orderedlist · farahank · Aug 14, 2020 · Aug 14, 2020 · Aug 14, 2020 · Aug 15, 2020
diff --git a/README.md b/README.md
@@ -1,14 +1,6 @@
 # Minimal Theme
 
-[Demo the Theme](http://orderedlist.github.com/minimal/)
-
-This is the raw HTML and styles that are used for the *minimal* theme on [GitHub Pages](http://pages.github.com/).
-
-Syntax highlighting is provided on GitHub Pages by [Pygments](http://pygments.org).
-
-# License
-
-This work is licensed under a [Creative Commons Attribution-ShareAlike 3.0 Unported License](http://creativecommons.org/licenses/by-sa/3.0/).
-
-
+This is the source for the website located at https://data4miccai.github.io/,
+which was put together for the respective tutorial at [MICCAI 2020](https://www.miccai2020.org/en/).
 
+This project is maintained by @fedorov.
diff --git a/assets/miccai-2020-logo.png b/assets/miccai-2020-logo.png
diff --git a/index.html b/index.html
@@ -3,7 +3,7 @@
   <head>
     <meta charset="utf-8">
     <meta http-equiv="X-UA-Compatible" content="chrome=1">
-    <title>Minimal by Steve Smith</title>
+    <title>DATA4MICCAI: NIH Cancer Imaging Data Repositories for Biomedical Data Science Research</title>
 
     <link rel="stylesheet" href="stylesheets/styles.css">
     <link rel="stylesheet" href="stylesheets/pygment_trac.css">
@@ -15,190 +15,113 @@
   <body>
     <div class="wrapper">
       <header>
-        <h1>Minimal</h1>
-        <p>A Theme for GitHub Pages</p>
-        <p class="view"><a href="http://github.com/orderedlist/minimal">View the Project on GitHub <small>orderedlist/minimal</small></a></p>
-        <ul>
-          <li><a href="https://github.com/orderedlist/minimal/zipball/master">Download <strong>ZIP File</strong></a></li>
-          <li><a href="https://github.com/orderedlist/minimal/tarball/master">Download <strong>TAR Ball</strong></a></li>
-          <li><a href="http://github.com/orderedlist/minimal">Fork On <strong>GitHub</strong></a></li>
-        </ul>
-      </header>
-      <section>
-        <h1>GitHub Flavored Markdown</h1>
-
-        <p><em>View the <a href="http://github.github.com/github-flavored-markdown/sample_content.html">source of this content</a>.</em></p>
-
-        <p>Let's get the whole "linebreak" thing out of the way. The next paragraph contains two phrases separated by a single newline character:</p>
-
-        <p>Roses are red<br>
-        Violets are blue</p>
+        <h1>DATA4MICCAI</h1>
 
-        <p>The next paragraph has the same phrases, but now they are separated by two spaces and a newline character:</p>
+        <h2>A <a href="https://www.miccai2021.org/en/">MICCAI 2021</a> Tutorial</h2>
 
-        <p>Roses are red<br><br>
-        Violets are blue</p>
-
-        <p>Oh, and one thing I cannot stand is the mangling of words with multiple underscores in them like perform_complicated_task or do_this_and_do_that_and_another_thing.</p>
-
-        <h2>A bit of the GitHub spice</h2>
-
-        <p>In addition to the changes in the previous section, certain references are auto-linked:</p>
+        <a href="https://www.miccai2021.org/en/"><img src="https://www.miccai2021.org/files/images/layout/en/miccai2021-logo.png" alt="MICCAI 2020"></a>
+      </header>
+      <section>
 
