Deploying to gh-pages from @ c3f63e0 🚀

about.html

@@ -124,7 +124,7 @@ <h1 class="title">About</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">30 September, 2023</p>
+      <p class="date">2 October, 2023</p>
     </div>
   </div>
 

core/core.html

@@ -247,7 +247,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#content" id="toc-content" class="nav-link active" data-scroll-target="#content">Content</a>
   <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-workflow-tips" id="toc-week-2-core-2-workflow-tips" class="nav-link" data-scroll-target="#week-2-core-2-workflow-tips">Week 2 Core 2 Workflow tips</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>
   </ul></li>
   </ul>
@@ -269,7 +269,7 @@ <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 September, 2023</p>
+      <p class="date">2 October, 2023</p>
     </div>
   </div>
 
@@ -285,19 +285,12 @@ <h1>Content</h1>
 <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>
-<p>This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work. We will also examine some file types and the concept of tidy data.</p>
+<p>This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work.</p>
 </section>
-<section id="week-2-core-2-workflow-tips" class="level2">
-<h2 class="anchored" data-anchor-id="week-2-core-2-workflow-tips">Week 2 Core 2 Workflow tips</h2>
+<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>
 <!-- Before  -->
 <!-- Apply to GitHub Global Campus as a student -->
-<!-- -   Reference managers: Zotero -->
-<!-- -   github copilot -->
-<!-- -   chat gtp -->
-<!-- -   Data management -->
-<!--     -   google drive: https://www.york.ac.uk/it-services/services/drive/#tab-6 -->
-<!-- Workshop -->
-<!-- Code formatting and style, 😎 Cool code Tips, Code 'algorithmically.', Writing functions (R and python??) (BIO00058M-Data-science-2020/slides/03_repro_and_intro_to_rmarkdown) -->
 <!-- After -->
 </section>
 <section id="week-6-core-3-reproducible-reporting" class="level2">

core/week-1/overview.html

@@ -266,7 +266,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">30 September, 2023</p>
+      <p class="date">2 October, 2023</p>
     </div>
   </div>
 

core/week-1/study_after_workshop.html

@@ -266,7 +266,7 @@ <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 September, 2023</p>
+      <p class="date">2 October, 2023</p>
     </div>
   </div>
 

core/week-1/study_before_workshop.html

@@ -259,7 +259,7 @@ <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 September, 2023</p>
+      <p class="date">2 October, 2023</p>
     </div>
   </div>
 

core/week-1/workshop.html

@@ -319,7 +319,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">30 September, 2023</p>
+      <p class="date">2 October, 2023</p>
     </div>
   </div>
 

core/week-2/overview.html

@@ -246,7 +246,7 @@
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
 <h1 class="title">Overview</h1>
-<p class="subtitle lead">Core 2: Workflow tips</p>
+<p class="subtitle lead">Core 2: File types, workflow tips and other tools</p>
 </div>
 
 
@@ -257,7 +257,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">30 September, 2023</p>
+      <p class="date">2 October, 2023</p>
     </div>
   </div>
 
@@ -267,33 +267,36 @@ <h1 class="title">Overview</h1>
 
 </header>
 
-<p>xxxxx</p>
+<p>This week</p>
 <section id="learning-objectives" class="level3">
 <h3 class="anchored" data-anchor-id="learning-objectives">Learning objectives</h3>
+<p>The successful student will be able to:</p>
 <ul>
-<li>dd</li>
-<li>dd.</li>
-<li>dd</li>
-<li>d</li>
+<li>explain why RStudio are useful/essential and be able to use the <strong><code>usethis</code></strong> package</li>
+<li>write cool 😎 code not 😩 ugly code</li>
+<li>explain the value of code which expresses the structure of the problem/solution.</li>
+<li>describe some common file types for biological data</li>
+<li>use some useful shortcuts to help write cool 😎 code</li>
+<li>know what the command line is and how to use it for simple tasks</li>
+<li>use Google colab to run code</li>
+<li>recognise some of the differences between R and Python</li>
 </ul>
 </section>
 <section id="instructions" class="level3">
 <h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
 <ol type="1">
-<li><p><a href="../../core/week-2/study_before_workshop.html">Prepare</a></p>
-<ol type="i">
-<li>📖 Read</li>
-</ol></li>
+<li><p><a href="../../core/week-2/study_before_workshop.html">Prepare</a> 20 mins reading on RStudio Projects revisited, formatting code and coding algorithmically</p></li>
 <li><p><a href="../../core/week-2/workshop.html">Workshop</a></p>
 <ol type="i">
-<li><p>💻 dd.</p></li>
-<li><p>💻 ddd</p></li>
-<li><p>💻 ddd</p></li>
+<li><p>💬 Types of biological data files</p></li>
+<li><p>🪄 Workflow tips and shortcuts</p></li>
+<li><p>💻 The command line</p></li>
+<li><p>💻 Google colab</p></li>
+<li><p>💻 Python</p></li>
 </ol></li>
 <li><p><a href="../../core/week-2/study_after_workshop.html">Consolidate</a></p>
 <ol type="i">
-<li><p>💻 dd</p></li>
-<li><p>💻 dd</p></li>
+<li>💻 not sure yet :)</li>
 </ol></li>
 </ol>