Open collaborative writing with Manubot

This manuscript (permalink) was automatically generated from greenelab/meta-review@4b6396b on July 27, 2018.



Scientific literature reviews are ideal for open, collaborative writing. Allowing any interested individual to contribute as an author can strengthen a review, providing broad and fair coverage of the subject matter. However, the traditional multi-author writing process breaks down at scale. We present techniques for overcoming the challenges of open manuscript writing. These include approaches for managing distributed authors and our new software, named Manubot, for automating citation and manuscript building.


The internet enables science to be shared in real-time at a low cost to a global audience. This development has decreased the barriers to making science open, while supporting new massively collaborative models of research. However, the scientific community requires tools whose workflows encourage openness rather than stifle it. For example, manuscripts are the cornerstone of scholarly communication, but drafting and publishing manuscripts has traditionally relied on proprietary or offline tools that do not support open scholarly writing, where anyone is able to contribute and the contribution history is preserved and public. Hence, we report a new tool and workflow for authoring scholarly manuscripts in the open, as well as the collaborative project which led to its creation.

Open scholarly writing, a form of crowdsourcing [1], has particular benefits for review articles, which present the state of the art in a scientific field [2]. Literature reviews are typically written in private by a closed team of colleagues. In contrast, broadly opening the process to anyone engaged in the topic — such that planning, organizing, writing, and editing occur collaboratively in a public forum where anyone is welcome to participate — can maximize a review’s value. Open drafting of reviews is especially helpful for capturing state-of-the-art knowledge about rapidly advancing research topics at the intersection of existing disciplines where contributors bring diverse opinions and expertise.

Based on our experience leading a recent open review [3], we discuss the pros and cons of open collaborative reviews as well as how they contribute to a living and frequently updated literature. Our review manuscript [4], code-named the Deep Review, surveyed deep learning’s role in biology and precision medicine, a research area undergoing explosive growth. In addition, we introduce Manubot, the infrastructure we created to enable open manuscript writing online for Deep Review, which was subsequently adopted by other projects.

We initiated the Deep Review by creating a GitHub repository ( to coordinate and manage contributions. GitHub is a platform designed for collaborative software development that’s adaptable for collaborative writing. From the start, we made the GitHub repository public, applying a Creative Commons Attribution License to the manuscript. Next, we encouraged anyone interested to contribute by proposing changes or additions. Although we invited some specific experts to participate, most authors discovered the manuscript organically through conferences or social media, deciding to contribute without solicitation. In total, the Deep Review attracted 36 authors who were not determined in advance from 20 different institutions.

Writing review articles in a public forum allows review authors to engage with the original researchers to clarify their methods and results and present them accurately, as exemplified here. Additionally, discussing manuscripts in the open generates valuable post-publication peer review [5,6,7] or pre-publication peer review of preprints [8]. Because incentives are commonly lacking to provide public peer review of existing literature [9], open collaborative reviews — where authorship is open to anyone who makes a valid contribution — could help spur more post-publication peer review. However, inviting wide authorship brings many technical and social challenges such as how to fairly distribute credit, coordinate the scientific content, and collaboratively manage extensive reference lists.

To address these challenges, we developed a manuscript writing process using the Markdown language, the GitHub platform, and our new Manubot tool for automating manuscript generation.

Contribution workflow

There are many existing collaborative writing platforms ranging from rich text editors, which support Microsoft Word documents or similar formats, to LaTeX-based systems for technical writing [10] such as Overleaf and Authorea. These platforms ideally offer version control, multiple permission levels, or other functionality to support multi-author document editing. Although they work well for editing text, they lack sufficient features for managing a collaborative manuscript and attributing precise credit, which are important for open writing (Table 1).

