diff --git a/core/core.html b/core/core.html
index 4fe2d4f..713303f 100644
--- a/core/core.html
+++ b/core/core.html
@@ -253,7 +253,7 @@ <h1 class="title">Core: Supporting Information</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-1-old/overview.html b/core/week-1-old/overview.html
index a18ab6a..e2dc79c 100644
--- a/core/week-1-old/overview.html
+++ b/core/week-1-old/overview.html
@@ -158,7 +158,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-1-old/study_after_workshop.html b/core/week-1-old/study_after_workshop.html
index 52e48b2..4425684 100644
--- a/core/week-1-old/study_after_workshop.html
+++ b/core/week-1-old/study_after_workshop.html
@@ -158,7 +158,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-1-old/study_before_workshop.html b/core/week-1-old/study_before_workshop.html
index fd6c5de..c40e4ba 100644
--- a/core/week-1-old/study_before_workshop.html
+++ b/core/week-1-old/study_before_workshop.html
@@ -151,7 +151,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-1-old/workshop.html b/core/week-1-old/workshop.html
index 44d331e..d88a066 100644
--- a/core/week-1-old/workshop.html
+++ b/core/week-1-old/workshop.html
@@ -212,7 +212,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-2-old/overview.html b/core/week-2-old/overview.html
index 41707de..d998ddb 100644
--- a/core/week-2-old/overview.html
+++ b/core/week-2-old/overview.html
@@ -149,7 +149,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-2-old/study_after_workshop.html b/core/week-2-old/study_after_workshop.html
index 80fc1bf..a785675 100644
--- a/core/week-2-old/study_after_workshop.html
+++ b/core/week-2-old/study_after_workshop.html
@@ -149,7 +149,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-2-old/study_before_workshop.html b/core/week-2-old/study_before_workshop.html
index 8be14af..628bddc 100644
--- a/core/week-2-old/study_before_workshop.html
+++ b/core/week-2-old/study_before_workshop.html
@@ -431,7 +431,7 @@
 </div>
 </div>
 
-  <p class="date">18 October, 2024</p>
+  <p class="date">20 October, 2024</p>
 </section><section id="overview" class="slide level2"><h2>Overview</h2>
 <ul>
 <li>RStudio Projects revisited
diff --git a/core/week-2-old/workshop.html b/core/week-2-old/workshop.html
index 94c261f..22e3f7b 100644
--- a/core/week-2-old/workshop.html
+++ b/core/week-2-old/workshop.html
@@ -233,7 +233,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
@@ -322,17 +322,17 @@ <h1 class="title">Workshop</h1>
 <div class="sourceCode cell-code" id="cb9"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-l</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 152
-drwxr-xr-x 2 runner docker  4096 Oct 18 10:37 data
-drwxr-xr-x 2 runner docker  4096 Oct 18 10:37 images
--rw-r--r-- 1 runner docker  1597 Oct 18 10:37 overview.qmd
--rw-r--r-- 1 runner docker 22717 Oct 18 10:42 study_after_workshop.html
--rw-r--r-- 1 runner docker   184 Oct 18 10:37 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  4807 Oct 18 10:37 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Oct 18 10:37 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 58063 Oct 18 10:37 workshop.html
--rw-r--r-- 1 runner docker  8550 Oct 18 10:37 workshop.qmd
--rw-r--r-- 1 runner docker  8577 Oct 18 10:42 workshop.rmarkdown
-drwxr-xr-x 3 runner docker  4096 Oct 18 10:37 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker  4096 Oct 20 13:00 data
+drwxr-xr-x 2 runner docker  4096 Oct 20 13:00 images
+-rw-r--r-- 1 runner docker  1597 Oct 20 13:00 overview.qmd
+-rw-r--r-- 1 runner docker 22717 Oct 20 13:04 study_after_workshop.html
+-rw-r--r-- 1 runner docker   184 Oct 20 13:00 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  4807 Oct 20 13:00 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Oct 20 13:00 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 58063 Oct 20 13:00 workshop.html
+-rw-r--r-- 1 runner docker  8550 Oct 20 13:00 workshop.qmd
+-rw-r--r-- 1 runner docker  8577 Oct 20 13:04 workshop.rmarkdown
+drwxr-xr-x 3 runner docker  4096 Oct 20 13:00 workshop_files</code></pre>
 </div>
 </div>
 <p>You can use more than one option at once. The <code>-h</code> option stands for “human readable” and makes the file sizes easier to understand for humans:</p>
@@ -340,17 +340,17 @@ <h1 class="title">Workshop</h1>
 <div class="sourceCode cell-code" id="cb11"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-hl</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 152K
-drwxr-xr-x 2 runner docker 4.0K Oct 18 10:37 data
-drwxr-xr-x 2 runner docker 4.0K Oct 18 10:37 images
--rw-r--r-- 1 runner docker 1.6K Oct 18 10:37 overview.qmd
--rw-r--r-- 1 runner docker  23K Oct 18 10:42 study_after_workshop.html
--rw-r--r-- 1 runner docker  184 Oct 18 10:37 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Oct 18 10:37 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct 18 10:37 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Oct 18 10:37 workshop.html
--rw-r--r-- 1 runner docker 8.4K Oct 18 10:37 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct 18 10:42 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Oct 18 10:37 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Oct 20 13:00 data
+drwxr-xr-x 2 runner docker 4.0K Oct 20 13:00 images
+-rw-r--r-- 1 runner docker 1.6K Oct 20 13:00 overview.qmd
+-rw-r--r-- 1 runner docker  23K Oct 20 13:04 study_after_workshop.html
+-rw-r--r-- 1 runner docker  184 Oct 20 13:00 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 4.7K Oct 20 13:00 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct 20 13:00 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  57K Oct 20 13:00 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Oct 20 13:00 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 20 13:04 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Oct 20 13:00 workshop_files</code></pre>
 </div>
 </div>
 <p>The <code>-a</code> option stands for “all” and shows us all the files, including hidden files.</p>
@@ -358,19 +358,19 @@ <h1 class="title">Workshop</h1>
 <div class="sourceCode cell-code" id="cb13"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-alh</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 160K
-drwxr-xr-x 5 runner docker 4.0K Oct 18 10:42 .