+        <h1>NIH Cancer Imaging Data Repositories for Biomedical Data Science Research</h1>
+
+        <h2>Date: Sept 27, 2021</h2>
+        <h2>Time: 10am-2pm (EDT) / 14:00-18:00 (UTC)</h2>
+<br><br>
+        The National Cancer Institute (NCI), of the National Institutes of Health (NIH), has made significant investments in the
+creation and development of public data repositories to enable and promote sharing and secondary analysis of cancer
+imaging data through an open science approach. Since its inception in 2011, <a href="https://www.cancerimagingarchive.net/">The Cancer Imaging Archive (TCIA)</a> has
+provided the imaging research community with a stable and reliable resource for sharing de-identified clinical
+radiology (DICOM), and more recently digital pathology images of a variety of cancers. A growing number of
+collections in TCIA contain clinical metadata, annotations, and third-party analysis results.
+<br><br>
+Recently NCI has launched the <a href="https://datacommons.cancer.gov">Cancer Research Data Commons (CRDC)</a>, an enterprise of cloud-based data
+repositories and resources dedicated to key information modalities in cancer research (including genomics,
+proteomics, and imaging) to provide the research community with a virtual and expandable infrastructure to enable
+cross-domain data analysis and archival. Adhering to FAIR principles in cancer informatics, CRDC aims to further
+enable innovations in data science in oncology. <a href="https://imaging.datacommons.cancer.gov">Imaging Data Commons (IDC)</a>, 
+the imaging node in CRDC, publicly
+released in October 2020, connects researchers with image collections from TCIA and beyond, through a robust
+infrastructure containing metadata, image-derived data (segmentations, annotations, and image-based analysis
+results), allowing image browsing and connectivity to Cloud Resources for image computation, data analysis, and
+archival of the results. Direct connectivity of IDC data to robust Google analytics and ML tools is an important feature
+of this platform.
+<br><br>
+This tutorial aims to familiarize attendees with TCIA, IDC, their similarities and differences in features and capabilities,
+including search, browsing, downloading (through TCIA), viewing and cohort collection (through IDC), and cloud
+computation through the NCI Cloud Resources. All levels are welcome.
+
+Attendees will be able to follow the demonstration session at their own pace, or during the tutorial, following
+the learning materials included in the IDC documentation. To be able to follow all of the exercises and demonstration
+notebooks the attendees will need to have a Google Cloud Project with billing activated. IDC provides free cloud 
+credits to facilitate exploration of the resource. The attendees are encouraged to request these credits in advance using
+the <a href="https://docs.google.com/forms/d/e/1FAIpQLSfXvXqficGaVEalJI3ym6rKqarmW_YUUWG6A4U8pclvR8MmRQ/viewform">IDC cloud credit application form</a>.
+<br><br>
+
+        <h2>Agenda</h2>
+
+        <b>10:00 – 10:50 am Cancer Imaging Data Repositories</b>
         <ul>
-          <li>SHA: be6a8cc1c1ecfe9489fb51e4869af15a13fc2cd2</li>
-          <li>User@SHA ref: <a href="https://github.com/mojombo/product/commit/be6a8cc1c1ecfe9489fb51e4869af15a13fc2cd2" class="commit-link">mojombo@<tt>be6a8cc</tt></a></li>
-          <li>User/Project@SHA: <a href="https://github.com/mojombo/god/commit/be6a8cc1c1ecfe9489fb51e4869af15a13fc2cd2" class="commit-link">mojombo/god@<tt>be6a8cc</tt></a></li>
-          <li>#Num: <a href="https://github.com/github/product/issues/1" class="issue-link" title="Baseline: What is up in the air right now?">#1</a></li>
-          <li>User/#Num: mojombo#1</li>
-          <li>User/Project#Num: <a href="https://github.com/mojombo/god/issues/1" class="issue-link" title="The server is not available (or you do not have permissions to access it)">mojombo/god#1</a></li>
+        <li>10 am - 10:10 am Introduction – K. Farahani</li> 
+        <li>10:10 am - 10:30 am The Cancer Imaging Archive (TCIA)– J. Freymann</li>
+        <li>10:30 am - 10:50 am Imaging Data Commons (IDC) – A. Fedorov, R. Kikinis <a href="https://docs.google.com/presentation/d/17IfcvwCrMkw2On3FZ3EjqjyzI6K_WA5BEXmjzvY9YWY/edit?usp=sharing">(slides)</a></li>
+        <li>10:50 am – 10:55 am Q &amp; A</li>
+        <li>10:55 am Break</li>
         </ul>
-
-        <p>These are dangerous goodies though, and we need to make sure email addresses don't get mangled:</p>
-
-        <p>My email addy is <a href="mailto:tom@github.com">tom@github.com</a>.</p>
-
-        <h2>Math is hard, let's go shopping</h2>
-
-        <p>In first grade I learned that 5 &gt; 3 and 2 &lt; 7. Maybe some arrows. 1 -&gt; 2 -&gt; 3. 9 &lt;- 8 &lt;- 7.</p>
-
-        <p>Triangles man! a^2 + b^2 = c^2</p>
-
-        <h2>We all like making lists</h2>
-
-        <p>The above header should be an H2 tag. Now, for a list of fruits:</p>
-
+
+        <b>11 am – 11:55 am Demonstration session: TCIA Features</b>
         <ul>
-          <li>Red Apples</li>
-          <li>Purple Grapes</li>
-          <li>Green Kiwifruits</li>
+        <li>11:00 am - 11: 15 am Browsing Radiology and Pathology Data – J. Kirby</li> 
+        <li>11:15 am - 11:30 am Searching with the Radiology Data Portal – L. Tarbox</li>
+        <li>11:30 am - 11:45 am Additional tools and resources – F. Prior</li>
+        <li>11:45 am – 11:55 am Q &amp; A</li>
+        <li>11:55 am Break</li>
+        </ul>
+
+        <b>12 pm – 12:30 pm Project MONAI and public data from TCIA and IDC – S. Aylward</b>
+        <ul>
+        <li>12:30 pm – 12:35 pm Q &amp; A</li>
+        <li>12:35 pm Break</li>
+        </ul>
+
+        <b>12:45 pm – 1:35 pm Demonstration session: IDC Features and Cloud Compute</b>
+        <ul>
+        <li>12:45 pm - 1:00 pm Imaging Data Commons Features - A. Fedorov</li> 
+        <ul>
+          <li>short demonstration videos available <a href="https://www.youtube.com/playlist?list=PLhawVWNiPvwb2H0D9UTOIL23bc5DuDJRu">here</a></li>
+          <li>overview paper about IDC published in "Cancer Research" is <a href="http://dx.doi.org/10.1158/0008-5472.CAN-21-0950">here</a></li>
+        </ul>
+        <li>1:00 pm - 1:15 pm Introduction to Google Cloud (GCP) Platform – W. Longabaugh <a href="https://docs.google.com/presentation/d/1HNZ34xkZCXt6WRDcEtmAUGNq5TM0xzPaK7sojKJfoBc/edit?usp=sharing">(slides)</a></li> 
+        <li>1:15 pm - 1:30 pm Utilizing IDC and GCP to support AI imaging research – D. Bontempi</li>
+        <ul>
+          <li>IDC notebooks are available <a href="https://github.com/ImagingDataCommons/IDC-Examples/tree/master/notebooks">here</a></li>
+        </ul>
+        <li>1:30 pm – 1:45 pm Q &amp;A</li>
         </ul>
 
