Upgrade Manubot Rootstock version (#2)

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735128a.

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Upgrade Manubot Rootstock version (#2)

Update to Manubot Rootstock at manubot/rootstock@b5644db

https://github.com/greenelab/manubot-rootstock/tree/b5644db59904b5563a79376e51765adf113a02cb

README.md

@@ -15,4 +15,4 @@ This directory contains the following files, which are mostly ignored on the `ma
 ## Source
 
 The manuscripts in this directory were built from
-[`b5953b1067f01f84f7b484a42823038f7d51edb0`](https://github.com/dhimmel/rephetio-manuscript/commit/b5953b1067f01f84f7b484a42823038f7d51edb0).
+[`735128a615ec804c31cca4046f66601ef2ea24d3`](https://github.com/dhimmel/rephetio-manuscript/commit/735128a615ec804c31cca4046f66601ef2ea24d3).

github-pandoc.css

@@ -1,3 +1,5 @@
+/* From https://gist.github.com/dashed/6714393 with Manubot modifications */
+
 /*! normalize.css v2.1.3 | MIT License | git.io/normalize */
 
 /* ==========================================================================
@@ -453,14 +455,14 @@ table {
 }
 
 .go-top {
-position: fixed;
-bottom: 2em;
-right: 2em;
-text-decoration: none;
-background-color: #E0E0E0;
-font-size: 12px;
-padding: 1em;
-display: inline;
+    position: fixed;
+    bottom: 2em;
+    right: 2em;
+    text-decoration: none;
+    background-color: #E0E0E0;
+    font-size: 12px;
+    padding: 1em;
+    display: inline;
 }
 
 /* Github css */

index.html

@@ -13,7 +13,7 @@
   <meta name="author" content="Ari Green">
   <meta name="author" content="Pouya Khankhanian">
   <meta name="author" content="Sergio E. Baranzini">
-  <meta name="dcterms.date" content="2017-09-05">
+  <meta name="dcterms.date" content="2017-09-06">
   <meta name="keywords" content="Rephetio, Hetionet, repurposing, hetnets, systems pharmacology, networks, machine learning, data science">
   <title>Systematic integration of biomedical knowledge prioritizes drugs for repurposing</title>
   <style type="text/css">code{white-space: pre;}</style>
@@ -30,7 +30,7 @@
 <header>
 <h1 class="title">Systematic integration of biomedical knowledge prioritizes drugs for repurposing</h1>
 </header>
-<p><small><em> This manuscript was automatically generated from <a href="https://github.com/dhimmel/rephetio-manuscript/tree/b5953b1067f01f84f7b484a42823038f7d51edb0">dhimmel/rephetio-manuscript@b5953b1</a> on September 5, 2017. </em></small></p>
+<p><small><em> This manuscript was automatically generated from <a href="https://github.com/dhimmel/rephetio-manuscript/tree/735128a615ec804c31cca4046f66601ef2ea24d3">dhimmel/rephetio-manuscript@735128a</a> on September 6, 2017. </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" height="13" /> <a href="https://orcid.org/0000-0002-3012-7446">0000-0002-3012-7446</a> · <img src="images/github.svg" alt="GitHub icon" height="13" /> <a href="https://github.com/dhimmel">dhimmel</a> · <img src="images/twitter.svg" alt="Twitter icon" height="13" /> <a href="https://twitter.com/dhimmel">dhimmel</a><br> <small> Program in Biological &amp; Medical Informatics, University of California, San Francisco; Department of Systems Pharmacology &amp; Translational Therapeutics, University of Pennsylvania </small></p></li>
@@ -712,8 +712,9 @@ <h3 id="realtime-open-science-thinklab">Realtime open science &amp; Thinklab</h3
 <h2 id="acknowledgements">Acknowledgements</h2>
 <p>We are immensely grateful to our <a href="https://think-lab.github.io/p/rephetio/leaderboard/" title="Rephetio Project Thinklab Leaderboard">Thinklab contributors</a> who joined us in our experiment of radically open science. The following non-team members provided contributions that received 5 or more Thinklab points: Lars Juhl Jensen, Frederic Bastian, Alexander Pico, Casey Greene, Benjamin Good, Craig Knox, Mike Gilson, Chris Mungall, Katie Fortney, Venkat Malladi, Tudor Oprea, MacKenzie Smith, Caty Chung, Allison McCoy, Alexey Strokach, Ritu Khare, Greg Way, Marina Sirota, Raghavendran Partha, Oleg Ursu, Jesse Spaulding, Gaya Nadarajan, Alex Ratner, Scooter Morris, Alessandro Didonna, Alex Pankov, Tong Shu Li, and Janet Piñero. Additionally, the founder of Thinklab, Jesse Spaulding, supported community contributions and developed the platform with Project Rephetio’s needs in mind. We also appreciate DigitalOcean’s sponsorship the Hetionet Browser to cover its hosting costs. Finally, we would like to thank Neo Technology, whose staff provided excellent technical support.</p>
 <p>This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant Number 1144247 to DSH. SEB is supported by the Heidrich Family and Friends Foundation. DH is supported by the the National Cancer Institute of the National Institutes of Health under Award Number UH2CA203792 and the National Library of Medicine under Award Number 1U01LM012675. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.</p>
-<h2 id="references" class="unnumbered page_break_before">References</h2>
-<div id="refs" class="references">
+<h2 id="references" class="page_break_before">References</h2>
+<!-- Explicitly insert bibliography here -->
+<div id="refs">
 <div id="ref-13c9OPizf">
 <p>1. <strong>Innovation in the pharmaceutical industry: New estimates of R&amp;D costs</strong><br />
 Joseph A. DiMasi, Henry G. Grabowski, Ronald W. Hansen<br />