts",
        "journal-title": "Nature",
        "DOI": "10.1038/nature.2017.22971",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib94",
        "doi-asserted-by": "publisher",
        "first-page": "137",
        "DOI": "10.1038/d41586-018-00093-7",
        "article-title": "Germany vs Elsevier: universities win temporary journal access after refusing to pay fees",
        "volume": "553",
        "author": "Schiermeier",
        "year": "2018",
        "journal-title": "Nature"
      },
      {
        "key": "bib95",
        "doi-asserted-by": "publisher",
        "first-page": "230",
        "DOI": "10.1186/s12916-015-0469-2",
        "article-title": "'Predatory' open access: a longitudinal study of article volumes and market characteristics",
        "volume": "13",
        "author": "Shen",
        "year": "2015",
        "journal-title": "BMC Medicine"
      },
      {
        "key": "bib96",
        "author": "Silver",
        "year": "2017",
        "unstructured": "Silver A. 2017. Sci-Hub domains inactive following court order. The Register. http://www.theregister.co.uk/2017/11/23/scihubs_become_inactive_following_court_order/ [Accessed February 7, 2018].",
        "article-title": "Sci-Hub domains inactive following court order",
        "volume-title": "The Register"
      },
      {
        "key": "bib97",
        "author": "Singh Chawla",
        "year": "2017",
        "article-title": "Publishers go after networking site for illicit sharing of journal papers",
        "journal-title": "Science",
        "DOI": "10.1126/science.aaq0132",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib98",
        "author": "Singh Chawla",
        "year": "2017",
        "article-title": "Publishers take ResearchGate to court, alleging massive copyright infringement",
        "journal-title": "Science",
        "DOI": "10.1126/science.aaq1560",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib99",
        "doi-asserted-by": "publisher",
        "first-page": "399",
        "DOI": "10.1038/d41586-017-05922-9",
        "article-title": "Need a paper? Get a plug-in",
        "volume": "551",
        "author": "Singh Chawla",
        "year": "2017",
        "journal-title": "Nature"
      },
      {
        "key": "bib100",
        "author": "Singh Chawla",
        "year": "2017",
        "article-title": "Unpaywall finds free versions of paywalled papers",
        "journal-title": "Nature",
        "DOI": "10.1038/nature.2017.21765",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib101",
        "author": "Standish",
        "year": "2017",
        "unstructured": "Standish R. 2017. The World’s Largest Free Scientific Resource Is Now Blocked in Russia. Foreign Policy. http://foreignpolicy.com/2017/09/06/the-worlds-largest-free-scientific-resource-is-now-blocked-in-russia/ [Accessed February 7, 2018].",
        "article-title": "The World’s Largest Free Scientific Resource Is Now Blocked in Russia",
        "volume-title": "Foreign Policy"
      },
      {
        "key": "bib102",
        "author": "Suber",
        "year": "2008",
        "unstructured": "Suber P. 2008. Gratis and libre open access. SPARC Open Access Newsletter. https://dash.harvard.edu/handle/1/4322580 [Accessed February 7, 2018].",
        "article-title": "Gratis and libre open access",
        "volume-title": "SPARC Open Access Newsletter"
      },
      {
        "key": "bib103",
        "author": "Suber",
        "year": "2017",
        "unstructured": "Suber P. 2017. Open Access. MIT Press. https://mitpress.mit.edu/books/open-access.",
        "article-title": "Open Access"
      },
      {
        "key": "bib104",
        "doi-asserted-by": "publisher",
        "first-page": "642",
        "DOI": "10.5860/crln.72.11.8671",
        "article-title": "Is free inevitable in scholarly communication?: The economics of open access",
        "volume": "72",
        "author": "Sutton",
        "year": "2011",
        "journal-title": "College & Research Libraries News"
      },
      {
        "key": "bib105",
        "author": "Sweet",
        "year": "2015",
        "unstructured": "Sweet RW. 2015. Memorandum & Opinion – Document #53 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS. Southern District Court of New York. https://www.courtlistener.com/docket/4355308/53/elsevier-inc-v-sci-hub/ [Accessed February 7, 2018].",
        "article-title": "Memorandum & Opinion – Document #53 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS",
        "volume-title": "Southern District Court of New York"
      },
      {
        "key": "bib106",
        "author": "Sweet",
        "year": "2017",
        "unstructured": "Sweet RW. 2017. Judgement – Document #87 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS. Southern District Court of New York. https://www.documentcloud.org/documents/3878258-2017-06-21-Elsevier-Sci-Hub-Final-Judgement.html [Accessed February 7, 2018].",
        "article-title": "Judgement – Document #87 of Elsevier Inc. v. Sci-Hub – Case 1:15-cv-04282-RWS",
        "volume-title": "Southern District Court of New York"
      },
      {
        "key": "bib107",
        "doi-asserted-by": "publisher",
        "first-page": "632",
        "DOI": "10.12688/f1000research.8460.3",
        "article-title": "The academic, economic and societal impacts of Open Access: an evidence-based review",
        "volume": "5",
        "author": "Tennant",
        "year": "2016",
        "journal-title": "F1000Research"
      },
      {
        "key": "bib108",
        "author": "Travis",