-        <p>Let's get crazy:</p>
-
-        <ol>
-          <li>
-            <p>This is a list item with two paragraphs. Lorem ipsum dolor<br>
-            sit amet, consectetuer adipiscing elit. Aliquam hendrerit<br>
-            mi posuere lectus.</p>
-
-            <p>Vestibulum enim wisi, viverra nec, fringilla in, laoreet<br>
-            vitae, risus. Donec sit amet nisl. Aliquam semper ipsum<br>
-            sit amet velit.</p>
-          </li>
-          <li><p>Suspendisse id sem consectetuer libero luctus adipiscing.</p></li>
-        </ol>
-
-        <p>What about some code <strong>in</strong> a list? That's insane, right?</p>
-
-        <ol>
-          <li>
-            <p>In Ruby you can map like this:</p>
-
-            <pre><code>['a', 'b'].map { |x| x.uppercase }</code></pre>
-          </li>
-          <li>
-            <p>In Rails, you can do a shortcut:</p>
-
-            <pre><code>['a', 'b'].map(&amp;:uppercase)</code></pre>
-          </li>
-        </ol>
-
-        <p>Some people seem to like definition lists</p>
-
-        <dl>
-          <dt>Lower cost</dt>
-          <dd>The new version of this product costs significantly less than the previous one!</dd>
-          <dt>Easier to use</dt>
-          <dd>We've changed the product so that it's much easier to use!</dd>
-        </dl>
-
-        <h2>I am a robot</h2>
-
-        <p>Maybe you want to print <code>robot</code> to the console 1000 times. Why not?</p>
-
-        <pre><code>def robot_invasion
-  puts("robot " * 1000)
-end
-</code></pre>
-
-        <p>You see, that was formatted as code because it's been indented by four spaces.</p>
-
-        <p>How about we throw some angle braces and ampersands in there?</p>
-
-        <pre><code>&lt;div class="footer"&gt;
-    &amp;copy; 2004 Foo Corporation
-&lt;/div&gt;
-</code></pre>
-
-        <h2>Set in stone</h2>
-
-        <p>Preformatted blocks are useful for ASCII art:</p>
-
-        <pre>             ,-.
-    ,     ,-.   ,-.
-   / \   (   )-(   )
-   \ |  ,.&gt;-(   )-&lt;
-    \|,' (   )-(   )
-     Y ___`-'   `-'
-     |/__/   `-'
-     |
-     |
-     |    -hrr-
-  ___|_____________
-</pre>
-
-        <h2>Playing the blame game</h2>
-
-        <p>If you need to blame someone, the best way to do so is by quoting them:</p>
-
-        <blockquote>
-        <p>I, at any rate, am convinced that He does not throw dice.</p>
-        </blockquote>
-
-        <p>Or perhaps someone a little less eloquent:</p>
-
-        <blockquote>
-        <p>I wish you'd have given me this written question ahead of time so I<br>
-        could plan for it... I'm sure something will pop into my head here in<br>
-        the midst of this press conference, with all the pressure of trying to<br>
-        come up with answer, but it hadn't yet...</p>
-
-        <p>I don't want to sound like<br>
-        I have made no mistakes. I'm confident I have. I just haven't - you<br>
-        just put me under the spot here, and maybe I'm not as quick on my feet<br>
-        as I should be in coming up with one.</p>
-        </blockquote>
+        <b>1:30 pm – 2:00 pm Open Discussion</b>
 