-drwxr-xr-x 8 runner docker 4.0K Oct 18 10:42 ..
-drwxr-xr-x 2 runner docker 4.0K Oct 18 10:37 data
-drwxr-xr-x 2 runner docker 4.0K Oct 18 10:37 images
--rw-r--r-- 1 runner docker 1.6K Oct 18 10:37 overview.qmd
--rw-r--r-- 1 runner docker  23K Oct 18 10:42 study_after_workshop.html
--rw-r--r-- 1 runner docker  184 Oct 18 10:37 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 4.7K Oct 18 10:37 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct 18 10:37 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Oct 18 10:37 workshop.html
--rw-r--r-- 1 runner docker 8.4K Oct 18 10:37 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct 18 10:42 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Oct 18 10:37 workshop_files</code></pre>
+drwxr-xr-x 5 runner docker 4.0K Oct 20 13:04 .
+drwxr-xr-x 8 runner docker 4.0K Oct 20 13:04 ..
+drwxr-xr-x 2 runner docker 4.0K Oct 20 13:00 data
+drwxr-xr-x 2 runner docker 4.0K Oct 20 13:00 images
+-rw-r--r-- 1 runner docker 1.6K Oct 20 13:00 overview.qmd
+-rw-r--r-- 1 runner docker  23K Oct 20 13:04 study_after_workshop.html
+-rw-r--r-- 1 runner docker  184 Oct 20 13:00 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 4.7K Oct 20 13:00 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct 20 13:00 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  57K Oct 20 13:00 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Oct 20 13:00 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct 20 13:04 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Oct 20 13:00 workshop_files</code></pre>
 </div>
 </div>
 <p>You can move about with the <code>cd</code> command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:</p>
diff --git a/core/week-2/overview.html b/core/week-2/overview.html
index 9eca06a..e1e160e 100644
--- a/core/week-2/overview.html
+++ b/core/week-2/overview.html
@@ -251,7 +251,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
@@ -263,7 +263,7 @@ <h1 class="title">Overview</h1>
 </header>
 
 
-<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>
+<p>This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. You will also ensure you know how to use the virtual desktop service (VDS) to access the software you need for your work. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work.</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>
@@ -276,6 +276,7 @@ <h3 class="anchored" data-anchor-id="learning-objectives">Learning objectives</h
 <li>write cool 😎 code not 😩 ugly code</li>
 <li>explain the value of code which expresses the structure of the problem/solution.</li>
 <li>use some useful shortcuts to help write cool 😎 code</li>
+<li>ensure they can use the VDS to access files and software required for the work</li>
 </ul>
 </section>
 <section id="instructions" class="level3">
@@ -285,6 +286,7 @@ <h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
 <ol type="i">
 <li>📖 Read Understanding file systems</li>
 <li>📖 Read Workflow in RStudio</li>
+<li>🖥️Set up the VDS and know how to use it.</li>
 </ol></li>
 <li><p><a href="../../core/week-2/workshop.html">Workshop</a></p></li>
 <li><p><a href="../../core/week-2/study_after_workshop.html">Consolidate</a></p></li>
diff --git a/core/week-2/study_after_workshop.html b/core/week-2/study_after_workshop.html
index 73885b3..6d28a86 100644
--- a/core/week-2/study_after_workshop.html
+++ b/core/week-2/study_after_workshop.html
@@ -244,7 +244,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
@@ -256,19 +256,24 @@ <h1 class="title">Independent Study to consolidate this week</h1>
 </header>
 
 
-<p>These are suggestions</p>
+<p>Before starting work on your strand specific data analysis. Ensure you have EITHER:</p>
 <ul>
-<li><p>Want github co-pilot?</p>
-<p>🎬 Create a <a href="https://github.com/">GitHub account</a></p>
-<p>🎬 Apply for <a href="https://education.github.com/discount_requests/application">student benefits</a></p></li>
-<li><p>Update R and RStudio</p>
-<p>🎬 <a href="https://www.r-project.org/">Update R</a></p>
-<p>🎬 <a href="https://posit.co/download/rstudio-desktop/">Update RStudio</a>.</p></li>
+<li>🎬 Set up the <a href="https://www.york.ac.uk/it-services/tools/vds/">Virtual Desktop Service</a> and been able to use it</li>
+</ul>
+<p>OR</p>
+<ul>
+<li><p>🎬 <a href="https://www.r-project.org/">Updated R</a></p></li>
+<li><p>🎬 <a href="https://posit.co/download/rstudio-desktop/">Updated RStudio</a>.</p></li>
 <li><p>Install package building tools</p>
 <p>🎬 Windows Install <a href="https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html">Rtools</a></p>
 <p>🎬 Mac install <a href="https://apps.apple.com/ca/app/xcode/id497799835?mt=12">Xcode from Mac App Store</a></p></li>
-<li><p>Update packages:</p>
-<p>🎬 devtools, tidyverse, BiocManager, readxl</p></li>
+<li><p>🎬 Installed packages: <strong><code>devtools</code></strong>, <strong><code>tidyverse</code></strong>, <strong><code>BiocManager</code></strong>, <strong><code>readxl</code></strong></p></li>
+</ul>
+<p>You might want to consider getting a GitHub account and applying for student benefits so that you can use GitHub co-pilot. GitHub copilot is an “AI pair programmer that offers autocomplete-style suggestions as you code”. GitHub Copilot is available as an opt-in integration with RStudio.</p>
+<ul>
+<li><p>Read more about <a href="https://docs.posit.co/ide/user/ide/guide/tools/copilot.html">GitHub Copilot integration with RStudio</a></p></li>
+<li><p>🎬 Create a <a href="https://github.com/">GitHub account</a></p></li>
+<li><p>🎬 Apply for <a href="https://education.github.com/discount_requests/application">student benefits</a>. You will need to upload an image of your student id, use your institutional email address and you will be required to use two factor authentication.</p></li>
 </ul>
 
 
diff --git a/core/week-2/study_before_workshop.html b/core/week-2/study_before_workshop.html
index e26ebfb..bb2d62f 100644
