Deploying to gh-pages from @ d705a90 🚀

core/core.html

@@ -202,7 +202,7 @@
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
             <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
- <span class="menu-text">Week 6: Quarto</span></a>
+ <span class="menu-text">Week 6: Core Drop-in</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -231,6 +231,42 @@
   <a href="../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
+</li>
+      </ul>
+  </li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true">
+ <span class="menu-text">Week 11: Research Compendia</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -248,7 +284,8 @@ <h2 id="toc-title">On this page</h2>
   <ul class="collapse">
   <li><a href="#week-1-core-1-organising-reproducible-data-analyses" id="toc-week-1-core-1-organising-reproducible-data-analyses" class="nav-link" data-scroll-target="#week-1-core-1-organising-reproducible-data-analyses">Week 1 Core 1 Organising reproducible data analyses</a></li>
   <li><a href="#week-2-core-2-file-types-workflow-tips-and-other-tools" id="toc-week-2-core-2-file-types-workflow-tips-and-other-tools" class="nav-link" data-scroll-target="#week-2-core-2-file-types-workflow-tips-and-other-tools">Week 2 Core 2 File types, workflow tips and other tools</a></li>
-  <li><a href="#week-6-core-3-reproducible-reporting" id="toc-week-6-core-3-reproducible-reporting" class="nav-link" data-scroll-target="#week-6-core-3-reproducible-reporting">Week 6 Core 3 Reproducible Reporting</a></li>
+  <li><a href="#week-6-core-drop-in" id="toc-week-6-core-drop-in" class="nav-link" data-scroll-target="#week-6-core-drop-in">Week 6 Core Drop-in</a></li>
+  <li><a href="#week-11-core-3-research-compendia-and-reproducible-reporting" id="toc-week-11-core-3-research-compendia-and-reproducible-reporting" class="nav-link" data-scroll-target="#week-11-core-3-research-compendia-and-reproducible-reporting">Week 11 Core 3 Research Compendia and Reproducible Reporting</a></li>
   </ul></li>
   </ul>
 </nav>
@@ -269,7 +306,7 @@ <h1 class="title">Core Data Analysis</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">30 October, 2023</p>
+      <p class="date">3 November, 2023</p>
     </div>
   </div>
 
@@ -281,7 +318,8 @@ <h1 class="title">Core Data Analysis</h1>
 
 <section id="content" class="level1">
 <h1>Content</h1>
-<p>There are three workshops taken by everyone on BIO00088H and BIO00070M. These are in weeks 1, 2 and 6. The first two cover some useful workflow tips and how to organise your analyses effectively so they are reproducible but you will also have the chance to revise material from stage 1 and 2.</p>
+<p>There are three workshops taken by everyone on BIO00088H. These are in weeks 1, 2 and 11. The first two cover some useful workflow tips and how to organise your analyses effectively so they are reproducible but you will also have the chance to revise material from stage 1 and 2. The third workshop covers Research Compendia and Reproducible Reporting. In week 6 there is a drop-in session where you can ask questions about the material covered in the first two workshops.</p>
+<p>Students doing BIO00070M will do week 1 and 2 of the core workshops, then 3-5 of the Omics workshops. You can also attend the week 6 drop-in. You do not do the week 11 session because your assessment differs. However, you will learn about Reproducible reporting in BIO00052M in week 10 because your that applies to your 52M assessment.</p>
 <p>Good organisation is important because you will want to be able to set work aside for holidays and assessment periods and then restart easily. You will also be assessed on the organisation, reproducibility and transparency of your work.</p>
 <section id="week-1-core-1-organising-reproducible-data-analyses" class="level2">
 <h2 class="anchored" data-anchor-id="week-1-core-1-organising-reproducible-data-analyses">Week 1 Core 1 Organising reproducible data analyses</h2>
@@ -290,10 +328,13 @@ <h2 class="anchored" data-anchor-id="week-1-core-1-organising-reproducible-data-
 <section id="week-2-core-2-file-types-workflow-tips-and-other-tools" class="level2">
 <h2 class="anchored" data-anchor-id="week-2-core-2-file-types-workflow-tips-and-other-tools">Week 2 Core 2 File types, workflow tips and other tools</h2>
 <p>This week we will consider File types, workflow tips and other tools. The independent study (~20 mins) reiterates the value of RStudio projects and shows you how you create them with usethis. You will also learn how to recognise and write cool 😎 code, not 😩 ugly code and code algorithmically. In the workshop we will examine some common biological data formats and discover some awesome short cuts to help you write cool 😎 code. You will also get a brief introduction to the command line and Google Colab.</p>
-<!-- After -->
 </section>
-<section id="week-6-core-3-reproducible-reporting" class="level2">
-<h2 class="anchored" data-anchor-id="week-6-core-3-reproducible-reporting">Week 6 Core 3 Reproducible Reporting</h2>
+<section id="week-6-core-drop-in" class="level2">
+<h2 class="anchored" data-anchor-id="week-6-core-drop-in">Week 6 Core Drop-in</h2>
+<p>This week there is a drop-in session where you can ask questions about the material particular covered in the first two workshops. However, we will also endeavour to answer questions about any of the material in the omics, images or structure strand.</p>
+</section>
+<section id="week-11-core-3-research-compendia-and-reproducible-reporting" class="level2">
+<h2 class="anchored" data-anchor-id="week-11-core-3-research-compendia-and-reproducible-reporting">Week 11 Core 3 Research Compendia and Reproducible Reporting</h2>
 <!-- Before -->
 <!--  (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown and BIO00058M-Data-science-2020/slides/04_advanced_rmarkdown.html) -->
 <!-- Literate programming -->