-        <h2>Table for two</h2>
+        <h3>Organizers</h3>
 
-        <table>
-          <tbody>
-        <tr>
-            <th>ID</th>
-        <th>Name</th>
-        <th>Rank</th>
-          </tr>
-          <tr>
-            <td>1</td>
-        <td>Tom Preston-Werner</td>
-        <td>Awesome</td>
-          </tr>
-          <tr>
-            <td>2</td>
-        <td>Albert Einstein</td>
-        <td>Nearly as awesome</td>
-          </tr>
-        </tbody>
-        </table>
+      <ul>
+          <li>Keyvan Farahani, National Cancer Institute</li>
+          <li>Andrey Fedorov, Brigham and Women's Hospital / Harvard Medical School</li>
+            <li>John Freymann, Fredrick National Laboratory for Cancer Research</li>
+            <li>Justin Kirby, Fredrick National Laboratory for Cancer Research</li>
+            <li>Ulrike Wagner, Fredrick National Laboratory for Cancer Research</li>
+            <li>Fred Prior, University of Arkansas Medical School</li>
+            <li>Lawrence Tarbox, University of Arkansas Medical School</li>
+            <li>Bill Longabaugh, Institute for Systems Biology</li>
+            <li>Suzanne Paquette, Institute for Systems Biology</li>
+            <li>David Pot, General Dynamics IT</li>
+            <li>Ron Kikinis, Brigham and Women's Hospital / Harvard Medical School</li>
+      </ul>
 
-        <h2>Crazy linking action</h2>
+      <a href="https://data4miccai.github.io/index_2020.html">MICCAI 2020 tutorial page</a>
 
-        <p>I get 10 times more traffic from <a href="http://google.com/" title="Google">Google</a> than from<br>
-        <a href="http://search.yahoo.com/" title="Yahoo Search">Yahoo</a> or <a href="http://search.msn.com/" title="MSN Search">MSN</a>.</p>
       </section>
       <footer>
-        <p>This project is maintained by <a href="http://github.com/orderedlist">Steve Smith</a></p>
+        <p>This page is maintained by <a href="http://github.com/fedorov">Andrey Fedorov</a></p>
         <p><small>Hosted on GitHub Pages &mdash; Theme by <a href="https://github.com/orderedlist">orderedlist</a></small></p>
       </footer>
     </div>