Add back-matter paragraph to replace front-matter funding info (#103)

This build is based on 12fd168. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/meta-review/builds/444327796 https://travis-ci.org/greenelab/meta-review/jobs/444327797 [ci skip] The full commit message that triggered this build is copied below: Add back-matter paragraph to replace front-matter funding info (#103) * Add Sloan foundation grant number https://sloan.org/grant-detail/8501 * Add funding section to back-matter * Revise funding statement to omit PI mentions * Suppress funders templating in front-matter * consistent ampersand / and
greenelab · Oct 21, 2018 · 937c297 · 937c297
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diff --git a/manuscript.html b/manuscript.html
@@ -9,7 +9,7 @@
   <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="2018-10-19" />
+  <meta name="dcterms.date" content="2018-10-21" />
   <meta name="keywords" content="collaborative review, continuous integration, publishing, Manubot" />
   <title>Open collaborative writing with Manubot</title>
   <style type="text/css">
@@ -96,13 +96,13 @@
 <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/b1f40073a670555c37ffb5a3260d17f67cc7a124/">permalink</a>) was automatically generated from <a href="https://github.com/greenelab/meta-review/tree/b1f40073a670555c37ffb5a3260d17f67cc7a124">greenelab/meta-review@b1f4007</a> on October 19, 2018. </em></small></p>
+<p><small><em> This manuscript (<a href="https://greenelab.github.io/meta-review/v/12fd1685f01d992e37f997a1daf6b523e1dc152a/">permalink</a>) was automatically generated from <a href="https://github.com/greenelab/meta-review/tree/12fd1685f01d992e37f997a1daf6b523e1dc152a">greenelab/meta-review@12fd168</a> on October 21, 2018. </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
-<li><p><strong>Daniel S. Himmelstein</strong><br> <img src="images/orcid.svg" alt="ORCID icon" width="13" height="13" /> <a href="https://orcid.org/0000-0002-3012-7446">0000-0002-3012-7446</a> · <img src="images/github.svg" alt="GitHub icon" width="13" height="13" /> <a href="https://github.com/dhimmel">dhimmel</a> · <img src="images/twitter.svg" alt="Twitter icon" width="13" height="13" /> <a href="https://twitter.com/dhimmel">dhimmel</a><br> <small> Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania · Funded by GBMF4552 </small></p></li>
+<li><p><strong>Daniel S. Himmelstein</strong><br> <img src="images/orcid.svg" alt="ORCID icon" width="13" height="13" /> <a href="https://orcid.org/0000-0002-3012-7446">0000-0002-3012-7446</a> · <img src="images/github.svg" alt="GitHub icon" width="13" height="13" /> <a href="https://github.com/dhimmel">dhimmel</a> · <img src="images/twitter.svg" alt="Twitter icon" width="13" height="13" /> <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>David R. Slochower</strong><br> <img src="images/orcid.svg" alt="ORCID icon" width="13" height="13" /> <a href="https://orcid.org/0000-0003-3928-5050">0000-0003-3928-5050</a> · <img src="images/github.svg" alt="GitHub icon" width="13" height="13" /> <a href="https://github.com/slochower">slochower</a> · <img src="images/twitter.svg" alt="Twitter icon" width="13" height="13" /> <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>Venkat S. Malladi</strong><br> <img src="images/orcid.svg" alt="ORCID icon" width="13" height="13" /> <a href="https://orcid.org/0000-0002-0144-0564">0000-0002-0144-0564</a> · <img src="images/github.svg" alt="GitHub icon" width="13" height="13" /> <a href="https://github.com/vsmalladi">vsmalladi</a> · <img src="images/twitter.svg" alt="Twitter icon" width="13" height="13" /> <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 · Funded by CPRIT RP150596 </small></p></li>
-<li><p><strong>Casey S. Greene</strong><br> <img src="images/orcid.svg" alt="ORCID icon" width="13" height="13" /> <a href="https://orcid.org/0000-0001-8713-9213">0000-0001-8713-9213</a> · <img src="images/github.svg" alt="GitHub icon" width="13" height="13" /> <a href="https://github.com/cgreene">cgreene</a> · <img src="images/twitter.svg" alt="Twitter icon" width="13" height="13" /> <a href="https://twitter.com/GreeneScientist">GreeneScientist</a><br> <small> Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania · Funded by GBMF4552 </small></p></li>