--- a/core/week-2/study_before_workshop.html
+++ b/core/week-2/study_before_workshop.html
@@ -244,7 +244,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
@@ -260,6 +260,17 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
 <li><p>📖 Read <a href="https://3mmarand.github.io/comp4biosci/file_systems.html">Understanding file systems</a>. This is an approximately 15 - 20 minute read revising file types and file systems. It covers concepts of working directories and paths. We learned these ideas in stage 1 and you may feel completely confident with them but many students will benefit from a refresher. For BIO00070M students, this is part of the work you will also be asked to complete for BIO00052M Data Analysis in R.</p></li>
 <li><p>📖 Read <a href="https://3mmarand.github.io/comp4biosci/workflow_rstudio.html">Workflow in RStudio</a>. You may find it helpful to remind yourself about RStudio Projects. In previous years, you have submitted an “RStudio Project” as part of your BABS work. In this module, you will submit “Supporting Information” for your Project Report. The Supporting Information is a documented and organised collection of all the digital parts of your research project. This includes data (or instructions for accessing data), code and/or non-coded processing, instructions for use, computational requirements and outputs. The Supporting Information could be a single RStudio Project (like you have done previously but with better documentation) or a folder that includes an RStudio Project and other material/scripts.</p></li>
 </ol>
+<p>3.💻 Set up the Virtual Desktop. I very strongly recommend working on the University computers for this work. You will be using more specialised R packages than you might be used to. This is especially important if you often have difficulty updating and or installing software on your own machine, wouldn’t know what what version of R you are using or don’t realise there is a difference between R and RStudio. The uni machines always have up-to-date R and R packages and all the packages that appear in teaching materials. It is my responsibility to ensure everything works on here.</p>
+<p>You can still work from home by using the <a href="https://www.york.ac.uk/it-services/tools/vds/">Virtual Desktop Service</a>. The VDS allows you to log on to a university computer from your own computer. It means you can access all software and filestores. When using the VDS for R and RStudio, it usually makes sense to use other software - such as a browser or file explorer - also through the VDS.</p>
+<p>If you are confident in your ability to set up your own machine, you need:</p>
+<ul>
+<li>to know the difference between R and RStudio</li>
+<li>to use R 4.4 and RStudio 2024.09.0 Build 375 (“Cranberry Hibiscus”)</li>
+<li>be certain you are actually using R 4.4 - it is written in the top edge of the console window. By default RStudio uses the latest version on R on your machine. However, windows users are able to change this to a “specific version”. You might have done that previously. Change it back using Tools | Global Options R version “Use your machine’s default 64-bit version of R”</li>
+<li>to make sure you do the independent study where it tells you what steps you need to take to get packages (and versions that are unlikely to cause issues) used in the workshop</li>
+</ul>
+<p>It is possible to access all your files on your university account without using the VDS. For example, if you want to work on uni machines at uni and your machine at home. You can best do this by mapping a drive: https://support.york.ac.uk/s/topic/0TO4K000000lA5ZWAU/filestores. If you store everything on google drive you can also read/write to that like any other drive using google drive app.</p>
+<p>Even if you plan to use your own machine I really recommend you take the time to set the VDS up now while you’re not time pressured so you always have that option ready.</p>
 
 
 
diff --git a/core/week-2/workshop.html b/core/week-2/workshop.html
index 9ac67bd..84a11b8 100644
--- a/core/week-2/workshop.html
+++ b/core/week-2/workshop.html
@@ -431,7 +431,7 @@
 </div>
 </div>
 
-  <p class="date">18 October, 2024</p>
+  <p class="date">20 October, 2024</p>
 </section><section><section id="introduction" class="title-slide slide level1 center"><h1>Introduction</h1>
 
 </section><section id="session-overview" class="slide level2"><h2>Session overview</h2>
diff --git a/core/week-6-old/overview.html b/core/week-6-old/overview.html
index 369f734..89e2842 100644
--- a/core/week-6-old/overview.html
+++ b/core/week-6-old/overview.html
@@ -157,7 +157,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-6-old/study_after_workshop.html b/core/week-6-old/study_after_workshop.html
index f0e7a80..456091c 100644
--- a/core/week-6-old/study_after_workshop.html
+++ b/core/week-6-old/study_after_workshop.html
@@ -151,7 +151,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-6-old/study_before_workshop.html b/core/week-6-old/study_before_workshop.html
index 4e4df6c..cc5cedc 100644
--- a/core/week-6-old/study_before_workshop.html
+++ b/core/week-6-old/study_before_workshop.html
@@ -151,7 +151,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-6-old/workshop.html b/core/week-6-old/workshop.html
index 89944c0..74a2092 100644
--- a/core/week-6-old/workshop.html
+++ b/core/week-6-old/workshop.html
@@ -187,7 +187,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-6/overview.html b/core/week-6/overview.html
index cb72530..73064bd 100644
--- a/core/week-6/overview.html
+++ b/core/week-6/overview.html
@@ -251,7 +251,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-6/study_after_workshop.html b/core/week-6/study_after_workshop.html
index c21ba8b..ed0d16e 100644
--- a/core/week-6/study_after_workshop.html
+++ b/core/week-6/study_after_workshop.html
@@ -251,7 +251,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-6/study_before_workshop.html b/core/week-6/study_before_workshop.html