        "year": "2016",
        "article-title": "In survey, most give thumbs-up to pirated papers",
        "journal-title": "Science",
        "DOI": "10.1126/science.aaf5704",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib109",
        "author": "Tzovaras",
        "year": "2018",
        "article-title": "Sci-Hub download log of 2017",
        "volume-title": "Zenodo",
        "DOI": "10.5281/zenodo.1158301",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib110",
        "author": "Van der Sar",
        "year": "2015",
        "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"
      },
      {
        "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"
      },
      {
        "key": "bib116",
        "doi-asserted-by": "publisher",
        "first-page": "134",
        "DOI": "10.1038/483134a",
        "article-title": "Trouble at the text mine",
        "volume": "483",
        "author": "Van Noorden",
        "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",
        "volume": "500",
        "author": "Van Noorden",
        "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",
        "volume": "495",
        "author": "Van Noorden",
        "year": "2013",
        "journal-title": "Nature"
      },
      {
        "key": "bib119",
        "doi-asserted-by": "publisher",
        "first-page": "161",
        "DOI": "10.1038/508161a",
        "article-title": "Funders punish open-access dodgers",
        "volume": "508",
        "author": "Van Noorden",
        "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"
      },
      {
        "key": "bib121",
        "author": "Van Noorden",
        "year": "2016",
        "article-title": "Alexandra Elbakyan: Paper pirate",
        "journal-title": "Nature",
        "DOI": "10.1038/540507a",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib122",
        "author": "Vogel",
        "year": "2017",
        "article-title": "A bold open-access push in Germany could change the future of academic publishing",
        "journal-title": "Science",
        "DOI": "10.1126/science.aap7562",
        "doi-asserted-by": "publisher"
      },
      {
        "key": "bib123",
        "doi-asserted-by": "publisher",
        "first-page": "161",
        "DOI": "10.1080/00987913.2007.10765116",
        "article-title": "Digital Object Identifiers and Their Use in Libraries",
        "volume": "33",
        "author": "Wang",
        "year": "2007",
        "journal-title": "Serials Review"
      },
      {
        "key": "bib124",
        "doi-asserted-by": "publisher",
        "first-page": "e1005962",
        "DOI": "10.1371/journal.pcbi.1005962",
        "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"
      },
      {
        "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"
      },
      {
        "key": "bib126",
        "author": "Woolston",
        "year": "2016",
        "article-title": "Paper piracy sparks online debate",
        "journal-title": "Nature",
        "DOI": "10.1038/nature.2016.19841",
        "doi-asserted-by": "publisher"
      }
    ],
    "container-title": "eLife",
    "original-title": [],
    "language": "en",
    "link": [
      {
        "URL": "https://cdn.elifesciences.org/articles/32822/elife-32822-v3.pdf",
        "content-type": "application/pdf",
        "content-version": "vor",
        "intended-application": "text-mining"
      },
      {
        "URL": "https://cdn.elifesciences.org/articles/32822/elife-32822-v3.xml",
        "content-type": "application/xml",
        "content-version": "vor",
        "intended-application": "text-mining"
      }
    ],
    "deposited": {
      "date-parts": [
        [
          2018,
          8,
          24
        ]
      ],
      "date-time": "2018-08-24T15:08:18Z",
      "timestamp": 1535123298000
    },
    "score": 1.0,
    "subtitle": [],
    "short-title": [],
    "issued": {
      "date-parts": [
        [
          2018,
          3,
          1
        ]
      ]
    },
    "references-count": 126,
    "alternative-id": [
      "10.7554/eLife.32822"
    ],
    "URL": "https://doi.org/ckcj",
    "relation": {
      "references": [
        {
          "id-type": "doi",
          "id": "10.6084/m9.figshare.4906367.v1",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.5061/dryad.q447c/1",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.5281/zenodo.472493",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.6084/m9.figshare.5231245.v1",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.6084/m9.figshare.4816720",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.6084/m9.figshare.1186832.v23",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.6084/m9.figshare.4542433.v6",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.6084/m9.figshare.5255368.v1",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.6084/m9.figshare.5255365.v1",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.6084/m9.figshare.3443876.v3",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.5281/zenodo.837902",
          "asserted-by": "subject"
        },
        {
          "id-type": "doi",
          "id": "10.5281/zenodo.1158301",
          "asserted-by": "subject"
        }
      ],
      "cites": []
    },
    "ISSN": [
      "2050-084X"
    ],
    "subject": [
      "General Biochemistry, Genetics and Molecular Biology",
      "General Immunology and Microbiology",
      "General Neuroscience",
      "General Medicine"
    ],
    "PMCID": "PMC5832410",
    "PMID": "29424689",
    "id": "IhliSZDo"
  }
]