+<li><p><strong>Venkat S. Malladi</strong><br> <img src="images/orcid.svg" alt="ORCID icon" width="13" height="13" /> <a href="https://orcid.org/0000-0002-0144-0564">0000-0002-0144-0564</a> · <img src="images/github.svg" alt="GitHub icon" width="13" height="13" /> <a href="https://github.com/vsmalladi">vsmalladi</a> · <img src="images/twitter.svg" alt="Twitter icon" width="13" height="13" /> <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" width="13" height="13" /> <a href="https://orcid.org/0000-0001-8713-9213">0000-0001-8713-9213</a> · <img src="images/github.svg" alt="GitHub icon" width="13" height="13" /> <a href="https://github.com/cgreene">cgreene</a> · <img src="images/twitter.svg" alt="Twitter icon" width="13" height="13" /> <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><br> <img src="images/orcid.svg" alt="ORCID icon" width="13" height="13" /> <a href="https://orcid.org/0000-0002-5324-9833">0000-0002-5324-9833</a> · <img src="images/github.svg" alt="GitHub icon" width="13" height="13" /> <a href="https://github.com/agitter">agitter</a> · <img src="images/twitter.svg" alt="Twitter icon" width="13" height="13" /> <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>
 <h2 id="abstract" class="page_break_before">Abstract</h2>
@@ -340,8 +340,10 @@ <h3 id="manubot-in-the-context-of-open-science">Manubot in the context of open s
 <p>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 <span class="citation" data-cites="PuP45jrB HQfvK1OF">[<a href="#ref-PuP45jrB">64</a>,<a href="#ref-HQfvK1OF">65</a>]</span>. More broadly, open licensing solves legal barriers to content reuse, enabling any type of scholarly output to become part of the commons <span class="citation" data-cites="g6WVoxNy 137tbemL9">[<a href="#ref-g6WVoxNy">66</a>,<a href="#ref-137tbemL9">67</a>]</span>. 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 <span class="citation" data-cites="gvyja7v1 rgo1TZr 1A97a4UwU">[<a href="#ref-gvyja7v1">68</a>,<a href="#ref-rgo1TZr">69</a>,<a href="#ref-1A97a4UwU">70</a>]</span>. 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.</p>
 <p>Greater openness in both research methods and publishing creates an opportunity to redefine peer review and the role journals play in communicating science <span class="citation" data-cites="52Q1v5nS">[<a href="#ref-52Q1v5nS">43</a>]</span>. At the extreme is real-time open science, whereby studies are performed entirely in the open from their inception <span class="citation" data-cites="17EdosXzD">[<a href="#ref-17EdosXzD">71</a>]</span>. Many such research projects have now been completed, benefiting from the associated early-stage peer review, additional opportunity for online collaboration, and increased visibility <span class="citation" data-cites="1pWYlPj4 O21tn8vf">[<a href="#ref-O21tn8vf">35</a>,<a href="#ref-1pWYlPj4">72</a>]</span>.</p>
 <p>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.</p>
-<h2 id="acknowledgements">Acknowledgements</h2>
+<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 Manubot template manuscript. We are grateful for additional Manubot discussion and testing by Alexander Dunkel, Ansel Halliburton, Achintya Rao, and other GitHub users.</p>
+<h2 id="funding">Funding</h2>
+<p>DSH 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 <a href="http://www.cprit.state.tx.us/files/funded-grants/RP150596.pdf">Grant RP150596</a> from the Cancer Prevention and Research Institute of Texas.</p>
 <h2 id="references" class="page_break_before">References</h2>
 <!-- Explicitly insert bibliography here -->
 <div id="refs">

diff --git a/manuscript.md b/manuscript.md
@@ -5,7 +5,7 @@ author-meta:
 - Venkat S. Malladi
 - Casey S. Greene
 - Anthony Gitter
-date-meta: '2018-10-19'
+date-meta: '2018-10-21'
 keywords:
 - collaborative review
 - continuous integration
@@ -22,10 +22,10 @@ title: Open collaborative writing with Manubot
 
