update

docs/build/html/_sources/index.txt

@@ -24,20 +24,12 @@ Contents
 
    sections/About-ISB-CGC
    sections/TCGA-Data
+   sections/TCGA_on_ISBCGC
    sections/Web-UI
    sections/Programmatic-API
    sections/Reference-Data
    sections/FAQ
    sections/Support
    sections/Other-Useful-Links
 
-Indices and Tables
-##################
-
-* :ref:`search`
-* :ref:`genindex`
-
-
-.. * :ref:`modindex`
-
 

docs/build/html/_sources/sections/FAQ.txt

@@ -15,10 +15,10 @@ already linked to a Google account, you can create_ a Google account with your c
 Please note, however that although these two accounts will then share the same *name*, they will
 still be two separate accounts, with two separate passwords, *etc*.  (It is also possible 
 that your institutional email address is *already* a Google account, if your institution uses
-Google Apps.  You can check here_).
+Google Apps.
+`Here <https://support.google.com/accounts/answer/40560?hl=en&ref_topic=3382296>`_ is how you can find out).
 
 .. _create: https://accounts.google.com/signupwithoutgmail
-.. _here:  https://support.google.com/accounts/answer/40560?hl=en&ref_topic=3382296
 
 
 Data Access

docs/build/html/_sources/sections/TCGA-Data.txt

@@ -34,9 +34,37 @@ Understanding the TCGA Data Types and Levels
 TCGA Data Types
 ===============
 
+The TCGA dataset is unique in that the tumor samples were assayed using a standard set of platforms and pipelines in order to produce a comprehensive dataset including:
+
+* DNA sequencing of tumor samples and matched-normals (typically blood samples) in order to detect somatic mutations;
+* SNP array based DNA copy-number and genotyping analysis of tumor samples and matched-normals;
+* DNA methylation of tumor samples;
+* messenger RNA (mRNA) expression analysis of the tumor samples to capture the gene expression profile;
+* micro-RNA (miRNA) expression profiling of the tumor samples;
+
+In addition, protein expression for a significant fraction (~20%) of all tumor samples was obtained using RPPA (reverse phase protein array).
+
 TCGA Data Levels
 ================
 
+For each *type* of data, there are typically three *levels* of data:
+* Level 1 typically represents raw, un-normalized data
+* Level 2 typically represents an intermediate level of processing and/or normalization of the data;
+* Level 3 typically represents aggregated, normalized, and/or segmented data.
+
+The results of integrative or pan-cancer analyses are sometimes referred to as "Level 4" data.  More information about
+`Data Level Classification <https://wiki.nci.nih.gov/display/TCGA/Data+level>`_ can be found on the NCI wiki.
+
+TCGA Data Platforms
+===================
+
+When working with any of the data types, it is important to also be aware of both the *platform* that was used to generate the underlying raw data as well as the 
+*pipeline* that was used to process the data.  For example, over the course of the TCGA study, DNA methlyation data was obtained using first the Illumina
+HumanMethylation27 platform, and later using the HumanMethylation450 platform.  Any analysis that combines data from these two platforms across a cohort of
+samples should take this into consideration.  Another example where multiple platforms and/or pipelines were used to produce a single data type is the Level-3 gene
+expression data: most tumor samples were processed at UNC and the normalized gene-expression values are based on the RSEM method, while some tumor samples were
+processed at BCGSC and the normalized gene-expression values are based on RPKM.
+
 Understanding Data Access
 #########################
 

docs/build/html/index.html

@@ -65,6 +65,12 @@ <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this head
 <li class="toctree-l2"><a class="reference internal" href="sections/TCGA-Data.html#understanding-data-access">Understanding Data Access</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="sections/TCGA_on_ISBCGC.html">TCGA Data hosted on the ISB-CGC Platform</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="sections/TCGA_on_ISBCGC.html#open-access-tcga-data">Open-Access TCGA Data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sections/TCGA_on_ISBCGC.html#controlled-access-tcga-data">Controlled-Access TCGA Data</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sections/TCGA_on_ISBCGC.html#tcga-metadata">TCGA Metadata</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="sections/Web-UI.html">Web Interface</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="sections/webapp/releases.html">Release Notes</a></li>
 <li class="toctree-l2"><a class="reference internal" href="sections/webapp/User-Dashboard.html">User Dashboard</a></li>
@@ -103,18 +109,9 @@ <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this head
 <li class="toctree-l1"><a class="reference internal" href="sections/Other-Useful-Links.html">Other Useful Links</a></li>
 </ul>
 </div>
-</div>
-<div class="section" id="indices-and-tables">
-<h2>Indices and Tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h2>
-<ul class="simple">
-<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
-<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
-</ul>
 <hr class="docutils" />
 <div class="isbcgcfooter container">
-Have feedback or corrections?  All improvements to these docs are welcome!
-You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a>
-or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
+Have feedback or corrections?  All improvements to these docs are welcome!  You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a> or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
 </div>
 </div>
 