index 134c493..8442c96 100644
--- a/core/week-6/study_before_workshop.html
+++ b/core/week-6/study_before_workshop.html
@@ -244,7 +244,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/core/week-6/workshop.html b/core/week-6/workshop.html
index 75dbea1..720512d 100644
--- a/core/week-6/workshop.html
+++ b/core/week-6/workshop.html
@@ -305,7 +305,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/images/images.html b/images/images.html
index 0b34e8d..f273e19 100644
--- a/images/images.html
+++ b/images/images.html
@@ -201,7 +201,7 @@ <h1 class="title">Image Data Analysis for Group Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/index.html b/index.html
index 0be0f8d..7212443 100644
--- a/index.html
+++ b/index.html
@@ -181,7 +181,7 @@ <h1 class="title">Data Analysis for the Group Research Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/search.json b/search.json
index 72cca15..5d86054 100644
--- a/search.json
+++ b/search.json
@@ -40,7 +40,7 @@
     "href": "core/week-2/study_before_workshop.html",
     "title": "Independent Study to prepare for workshop",
     "section": "",
-    "text": "📖 Read Understanding file systems. This is an approximately 15 - 20 minute read revising file types and file systems. It covers concepts of working directories and paths. We learned these ideas in stage 1 and you may feel completely confident with them but many students will benefit from a refresher. For BIO00070M students, this is part of the work you will also be asked to complete for BIO00052M Data Analysis in R.\n📖 Read Workflow in RStudio. You may find it helpful to remind yourself about RStudio Projects. In previous years, you have submitted an “RStudio Project” as part of your BABS work. In this module, you will submit “Supporting Information” for your Project Report. The Supporting Information is a documented and organised collection of all the digital parts of your research project. This includes data (or instructions for accessing data), code and/or non-coded processing, instructions for use, computational requirements and outputs. The Supporting Information could be a single RStudio Project (like you have done previously but with better documentation) or a folder that includes an RStudio Project and other material/scripts.",
+    "text": "📖 Read Understanding file systems. This is an approximately 15 - 20 minute read revising file types and file systems. It covers concepts of working directories and paths. We learned these ideas in stage 1 and you may feel completely confident with them but many students will benefit from a refresher. For BIO00070M students, this is part of the work you will also be asked to complete for BIO00052M Data Analysis in R.\n📖 Read Workflow in RStudio. You may find it helpful to remind yourself about RStudio Projects. In previous years, you have submitted an “RStudio Project” as part of your BABS work. In this module, you will submit “Supporting Information” for your Project Report. The Supporting Information is a documented and organised collection of all the digital parts of your research project. This includes data (or instructions for accessing data), code and/or non-coded processing, instructions for use, computational requirements and outputs. The Supporting Information could be a single RStudio Project (like you have done previously but with better documentation) or a folder that includes an RStudio Project and other material/scripts.\n\n3.💻 Set up the Virtual Desktop. I very strongly recommend working on the University computers for this work. You will be using more specialised R packages than you might be used to. This is especially important if you often have difficulty updating and or installing software on your own machine, wouldn’t know what what version of R you are using or don’t realise there is a difference between R and RStudio. The uni machines always have up-to-date R and R packages and all the packages that appear in teaching materials. It is my responsibility to ensure everything works on here.\nYou can still work from home by using the Virtual Desktop Service. The VDS allows you to log on to a university computer from your own computer. It means you can access all software and filestores. When using the VDS for R and RStudio, it usually makes sense to use other software - such as a browser or file explorer - also through the VDS.\nIf you are confident in your ability to set up your own machine, you need:\n\nto know the difference between R and RStudio\nto use R 4.4 and RStudio 2024.09.0 Build 375 (“Cranberry Hibiscus”)\nbe certain you are actually using R 4.4 - it is written in the top edge of the console window. By default RStudio uses the latest version on R on your machine. However, windows users are able to change this to a “specific version”. You might have done that previously. Change it back using Tools | Global Options R version “Use your machine’s default 64-bit version of R”\nto make sure you do the independent study where it tells you what steps you need to take to get packages (and versions that are unlikely to cause issues) used in the workshop\n\nIt is possible to access all your files on your university account without using the VDS. For example, if you want to work on uni machines at uni and your machine at home. You can best do this by mapping a drive: https://support.york.ac.uk/s/topic/0TO4K000000lA5ZWAU/filestores. If you store everything on google drive you can also read/write to that like any other drive using google drive app.\nEven if you plan to use your own machine I really recommend you take the time to set the VDS up now while you’re not time pressured so you always have that option ready.",
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@@ -52,7 +52,7 @@
     "href": "core/week-2/study_after_workshop.html",
     "title": "Independent Study to consolidate this week",
