Learning environ documentation

css/index.css

@@ -129,7 +129,7 @@ a:hover{
 }
 
 .titlefont {
-		font-size: 24px;
+   font-size: 22px;
    font-family: "HelveticaNeue-Light", "Helvetica Neue Light", "Helvetica Neue", Helvetica, Arial, "Lucida Grande", sans-serif; 
    font-weight: 100;
 
@@ -150,6 +150,7 @@ a:hover{
 }
 
 #infotext {
+    font-size: 12px;
 	margin-top: 8px;
 	font-style:oblique;
 	float:left;
@@ -179,16 +180,24 @@ a:hover{
 }
 
 #view {
-	width: 3em;
+	width: 2.5em;
 }
 
 
 #embed {
-	width: 4em;
+	width: 3.5em;
 }
 
 #develop {
-	width: 5em;
+	width: 4.5em;
+}
+
+#teach {
+    width: 3em;
+}
+
+#jupyter {
+    width: 3.75em;
 }
 
 #issues {

index.html

@@ -76,6 +76,7 @@
 	  $("#text3Dmol").hide();
 	    $("#viewtext").hide();
 	    $("#embedtext").hide();
+	    $("#teachtext").hide();
 	    $("#jupytertext").hide();
 	    $("#developtext").hide();
   };
@@ -97,6 +98,17 @@
 	    hidetext();
 		$("#text3Dmol").show();
   });
+
+    $('#teach').hover(
+  function () {
+	    hidetext();
+    $("#teachtext").show();
+  }, 
+  function () {
+	    hidetext();
+		$("#text3Dmol").show();
+  });
+
     $('#jupyter').hover(
   function () {
 	    hidetext();
@@ -128,13 +140,15 @@
    <div id="strip" class = "titlefont">
     <a href="doc/tutorial-url.html" id="view" class="titletext">View</a>
     <a href="doc/tutorial-embeddable.html" id="embed" class="titletext">Embed</a>
-    <a href="http://nbviewer.jupyter.org/github/3dmol/3Dmol.js/blob/9050b97144e81f065df7eecc87ba9a16723ab14b/py3Dmol/examples.ipynb" id="jupyter" class="titletext">Jupyter&nbsp;&nbsp</a>
+    <a href="doc/tutorial-learning_environment.html" id="teach" class="titletext">Teach</a>
+    <a href="http://nbviewer.jupyter.org/github/3dmol/3Dmol.js/blob/9050b97144e81f065df7eecc87ba9a16723ab14b/py3Dmol/examples.ipynb" id="jupyter" class="titletext">Jupyter</a>
     <a href="doc/index.html" id="develop" class="titletext">Develop</a>
    </div>
    <div id="infotext">
     <span id="text3Dmol" class="floattext">A modern, object-oriented JavaScript library for visualizing molecular data</span>
     <span id="viewtext" class="floattext">View structures through a declarative URL interface</span>
     <span id="embedtext" class="floattext">Embed molecular viewers in webpages with two lines of code</span>
+    <span id="teachtext" class="floattext">Engage students while teaching molecular structures</span>
     <span id="jupytertext" class="floattext">Include interactive 3D structures in Jupyter notebooks</span>
     <span id="developtext" class="floattext">Develop web applications using a full featured API</span>
 

tutorials/learning_environment.json

@@ -0,0 +1,3 @@
+{
+	"title" : "Active Learning with 3Dmol.js"
+}

tutorials/learning_environment.md

@@ -0,0 +1,47 @@
+<script src="../build/3Dmol-min.js"></script> 
+
+The [hosted 3Dmol.js viewer](tutorial-url.html) can serve as an active learning environment of engaging and querying students when teaching properties of 3D molecular structures.  The instructor creates a session using the share button in the upper right corner.  When students connect to this session, they see the same molecular view as the instructor.  Although the students can independently manipulate the view, the instructor can override their view.
+
+The instructor can pose questions that the students then answer by clicking on atoms.  The accumulated and anonymous answers can then be displayed in the instructor's view.
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/90UhGlzLcdc" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
+## Self-Hosting
+
+The easiest way to use the 3Dmol.js active learning environment is through the hosted viewer at [https://3dmol.csb.pitt.edu].  However, it may be desirable to host your own instance for your class.  A light-weight Flask webserver can quickly be brought up on a Ubuntu Linux machine with a few commands:
+
+
+```
+{@lang bash}#install dependencies
+apt install npm python3-pip
+pip3 install flask flask_socketio eventlet
+#use npm to install and build 3Dmol.js
+npm install 3dmol
+#run a standalone flask server
+cd node_modules/3dmol/learning-environment
+#can optionally specify a port with -p <PORT>, default is 5000
+python3 server.py
+```
+
+By default, this will launch a server on port 5000, e.g. <tt>http://HOSTNAME:5000/</tt>.  Do <b>not</b> run this command as superuser to run the server on the privileged default webserver port 80 without consulting with a network security specialist.
+
+
+If you already have a webserver running, you can redirect the websocket requests used by 3Dmol.js to the server running on port 5000.  For example, for apache the following is added to the configuration (see [here](https://stackoverflow.com/questions/36472920/apache-proxy-configuration-for-socket-io-project-not-in-root)</a>):
+
+
+<pre>
+<font color='black'>RewriteEngine On
+RewriteCond %{REQUEST_URI}  ^/socket.io            [NC]
+RewriteCond %{QUERY_STRING} transport=websocket    [NC]
+RewriteRule /(.*)           ws://localhost:5000/$1 [P,L]
+
+ProxyPass        /socket.io http://localhost:5000/socket.io
+ProxyPassReverse /socket.io http://localhost:5000/socket.io
+<font>
+</pre>
+
+The [flask-SocketIO documentation](https://flask-socketio.readthedocs.io/en/latest/) provides more information for running in other setups such as gunicorn, uwsgi, and nginx.
+
+
+
+