aesthetic changes to be closer to style of pmbio and rnabio

_includes/figure.html

@@ -1,5 +1,5 @@
-<figure class="figure{% if include.position %}  figure--{{ include.position }}{% endif %}" {% if include.width %} width="{{ include.width }}"{% endif %}>
-    <img class="image" src="{{ include.image | relative_url }}" {% if include.width %} width="{{ include.width }}"{% endif %}>
+<<figure class="figure{% if include.position %}  figure--{{ include.position }}{% endif %}" {% if include.width %} width="{{ include.width }}"{% endif %}>
+    <img class="image {% if include.class %} {{ include.class }}{% endif %}" src="{{ include.image | relative_url }}" {% if include.width %} width="{{ include.width }}"{% endif %}>
     {% if include.caption %}<figcaption class="caption">{{ include.caption }}</figcaption>{% endif %}
     {% if include.license %}
     <figcaption class="caption">

_includes/post-categories.html

@@ -1,15 +1,13 @@
 {% assign sorted_categories = site.categories | sort %}
 {% for category in sorted_categories %}
 	{% assign category_name = category | first %}
-	<section class="section  typeset">
-		<h2 id="{{ category_name | slugify }}">{{ category_name }}</h2>
+	<section class="section typeset">
+		<h3 id="{{ category_name | slugify }}">{{ category_name }}</h3>
 		<ul class="list  list--posts">
 			{% for page in site.categories[category_name] reversed %}
 				<li class="item  item--post">
 				 	<article class="article  article--post  typeset">
-					 	<h3><a href="{{ page.url | relative_url }}" title="Post - {{ page.title }}">{{ page.title }}</a></h3>
-						{% include post-meta.html %}
-						{{ page.excerpt | markdownify | truncatewords: 20 }}
+					 	<h4><a href="{{ page.url | relative_url }}" title="Post - {{ page.title }}">{{ page.title }}</a></h4>
 				 	</article>
 			 </li>
 		 {% endfor %}

_includes/site-footer.html

@@ -10,3 +10,21 @@
     {% include nav-social.html %}
   </div>
 </footer>
+
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<!--
+<script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.3/umd/popper.min.js" integrity="sha384-ZMP7rVo3mIykV+2+9J3UJ46jBk0WLaUAdn689aCwoqbBJiSnjAK/l8WvCWPIPm49" crossorigin="anonymous"></script>
+<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js" integrity="sha384-ChfqqxuZUCnJSK3+MXmPNIyE6ZbWh2IMqE241rYiqJxyMiZ6OW/JmZQ5stwEULTy" crossorigin="anonymous"></script>
+-->
+<script>
+$(function () {
+  $('[data-toggle="popover"]').popover()
+})
+</script>
+
+<script>
+$('.popover-dismiss').popover({
+  trigger: 'focus'
+})
+</script>

_layouts/default.html

@@ -20,6 +20,7 @@
 			{% seo %}
 		{% endif %}
 
+    <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
     <link rel="stylesheet" href="{{ "/assets/styles.css" | relative_url }}">
 
 		{% include site-favicons.html %}

_sass/sassline-base/_typography.scss

@@ -360,8 +360,8 @@ table tr th, table tr td
     background-size: 100% 0.15rem;
     border: 0;
     margin: 0;
-    padding-bottom: 3rem;
-    padding-top: 3rem;
+    padding-bottom: 1rem;
+    padding-top: 1rem;
   }
 
   // Code block.
@@ -410,3 +410,8 @@ table tr th, table tr td
     font-feature-settings: 'onum', 'kern';
   }
 }
+
+.article{
+  padding-top: 1px;
+  padding-bottom: 1px;
+}

authors.md

@@ -18,7 +18,7 @@ layout: "home"
 <a class="link" target="_blank" href="{{refer}}" title="{{link[0]}}">{% include icon.html id=id %}</a>
 {% endfor %}
 </nav>
-{% include figure.html image="/assets/Authors/obig2.jpg" position="right" %}
+{% include figure.html image="/assets/Authors/obig2.jpg" position="right" class="rounded-circle" width="300" %}
 Dr. Obi Griffith is Assistant Professor of Medicine and Assistant Director at the McDonnell Genome Institute. Dr. Griffith's research is focused on the development of personalized medicine strategies for cancer using genomic technologies with a particular focus on gene regulatory changes associated with breast cancer. He develops and uses bioinformatics and statistical methods for the analysis of high throughput sequence data and identification of biomarkers for diagnostic, prognostic and drug response prediction. Dr. Griffith has developed and instructs a workshop on RNA sequence analysis for Cold Spring Harbor Laboratories and is a regular instructor for the Canadian Bioinformatics Workshops series. Before coming to Washington University, Dr. Griffith completed bioinformatics post-doctoral fellowships at Lawrence Berkeley National Laboratory in Berkeley, California and at the BC Cancer Agency Genome Sciences Centre in Vancouver, British Columbia. He received his Ph.D. (Medical Genetics, 2008) from the University of British Columbia and B.S. (Biochemistry and Biology with Honors, 2002) from the University of Winnipeg.
 
 ***
@@ -31,7 +31,7 @@ Dr. Obi Griffith is Assistant Professor of Medicine and Assistant Director at th
 <a class="link" target="_blank" href="{{refer}}" title="{{link[0]}}">{% include icon.html id=id %}</a>
 {% endfor %}
 </nav>
-{% include figure.html image="/assets/Authors/MG14.jpg" position="right" %}
+{% include figure.html image="/assets/Authors/MG14.jpg" position="right" class="rounded-circle" width="300" %}
 Dr. Malachi Griffith is an Assistant Director of the McDonnell Genome Institute and an Assistant Professor in the Department of Medicine. Dr. Griffith's research is focused on the development of genomics, bioinformatics and statistical methods as they apply to the study of cancer biology and medicine. A particular focus of his work is in the translation of genomics data from whole genome, exome and transcriptome sequencing into clinically actionable observations and personalized cancer therapies.
  Dr. Griffith is a regular instructor for the Canadian Bioinformatics Workshops series and Cold Spring Harbor Laboratories. Dr. Griffith is currently supported by an NIH R00 pathway to independence grant. Before coming to Washington University Dr. Griffith was a bioinformatics post-doctoral fellow at the BC Cancer Agency Genome Sciences center in Vancouver, British Columbia. He received his Ph.D. (Medical Genetics, 2009) from the University of British Columbia and B.S. (Biochemistry and Biology with Honors, 2002) from the University of Winnipeg.
 
@@ -45,5 +45,5 @@ Dr. Malachi Griffith is an Assistant Director of the McDonnell Genome Institute
 <a class="link" target="_blank" href="{{refer}}" title="{{link[0]}}">{% include icon.html id=id %}</a>
 {% endfor %}
 </nav>
-{% include figure.html image="/assets/Authors/ZacharySkidmore.png" position="right" %}
+{% include figure.html image="/assets/Authors/ZacharySkidmore.png" position="right" class="rounded-circle" width="300" %}
 Zachary Skidmore is a staff scientist at the McDonell Genome Institute at Washington University in Saint Louis. His undergraduate work was completed at the Ohio State University where he obtained a B.Sc. in molecular biology. Graduate work was performed at the University of Illinois where he obtained a M.eng in bioinformatics. His research focus is in the realm of cancer biology where he uses and develops tools and techniques to aid in the analysis and interpretation of cancer sequencing data. He have worked on several large sequencing projects across many cancer types and has expertise in a variety of languages (perl, R, bash, python, typescript, angular2). He is the creator and maintainer of the bioconductor package GenVisR, a graphics program designed to help visualize cohort level genomic data.