Table 1: Collaborative writing platforms. A summary of features that differentiate Manubot from existing collaborative writing platforms. We assessed features on June 15, 2018 using the free version of each platform. Some platforms offer additional features through a paid subscription or software. 1Additional functionality, such as bibliography management, is available by editing the Word document stored in OneDrive with the paid Word desktop application. 2Conversations about modifications take place on the document as comments, annotations, or unsaved chats. There is no separate integrated forum for discussing and editing revisions. 3Simultaneous edits online can be attributed to a single author in a git commit.
Feature Manubot Authorea + BibTeX Overleaf + BibTeX Google Docs + Paperpile Word Online1 Markdown on GitHub
Multi-author editing Yes Yes Yes Yes Yes Yes
Propose changes Yes No No Yes No Yes
Continuous integration testing Yes No No No No No
Multi-participant conversation for changes Yes No2 No2 No2 No2 Yes
Character-level provenance for text Yes No (versions tracked by day) No3 Requires manual inspection of history Not after changes are accepted Yes
Bibliography management Yes Yes Yes Yes No, requires the Word desktop application No
Cite by common identifiers Yes No No No No No
Editing software Any text editor Web interface Web interface Web interface Web interface Any text editor
Document format Markdown LaTeX LaTeX Proprietary Proprietary Markdown
Templating Yes Yes Yes No No No
Technial expertise required Yes Yes Yes No No Yes

In our workflow, we adopt standard software development strategies in order to enable any contributor to edit any part of the manuscript but enforce discussion and review of all proposed changes. The GitHub platform provides support for organizing and editing the manuscript. We use GitHub issues for organization, opening a new issue for each discussion topic. For a review manuscript, this includes each primary paper under consideration. Within a paper’s issue, contributors summarize the research, discuss it (sometimes with the original authors), and assess its relevance to the review. Issues also serve as an open to-do list and a forum for debating the main message, themes, and topics of the review.

GitHub and the underlying git version control system [11,12] also structure the writing process. The official version of the manuscript is forked by individual contributors. A contributor then adds and revises files, grouping these changes into commits. When the changes are ready to be reviewed, the series of commits are submitted as a pull request through GitHub, which notifies other authors of the pending changes. GitHub’s review interface allows anyone to comment on the changes, globally or at specific lines, asking questions or requesting modifications as depicted in 13. Conversations during review can reference other pull requests, issues, or authors, linking the relevant people and content, as illustrated in Figure 1. Reviewing batches of revisions that focus on a single theme is more efficient than independently discussing isolated comments and edits, and it helps maintain consistent content and tone across different authors and reviewers. Once all requested modifications are made, the manuscript maintainers, a subset of authors with elevated GitHub permissions, formally approve the pull request and merge the changes into the official version. The process of writing and revising material can be orchestrated through GitHub with a web browser or a local text editor.

Figure 1: Deep Review editing workflow. Any reader can become a contributor by proposing a change through a pull request. In this example, the contributor opens an issue to discuss a manuscript modification. A maintainer and additional participant provide feedback, and the maintainer recommends creating a pull request to update the text. The contributor creates the pull request, it is reviewed by a maintainer and a participant, and the contributor updates the pull request in response. Once the pull request is approved, the maintainer merges the changes into the official version of the manuscript.
Figure 1: Deep Review editing workflow. Any reader can become a contributor by proposing a change through a pull request. In this example, the contributor opens an issue to discuss a manuscript modification. A maintainer and additional participant provide feedback, and the maintainer recommends creating a pull request to update the text. The contributor creates the pull request, it is reviewed by a maintainer and a participant, and the contributor updates the pull request in response. Once the pull request is approved, the maintainer merges the changes into the official version of the manuscript.

The Deep Review issue and pull request on protein-protein interactions demonstrate this process in practice. A new contributor identified a relevant research topic that was missing from the review manuscript with examples of how the literature would be synthesized. A maintainer confirmed that this was a desirable topic and referred to related open issues. The contributor made the pull request, and two maintainers and another participant made recommendations. After four rounds of reviews and pull request edits, a maintainer merged the changes.

We found that this workflow was an effective compromise between fully unrestricted editing and a more heavily-structured approach that limited the authors or the sections they could edit. In addition, authors are associated with their commits, which makes it easy for contributors to receive credit for their work and helps prevent ghostwriting [14]. Figure 2 and the GitHub contributors page summarize all edits and commits from each author, providing aggregated information that is not available on other collaborative writing platforms. Because our writing process tracks the complete history through git commits, it enables detailed retrospective contribution analysis.

