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This build is based on 362b839. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/540980410 https://travis-ci.org/greenelab/meta-review/jobs/540980412 [ci skip] The full commit message that triggered this build is copied below: Switch affiliations to a numbered list Merges #236 Closes #230 Switch affiliations to a numbered list and add city / country to affiliations As per PLOS Computational Biology request: > Please modify the Affiliations section of your manuscript so that all affiliations listed contain a Department, Institution, City, and Country
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diff --git a/manuscript.docx b/manuscript.docx
diff --git a/manuscript.html b/manuscript.html
@@ -91,19 +91,105 @@
 <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/95da0bdf3063b5a470f567f5df8f5e33e1823647/">permalink</a>) was automatically generated from <a href="https://github.com/greenelab/meta-review/tree/95da0bdf3063b5a470f567f5df8f5e33e1823647">greenelab/meta-review@95da0bd</a> on June 3, 2019. </em></small></p>
+<p><small><em> This manuscript (<a href="https://greenelab.github.io/meta-review/v/362b839108fdcb109ede7dc29a2492303cec62fe/">permalink</a>) was automatically generated from <a href="https://github.com/greenelab/meta-review/tree/362b839108fdcb109ede7dc29a2492303cec62fe">greenelab/meta-review@362b839</a> on June 3, 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>
-<li><p><strong>Vincent Rubinetti</strong> <br> <img src="images/orcid.svg" alt="ORCID icon" class="inline_icon" /> <a href="https://orcid.org/0000-0002-4655-3773">0000-0002-4655-3773</a> · <img src="images/github.svg" alt="GitHub icon" class="inline_icon" /> <a href="https://github.com/vincerubinetti">vincerubinetti</a> · <img src="images/twitter.svg" alt="Twitter icon" class="inline_icon" /> <a href="https://twitter.com/vincerubinetti">vincerubinetti</a><br> <small> Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania </small></p></li>
-<li><p><strong>David R. Slochower</strong> <br> <img src="images/orcid.svg" alt="ORCID icon" class="inline_icon" /> <a href="https://orcid.org/0000-0003-3928-5050">0000-0003-3928-5050</a> · <img src="images/github.svg" alt="GitHub icon" class="inline_icon" /> <a href="https://github.com/slochower">slochower</a> · <img src="images/twitter.svg" alt="Twitter icon" class="inline_icon" /> <a href="https://twitter.com/drslochower">drslochower</a><br> <small> Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego </small></p></li>
-<li><p><strong>Dongbo Hu</strong> <br> <img src="images/orcid.svg" alt="ORCID icon" class="inline_icon" /> <a href="https://orcid.org/0000-0003-2606-3969">0000-0003-2606-3969</a> · <img src="images/github.svg" alt="GitHub icon" class="inline_icon" /> <a href="https://github.com/dongbohu">dongbohu</a> · <img src="images/twitter.svg" alt="Twitter icon" class="inline_icon" /> <a href="https://twitter.com/dongbohu">dongbohu</a><br> <small> Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania </small></p></li>
-<li><p><strong>Venkat S. Malladi</strong> <br> <img src="images/orcid.svg" alt="ORCID icon" class="inline_icon" /> <a href="https://orcid.org/0000-0002-0144-0564">0000-0002-0144-0564</a> · <img src="images/github.svg" alt="GitHub icon" class="inline_icon" /> <a href="https://github.com/vsmalladi">vsmalladi</a> · <img src="images/twitter.svg" alt="Twitter icon" class="inline_icon" /> <a href="https://twitter.com/katatonikkat">katatonikkat</a><br> <small> Department of Bioinformatics, University of Texas Southwestern Medical Center; Bioinformatics Core Facility, University of Texas Southwestern Medical Center </small></p></li>
-<li><p><strong>Casey S. Greene</strong> <br> <img src="images/orcid.svg" alt="ORCID icon" class="inline_icon" /> <a href="https://orcid.org/0000-0001-8713-9213">0000-0001-8713-9213</a> · <img src="images/github.svg" alt="GitHub icon" class="inline_icon" /> <a href="https://github.com/cgreene">cgreene</a> · <img src="images/twitter.svg" alt="Twitter icon" class="inline_icon" /> <a href="https://twitter.com/GreeneScientist">GreeneScientist</a><br> <small> Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania </small></p></li>
-<li><p><strong>Anthony Gitter</strong> <sup><a href="#correspondence">✉</a></sup><br> <img src="images/orcid.svg" alt="ORCID icon" class="inline_icon" /> <a href="https://orcid.org/0000-0002-5324-9833">0000-0002-5324-9833</a> · <img src="images/github.svg" alt="GitHub icon" class="inline_icon" /> <a href="https://github.com/agitter">agitter</a> · <img src="images/twitter.svg" alt="Twitter icon" class="inline_icon" /> <a href="https://twitter.com/anthonygitter">anthonygitter</a><br> <small> Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison; Morgridge Institute for Research </small></p></li>
-</ul>
+<!-- commented out for https://github.com/greenelab/meta-review/issues/230
+
+
++ **Daniel S. Himmelstein** ^[✉](#correspondence)^<br>