CSL Schema Pruning

CSL Data Validation

tidbits

end-to-end reproducibility

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)

Embed images using versioned links to source 

{
  "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.

Directly insert output using template variables

JSON provides analysis output

the future: living 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

tracking prose in git: newlines

no newlines

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.

word wrap at 25 chars

one sentence per line

"semantic newlines" create the best diffs & minimize conflict

current usage

As of January 2019, there are about 50 public Manubot manuscripts. https://git.io/fx4g9

The Deep Review

  • review article on deep learning in precision medicine
  • 27 authors from 20 different institutions
  • readers appreciate the breadth of perspectives

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

The people of the 24ᵗʰ annual PSB

contribute to this historic manuscript

github.com/dhimmel/psb-manuscript

https://git.dhimmel.com/psb-manuscript/

  • Introduce yourself briefly.
  • What do you research? Include any relevant links to your lab or personal website.
  • What is your favorite study from your career or what study was your biggest discovery?
  • What was your first scholarly publication?
  • Add a code snippet or mathematical equation.
  • Add a figure with a caption. This could be a picture of you in Hawaii or a figure from your previous work if the license is permissive enough to allow reuse.
  • Feel free to include other things!

what to write?

the one time self-citations are officially encouraged!

goal: create a pull request to add your section

content/metadata.yaml

content/02.author-sections.md

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

contribution workflow

  1. Go to 02.author-sections.md:
    
    git.io/fh3Ty
  2. Click edit pencil, add section about self, create pull request.

  3. Uncomment author info at:
    github.com/{username}/psb-manuscript/edit/patch-1/content/metadata.yaml
  4. See if continuous integration passes. Wait for review.
github.com/dhimmel/psb-manuscript
USAGE: git.io/fh3I8

getting started

manubot-rootstock

manubot.org

Acknowledgments

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.

Funding

Questions?

@dhimmel

0000-0002-3012-7446

Getting started
https://manubot.org
Slides
https://slides.com/dhimmel/psb

Big Island Adventure Map

https://goo.gl/R8EpcA

PSB 2019: Writing bio-computational manuscripts with Manubot

By Daniel Himmelstein

PSB 2019: Writing bio-computational manuscripts with Manubot

Special Working Group in Hawaii at the Pacific Symposium on Biocomputing on 2019-01-04. This presentation is released under a CC BY 4.0 License.

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