Figure 2: Deep Review contributions by author over time. The total words added to the Deep Review by each author is plotted over time (final values in parentheses). These statistics were extracted from git commit diffs of the manuscript’s Markdown source. This figure reveals the composition of written contributions to the manuscript at every point in its history. Deep Review was initiated in August 2016, and the first complete manuscript was released as a preprint [15] in May 2017. While the article was under review, we continued to maintain the project and accepted new contributions. The preprint was updated in January 2018, and the article was accepted by the journal in March 2018 [4]. As of June 15, 2018, the Deep Review repository accumulated 755 git commits, 315 merged pull requests, 537 issues, and 616 GitHub stars.
Figure 2: Deep Review contributions by author over time. The total words added to the Deep Review by each author is plotted over time (final values in parentheses). These statistics were extracted from git commit diffs of the manuscript’s Markdown source. This figure reveals the composition of written contributions to the manuscript at every point in its history. Deep Review was initiated in August 2016, and the first complete manuscript was released as a preprint [15] in May 2017. While the article was under review, we continued to maintain the project and accepted new contributions. The preprint was updated in January 2018, and the article was accepted by the journal in March 2018 [4]. As of June 15, 2018, the Deep Review repository accumulated 755 git commits, 315 merged pull requests, 537 issues, and 616 GitHub stars.


Manubot is a system for writing scholarly manuscripts via GitHub. With Manubot, manuscripts are written as plain-text Markdown files, which is well suited for version control using git. The Markdown standard itself provides limited yet crucial formatting syntax, including the ability to embed images and format text via bold, italics, hyperlinks, headers, inline code, codeblocks, blockquotes, and numbered or bulleted lists. In addition, Manubot relies on extensions from Pandoc Markdown to enable citations, tables, captions, and equations specified using the popular TeX math syntax.

Manubot includes an additional layer of citation processing, currently unique to the system. All citations point to a standard identifier, for which Manubot automatically retrieves bibliographic metadata. Table 2 presents the supported identifiers and example citations before and after Manubot processing. Authors can optionally define citation tags to provide short readable alternatives to the citation identifiers. Metadata is exported to Citation Style Language (CSL) JSON Items, an open standard that is widely supported by reference managers [16,17]. In cases where automatic retrieval of metadata fails or produces incorrect references — which is most common for URL citations — users can manually provide the correct CSL JSON.

Table 2: Citation types supported by Manubot. Authors may optionally map a named tag to one of the other supported identifier types. In this example, the tag Avasthi2018_preprints represents the DOI identifier doi:10.7554/eLife.38532.
Identifier Metadata source Example citation Processed citation
Digital Object Identifier (DOI) DOI Content Negotiation doi:10.1098/rsif.2017.0387 [4]
PubMed Identifier (PMID) NCBI’s E-utilities pmid:25851694 [5]
PubMed Central Identifier (PMCID) NCBI’s Citation Exporter pmcid:PMC4719068 [1]
arXiv identifier arXiv API arxiv:1502.04015v1 [18]
URL Greycite [19] url: [20]
Tag Source for tagged identifier tag:Avasthi2018_preprints [8]

Manubot formats bibliographies according to a CSL specification. As a result, users can choose from thousands of existing CSL styles or use Manubot’s default style. Styles define how references are constructed from bibliographic metadata, controlling layout details such as the maximum number of authors to list per reference. Thousands of journals have predefined styles. As a result, adopting the specific bibliographic format required by a journal usually just requires specifying the style’s source URL in the Manubot configuration.

Manubot uses Pandoc to convert manuscripts from Markdown to HTML, PDF, and optionally DOCX outputs. Pandoc supports conversion between additional formats — such as LaTeX, AsciiDoc, EPUB, and JATS — offering Manubot users broad interoperability. Journal Article Tag Suite (JATS) is a standard XML format for scholarly articles that is used by publishers, archives, and text miners [21,22,23]. Pandoc’s JATS support provides an avenue to integrate Manubot with the larger JATS ecosystem. For now, however, the primary Manubot output is HTML intended to be viewed in a web browser.

Manubot performs continuous publication: every update to a manuscript’s source is automatically reflected in the online outputs. The approach uses continuous integration (CI) [24,25,26], specifically Travis CI at the moment, to monitor changes. When changes occur, the CI service attempts to generate an updated manuscript. If this process is error free, the CI service timestamps the manuscript and uploads the output files to the GitHub repository. Because the HTML manuscript is hosted using GitHub Pages, the CI service automatically deploys the new manuscript version when it pushes the updated outputs to GitHub. Using CI to build the manuscript automatically catches many common errors, such as misspelled citations, invalid formatting, or misconfigured software dependencies.