+    ![ORCID icon](images/orcid.svg){.inline_icon}
+    [0000-0002-3012-7446](https://orcid.org/0000-0002-3012-7446)
+    · ![GitHub icon](images/github.svg){.inline_icon}
+    [dhimmel](https://github.com/dhimmel)
+    · ![Twitter icon](images/twitter.svg){.inline_icon}
+    [dhimmel](https://twitter.com/dhimmel)<br>
+  <small>
+     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
+  </small>
+
++ **Vincent Rubinetti** <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon}
+    [0000-0002-4655-3773](https://orcid.org/0000-0002-4655-3773)
+    · ![GitHub icon](images/github.svg){.inline_icon}
+    [vincerubinetti](https://github.com/vincerubinetti)
+    · ![Twitter icon](images/twitter.svg){.inline_icon}
+    [vincerubinetti](https://twitter.com/vincerubinetti)<br>
+  <small>
+     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
+  </small>
+
++ **David R. Slochower** <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon}
+    [0000-0003-3928-5050](https://orcid.org/0000-0003-3928-5050)
+    · ![GitHub icon](images/github.svg){.inline_icon}
+    [slochower](https://github.com/slochower)
+    · ![Twitter icon](images/twitter.svg){.inline_icon}
+    [drslochower](https://twitter.com/drslochower)<br>
+  <small>
+     Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, San Diego, United States of America
+  </small>
+
++ **Dongbo Hu** <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon}
+    [0000-0003-2606-3969](https://orcid.org/0000-0003-2606-3969)
+    · ![GitHub icon](images/github.svg){.inline_icon}
+    [dongbohu](https://github.com/dongbohu)
+    · ![Twitter icon](images/twitter.svg){.inline_icon}
+    [dongbohu](https://twitter.com/dongbohu)<br>
+  <small>
+     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
+  </small>
+
++ **Venkat S. Malladi** <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon}
+    [0000-0002-0144-0564](https://orcid.org/0000-0002-0144-0564)
+    · ![GitHub icon](images/github.svg){.inline_icon}
+    [vsmalladi](https://github.com/vsmalladi)
+    · ![Twitter icon](images/twitter.svg){.inline_icon}
+    [katatonikkat](https://twitter.com/katatonikkat)<br>
+  <small>
+     Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America; Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
+  </small>
+
++ **Casey S. Greene** <br>
+    ![ORCID icon](images/orcid.svg){.inline_icon}
+    [0000-0001-8713-9213](https://orcid.org/0000-0001-8713-9213)
+    · ![GitHub icon](images/github.svg){.inline_icon}
+    [cgreene](https://github.com/cgreene)
+    · ![Twitter icon](images/twitter.svg){.inline_icon}
+    [GreeneScientist](https://twitter.com/GreeneScientist)<br>
+  <small>
+     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
+  </small>
+
++ **Anthony Gitter** ^[✉](#correspondence)^<br>
+    ![ORCID icon](images/orcid.svg){.inline_icon}
+    [0000-0002-5324-9833](https://orcid.org/0000-0002-5324-9833)
+    · ![GitHub icon](images/github.svg){.inline_icon}
+    [agitter](https://github.com/agitter)
+    · ![Twitter icon](images/twitter.svg){.inline_icon}
+    [anthonygitter](https://twitter.com/anthonygitter)<br>
+  <small>
+     Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Morgridge Institute for Research, Madison, Wisconsin, United States of America
+  </small>
+
+
+::: {#correspondence}
+✉ — correspondence preferred via [GitHub Issues](https://github.com/greenelab/meta-review/issues).
+Otherwise, address correspondence to <[email protected]> and <[email protected]>.
+:::
+-->
+<p>Daniel S. Himmelstein<sup>1<a href="#correspondence">*</a></sup>, Vincent Rubinetti<sup>1</sup>, David R. Slochower<sup>2</sup>, Dongbo Hu<sup>1</sup>, Venkat S. Malladi<sup>3,4</sup>, Casey S. Greene<sup>1</sup>, Anthony Gitter<sup>5,6<a href="#correspondence">*</a></sup></p>
+<ol type="1">
+<li>Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America</li>
+<li>Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, San Diego, United States of America</li>
+<li>Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America</li>
+<li>Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America</li>
+<li>Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America</li>
+<li>Morgridge Institute for Research, Madison, Wisconsin, United States of America</li>
+</ol>
 <div id="correspondence">
-<p>✉ — correspondence preferred via <a href="https://github.com/greenelab/meta-review/issues">GitHub Issues</a>. Otherwise, address correspondence to <a href="mailto:[email protected]" class="email">[email protected]</a> and <a href="mailto:[email protected]" class="email">[email protected]</a>.</p>
+<p>* — correspondence preferred via <a href="https://github.com/greenelab/meta-review/issues">GitHub Issues</a>. Otherwise, address correspondence to <a href="mailto:[email protected]" class="email">[email protected]</a> and <a href="mailto:[email protected]" class="email">[email protected]</a>.</p>
 </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>