@@ -128,7 +125,6 @@ <h3><a href="#">Table Of Contents</a></h3>
   <ul>
 <li><a class="reference internal" href="#">The ISB Cancer Genomics Cloud</a><ul>
 <li><a class="reference internal" href="#contents">Contents</a></li>
-<li><a class="reference internal" href="#indices-and-tables">Indices and Tables</a></li>
 </ul>
 </li>
 </ul>

docs/build/html/sections/About-ISB-CGC.html

@@ -26,7 +26,7 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/custom.js"></script>
     <link rel="top" title="ISB Cancer Genomics Cloud 1.0.0 documentation" href="../index.html" />
-    <link rel="next" title="Web Interface" href="Web-UI.html" />
+    <link rel="next" title="About the TCGA Data" href="TCGA-Data.html" />
     <link rel="prev" title="The ISB Cancer Genomics Cloud" href="../index.html" /> 
   </head>
   <body role="document">
@@ -37,7 +37,7 @@ <h3>Navigation</h3>
           <a href="../genindex.html" title="General Index"
              accesskey="I">index</a></li>
         <li class="right" >
-          <a href="Web-UI.html" title="Web Interface"
+          <a href="TCGA-Data.html" title="About the TCGA Data"
              accesskey="N">next</a> |</li>
         <li class="right" >
           <a href="../index.html" title="The ISB Cancer Genomics Cloud"
@@ -74,9 +74,7 @@ <h1>About the ISB Cancer Genomics Cloud<a class="headerlink" href="#about-the-is
 collaborators around the globe.</p>
 <hr class="docutils" />
 <div class="isbcgcfooter container">
-Have feedback or corrections?  All improvements to these docs are welcome!
-You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a>
-or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
+Have feedback or corrections?  All improvements to these docs are welcome!  You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a> or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
 </div>
 
 
@@ -89,8 +87,8 @@ <h4>Previous topic</h4>
   <p class="topless"><a href="../index.html"
                         title="previous chapter">The ISB Cancer Genomics Cloud</a></p>
   <h4>Next topic</h4>
-  <p class="topless"><a href="Web-UI.html"
-                        title="next chapter">Web Interface</a></p>
+  <p class="topless"><a href="TCGA-Data.html"
+                        title="next chapter">About the TCGA Data</a></p>
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
     <ul class="this-page-menu">
@@ -122,7 +120,7 @@ <h3>Navigation</h3>
           <a href="../genindex.html" title="General Index"
              >index</a></li>
         <li class="right" >
-          <a href="Web-UI.html" title="Web Interface"
+          <a href="TCGA-Data.html" title="About the TCGA Data"
              >next</a> |</li>
         <li class="right" >
           <a href="../index.html" title="The ISB Cancer Genomics Cloud"

docs/build/html/sections/FAQ.html

@@ -64,7 +64,8 @@ <h2>ISB-CGC Accounts and Cloud Projects<a class="headerlink" href="#isb-cgc-acco
 Please note, however that although these two accounts will then share the same <em>name</em>, they will
 still be two separate accounts, with two separate passwords, <em>etc</em>.  (It is also possible
 that your institutional email address is <em>already</em> a Google account, if your institution uses
-Google Apps.  You can check <a href="#id2"><span class="problematic" id="id3">here_</span></a>).</p>
+Google Apps.
+<a class="reference external" href="https://support.google.com/accounts/answer/40560?hl=en&amp;ref_topic=3382296">Here</a> is how you can find out).</p>
 </div>
 <div class="section" id="data-access">
 <h2>Data Access<a class="headerlink" href="#data-access" title="Permalink to this headline">¶</a></h2>
@@ -116,9 +117,7 @@ <h2>R and Bioconductor Users<a class="headerlink" href="#r-and-bioconductor-user
 the documentation from the Google Genomics <a class="reference external" href="http://googlegenomics.readthedocs.org/en/latest/workshops/bioc-2015.html">workshop</a> at BioConductor 2015.</p>
 <hr class="docutils" />
 <div class="isbcgcfooter container">
-Have feedback or corrections?  All improvements to these docs are welcome!
-You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a>
-or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
+Have feedback or corrections?  All improvements to these docs are welcome!  You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a> or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
 </div>
 </div>
 