     "section": "",
-    "text": "These are suggestions\n\nWant github co-pilot?\n🎬 Create a GitHub account\n🎬 Apply for student benefits\nUpdate R and RStudio\n🎬 Update R\n🎬 Update RStudio.\nInstall package building tools\n🎬 Windows Install Rtools\n🎬 Mac install Xcode from Mac App Store\nUpdate packages:\n🎬 devtools, tidyverse, BiocManager, readxl",
+    "text": "Before starting work on your strand specific data analysis. Ensure you have EITHER:\n\n🎬 Set up the Virtual Desktop Service and been able to use it\n\nOR\n\n🎬 Updated R\n🎬 Updated RStudio.\nInstall package building tools\n🎬 Windows Install Rtools\n🎬 Mac install Xcode from Mac App Store\n🎬 Installed packages: devtools, tidyverse, BiocManager, readxl\n\nYou might want to consider getting a GitHub account and applying for student benefits so that you can use GitHub co-pilot. GitHub copilot is an “AI pair programmer that offers autocomplete-style suggestions as you code”. GitHub Copilot is available as an opt-in integration with RStudio.\n\nRead more about GitHub Copilot integration with RStudio\n🎬 Create a GitHub account\n🎬 Apply for student benefits. You will need to upload an image of your student id, use your institutional email address and you will be required to use two factor authentication.",
     "crumbs": [
       "Core Supporting Info",
       "Week 2: Supporting Information 1",
@@ -2585,7 +2585,7 @@
     "href": "core/week-2-old/workshop.html#rstudio-terminal",
     "title": "Workshop",
     "section": "RStudio terminal",
-    "text": "RStudio terminal\nThe RStudio terminal is a convenient interface to the shell without leaving RStudio. It is useful for running commands that are not available in R. For example, you can use it to run other programs like fasqc, git, ftp, ssh\nNavigating your file system\nSeveral commands are frequently used to create, inspect, rename, and delete files and directories.\n$\nThe dollar sign is the prompt (like &gt; on the R console), which shows us that the shell is waiting for input.\nYou can find out where you are using the pwd command, which stands for “print working directory”.\n\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old\n\n\nYou can find out what you can see with ls which stands for “list”.\n\nls\n\ndata\nimages\noverview.qmd\nstudy_after_workshop.html\nstudy_after_workshop.qmd\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.html\nworkshop.qmd\nworkshop.rmarkdown\nworkshop_files\n\n\nYou might have noticed that unlike R, the commands do not have brackets after them. Instead, options (or switches) are given after the command. For example, we can modify the ls command to give us more information with the -l option, which stands for “long”.\n\nls -l\n\ntotal 152\ndrwxr-xr-x 2 runner docker  4096 Oct 18 10:37 data\ndrwxr-xr-x 2 runner docker  4096 Oct 18 10:37 images\n-rw-r--r-- 1 runner docker  1597 Oct 18 10:37 overview.qmd\n-rw-r--r-- 1 runner docker 22717 Oct 18 10:42 study_after_workshop.html\n-rw-r--r-- 1 runner docker   184 Oct 18 10:37 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker  4807 Oct 18 10:37 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Oct 18 10:37 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 58063 Oct 18 10:37 workshop.html\n-rw-r--r-- 1 runner docker  8550 Oct 18 10:37 workshop.qmd\n-rw-r--r-- 1 runner docker  8577 Oct 18 10:42 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker  4096 Oct 18 10:37 workshop_files\n\n\nYou can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:\n\nls -hl\n\ntotal 152K\ndrwxr-xr-x 2 runner docker 4.0K Oct 18 10:37 data\ndrwxr-xr-x 2 runner docker 4.0K Oct 18 10:37 images\n-rw-r--r-- 1 runner docker 1.6K Oct 18 10:37 overview.qmd\n-rw-r--r-- 1 runner docker  23K Oct 18 10:42 study_after_workshop.html\n-rw-r--r-- 1 runner docker  184 Oct 18 10:37 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Oct 18 10:37 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker  13K Oct 18 10:37 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker  57K Oct 18 10:37 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Oct 18 10:37 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 18 10:42 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Oct 18 10:37 workshop_files\n\n\nThe -a option stands for “all” and shows us all the files, including hidden files.\n\nls -alh\n\ntotal 160K\ndrwxr-xr-x 5 runner docker 4.0K Oct 18 10:42 .\ndrwxr-xr-x 8 runner docker 4.0K Oct 18 10:42 ..\ndrwxr-xr-x 2 runner docker 4.0K Oct 18 10:37 data\ndrwxr-xr-x 2 runner docker 4.0K Oct 18 10:37 images\n-rw-r--r-- 1 runner docker 1.6K Oct 18 10:37 overview.qmd\n-rw-r--r-- 1 runner docker  23K Oct 18 10:42 study_after_workshop.html\n-rw-r--r-- 1 runner docker  184 Oct 18 10:37 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Oct 18 10:37 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker  13K Oct 18 10:37 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker  57K Oct 18 10:37 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Oct 18 10:37 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 18 10:42 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Oct 18 10:37 workshop_files\n\n\nYou can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:\n\ncd data\npwd\ncd ..