 <small><em>
 This manuscript
-([permalink](https://greenelab.github.io/meta-review/v/b1f40073a670555c37ffb5a3260d17f67cc7a124/))
+([permalink](https://greenelab.github.io/meta-review/v/12fd1685f01d992e37f997a1daf6b523e1dc152a/))
 was automatically generated
-from [greenelab/meta-review@b1f4007](https://github.com/greenelab/meta-review/tree/b1f40073a670555c37ffb5a3260d17f67cc7a124)
-on October 19, 2018.
+from [greenelab/meta-review@12fd168](https://github.com/greenelab/meta-review/tree/12fd1685f01d992e37f997a1daf6b523e1dc152a)
+on October 21, 2018.
 </em></small>
 
 ## Authors
@@ -41,7 +41,6 @@ on October 19, 2018.
     [dhimmel](https://twitter.com/dhimmel)<br>
   <small>
      Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
-     · Funded by GBMF4552
   </small>
 
 + **David R. Slochower**<br>
@@ -64,7 +63,6 @@ on October 19, 2018.
     [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
-     · Funded by CPRIT RP150596
   </small>
 
 + **Casey S. Greene**<br>
@@ -76,7 +74,6 @@ on October 19, 2018.
     [GreeneScientist](https://twitter.com/GreeneScientist)<br>
   <small>
      Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania
-     · Funded by GBMF4552
   </small>
 
 + **Anthony Gitter**<br>
@@ -399,13 +396,18 @@ Specifically, Manubot demonstrates a system for publishing that is transparent,
 These attributes empower integrating Manubot with an ecosystem of other community-driven tools to make science as open and collaborative as possible.
 
 
-## Acknowledgements
+## Acknowledgments
 
 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.
 
+## Funding
+
+DSH 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](http://www.cprit.state.tx.us/files/funded-grants/RP150596.pdf) from the Cancer Prevention and Research Institute of Texas.
+
 ## References {.page_break_before}
 
 <!-- Explicitly insert bibliography here -->

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/variables.json b/variables.json
@@ -1,5 +1,5 @@
 {
-  "date": "October 19, 2018",
+  "date": "October 21, 2018",
   "authors": [
     {
       "github": "dhimmel",
@@ -11,7 +11,7 @@
       "affiliations": [
         "Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania"
       ],
-      "funders": "GBMF4552",
+      "funders": "G-2018-11163 and GBMF4552",
       "affiliation_numbers": [
         1
       ]
@@ -57,7 +57,7 @@
       "affiliations": [
         "Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania"
       ],
-      "funders": "GBMF4552",
+      "funders": "G-2018-11163 and GBMF4552",
       "affiliation_numbers": [
         1
       ]
@@ -109,7 +109,7 @@
     "repo_slug": "greenelab/meta-review",
     "repo_owner": "greenelab",
     "repo_name": "meta-review",
-    "commit": "b1f40073a670555c37ffb5a3260d17f67cc7a124"
+    "commit": "12fd1685f01d992e37f997a1daf6b523e1dc152a"
   },
   "creation_time_utc": "2018-06-15T14:25:26.787993",
   "commit": "63d2468883ea69ad7ad638c39efab0fcbe026298",
@@ -133,6 +133,6 @@
       "url": 21,
       "total": 72
     },
-    "word_count": 4838
+    "word_count": 4881
   }
 }