core/week-1/overview.html

@@ -202,7 +202,7 @@
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
             <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
- <span class="menu-text">Week 6: Quarto</span></a>
+ <span class="menu-text">Week 6: Core Drop-in</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -231,6 +231,42 @@
   <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
+</li>
+      </ul>
+  </li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true">
+ <span class="menu-text">Week 11: Research Compendia</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -266,7 +302,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">30 October, 2023</p>
+      <p class="date">3 November, 2023</p>
     </div>
   </div>
 

core/week-1/study_after_workshop.html

@@ -202,7 +202,7 @@
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
             <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
- <span class="menu-text">Week 6: Quarto</span></a>
+ <span class="menu-text">Week 6: Core Drop-in</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -231,6 +231,42 @@
   <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
+</li>
+      </ul>
+  </li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true">
+ <span class="menu-text">Week 11: Research Compendia</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -266,7 +302,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">30 October, 2023</p>
+      <p class="date">3 November, 2023</p>
     </div>
   </div>
 

core/week-1/study_before_workshop.html

@@ -202,7 +202,7 @@
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
             <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
- <span class="menu-text">Week 6: Quarto</span></a>
+ <span class="menu-text">Week 6: Core Drop-in</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -231,6 +231,42 @@
   <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
+</li>
+      </ul>
+  </li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true">
+ <span class="menu-text">Week 11: Research Compendia</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -259,7 +295,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">30 October, 2023</p>
+      <p class="date">3 November, 2023</p>
     </div>
   </div>
 

core/week-1/workshop.html

@@ -221,7 +221,7 @@
         <li class="sidebar-item sidebar-item-section">
       <div class="sidebar-item-container"> 
             <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
- <span class="menu-text">Week 6: Quarto</span></a>
+ <span class="menu-text">Week 6: Core Drop-in</span></a>
           <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
             <i class="bi bi-chevron-right ms-2"></i>
           </a> 
@@ -250,6 +250,42 @@
   <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Consolidate!</span></a>
   </div>
+</li>
+      </ul>
+  </li>
+        <li class="px-0"><hr class="sidebar-divider hi "></li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true">
+ <span class="menu-text">Week 11: Research Compendia</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/overview.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">About</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_before_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Prepare!</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Workshop</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="../../core/week-6/study_after_workshop.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Consolidate!</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -319,7 +355,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">30 October, 2023</p>
+      <p class="date">3 November, 2023</p>
     </div>
   </div>