Author statement & hide funders section for PLOS

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Author statement & hide funders section for PLOS

Merges #220
Closes #219

Adds author summary for PLOS Computational Biology
https://journals.plos.org/ploscompbiol/s/submission-guidelines#loc-author-summary
Current word count is 200 (the max).

manuscript.html

@@ -11,7 +11,7 @@
   <meta name="author" content="Venkat S. Malladi" />
   <meta name="author" content="Casey S. Greene" />
   <meta name="author" content="Anthony Gitter" />
-  <meta name="dcterms.date" content="2019-04-12" />
+  <meta name="dcterms.date" content="2019-04-17" />
   <meta name="keywords" content="manubot, deep review, publishing, open science, open access, collaboration, writing, github, git, continuous integration, markdown, pandoc" />
   <title>Open collaborative writing with Manubot</title>
   <style>
@@ -91,7 +91,7 @@
 <header id="title-block-header">
 <h1 class="title">Open collaborative writing with Manubot</h1>
 </header>
-<p><small><em> This manuscript (<a href="https://greenelab.github.io/meta-review/v/4ef4d9fe9f85e90a232018b5aa111903449fd231/">permalink</a>) was automatically generated from <a href="https://github.com/greenelab/meta-review/tree/4ef4d9fe9f85e90a232018b5aa111903449fd231">greenelab/meta-review@4ef4d9f</a> on April 12, 2019. </em></small></p>
+<p><small><em> This manuscript (<a href="https://greenelab.github.io/meta-review/v/b60d60ef188bdbf4694dd1d8a442737296380260/">permalink</a>) was automatically generated from <a href="https://github.com/greenelab/meta-review/tree/b60d60ef188bdbf4694dd1d8a442737296380260">greenelab/meta-review@b60d60e</a> on April 17, 2019. </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
 <li><p><strong>Daniel S. Himmelstein</strong> <sup><a href="#correspondence">✉</a></sup><br> <img src="images/orcid.svg" alt="ORCID icon" class="inline_icon" /> <a href="https://orcid.org/0000-0002-3012-7446">0000-0002-3012-7446</a> · <img src="images/github.svg" alt="GitHub icon" class="inline_icon" /> <a href="https://github.com/dhimmel">dhimmel</a> · <img src="images/twitter.svg" alt="Twitter icon" class="inline_icon" /> <a href="https://twitter.com/dhimmel">dhimmel</a><br> <small> Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania </small></p></li>
@@ -107,6 +107,10 @@ <h2 id="authors">Authors</h2>
 </div>
 <h2 id="abstract" class="page_break_before">Abstract</h2>
 <p>Open, collaborative research is a powerful paradigm that can immensely strengthen the scientific process by integrating broad and diverse expertise. However, traditional research and multi-author writing processes break down at scale. We present new software named Manubot, available at <a href="https://manubot.org" class="uri">https://manubot.org</a>, to address the challenges of open scholarly writing. Manubot adopts the contribution workflow used by many large-scale open source software projects to enable collaborative authoring of scholarly manuscripts. With Manubot, manuscripts are written in Markdown and stored in a Git repository to precisely track changes over time. By hosting manuscript repositories publicly, such as on GitHub, multiple authors can simultaneously propose and review changes. A cloud service automatically evaluates proposed changes to catch errors. Publication with Manubot is continuous: When a manuscript’s source changes, the rendered outputs are rebuilt and republished to a web page. Manubot automates bibliographic tasks by implementing citation by identifier, where users cite persistent identifiers (e.g. DOIs, PubMed IDs, ISBNs, URLs), whose metadata is then retrieved and converted to a user-specified style. Manubot modernizes publishing to align with the ideals of open science by making it transparent, reproducible, immediate, versioned, collaborative, and free of charge.</p>
+<h2 id="author-summary">Author summary</h2>
+<p>Traditionally, scholarly manuscripts have been written in private by a predefined team of collaborators. But now the internet enables realtime open science, where project communication occurs online in a public venue and anyone is able to contribute. Dispersed teams of online contributors require new tools to jointly prepare manuscripts.</p>
+<p>Existing tools fail to scale beyond tens of authors and struggle to support iterative refinement of proposed changes. Therefore, we created a system called Manubot for writing manuscripts based on collaborative version control. Manubot adopts the workflow from open source software development, which has enabled hundreds of contributors to simultaneously develop complex codebases such as Python and Linux, and applies it to open collaborative writing.</p>
