Merge branch 'master' into staging

merging staging changes accidentally committed to master

_config.yml

@@ -38,6 +38,11 @@ author :
 #
 production_url : http://drummondlab.org
 
+# The excerpt_separator can be used to define a cutoff for previewing on pages
+# like the main Blog page. Warning: it is case sensitive! Use it exactly
+# as written here.
+excerpt_separator: "<!-- more -->"
+
 # All Jekyll-Bootstrap specific configurations are namespaced into this hash
 #
 JB :

_includes/themes/lab/home.html

@@ -56,7 +56,9 @@
 
   <div class="hugespacer"></div>
 
+  <!-- Main dynamic-content portion of the front page: news, blog posts, papers -->
   <div class="row">
+    <!-- Column to display blog posts -->
     <div class="col-md-4">
       <div class="head">
         <a class="off" href="/news/">News</a>
@@ -94,40 +96,80 @@
       </div>
       <div class="bigspacer"></div>   
     </div>
+
+    <!-- Column to display blog posts -->
     <div class="col-md-4">
-      <div class="head">
-        <a class="off" href="/blog/">Posts</a>
+      <div class="row">
+        <div class="head">
+          <a class="off" href="/blog/">Posts</a>
+        </div>
+        <div class="bigspacer"></div>
+        <div class="feedbox pad-left">
+          {% for post in site.categories.blog limit:3 %}
+
+            {% for member in site.categories.team %}
+              {% if member.handle == post.author_handle %}
+                {% assign author = member %}
+              {% endif %}
+            {% endfor %}    
+
+            <div class="note-title">
+              <i class="fa fa-comment-o fa-fw"></i>
+              <a class="off" href="{{ post.url }}">
+              {{ post.title }}
+              </a>
+            </div>
+            <div class="smallspacer"></div>
+            <div class="smallnote">
+              Posted
+              {{ post.date | date_to_string }}
+              {% if author %}
+              by <a class="off" href="{{ author.url }}">{{ author.nickname }}</a>
+              {% endif %}           
+            </div>
+            <div class="spacer"></div>  
+            <div class="spacer"></div>        
+          {% endfor %}
+        </div>
+        <div class="bigspacer"></div>   
       </div>
-      <div class="bigspacer"></div>
-      <div class="feedbox pad-left">
-        {% for post in site.categories.blog limit:4 %}
-
-          {% for member in site.categories.team %}
-            {% if member.handle == post.author_handle %}
-              {% assign author = member %}
-            {% endif %}
-          {% endfor %}    
+     <div class="row">
+        <div class="head">
+          <a class="off" href="/blog/">Outreach</a>
+        </div>
+        <div class="bigspacer"></div>
+        <div class="feedbox pad-left">
+          {% for post in site.categories.outreach limit:3 %}
 
-          <div class="note-title">
-            <i class="fa fa-comment-o fa-fw"></i>
-            <a class="off" href="{{ post.url }}">
-            {{ post.title }}
-            </a>
-          </div>
-          <div class="smallspacer"></div>
-          <div class="smallnote">
-            Posted
-            {{ post.date | date_to_string }}
-            {% if author %}
-            by <a class="off" href="{{ author.url }}">{{ author.nickname }}</a>
-            {% endif %}           
-          </div>
-          <div class="spacer"></div>  
-          <div class="spacer"></div>        
-        {% endfor %}
+            {% for member in site.categories.team %}
+              {% if member.handle == post.author_handle %}
+                {% assign author = member %}
+              {% endif %}
+            {% endfor %}    
+
+            <div class="note-title">
+              <i class="fa fa-comment-o fa-fw"></i>
+              <a class="off" href="{{ post.url }}">
+              {{ post.title }}
+              </a>
+            </div>
+            <div class="smallspacer"></div>
+            <div class="smallnote">
+              Posted
+              {{ post.date | date_to_string }}
+              {% if author %}
+              by <a class="off" href="{{ author.url }}">{{ author.nickname }}</a>
+              {% endif %}           
+            </div>
+            <div class="spacer"></div>  
+            <div class="spacer"></div>        
+          {% endfor %}
+        </div>
+        <div class="bigspacer"></div>   
       </div>
-      <div class="bigspacer"></div>   
     </div>
+
+   <!-- Column to display papers -->
     <div class="col-md-4">
       <div class="head">
         <a class="off" href="/papers/">Papers

news/index.html

@@ -3,7 +3,7 @@
 title: "News"
 description: "The Drummond Lab blog"
 group: subnavigation
-navorder: 6
+navorder: 7
 ---
 {% include JB/setup %}
 