\npwd\ncd data\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old/data\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old/data\n\n\nhead 1cq2.pdb\nHEADER    OXYGEN STORAGE/TRANSPORT                04-AUG-99   1CQ2              \nTITLE     NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0    \nTITLE    2 ANGSTROM                                                             \nCOMPND    MOL_ID: 1;                                                            \nCOMPND   2 MOLECULE: MYOGLOBIN;                                                 \nCOMPND   3 CHAIN: A;                                                            \nCOMPND   4 ENGINEERED: YES;                                                     \nCOMPND   5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED                           \nSOURCE    MOL_ID: 1;                                                            \nSOURCE   2 ORGANISM_SCIENTIFIC: PHYSETER CATODON;      \nhead -20 data/1cq2.pdb\nHEADER    OXYGEN STORAGE/TRANSPORT                04-AUG-99   1CQ2              \nTITLE     NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0    \nTITLE    2 ANGSTROM                                                             \nCOMPND    MOL_ID: 1;                                                            \nCOMPND   2 MOLECULE: MYOGLOBIN;                                                 \nCOMPND   3 CHAIN: A;                                                            \nCOMPND   4 ENGINEERED: YES;                                                     \nCOMPND   5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED                           \nSOURCE    MOL_ID: 1;                                                            \nSOURCE   2 ORGANISM_SCIENTIFIC: PHYSETER CATODON;                               \nSOURCE   3 ORGANISM_COMMON: SPERM WHALE;                                        \nSOURCE   4 ORGANISM_TAXID: 9755;                                                \nSOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 \nSOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        \nSOURCE   7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              \nSOURCE   8 EXPRESSION_SYSTEM_PLASMID: PET15A                                    \nKEYWDS    HELICAL, GLOBULAR, ALL-HYDROGEN CONTAINING STRUCTURE, OXYGEN STORAGE- \nKEYWDS   2 TRANSPORT COMPLEX                                                    \nEXPDTA    NEUTRON DIFFRACTION                                                   \nAUTHOR    F.SHU,V.RAMAKRISHNAN,B.P.SCHOENBORN   \nless 1cq2.pdb\nless is a program that displays the contents of a file, one page at a time. It is useful for viewing large files because it does not load the whole file into memory before displaying it. Instead, it reads and displays a few lines at a time. You can navigate forward through the file with the spacebar, and backwards with the b key. Press q to quit.\nA wildcard is a character that can be used as a substitute for any of a class of characters in a search, The most common wildcard characters are the asterisk (*) and the question mark (?).\nls *.csv\ncp stands for “copy”. You can copy a file from one directory to another by giving cp the path to the file you want to copy and the path to the destination directory.\ncp 1cq2.pdb copy_of_1cq2.pdb\ncp 1cq2.pdb ../copy_of_1cq2.pdb\ncp 1cq2.pdb ../bob.txt\nTo delete a file use the rm command, which stands for “remove”.\nrm ../bob.txt\nbut be careful because the file will be gone forever. There is no “are you sure?” or undo.\nTo move a file from one directory to another, use the mv command. mv works like cp except that it also deletes the original file.\nmv ../copy_of_1cq2.pdb .\nMake a directory\nmkdir mynewdir"
+    "text": "RStudio terminal\nThe RStudio terminal is a convenient interface to the shell without leaving RStudio. It is useful for running commands that are not available in R. For example, you can use it to run other programs like fasqc, git, ftp, ssh\nNavigating your file system\nSeveral commands are frequently used to create, inspect, rename, and delete files and directories.\n$\nThe dollar sign is the prompt (like &gt; on the R console), which shows us that the shell is waiting for input.\nYou can find out where you are using the pwd command, which stands for “print working directory”.\n\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old\n\n\nYou can find out what you can see with ls which stands for “list”.\n\nls\n\ndata\nimages\noverview.qmd\nstudy_after_workshop.html\nstudy_after_workshop.qmd\nstudy_before_workshop.ipynb\nstudy_before_workshop.qmd\nworkshop.html\nworkshop.qmd\nworkshop.rmarkdown\nworkshop_files\n\n\nYou might have noticed that unlike R, the commands do not have brackets after them. Instead, options (or switches) are given after the command. For example, we can modify the ls command to give us more information with the -l option, which stands for “long”.\n\nls -l\n\ntotal 152\ndrwxr-xr-x 2 runner docker  4096 Oct 20 13:00 data\ndrwxr-xr-x 2 runner docker  4096 Oct 20 13:00 images\n-rw-r--r-- 1 runner docker  1597 Oct 20 13:00 overview.qmd\n-rw-r--r-- 1 runner docker 22717 Oct 20 13:04 study_after_workshop.html\n-rw-r--r-- 1 runner docker   184 Oct 20 13:00 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker  4807 Oct 20 13:00 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker 13029 Oct 20 13:00 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker 58063 Oct 20 13:00 workshop.html\n-rw-r--r-- 1 runner docker  8550 Oct 20 13:00 workshop.qmd\n-rw-r--r-- 1 runner docker  8577 Oct 20 13:04 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker  4096 Oct 20 13:00 workshop_files\n\n\nYou can use more than one option at once. The -h option stands for “human readable” and makes the file sizes easier to understand for humans:\n\nls -hl\n\ntotal 152K\ndrwxr-xr-x 2 runner docker 4.0K Oct 20 13:00 data\ndrwxr-xr-x 2 runner docker 4.0K Oct 20 13:00 images\n-rw-r--r-- 1 runner docker 1.6K Oct 20 13:00 overview.qmd\n-rw-r--r-- 1 runner docker  23K Oct 20 13:04 study_after_workshop.html\n-rw-r--r-- 1 runner docker  184 Oct 20 13:00 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Oct 20 13:00 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker  13K Oct 20 13:00 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker  57K Oct 20 13:00 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Oct 20 13:00 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 20 13:04 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Oct 20 13:00 workshop_files\n\n\nThe -a option stands for “all” and shows us all the files, including hidden files.