To illustrate, the source GitHub repository for this article is When this repository changes, Travis CI rebuilds the manuscript. If successful, the output is deployed back to GitHub (to dedicated output and gh-pages branches). As a result, stays up to date with the latest HTML manuscript. Furthermore, versioned URLs, such as, provide access to previous manuscript versions.

The idea of the “priority of discovery” is important to science, and Vale and Hyman discuss the importance of both disclosure and validation [27]. In their framework, disclosure occurs when a scientific output is released to the world. However, for a manuscript that is shared as it is written, being able to establish priority could be challenging. Manubot supports OpenTimestamps to timestamp the HTML and PDF outputs on the Bitcoin blockchain. This procedure allows one to retrospectively prove that a manuscript version existed prior to its blockchain-verifiable timestamp [18,28,29,30]. Timestamps protect against attempts to rewrite a manuscript’s history and ensure accurate histories, potentially alleviating certain authorship or priority disputes. Because all bitcoin transactions compete for limited space on the blockchain, the fees required to send a single transaction can be high. OpenTimestamps avoids this fee by encoding many timestamps into a single Bitcoin transaction [31]. There can be a lag of a few hours before the transaction is made, which is suitable for the purposes of scientific writing.

Manubot has the potential to transform publication, making it permissionless, reproducible, free of charge, and largely open source. It does rely on gratis services from two proprietary platforms: GitHub and Travis CI. Fortunately, lock-in to these services is minimal, and several substitutes already exist. One direction Manubot is working towards is end-to-end document reproducibility, where every figure or piece of data in a manuscript can be traced back to its origin [32]. Manubot is well suited for preserving provenance. For example, figures can be specified using versioned URLs that refer to the code that created them. In addition, manuscripts can be templated, so that numerical values or tables are inserted directly from the repository that created them. An example repository demonstrates Manubot’s features and serves as a template for users to write their own manuscript with Manubot.

Since its creation to facilitate the Deep Review, Manubot has been used to write a variety of scholarly documents. The Sci-Hub Coverage Study — performed openly on GitHub from its inception — investigated Sci-Hub’s repository of pirated articles [33]. Sci-Hub reviewed the initial preprint from this study in a series of tweets, pointing out a major error in one of the analyses. Within hours, the authors used Markdown’s strikethrough formatting in Manubot to cross-out the errant sentences (commit, versioned manuscript), thereby alerting readers to the mistake and preventing further propagation of misinformation. One month later, a larger set of revisions explained the error in more detail and was included in a second version of the preprint. As such, continuous publishing via Manubot helped the authors address the error without delay, while retaining a public version history of the process. This Sci-Hub Coverage Study preprint was the most viewed 2017 PeerJ Preprint, while the Deep Review was the most viewed 2017 bioRxiv preprint [34]. Hence, in Manubot’s first year, two of the most popular preprints were written using its collaborative, open, and review-driven authoring process.

Additional research studies in progress are being authored using Manubot, spanning the fields of genomics, climate science, and data visualization. Manubot is also being used for documents beyond traditional journal publications, such as grant proposals, progress reports, undergraduate research reports [35], literature reviews, and lab notebooks. Finally, manuscripts written with other authoring systems have been successfully ported to Manubot, including the Bitcoin Whitepaper [36] and Project Rephetio manuscript [37].


To determine authorship for the Deep Review, we followed the International Committee of Medical Journal Editors (ICMJE) guidelines and used GitHub to track contributions. ICMJE recommends authors substantially contribute to, draft, approve, and agree to be accountable for the manuscript. We acknowledged other contributors who did not meet all four criteria, including contributors who provided text but did not review and approve the complete manuscript. Although these criteria provided a straightforward, equitable way to determine who would be an author, they did not produce a traditionally ordered author list. In biomedical journals, the convention is that the first and last authors made the most substantial contributions to the manuscript. This convention can be difficult to reconcile in a collaborative effort. Using git, we could quantify the number of commits each author made or the number of sentences an author wrote or edited, but these metrics discount intellectual contributions such as discussing primary literature and reviewing pull requests. However, there is no objective system to compare and weight the different types of contributions and produce an ordered author list.

