Merge branch 'master' into release-16

rnacentral/portal/templates/portal/docs/secondary-structure.md

@@ -3,7 +3,8 @@
 
 RNAcentral generates secondary structure (2D) diagrams using
 the [R2DT](https://github.com/RNAcentral/R2DT) software that
-visualises RNA structure using standard layouts or templates (*manuscript in preparation*).
+visualises RNA structure using standard layouts or templates.
+Learn more in the [R2DT preprint](https://www.biorxiv.org/content/10.1101/2020.09.10.290924v1)
 
 <iframe width="560" height="315" src="https://www.youtube.com/embed/La7HA8i_h5I" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
 

rnacentral/portal/templates/portal/docs/text-search.md

@@ -82,6 +82,14 @@ Use parentheses to group and nest logical terms.
 
 ---
 
+## RNAcentral CPB protocol
+
+Our latest article describes different ways of accessing the data. 
+
+<a href='https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpbi.104#cpbi104-fig-0003' class="btn btn-primary" target="_blank">See the text search section</a>
+
+---
+
 ## About RNAcentral search <a style="cursor: pointer" id="ebi-search" ng-click="scrollTo('ebi-search')" name="ebi-search" class="text-muted smaller"><i class="fa fa-link"></i></a>
 
 RNAcentral is powered by the [EBI search](http://www.ebi.ac.uk/ebisearch/),

rnacentral/portal/templates/portal/docs/training.md

@@ -22,6 +22,13 @@ Watch a recording of an online webinar to see RNAcentral in action:
 RNAcentral has been described in several papers:
 
 <blockquote class="callout-info">
+  <p>Exploring non‐coding RNAs in RNAcentral</p>
+  <footer>Sweeney, B. A., Tagmazian, A. A., Ribas, C. E., Finn, R. D., Bateman, A., & Petrov, A. I., 2020</footer>
+  <footer><em>Current Protocols in Bioinformatics</em></footer>
+  <a href="https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpbi.104">CPB</a>
+</blockquote>
+
+<blockquote>
   <p>RNAcentral: a hub of information for non-coding RNA sequences</p>
   <footer>The RNAcentral Consortium, 2019</footer>
   <footer><em>Nucleic Acids Research (Database issue)</em></footer>

rnacentral/portal/templates/portal/homepage.html

@@ -187,7 +187,7 @@ RNAcentral: The non-coding RNA sequence database
             </ul>
 
             <p class="margin-top-5px">
-              Try the new RNAcentral <a href="{% url 'sequence-search' %}">sequence search</a>, <a href="/search?q=has_secondary_structure:%22True%22">browse secondary structures</a>, or read about the <a href="https://blog.rnacentral.org">new member databases</a> on the blog.
+                <span class="label label-success">New</span> Read new RNAcentral paper in <a href="https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpbi.104" target="_blank">Current Protocols in Biodinformatics</a>
             </p>
           </div>
         </div>

rnacentral/portal/templates/portal/r2dt.html

@@ -20,8 +20,9 @@
 
 {% block content %}
     <h1><i class="fa fa-search"></i> R2DT</h1>
-    <p class="lead">Visualise RNA secondary structure in standard orientations using RNA 2D Templates (R2DT)
-      <br /><a href="https://github.com/RNAcentral/R2DT" target="_blank" class="no-icon">Learn more →</a>
+    <p class="lead">
+        Visualise RNA secondary structure in standard orientations using RNA 2D Templates (R2DT).
+        <br>Learn more in the <a href="https://www.biorxiv.org/content/10.1101/2020.09.10.290924v1" target="_blank">R2DT preprint</a>
     </p>
     <r2dt-web
         examples='[

rnacentral/sequence_search/templates/sequence-search-embed.html

@@ -38,6 +38,7 @@
           "h3Color": "#BF8E3E",
           "facetColor": "#BF8E3E",
           "hideRnacentral": "true",
+          "urlWithJobId": "true",
           "trackingID": "UA-51212613-1"
         }'
     />