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diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -63,6 +63,20 @@ Reference
 | `On the Design of Oligos for Gene Synthesis. <http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4375554>`_
 | *Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering* **2007**: 123-130.
 
+----------
+
+Workflows
+----------------------------
+
+* `I have just discovered an RNA molecule </workflows/from_scratch/>`_
+
+* `I want to learn an RNA’s secondary structure </workflows/2D_modeling/>`_
+
+* `I want to test an RNA secondary structure model </workflows/mutation_rescue/>`_
+
+* `I think my RNA has interesting alternative states </workflows/alternative_states/>`_
+
+
 ----------
 
 Developed by **Das lab**, `Leland Stanford Junior University`.

diff --git a/_sources/install.rst.txt b/_sources/install.rst.txt
@@ -7,7 +7,7 @@ Installation
 
 .. code-block:: bash
 
-    git clone https://github.com/DasLab/Primerize.git
+    git clone https://github.com/ribokit/Primerize.git
 
 * To install ``Primerize``, simply:
 

diff --git a/_sources/matlab.rst.txt b/_sources/matlab.rst.txt
@@ -12,7 +12,7 @@ To install ``NA_Thermo``, simply:
 
 .. code-block:: bash
 
-    git clone https://github.com/DasLab/Primerize.git
+    git clone https://github.com/ribokit/Primerize.git
 
 * In *MATLAB*, go to "**Set Path**". Then "**Add with Subfolders**" of the target ``path/to/Primerize/MATLAB/Scripts/``.
 

diff --git a/_static/doctools.js b/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/_static/searchtools.js b/_static/searchtools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/_static/websupport.js b/_static/websupport.js
@@ -4,7 +4,7 @@
  *
  * sphinx.websupport utilities for all documentation.
  *
- * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2017 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/content.html b/content.html
@@ -8,7 +8,7 @@
     <meta http-equiv="X-UA-Compatible" content="chrome=1">
     <meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no">
 
-    <title>Modules &mdash; Primerize 1.6.2 : PCR Assembly Primer Design | RiboKit</title>
+    <title>Modules &mdash; Primerize 1.6.4 : PCR Assembly Primer Design | RiboKit</title>
 
 
 
@@ -27,7 +27,7 @@
           <link rel="index" title="Index"
                 href="genindex.html"/>
           <link rel="search" title="Search" href="search.html"/>
-      <link rel="top" title="Primerize 1.6.2 : PCR Assembly Primer Design" href="index.html"/>
+      <link rel="top" title="Primerize 1.6.4 : PCR Assembly Primer Design" href="index.html"/>
           <link rel="next" title="primerize.primerize_1d Module" href="primerize.primerize_1d.html"/>
           <link rel="prev" title="Example Scripts" href="example.html"/> 
 
@@ -60,7 +60,7 @@ <h1>
     <span id="logo"><span class="octicon octicon-mark-github"></span></span>
 
 
-      <a href="https://github.com/DasLab/Primerize" target="_blank" class="button fork"><strong>View On GitHub</strong></a>
+      <a href="https://github.com/ribokit/Primerize" target="_blank" class="button fork"><strong>View On GitHub</strong></a>
 
 
 
@@ -73,7 +73,7 @@ <h1>
 
 
 
-        <div class="version"><span>1.6.2</span></div>
+        <div class="version"><span>1.6.4</span></div>
 
 
 
@@ -158,13 +158,13 @@ <h1>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
 
     <p class="wrapper">
       <small>
-        &copy; Copyright 2008-2016 The Board of Trustees of the Leland Stanford Junior University. All Rights Reserved.
+        &copy; Copyright 2008-2017 The Board of Trustees of the Leland Stanford Junior University. All Rights Reserved.
       </small>
     </p>
 
     <p class="wrapper">
 
-      <small>Last updated on</small> Dec 20, 2016.
+      <small>Last updated on</small> Jun 22, 2017.
 