+<p>Manubot also addresses other shortcomings of current publishing tools. Specifically, all changes to a manuscript are tracked, enabling transparency and better attribution of credit. Manubot automates many tasks, including creating the bibliography and deploying the manuscript as a webpage. Manubot webpages preserve old versions and provide a simple yet interactive interface for reading. As such, Manubot is a suitable foundation for next-generation preprints. Manuscript readers have ample opportunity to not only provide public peer review but also to contribute improvements, before and after journal publication.</p>
 <h2 id="introduction" class="page_break_before">Introduction</h2>
 <p>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 <span class="citation" data-cites="1DiVJ3t6P">[<a href="#ref-1DiVJ3t6P">1</a>]</span>. However, the scientific community requires tools whose workflows encourage openness <span class="citation" data-cites="IWBJQIkl">[<a href="#ref-IWBJQIkl">2</a>]</span>. Manuscripts are the cornerstone of scholarly communication, but drafting and publishing manuscripts has traditionally relied on proprietary or offline tools that do not support <em>open scholarly writing</em>, in which anyone is able to contribute and the contribution history is preserved and public. We introduce <a href="https://manubot.org">Manubot</a>, a new tool and infrastructure for authoring scholarly manuscripts in the open, and report how it was instrumental for the collaborative project that led to its creation.</p>
 <p>Based on our experience leading a recent open review <span class="citation" data-cites="16CgM2x0z">[<a href="#ref-16CgM2x0z">3</a>]</span>, we discuss the advantages and challenges of open collaborative writing, a form of crowdsourcing <span class="citation" data-cites="12sHvZy1a">[<a href="#ref-12sHvZy1a">4</a>]</span>. Our review manuscript <span class="citation" data-cites="PZMP42Ak">[<a href="#ref-PZMP42Ak">5</a>]</span> was code-named the Deep Review and surveyed deep learning’s role in biology and precision medicine, a research area undergoing explosive growth. We initiated the Deep Review in August 2016 by creating a GitHub repository (<a href="https://github.com/greenelab/deep-review" class="uri">https://github.com/greenelab/deep-review</a>) to coordinate and manage contributions. GitHub is a platform designed for collaborative software development that is adaptable for collaborative writing. From the start, we made the GitHub repository public under a Creative Commons Attribution License (<a href="https://github.com/greenelab/deep-review/blob/master/LICENSE.md" title="Creative Commons Attribution 4.0 International License">CC BY 4.0</a>). 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 in less than two years.</p>
@@ -446,8 +450,13 @@ <h2 id="supporting-information">Supporting Information</h2>
 </p>
 <h2 id="acknowledgments">Acknowledgments</h2>
 <p>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 Rootstock manuscript. We are grateful for additional Manubot discussion and testing by Alexander Dunkel, Ansel Halliburton, Benjamin J. Heil, Zach Hensel, Alexandra J. Lee, YoSon Park, Achintya Rao, and other GitHub users. We thank John MacFarlane and Nikolay Yakimov for assistance with Pandoc and the global Binder team for advice on Binder. Finally, we thank C. Titus Brown and the other anonymous reviewers for their help improving this manuscript.</p>
-<h2 id="funding">Funding</h2>
-<p>DSH, DH, VR, and CSG were supported by <a href="https://sloan.org/grant-detail/8501">Grant G-2018-11163</a> from the Alfred P. Sloan Foundation and <a href="https://www.moore.org/grant-detail?grantId=GBMF4552">Grant GBMF4552</a> from the Gordon and Betty Moore Foundation. VSM was supported by Grant RP150596 from the Cancer Prevention and Research Institute of Texas.</p>
+<!--
+## Funding
+
+DSH, DH, VR, and CSG were supported by [Grant G-2018-11163](https://sloan.org/grant-detail/8501) from the Alfred P. Sloan Foundation and [Grant GBMF4552](https://www.moore.org/grant-detail?grantId=GBMF4552) from the Gordon and Betty Moore Foundation.
+VSM was supported by Grant RP150596 from the Cancer Prevention and Research Institute of Texas.
+The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
+-->
 <h2 id="references" class="page_break_before">References</h2>
 <!-- Explicitly insert bibliography here -->
 <div id="refs">