To address this issue, we generalized the concept of “co-first” authorship, in which two or more authors are denoted as making equal contributions to a paper. We defined four types of contributions [4], from major to minor, and reviewed the GitHub discussions and commits to assign authors to these categories. A randomized algorithm then arbitrarily ordered authors within each contribution category, and we combined the category-specific author lists to produce a traditional ordering. The randomization procedure was shared with the authors in advance (pre-registered) and run in a deterministic manner. Given the same author contributions, it always produced the same ordered author list. We annotated the author list to indicate that author order was partly randomized and emphasize that the order did not indicate one author contributed more than another from the same category.


Additional collaborative writing projects

The Deep Review was not the first scholarly manuscript written online via an open collaborative process. Interestingly, the collaborative scholarly works (of which we’re aware) tend to have dealt with rapidly developing topics. In 2013, two dozen mathematicians created the 600-page “HoTT Book” on “Homotopy Type Theory”, writing collaboratively in LaTeX on GitHub [38,39]. Two technical books on cryptocurrency — Mastering Bitcoin and Mastering Ethereum — written on GitHub in asciidoc format have engaged hundreds of contributors. Both The HoTT Book and Mastering Bitcoin continue to be maintained years after their initial publication. A 2017 perspective on the future of peer review was written collaboratively on Overleaf, with contributions from 32 authors [40]. While debate was raging over tightening the default threshold for statistical significance, nearly 150 scientists contributed to a Google Doc discussion that was condensed into a traditional journal commentary [41,42]. The greatest success to date of open collaborative writing is arguably Wikipedia, whose English version contains over 5.5 million articles. Wikipedia scaled encyclopedias far beyond any privately-written alternative. As the examples above illustrate, open collaborative writing appears to scale scholarly manuscripts where diverse opinion and expertise are paramount beyond what would otherwise be possible.

Concepts for the future of scholarly publishing extend beyond collaborative writing [43,44]. Bookdown [45] and Pandoc Scholar [46] both extend traditional Markdown to better support publishing. Examples of continuous integration to automate manuscript generation include gh-publisher and Continuous Publishing [47], which was used to produce the book Opening Science [48]. Distill journal articles [49], Idyll [50], and Stencila [51] support manuscripts with interactive graphics and close integration with the underlying code. As an open source project, Manubot can be extended to adopt best practices from these other emerging platforms.

Several open science efforts are GitHub-based like our collaborative writing process. The ReScience [52], the Journal of Open Source Software [53], and some other Open Journals rely on GitHub for peer review and hosting. GitHub is also increasingly used for resource curation [54], and collaborative scholarly reviews combine literature curation with discussion and interpretation.


There are potential limitations of our GitHub-based approach. Because our review manuscript pertained to a computational topic, most of the authors had computational backgrounds, including previous experience with version control workflows and GitHub. In other disciplines, collaborative writing via GitHub and Manubot could present a steeper barrier to entry and deter participants. In addition, git carefully tracks all revisions to the manuscript text but not the surrounding conversations that take place through GitHub issues and pull requests. These discussions must be archived to ensure that important decisions about the manuscript are preserved and authors receive credit for intellectual contributions that are not directly reflected in the manuscript’s text. GitHub supports programmatic access to issues, pull requests, and reviews so tracking these conversations is feasible in the future.

In our open review paper, we established contributor guidelines that discussed norms in the areas of text contribution, peer review, and authorship, which we identified in advance as potential areas of disagreement. Our contributor guidelines required verifiable participation: either directly attributable changes to the text or participation in the discussion on GitHub. We maintained our guidelines, even when a case arose where two authors had written text together but only one had directly attributable changes and participation. These guidelines did not discuss broader community norms that may have improved inclusiveness. It is also important to consider how the move to an open contribution model affects under-represented minority members of the scientific community [20]. Recent work has identified clear social norms and processes as helpful to maintaining a collaborative culture [55]. Conferences and open source projects have used codes of conduct to establish these norms [56,57]. We would encourage the maintainers of similar projects to consider broader codes of conduct for project participants that establish on social as well as academic norms.