     </p>
 
@@ -188,7 +188,7 @@ <h1>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
       <script type="text/javascript">
           var DOCUMENTATION_OPTIONS = {
               URL_ROOT:'./',
-              VERSION:'1.6.2',
+              VERSION:'1.6.4',
               COLLAPSE_INDEX:false,
               FILE_SUFFIX:'.html',
               HAS_SOURCE:  true
@@ -203,7 +203,7 @@ <h1>Modules<a class="headerlink" href="#modules" title="Permalink to this headli
           <script type="text/javascript" src="_static/doctools.js"></script>
 
 
-          <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+          <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
 
 

diff --git a/example.html b/example.html
@@ -8,7 +8,7 @@
     <meta http-equiv="X-UA-Compatible" content="chrome=1">
     <meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no">
 
-    <title>Example Scripts &mdash; Primerize 1.6.2 : PCR Assembly Primer Design | RiboKit</title>
+    <title>Example Scripts &mdash; Primerize 1.6.4 : PCR Assembly Primer Design | RiboKit</title>
 
 
 
@@ -27,7 +27,7 @@
           <link rel="index" title="Index"
                 href="genindex.html"/>
           <link rel="search" title="Search" href="search.html"/>
-      <link rel="top" title="Primerize 1.6.2 : PCR Assembly Primer Design" href="index.html"/>
+      <link rel="top" title="Primerize 1.6.4 : PCR Assembly Primer Design" href="index.html"/>
           <link rel="next" title="Modules" href="content.html"/>
           <link rel="prev" title="Installation" href="install.html"/> 
 
@@ -60,7 +60,7 @@ <h1>
     <span id="logo"><span class="octicon octicon-mark-github"></span></span>
 
 
-      <a href="https://github.com/DasLab/Primerize" target="_blank" class="button fork"><strong>View On GitHub</strong></a>
+      <a href="https://github.com/ribokit/Primerize" target="_blank" class="button fork"><strong>View On GitHub</strong></a>
 
 
 
@@ -73,7 +73,7 @@ <h1>
 
 
 
-        <div class="version"><span>1.6.2</span></div>
+        <div class="version"><span>1.6.4</span></div>
 
 
 
@@ -197,13 +197,13 @@ <h1>Example Scripts<a class="headerlink" href="#example-scripts" title="Permalin
 
     <p class="wrapper">
       <small>
-        &copy; Copyright 2008-2016 The Board of Trustees of the Leland Stanford Junior University. All Rights Reserved.
+        &copy; Copyright 2008-2017 The Board of Trustees of the Leland Stanford Junior University. All Rights Reserved.
       </small>
     </p>
 
     <p class="wrapper">
 
-      <small>Last updated on</small> Dec 20, 2016.
+      <small>Last updated on</small> Jun 22, 2017.
 
     </p>
 
@@ -227,7 +227,7 @@ <h1>Example Scripts<a class="headerlink" href="#example-scripts" title="Permalin
       <script type="text/javascript">
           var DOCUMENTATION_OPTIONS = {
               URL_ROOT:'./',
-              VERSION:'1.6.2',
+              VERSION:'1.6.4',
               COLLAPSE_INDEX:false,
               FILE_SUFFIX:'.html',
               HAS_SOURCE:  true
@@ -242,7 +242,7 @@ <h1>Example Scripts<a class="headerlink" href="#example-scripts" title="Permalin
           <script type="text/javascript" src="_static/doctools.js"></script>
 
 
-          <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+          <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
 
 

diff --git a/genindex.html b/genindex.html
@@ -9,7 +9,7 @@
     <meta http-equiv="X-UA-Compatible" content="chrome=1">
     <meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no">
 
-    <title>Index &mdash; Primerize 1.6.2 : PCR Assembly Primer Design | RiboKit</title>
+    <title>Index &mdash; Primerize 1.6.4 : PCR Assembly Primer Design | RiboKit</title>
 