\n\nls -alh\n\ntotal 160K\ndrwxr-xr-x 5 runner docker 4.0K Oct 20 13:04 .\ndrwxr-xr-x 8 runner docker 4.0K Oct 20 13:04 ..\ndrwxr-xr-x 2 runner docker 4.0K Oct 20 13:00 data\ndrwxr-xr-x 2 runner docker 4.0K Oct 20 13:00 images\n-rw-r--r-- 1 runner docker 1.6K Oct 20 13:00 overview.qmd\n-rw-r--r-- 1 runner docker  23K Oct 20 13:04 study_after_workshop.html\n-rw-r--r-- 1 runner docker  184 Oct 20 13:00 study_after_workshop.qmd\n-rw-r--r-- 1 runner docker 4.7K Oct 20 13:00 study_before_workshop.ipynb\n-rw-r--r-- 1 runner docker  13K Oct 20 13:00 study_before_workshop.qmd\n-rw-r--r-- 1 runner docker  57K Oct 20 13:00 workshop.html\n-rw-r--r-- 1 runner docker 8.4K Oct 20 13:00 workshop.qmd\n-rw-r--r-- 1 runner docker 8.4K Oct 20 13:04 workshop.rmarkdown\ndrwxr-xr-x 3 runner docker 4.0K Oct 20 13:00 workshop_files\n\n\nYou can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:\n\ncd data\npwd\ncd ..\npwd\ncd data\npwd\n\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old/data\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old\n/home/runner/work/BIO00088H-data/BIO00088H-data/core/week-2-old/data\n\n\nhead 1cq2.pdb\nHEADER    OXYGEN STORAGE/TRANSPORT                04-AUG-99   1CQ2              \nTITLE     NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0    \nTITLE    2 ANGSTROM                                                             \nCOMPND    MOL_ID: 1;                                                            \nCOMPND   2 MOLECULE: MYOGLOBIN;                                                 \nCOMPND   3 CHAIN: A;                                                            \nCOMPND   4 ENGINEERED: YES;                                                     \nCOMPND   5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED                           \nSOURCE    MOL_ID: 1;                                                            \nSOURCE   2 ORGANISM_SCIENTIFIC: PHYSETER CATODON;      \nhead -20 data/1cq2.pdb\nHEADER    OXYGEN STORAGE/TRANSPORT                04-AUG-99   1CQ2              \nTITLE     NEUTRON STRUCTURE OF FULLY DEUTERATED SPERM WHALE MYOGLOBIN AT 2.0    \nTITLE    2 ANGSTROM                                                             \nCOMPND    MOL_ID: 1;                                                            \nCOMPND   2 MOLECULE: MYOGLOBIN;                                                 \nCOMPND   3 CHAIN: A;                                                            \nCOMPND   4 ENGINEERED: YES;                                                     \nCOMPND   5 OTHER_DETAILS: PROTEIN IS FULLY DEUTERATED                           \nSOURCE    MOL_ID: 1;                                                            \nSOURCE   2 ORGANISM_SCIENTIFIC: PHYSETER CATODON;                               \nSOURCE   3 ORGANISM_COMMON: SPERM WHALE;                                        \nSOURCE   4 ORGANISM_TAXID: 9755;                                                \nSOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 \nSOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        \nSOURCE   7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              \nSOURCE   8 EXPRESSION_SYSTEM_PLASMID: PET15A                                    \nKEYWDS    HELICAL, GLOBULAR, ALL-HYDROGEN CONTAINING STRUCTURE, OXYGEN STORAGE- \nKEYWDS   2 TRANSPORT COMPLEX                                                    \nEXPDTA    NEUTRON DIFFRACTION                                                   \nAUTHOR    F.SHU,V.RAMAKRISHNAN,B.P.SCHOENBORN   \nless 1cq2.pdb\nless is a program that displays the contents of a file, one page at a time. It is useful for viewing large files because it does not load the whole file into memory before displaying it. Instead, it reads and displays a few lines at a time. You can navigate forward through the file with the spacebar, and backwards with the b key. Press q to quit.\nA wildcard is a character that can be used as a substitute for any of a class of characters in a search, The most common wildcard characters are the asterisk (*) and the question mark (?).\nls *.csv\ncp stands for “copy”. You can copy a file from one directory to another by giving cp the path to the file you want to copy and the path to the destination directory.\ncp 1cq2.pdb copy_of_1cq2.pdb\ncp 1cq2.pdb ../copy_of_1cq2.pdb\ncp 1cq2.pdb ../bob.txt\nTo delete a file use the rm command, which stands for “remove”.\nrm ../bob.txt\nbut be careful because the file will be gone forever. There is no “are you sure?” or undo.\nTo move a file from one directory to another, use the mv command. mv works like cp except that it also deletes the original file.\nmv ../copy_of_1cq2.pdb .\nMake a directory\nmkdir mynewdir"
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@@ -3086,7 +3086,7 @@
     "href": "core/week-2/overview.html",
     "title": "Overview",
     "section": "",
-    "text": "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.\n\nLearning objectives\nThe successful student will be able to:\n\nexplain the organisation of files and directories in a file systems including root, home and working directories\nexplain absolute and relative file paths\nexplain why working reproducibly is important\nknow how to use a project-oriented workflow to organise work\nbe able to give files human- and machine-readable names\nwrite cool 😎 code not 😩 ugly code\nexplain the value of code which expresses the structure of the problem/solution.\nuse some useful shortcuts to help write cool 😎 code\n\n\n\nInstructions\n\nPrepare\n\n📖 Read Understanding file systems\n📖 Read Workflow in RStudio\n\nWorkshop\nConsolidate",