manuscript.md

@@ -7,7 +7,7 @@ author-meta:
 - Venkat S. Malladi
 - Casey S. Greene
 - Anthony Gitter
-date-meta: '2019-04-12'
+date-meta: '2019-04-17'
 keywords:
 - manubot
 - deep review
@@ -32,10 +32,10 @@ title: Open collaborative writing with Manubot
 
 <small><em>
 This manuscript
-([permalink](https://greenelab.github.io/meta-review/v/4ef4d9fe9f85e90a232018b5aa111903449fd231/))
+([permalink](https://greenelab.github.io/meta-review/v/b60d60ef188bdbf4694dd1d8a442737296380260/))
 was automatically generated
-from [greenelab/meta-review@4ef4d9f](https://github.com/greenelab/meta-review/tree/4ef4d9fe9f85e90a232018b5aa111903449fd231)
-on April 12, 2019.
+from [greenelab/meta-review@b60d60e](https://github.com/greenelab/meta-review/tree/b60d60ef188bdbf4694dd1d8a442737296380260)
+on April 17, 2019.
 </em></small>
 
 ## Authors
@@ -140,6 +140,23 @@ When a manuscript's source changes, the rendered outputs are rebuilt and republi
 Manubot automates bibliographic tasks by implementing citation by identifier, where users cite persistent identifiers (e.g. DOIs, PubMed IDs, ISBNs, URLs), whose metadata is then retrieved and converted to a user-specified style.
 Manubot modernizes publishing to align with the ideals of open science by making it transparent, reproducible, immediate, versioned, collaborative, and free of charge.
 
+## Author summary
+
+Traditionally, scholarly manuscripts have been written in private by a predefined team of collaborators.
+But now the internet enables realtime open science, where project communication occurs online in a public venue and anyone is able to contribute.
+Dispersed teams of online contributors require new tools to jointly prepare manuscripts.
+
+Existing tools fail to scale beyond tens of authors and struggle to support iterative refinement of proposed changes.
+Therefore, we created a system called Manubot for writing manuscripts based on collaborative version control.
+Manubot adopts the workflow from open source software development, which has enabled hundreds of contributors to simultaneously develop complex codebases such as Python and Linux, and applies it to open collaborative writing.
+
+Manubot also addresses other shortcomings of current publishing tools.
+Specifically, all changes to a manuscript are tracked, enabling transparency and better attribution of credit.
+Manubot automates many tasks, including creating the bibliography and deploying the manuscript as a webpage.
+Manubot webpages preserve old versions and provide a simple yet interactive interface for reading.
+As such, Manubot is a suitable foundation for next-generation preprints.
+Manuscript readers have ample opportunity to not only provide public peer review but also to contribute improvements, before and after journal publication.
+
 
 ## Introduction {.page_break_before}
 
@@ -644,10 +661,13 @@ We are grateful for additional Manubot discussion and testing by Alexander Dunke
 We thank John MacFarlane and Nikolay Yakimov for assistance with Pandoc and the global Binder team for advice on Binder.
 Finally, we thank C. Titus Brown and the other anonymous reviewers for their help improving this manuscript.
 
+<!--
 ## Funding
 
 DSH, DH, VR, and CSG were supported by [Grant G-2018-11163](https://sloan.org/grant-detail/8501) from the Alfred P. Sloan Foundation and [Grant GBMF4552](https://www.moore.org/grant-detail?grantId=GBMF4552) from the Gordon and Betty Moore Foundation.
 VSM was supported by Grant RP150596 from the Cancer Prevention and Research Institute of Texas.
+The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
+-->
 
 ## References {.page_break_before}
 

references.json

@@ -28315,7 +28315,7 @@
         [
           "2019",
           4,
-          12
+          17
         ]
       ]
     },
@@ -28434,7 +28434,7 @@
         [
           "2019",
           4,
-          12
+          17
         ]
       ]
     },
@@ -28532,7 +28532,7 @@
         [
           "2019",
           4,
-          12
+          17
         ]
       ]
     },
@@ -28565,7 +28565,7 @@
         [
           "2019",
           4,
-          12
+          17
         ]
       ]
     },
@@ -28731,7 +28731,7 @@
         [
           "2019",
           4,
-          12
+          17
         ]
       ]
     },
@@ -28829,7 +28829,7 @@
         [
           "2019",
           4,
-          12
+          17
         ]
       ]
     },

variables.json

@@ -1,5 +1,5 @@
 {
-  "date": "April 12, 2019",
+  "date": "April 17, 2019",
   "authors": [
     {
       "github": "dhimmel",
@@ -449,7 +449,7 @@
     "repo_slug": "greenelab/meta-review",
     "repo_owner": "greenelab",
     "repo_name": "meta-review",
-    "commit": "4ef4d9fe9f85e90a232018b5aa111903449fd231"
+    "commit": "b60d60ef188bdbf4694dd1d8a442737296380260"
   },
   "creation_time_utc": "2019-03-06T15:41:48.892633",
   "creation_date_pretty": "March 06, 2019",
@@ -477,6 +477,6 @@
       "wikidata": 1,
       "total": 92
     },
-    "word_count": 7653
+    "word_count": 7877
   }
 }