 
 
@@ -28,7 +28,7 @@
           <link rel="index" title="Index"
                 href="#"/>
           <link rel="search" title="Search" href="search.html"/>
-      <link rel="top" title="Primerize 1.6.2 : PCR Assembly Primer Design" href="index.html"/> 
+      <link rel="top" title="Primerize 1.6.4 : PCR Assembly Primer Design" href="index.html"/> 
 
     <script type="text/javascript">
       if (window.location.protocol.indexOf('https') == -1 && window.location.hostname.indexOf('.github.io') != -1) { window.location.href = window.location.href.replace('http:', 'https:'); }
@@ -59,7 +59,7 @@ <h1>
     <span id="logo"><span class="octicon octicon-mark-github"></span></span>
 
 
-      <a href="https://github.com/DasLab/Primerize" target="_blank" class="button fork"><strong>View On GitHub</strong></a>
+      <a href="https://github.com/ribokit/Primerize" target="_blank" class="button fork"><strong>View On GitHub</strong></a>
 
 
 
@@ -72,7 +72,7 @@ <h1>
 
 
 
-        <div class="version"><span>1.6.2</span></div>
+        <div class="version"><span>1.6.4</span></div>
 
 
 
@@ -81,8 +81,8 @@ <h1>
       <div class="downloads">
         <span>Downloads</span>
         <ul>
-          <li><a href="https://github.com/DasLab/Primerize/zipball/master" target="_blank" class="button">ZIP</a></li>
-          <li><a href="https://github.com/DasLab/Primerize/tarball/master" target="_blank" class="button">TAR</a></li>
+          <li><a href="https://github.com/ribokit/Primerize/zipball/master" target="_blank" class="button">ZIP</a></li>
+          <li><a href="https://github.com/ribokit/Primerize/tarball/master" target="_blank" class="button">TAR</a></li>
         </ul>
       </div>
 
@@ -571,13 +571,13 @@ <h2 id="V">V</h2>
 
     <p class="wrapper">
       <small>
-        &copy; Copyright 2008-2016 The Board of Trustees of the Leland Stanford Junior University. All Rights Reserved.
+        &copy; Copyright 2008-2017 The Board of Trustees of the Leland Stanford Junior University. All Rights Reserved.
       </small>
     </p>
 
     <p class="wrapper">
 
-      <small>Last updated on</small> Dec 20, 2016.
+      <small>Last updated on</small> Jun 22, 2017.
 
     </p>
 
@@ -601,7 +601,7 @@ <h2 id="V">V</h2>
       <script type="text/javascript">
           var DOCUMENTATION_OPTIONS = {
               URL_ROOT:'./',
-              VERSION:'1.6.2',
+              VERSION:'1.6.4',
               COLLAPSE_INDEX:false,
               FILE_SUFFIX:'.html',
               HAS_SOURCE:  true
@@ -616,7 +616,7 @@ <h2 id="V">V</h2>
           <script type="text/javascript" src="_static/doctools.js"></script>
 
 
-          <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+          <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
 
 

diff --git a/index.html b/index.html
@@ -8,7 +8,7 @@
     <meta http-equiv="X-UA-Compatible" content="chrome=1">
     <meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no">
 
-    <title>Primerize Documentation &mdash; Primerize 1.6.2 : PCR Assembly Primer Design | RiboKit</title>
+    <title>Primerize Documentation &mdash; Primerize 1.6.4 : PCR Assembly Primer Design | RiboKit</title>
 
 
 
@@ -27,7 +27,7 @@
           <link rel="index" title="Index"
                 href="genindex.html"/>
           <link rel="search" title="Search" href="search.html"/>
-      <link rel="top" title="Primerize 1.6.2 : PCR Assembly Primer Design" href="#"/>
+      <link rel="top" title="Primerize 1.6.4 : PCR Assembly Primer Design" href="#"/>
           <link rel="next" title="Installation" href="install.html"/> 
 