Open writing presents new opportunities for scholarly communication. Though it is still valuable to have versioned drafts of a review manuscript with digital identifiers, journal publication may not be the terminal endpoint for collaborative manuscripts. After releasing the first version of our collaborative review [15], 14 new contributors have updated the manuscript (Figure 2) and existing authors continue to discuss new literature, creating a living document. Manubot provides an ideal platform for perpetual reviews [58,59].

Manubot in the context of open science

Science is undergoing a transition towards openness. The internet provides a global information commons, where scholarship can be publicly shared at a minimal cost. For example, open access publishing provides an economic model that encourages maximal dissemination and reuse of scholarly articles [60,61]. More broadly, open licensing solves legal barriers to content reuse, enabling any type of scholarly output to become part of the commons [62,63]. The opportunity to reuse data and code for new investigations, as well as a push for increased reproducibility, has begot a movement to make all research outputs public, unless there are bonafide privacy or security concerns [64,65,66]. New tools and services make it increasingly feasible to publicly share the unabridged methods of a study, especially for computational research, which consists solely of software and data. Greater openness in both research methods and publishing is creating an opportunity to redefine peer review and the role journals play in communicating science [67]. At the extreme is real-time open science, whereby studies are performed entirely in the open from their inception [68]. Many such research projects have now been completed, benefiting from the associated early-stage peer review, additional opportunity for online collaboration, and increased visibility [37,69].

Manubot is designed to be an authoring protocol for real-time open science, with especial relevance for projects that are already using the 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. We hope that these attributes help integrate Manubot with an ecosystem of other community-driven tools to make science as open and collaborative as possible.


We would like to thank the authors of the Deep Review who helped us test collaborative writing with Manubot. The authors who responded favorably to being acknowledged are 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. In addition, we thank Ogun Adebali, Evan M. Cofer, and Robert Gieseke for contributing to the Manubot template manuscript. We are grateful for additional Manubot discussion and testing by Alexander Dunkel, Ansel Halliburton, Achintya Rao, and other GitHub users.


1. Crowdsourcing in biomedicine: challenges and opportunities
Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu
Briefings in Bioinformatics (2016-01)

2. Ten Simple Rules for Writing a Literature Review
Marco Pautasso
PLoS Computational Biology (2013-07-18)

3. TechBlog: “Manubot” powers a crowdsourced “deep-learning” review
Jeffrey Perkel
Naturejobs (2018-02-20)

4. 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)

5. Reviewing post-publication peer review.
Paul Knoepfler
Trends in genetics : TIG (2015-04-04)

6. A Stronger Post-Publication Culture Is Needed for Better Science
Hilda Bastian
PLoS Medicine (2014-12-30)

7. Post-Publication Peer Review: Opening Up Scientific Conversation
Jane Hunter
Frontiers in Computational Neuroscience (2012)

8. Journal clubs in the time of preprints
Prachee Avasthi, Alice Soragni, Joshua N Bembenek
eLife (2018-06-11)

9. Post-publication peer review, in all its guises, is here to stay
Michael Markie
Insights the UKSG journal (2015-07-07)

10. Scientific writing: the online cooperative
Jeffrey M. Perkel
Nature (2014-10-01)

11. A Quick Introduction to Version Control with Git and GitHub
John D. Blischak, Emily R. Davenport, Greg Wilson
PLOS Computational Biology (2016-01-19)

12. Ten Simple Rules for Taking Advantage of Git and GitHub
Yasset Perez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, … Juan Antonio Vizcaíno
PLOS Computational Biology (2016-07-14)

13. Opportunities And Obstacles For Deep Learning In Biology And Medicine
Johnny Israeli
Medium (2017-05-31)

14. What Should Be Done To Tackle Ghostwriting in the Medical Literature?
Peter C Gøtzsche, Jerome P Kassirer, Karen L Woolley, Elizabeth Wager, Adam Jacobs, Art Gertel, Cindy Hamilton
PLoS Medicine (2009-02-03)

15. 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
Cold Spring Harbor Laboratory (2017-05-28)

16. Reference Management
Martin Fenner, Kaja Scheliga, Sönke Bartling
Opening Science (2013-12-17)

17. Comparison of Select Reference Management Tools
Yingting Zhang
Medical Reference Services Quarterly (2012-01)

18. Decentralized Trusted Timestamping using the Crypto Currency Bitcoin
Bela Gipp, Norman Meuschke, André Gernandt
arXiv (2015-02-13)