+    "text": "This week you will revise some essential concepts for scientific computing: file system organisation, file types, working directories and paths. You will also ensure you know how to use the virtual desktop service (VDS) to access the software you need for your work. The workshop will cover a rationale for working reproducibly, project oriented workflow, naming things and documenting your work.\n\nLearning objectives\nThe successful student will be able to:\n\nexplain the organisation of files and directories in a file systems including root, home and working directories\nexplain absolute and relative file paths\nexplain why working reproducibly is important\nknow how to use a project-oriented workflow to organise work\nbe able to give files human- and machine-readable names\nwrite cool 😎 code not 😩 ugly code\nexplain the value of code which expresses the structure of the problem/solution.\nuse some useful shortcuts to help write cool 😎 code\nensure they can use the VDS to access files and software required for the work\n\n\n\nInstructions\n\nPrepare\n\n📖 Read Understanding file systems\n📖 Read Workflow in RStudio\n🖥️Set up the VDS and know how to use it.\n\nWorkshop\nConsolidate",
     "crumbs": [
       "Core Supporting Info",
       "Week 2: Supporting Information 1",
diff --git a/structures/structures.html b/structures/structures.html
index 3c07cf0..75679a7 100644
--- a/structures/structures.html
+++ b/structures/structures.html
@@ -200,7 +200,7 @@ <h1 class="title">Structure Data Analysis for Group Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/transcriptomics/transcriptomics.html b/transcriptomics/transcriptomics.html
index 28e8b78..9977839 100644
--- a/transcriptomics/transcriptomics.html
+++ b/transcriptomics/transcriptomics.html
@@ -289,7 +289,7 @@ <h1 class="title">Transcriptomics Data Analysis for Group Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/transcriptomics/week-3/overview.html b/transcriptomics/week-3/overview.html
index feec867..1eb36d7 100644
--- a/transcriptomics/week-3/overview.html
+++ b/transcriptomics/week-3/overview.html
@@ -286,7 +286,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/transcriptomics/week-3/study_after_workshop.html b/transcriptomics/week-3/study_after_workshop.html
index c141b23..edc05da 100644
--- a/transcriptomics/week-3/study_after_workshop.html
+++ b/transcriptomics/week-3/study_after_workshop.html
@@ -288,7 +288,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/transcriptomics/week-3/study_before_workshop.html b/transcriptomics/week-3/study_before_workshop.html
index 36897e8..2aebf92 100644
--- a/transcriptomics/week-3/study_before_workshop.html
+++ b/transcriptomics/week-3/study_before_workshop.html
@@ -368,7 +368,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
 </div>
 </div>
 
-  <p class="date">18 October, 2024</p>
+  <p class="date">20 October, 2024</p>
 </section>
 <section id="overview" class="slide level2">
 <h2>Overview</h2>
diff --git a/transcriptomics/week-3/workshop.html b/transcriptomics/week-3/workshop.html
index a3ffd69..11e0f56 100644
--- a/transcriptomics/week-3/workshop.html
+++ b/transcriptomics/week-3/workshop.html
@@ -389,7 +389,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/transcriptomics/week-4/overview.html b/transcriptomics/week-4/overview.html
index fb45851..dc5abe9 100644
--- a/transcriptomics/week-4/overview.html
+++ b/transcriptomics/week-4/overview.html
@@ -307,7 +307,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/transcriptomics/week-4/study_after_workshop.html b/transcriptomics/week-4/study_after_workshop.html
index fb1d2c1..db8d4bb 100644
--- a/transcriptomics/week-4/study_after_workshop.html
+++ b/transcriptomics/week-4/study_after_workshop.html
@@ -279,7 +279,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/transcriptomics/week-4/study_before_workshop.html b/transcriptomics/week-4/study_before_workshop.html
index 0724caa..515e088 100644
--- a/transcriptomics/week-4/study_before_workshop.html
+++ b/transcriptomics/week-4/study_before_workshop.html
@@ -429,7 +429,7 @@
 </div>
 </div>
 
-  <p class="date">18 October, 2024</p>
+  <p class="date">20 October, 2024</p>
 </section><section id="overview" class="slide level2"><h2>Overview</h2>
 <p>In these slides we will:</p>
 <div>
diff --git a/transcriptomics/week-4/workshop.html b/transcriptomics/week-4/workshop.html
index 7598b42..b3d61be 100644
--- a/transcriptomics/week-4/workshop.html
+++ b/transcriptomics/week-4/workshop.html
@@ -397,7 +397,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/transcriptomics/week-5/overview.html b/transcriptomics/week-5/overview.html
index edd211b..ad9f83e 100644
--- a/transcriptomics/week-5/overview.html
+++ b/transcriptomics/week-5/overview.html
@@ -287,7 +287,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/transcriptomics/week-5/study_after_workshop.html b/transcriptomics/week-5/study_after_workshop.html
index e8e005f..9020144 100644
--- a/transcriptomics/week-5/study_after_workshop.html
+++ b/transcriptomics/week-5/study_after_workshop.html
@@ -279,7 +279,7 @@ <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">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
diff --git a/transcriptomics/week-5/study_before_workshop.html b/transcriptomics/week-5/study_before_workshop.html
index 8c1e6a5..bfb86c8 100644
--- a/transcriptomics/week-5/study_before_workshop.html
+++ b/transcriptomics/week-5/study_before_workshop.html
@@ -429,7 +429,7 @@
 </div>
 </div>
 
-  <p class="date">18 October, 2024</p>
+  <p class="date">20 October, 2024</p>
 </section><section id="overview" class="slide level2"><h2>Overview</h2>
 <p>In these slides we will:</p>
 <div>
diff --git a/transcriptomics/week-5/workshop.html b/transcriptomics/week-5/workshop.html
index a6fdd0a..4e0ed4c 100644
--- a/transcriptomics/week-5/workshop.html
+++ b/transcriptomics/week-5/workshop.html
@@ -378,7 +378,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">18 October, 2024</p>
+      <p class="date">20 October, 2024</p>
     </div>
   </div>
   
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