docs/build/html/sections/Other-Useful-Links.html

@@ -26,7 +26,6 @@
     <script type="text/javascript" src="../_static/doctools.js"></script>
     <script type="text/javascript" src="../_static/custom.js"></script>
     <link rel="top" title="ISB Cancer Genomics Cloud 1.0.0 documentation" href="../index.html" />
-    <link rel="next" title="THIS IS THE MAIN SECTION TITLE" href="CrashTestDummy.html" />
     <link rel="prev" title="Contacts &amp; Support" href="Support.html" /> 
   </head>
   <body role="document">
@@ -36,9 +35,6 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="../genindex.html" title="General Index"
              accesskey="I">index</a></li>
-        <li class="right" >
-          <a href="CrashTestDummy.html" title="THIS IS THE MAIN SECTION TITLE"
-             accesskey="N">next</a> |</li>
         <li class="right" >
           <a href="Support.html" title="Contacts &amp; Support"
              accesskey="P">previous</a> |</li>
@@ -73,9 +69,7 @@ <h1>Other Useful Links<a class="headerlink" href="#other-useful-links" title="Pe
 some of the tools at your disposal.</p>
 <hr class="docutils" />
 <div class="isbcgcfooter container">
-Have feedback or corrections?  All improvements to these docs are welcome!
-You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a>
-or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
+Have feedback or corrections?  All improvements to these docs are welcome!  You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a> or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
 </div>
 
 
@@ -87,9 +81,6 @@ <h1>Other Useful Links<a class="headerlink" href="#other-useful-links" title="Pe
   <h4>Previous topic</h4>
   <p class="topless"><a href="Support.html"
                         title="previous chapter">Contacts &amp; Support</a></p>
-  <h4>Next topic</h4>
-  <p class="topless"><a href="CrashTestDummy.html"
-                        title="next chapter">THIS IS THE MAIN SECTION TITLE</a></p>
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
     <ul class="this-page-menu">
@@ -120,9 +111,6 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="../genindex.html" title="General Index"
              >index</a></li>
-        <li class="right" >
-          <a href="CrashTestDummy.html" title="THIS IS THE MAIN SECTION TITLE"
-             >next</a> |</li>
         <li class="right" >
           <a href="Support.html" title="Contacts &amp; Support"
              >previous</a> |</li>

docs/build/html/sections/Reference-Data.html

@@ -95,9 +95,7 @@ <h2>Other Reference Data Sources<a class="headerlink" href="#other-reference-dat
 the <strong>Illumina Platinum Genomes</strong>, information about the <strong>Tute Genomics Annotation</strong> table, <em>etc</em>.</p>
 <hr class="docutils" />
 <div class="isbcgcfooter container">
-Have feedback or corrections?  All improvements to these docs are welcome!
-You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a>
-or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
+Have feedback or corrections?  All improvements to these docs are welcome!  You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a> or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
 </div>
 </div>
 

docs/build/html/sections/Support.html

@@ -80,9 +80,7 @@ <h2>Contact Us<a class="headerlink" href="#contact-us" title="Permalink to this
 <p>For feature-requests or bug-reports, please send e-mail to <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</p>
 <hr class="docutils" />
 <div class="isbcgcfooter container">
-Have feedback or corrections?  All improvements to these docs are welcome!
-You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a>
-or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
+Have feedback or corrections?  All improvements to these docs are welcome!  You can file an issue <a class="reference external" href="https://github.com/isb-cgc/readthedocs/issues">here</a> or email us at <a class="reference external" href="mailto:feedback&#37;&#52;&#48;isb-cgc&#46;org">feedback<span>&#64;</span>isb-cgc<span>&#46;</span>org</a>.</div>
 </div>
 </div>