19. Twenty-Five Shades of Greycite: Semantics for referencing and preservation
Phillip Lord, Lindsay Marshall
arXiv (2013-04-26)

20. Open science and open science
Laurent Gatto

21. JATS: Journal Article Tag Suite, version 1.1
National Information Standards Organization

22. Journal Article Tag Suite 1.0: National Information Standards Organization standard of journal extensible markup language
Sun Huh
Science Editing (2014-08-18)

23. NISO Z39.96-201x, JATS: Journal Article Tag Suite
Mark H. Needleman
Serials Review (2012-09)

24. Collaborative software development made easy
Andrew Silver
Nature (2017-10-04)

25. Reproducibility of computational workflows is automated using continuous analysis
Brett K Beaulieu-Jones, Casey S Greene
Nature Biotechnology (2017-03-13)

26. Developing a modern data workflow for living data
Glenda M Yenni, Erica M Christensen, Ellen K Bledsoe, Sarah R Supp, Renata M Diaz, Ethan P White, SK Morgan Ernest
Cold Spring Harbor Laboratory (2018-06-12)

27. Priority of discovery in the life sciences
Ronald D Vale, Anthony A Hyman
eLife (2016-06-16)

28. The Grey Literature — Proof of prespecified endpoints in medical research with the bitcoin blockchain
Benjamin Gregory Carlisle

29. The most interesting case of scientific irreproducibility?
Daniel Himmelstein
Satoshi Village (2017-03-08)

30. Bitcoin: A Peer-to-Peer Electronic Cash System
Satoshi Nakamoto

31. OpenTimestamps: Scalable, Trustless, Distributed Timestamping with BitcoinPeter Todd (2018-02-10)

32. eLife supports development of open technology stack for publishing reproducible manuscripts online
Emily Packer

33. 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)

34. 2017 in news: The science events that shaped the year
Ewen Callaway, Davide Castelvecchi, David Cyranoski, Elizabeth Gibney, Heidi Ledford, Jane J. Lee, Lauren Morello, Nicky Phillips, Quirin Schiermeier, Jeff Tollefson, … Alexandra Witze
Nature (2017-12-21)

35. Vagelos Report Summer 2017
Michael Zietz
Figshare (2017)

36. How I used the Manubot to reproduce the Bitcoin Whitepaper
Daniel Himmelstein
Steem (2017-09-20)

37. Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini
eLife (2017-09-22)

38. Homotopy Type Theory: Univalent Foundations of Mathematics
The Univalent Foundations Program
Institute for Advanced Study (2013)

39. The HoTT book
Andrej Bauer
Mathematics and Computation (2013-06-20)

40. A multi-disciplinary perspective on emergent and future innovations in peer review
Jonathan P. Tennant, Jonathan M. Dugan, Daniel Graziotin, Damien C. Jacques, François Waldner, Daniel Mietchen, Yehia Elkhatib, Lauren B. Collister, Christina K. Pikas, Tom Crick, … Julien Colomb
F1000Research (2017-11-01)

41. Nearly 100 scientists spent 2 months on Google Docs to redefine the p-value. Here’s what they came up with
Jop Vrieze
Science (2018-01-18)

42. Justify your alpha
Daniel Lakens, Federico G. Adolfi, Casper J. Albers, Farid Anvari, Matthew A. J. Apps, Shlomo E. Argamon, Thom Baguley, Raymond B. Becker, Stephen D. Benning, Daniel E. Bradford, … Rolf A. Zwaan
Nature Human Behaviour (2018-02-26)

43. The arXiv of the future will not look like the arXiv
Alberto Pepe, Matteo Cantiello, Josh Nicholson

44. TechBlog: C. Titus Brown: Predicting the paper of the future
C. Titus Brown
Naturejobs (2017-06-01)

45. bookdown
Yihui Xie
Chapman &Hall/CRC The R Series (2016-12-21)

46. Formatting Open Science: agilely creating multiple document formats for academic manuscripts with Pandoc Scholar
Albert Krewinkel, Robert Winkler
PeerJ Computer Science (2017-05-08)

