Deploying to gh-pages from @ ee801e7 🚀

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>
 

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>
 

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>
 

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>
 

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>
 

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>
 

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>
 

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

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>
 
@@ -322,55 +322,55 @@ <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>
 <div class="cell">
 <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>
 <div class="cell">
 <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>

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>

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>
 
 

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>
 
 
 

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>

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>
 

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>
 

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>
 

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>
 

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>
 

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>
 

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>