diff --git a/manuscript.md b/manuscript.md
@@ -32,14 +32,15 @@ title: Open collaborative writing with Manubot
 
 <small><em>
 This manuscript
-([permalink](https://greenelab.github.io/meta-review/v/95da0bdf3063b5a470f567f5df8f5e33e1823647/))
+([permalink](https://greenelab.github.io/meta-review/v/362b839108fdcb109ede7dc29a2492303cec62fe/))
 was automatically generated
-from [greenelab/meta-review@95da0bd](https://github.com/greenelab/meta-review/tree/95da0bdf3063b5a470f567f5df8f5e33e1823647)
+from [greenelab/meta-review@362b839](https://github.com/greenelab/meta-review/tree/362b839108fdcb109ede7dc29a2492303cec62fe)
 on June 3, 2019.
 </em></small>
 
 ## Authors
 
+<!-- commented out for https://github.com/greenelab/meta-review/issues/230
 
 
 + **Daniel S. Himmelstein** ^[✉](#correspondence)^<br>
@@ -50,7 +51,7 @@ on June 3, 2019.
     · ![Twitter icon](images/twitter.svg){.inline_icon}
     [dhimmel](https://twitter.com/dhimmel)<br>
   <small>
-     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
+     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
   </small>
 
 + **Vincent Rubinetti** <br>
@@ -61,7 +62,7 @@ on June 3, 2019.
     · ![Twitter icon](images/twitter.svg){.inline_icon}
     [vincerubinetti](https://twitter.com/vincerubinetti)<br>
   <small>
-     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
+     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
   </small>
 
 + **David R. Slochower** <br>
@@ -72,7 +73,7 @@ on June 3, 2019.
     · ![Twitter icon](images/twitter.svg){.inline_icon}
     [drslochower](https://twitter.com/drslochower)<br>
   <small>
-     Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
+     Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, San Diego, United States of America
   </small>
 
 + **Dongbo Hu** <br>
@@ -83,7 +84,7 @@ on June 3, 2019.
     · ![Twitter icon](images/twitter.svg){.inline_icon}
     [dongbohu](https://twitter.com/dongbohu)<br>
   <small>
-     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
+     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
   </small>
 
 + **Venkat S. Malladi** <br>
@@ -94,7 +95,7 @@ on June 3, 2019.
     · ![Twitter icon](images/twitter.svg){.inline_icon}
     [katatonikkat](https://twitter.com/katatonikkat)<br>
   <small>
-     Department of Bioinformatics, University of Texas Southwestern Medical Center; Bioinformatics Core Facility, University of Texas Southwestern Medical Center
+     Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America; Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
   </small>
 
 + **Casey S. Greene** <br>
@@ -105,7 +106,7 @@ on June 3, 2019.
     · ![Twitter icon](images/twitter.svg){.inline_icon}
     [GreeneScientist](https://twitter.com/GreeneScientist)<br>
   <small>
-     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
+     Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
   </small>
 
 + **Anthony Gitter** ^[✉](#correspondence)^<br>
@@ -116,14 +117,40 @@ on June 3, 2019.
     · ![Twitter icon](images/twitter.svg){.inline_icon}
     [anthonygitter](https://twitter.com/anthonygitter)<br>
   <small>
-     Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison; Morgridge Institute for Research
+     Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America; Morgridge Institute for Research, Madison, Wisconsin, United States of America
   </small>
 
 
 ::: {#correspondence}
 ✉ — correspondence preferred via [GitHub Issues](https://github.com/greenelab/meta-review/issues).
 Otherwise, address correspondence to <[email protected]> and <[email protected]>.
 :::
+-->
+
+
+
+Daniel S. Himmelstein^1[*](#correspondence)^,
+Vincent Rubinetti^1^,
+David R. Slochower^2^,
+Dongbo Hu^1^,
+Venkat S. Malladi^3,4^,
+Casey S. Greene^1^,
+Anthony Gitter^5,6[*](#correspondence)^
+
+
+
+1. Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
+2. Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, San Diego, United States of America
+3. Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
+4. Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
+5. Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
+6. Morgridge Institute for Research, Madison, Wisconsin, United States of America
+
+
+::: {#correspondence}
+\* — correspondence preferred via [GitHub Issues](https://github.com/greenelab/meta-review/issues).
+Otherwise, address correspondence to <[email protected]> and <[email protected]>.
+:::
 
 
 ## Abstract {.page_break_before}

diff --git a/manuscript.pdf b/manuscript.pdf