47. Continuous Publishing
Martin Fenner
Gobbledygook (2014-03-10)

48. Opening ScienceSpringer International Publishing (2014)

49. The Building Blocks of Interpretability
Chris Olah, Arvind Satyanarayan, Ian Johnson, Shan Carter, Ludwig Schubert, Katherine Ye, Alexander Mordvintsev
Distill (2018-03-06)

50. Announcing
Matthew Conlen, Andrew Osheroff
Idyll (2018-06-26)

51. Stencila – an office suite for reproducible research
Michael Aufreiter, Aleksandra Pawlik, Nokome Bentley
eLife Labs (2018-07-02)

52. Sustainable computational science: the ReScience initiative
Nicolas P. Rougier, Konrad Hinsen, Frédéric Alexandre, Thomas Arildsen, Lorena A. Barba, Fabien C.Y. Benureau, C. Titus Brown, Pierre de Buyl, Ozan Caglayan, Andrew P. Davison, … Tiziano Zito
PeerJ Computer Science (2017-12-18)

53. Journal of Open Source Software (JOSS): design and first-year review
Arfon M. Smith, Kyle E. Niemeyer, Daniel S. Katz, Lorena A. Barba, George Githinji, Melissa Gymrek, Kathryn D. Huff, Christopher R. Madan, Abigail Cabunoc Mayes, Kevin M. Moerman, … Jacob T. Vanderplas
PeerJ Computer Science (2018-02-12)

54. The appropriation of GitHub for curation
Yu Wu, Na Wang, Jessica Kropczynski, John M. Carroll
PeerJ Computer Science (2017-10-09)

55. Innovating Collaborative Content Creation: The Role of Altruism and Wiki Technology
Christian Wagner, Pattarawan Prasarnphanich
2007 40th Annual Hawaii International Conference on System Sciences (HICSS’07) (2007)

56. Code of conduct evaluationsGeek Feminism Wiki (2017-06-13)

57. Contributor Covenant: A Code of Conduct for Open Source Projects
Coraline Ada Ehmke

58. A proposal for regularly updated review/survey articles: “Perpetual Reviews”
David L. Mobley, Daniel M. Zuckerman
arXiv (2015-02-03)

59. Why we need the Living Journal of Computational Molecular Science
David L. Mobley, Michael R. Shirts, Daniel M. Zuckerman
Living Journal of Computational Molecular Science (2017-08-22)

60. The academic, economic and societal impacts of Open Access: an evidence-based review
Jonathan P. Tennant, François Waldner, Damien C. Jacques, Paola Masuzzo, Lauren B. Collister, Chris. H. J. Hartgerink
F1000Research (2016-09-21)

61. How open science helps researchers succeed
Erin C McKiernan, Philip E Bourne, C Titus Brown, Stuart Buck, Amye Kenall, Jennifer Lin, Damon McDougall, Brian A Nosek, Karthik Ram, Courtney K Soderberg, … Tal Yarkoni
eLife (2016-07-07)

62. The Legal Framework for Reproducible Scientific Research: Licensing and Copyright
Victoria Stodden
Computing in Science & Engineering (2009-01)

63. Legal confusion threatens to slow data science
Simon Oxenham
Nature (2016-08-03)

64. Enhancing reproducibility for computational methods
V. Stodden, M. McNutt, D. H. Bailey, E. Deelman, Y. Gil, B. Hanson, M. A. Heroux, J. P. A. Ioannidis, M. Taufer
Science (2016-12-08)

65. The case for open computer programs
Darrel C. Ince, Leslie Hatton, John Graham-Cumming
Nature (2012-02-22)

66. The Open Knowledge Foundation: Open Data Means Better Science
Jennifer C. Molloy
PLoS Biology (2011-12-06)

67. A multi-disciplinary perspective on emergent and future innovations in peer review
Jonathan P. Tennant, Jonathan M. Dugan, Daniel Graziotin, Damien C. Jacques, François Waldner, Daniel Mietchen, Yehia Elkhatib, Lauren B. Collister, Christina K. Pikas, Tom Crick, … Julien Colomb
F1000Research (2017-07-20)

68. This revolution will be digitized: online tools for radical collaboration
C. Patil, V. Siegel
Disease Models & Mechanisms (2009-04-30)

69. Publishing the research process
Daniel Mietchen, Ross Mounce, Lyubomir Penev
Research Ideas and Outcomes (2015-12-17)