outreach/_posts/2024-10-05-south-side-science-festival.md

@@ -0,0 +1,20 @@
+---
+layout: post
+title: "South Side Science Festival"
+author: "D. Allan Drummond"
+author_handle: "dad"
+image: /assets/images/news/default-news.png
+category: outreach
+published: true
+tags: [outreach]
+---
+We had a great time at the [South Side Science Festival][1]! 
+
+![team-at-ss-fest](/assets/images/outreach/team-at-ss-science-festival-20241005.jpg){:width="75%" style=".center"}
+
+<!-- more -->
+
+Dozens of families from the South Side of Chicago came by to experience our demonstrations of phase separation (vortexing was a huge hit with kids), color in diagrams of yeast cells, gaze in wonder at our 3D-printed cell models, and hang out with our team as we dropped some knowledge (and, okay, also some candy...). Can't wait to do it again next year!
+
+[1]: https://southsidescience.event.uchicago.edu/
+

outreach/_posts/2024-10-06-cell-coloring-page.md

@@ -0,0 +1,25 @@
+---
+layout: post
+title: "Color inside the cell"
+author: "D. Allan Drummond"
+author_handle: "dad"
+image: /assets/images/news/default-news.png
+category: outreach
+published: true
+tags: [outreach]
+---
+We made a coloring page to help you learn yeast cell biology!
+
+![cell](/assets/images/outreach/yeast-cell-unannotated.jpg){:width="75%" style=".center"}
+
+<!-- more -->
+
+You can download a high-resolution PDF file [here](/assets/images/outreach/yeast-cell-unannotated.pdf).
+
+We encourage you to be free with your colors. You many notice some places where the seemingly different shapes/spaces seem to be continuous...that's biology! So much of cell biology is discovery and an attempt by us humans to understand something too tiny to see with our naked eyes, so ancient and unfamiliar that we've had to give things names without knowing quite what they do, and so complex that we don't have it all figured out yet. Hope you enjoy seeing just a taste of what researchers have been able to identify.
+
+![cell-annotated](/assets/images/outreach/yeast-cell-annotated.png){:width="75%" style=".center"}
+
+You can download a high-resolution PDF file of the answer key [here](/assets/images/outreach/yeast-cell-annotated.pdf).
+
+

outreach/index.html

@@ -0,0 +1,76 @@
+---
+layout: default
+title: "Outreach"
+description: "Drummond Lab outreach"
+group: subnavigation
+navorder: 5
+---
+{% include JB/setup %}
+
+
+<div class="pager">
+
+	{% if paginator.previous_page %}
+		{% if paginator.previous_page == 1 %}
+		<a class="prev" href="/{{ page.category }}/">
+			<i class="fa fa-chevron-left fa-lg"></i>
+		</a>
+		{% else %}
+		<a class="prev" href="/{{ page.category }}/page{{ paginator.previous_page }}">
+			<i class="fa fa-chevron-left fa-lg"></i>
+		</a>
+		{% endif %}  		
+	{% endif %}  
+
+	{% if paginator.next_page %}  
+	<a class="next" href="/{{ page.category }}/page{{ paginator.next_page }}">
+		<i class="fa fa-chevron-right fa-lg"></i>
+	</a>	
+	{% endif %}  	
+
+</div>
+
+{% for post in site.categories.outreach %}
+
+	{% for member in site.categories.team %}
+		{% if member.handle == post.author_handle %}
+			{% assign author = member %}
+		{% endif %}
+	{% endfor %}
+
+	<div class="bigspacer"></div>
+	<div class="row">
+		<div class="col-md-3">
+			<div class="head">
+				<a href="{{ post.url }}" class="off">{{ post.title }}</a>
+			</div>
+			<div class="smallnote">
+				{{ post.date | date_to_string }}
+				{% if author %}
+				by <a class="off" href="{{ author.url }}">{{ author.nickname }}</a>
+				{% endif %}				
+			</div>	
+		</div>
+		<div class="col-md-8">		
+			<div style="height:5px;"></div>			
+			<!--{% if post.image %}
+			<a href="{{ post.url }}"><img class="offset" src="{{ post.image }}"></a>
+			{% endif %}-->
+			<div class="post">
+				{{ post.excerpt }}
+			</div>
+		</div>			
+		<div class="col-md-1"></div>
+	</div>		
+
+{% endfor %}
+
+<div class="bigspacer"></div>	
+<div class="row">
+	<div class="col-md-12 text-center">
+		<a class="off" href="/{{ page.category }}/archive/">
+			<div class="smallhead">Archive</div>
+			<i class="text-gray fa fa-chevron-circle-down fa-2x"></i>
+		</a>
+	</div>
+</div>

protocols/index.html

@@ -1,9 +1,9 @@
 ---
 layout: default
 title: "Protocols"
-description: ""
+description: "Drummond Lab experimental protocols"
 group: subnavigation
-navorder: 5
+navorder: 6
 ---
 {% include JB/setup %}