     <script type="text/javascript">
@@ -59,7 +59,7 @@ <h1>
     <span id="logo"><span class="octicon octicon-mark-github"></span></span>
 
 
-      <a href="https://github.com/DasLab/Primerize" target="_blank" class="button fork"><strong>View On GitHub</strong></a>
+      <a href="https://github.com/ribokit/Primerize" target="_blank" class="button fork"><strong>View On GitHub</strong></a>
 
 
 
@@ -72,7 +72,7 @@ <h1>
 
 
 
-        <div class="version"><span>1.6.2</span></div>
+        <div class="version"><span>1.6.4</span></div>
 
 
 
@@ -81,8 +81,8 @@ <h1>
       <div class="downloads">
         <span>Downloads</span>
         <ul>
-          <li><a href="https://github.com/DasLab/Primerize/zipball/master" target="_blank" class="button">ZIP</a></li>
-          <li><a href="https://github.com/DasLab/Primerize/tarball/master" target="_blank" class="button">TAR</a></li>
+          <li><a href="https://github.com/ribokit/Primerize/zipball/master" target="_blank" class="button">ZIP</a></li>
+          <li><a href="https://github.com/ribokit/Primerize/tarball/master" target="_blank" class="button">TAR</a></li>
         </ul>
       </div>
 
@@ -177,6 +177,16 @@ <h2>Reference<a class="headerlink" href="#reference" title="Permalink to this he
 <div class="line"><a class="reference external" href="http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4375554">On the Design of Oligos for Gene Synthesis.</a></div>
 <div class="line"><em>Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering</em> <strong>2007</strong>: 123-130.</div>
 </div>
+</div>
+<hr class="docutils" />
+<div class="section" id="workflows">
+<h2>Workflows<a class="headerlink" href="#workflows" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li><a class="reference external" href="/workflows/from_scratch/">I have just discovered an RNA molecule</a></li>
+<li><a class="reference external" href="/workflows/2D_modeling/">I want to learn an RNA’s secondary structure</a></li>
+<li><a class="reference external" href="/workflows/mutation_rescue/">I want to test an RNA secondary structure model</a></li>
+<li><a class="reference external" href="/workflows/alternative_states/">I think my RNA has interesting alternative states</a></li>
+</ul>
 <hr class="docutils" />
 <p>Developed by <strong>Das lab</strong>, <cite>Leland Stanford Junior University</cite>.</p>
 <p>README by <a class="reference external" href="https://t47.io/">t47</a>, <em>January 2016</em>.</p>
@@ -197,13 +207,13 @@ <h2>Reference<a class="headerlink" href="#reference" title="Permalink to this he
 
     <p class="wrapper">
       <small>
-        &copy; Copyright 2008-2016 The Board of Trustees of the Leland Stanford Junior University. All Rights Reserved.
+        &copy; Copyright 2008-2017 The Board of Trustees of the Leland Stanford Junior University. All Rights Reserved.
       </small>
     </p>
 
     <p class="wrapper">
 
-      <small>Last updated on</small> Dec 20, 2016.
+      <small>Last updated on</small> Jun 22, 2017.
 
     </p>
 
@@ -227,7 +237,7 @@ <h2>Reference<a class="headerlink" href="#reference" title="Permalink to this he
       <script type="text/javascript">
           var DOCUMENTATION_OPTIONS = {
               URL_ROOT:'./',
-              VERSION:'1.6.2',
+              VERSION:'1.6.4',
               COLLAPSE_INDEX:false,
               FILE_SUFFIX:'.html',
               HAS_SOURCE:  true
@@ -242,7 +252,7 @@ <h2>Reference<a class="headerlink" href="#reference" title="Permalink to this he
           <script type="text/javascript" src="_static/doctools.js"></script>
 
 
-          <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+          <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>