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core/week-1/study_after_workshop.html

@@ -270,20 +270,17 @@ <h1 class="title">Independent Study to consolidate this week</h1>
 
 </header>
 
+<p>These are suggestions</p>
 <section id="bio00088h-group-research-project-students" class="level2">
 <h2 class="anchored" data-anchor-id="bio00088h-group-research-project-students">BIO00088H Group Research Project students</h2>
 <ol type="1">
-<li><h2 id="start-to-build-the-the-file-and-folder-infrastructure-for-your-project" class="anchored">Start to build the the file and folder infrastructure for your project</h2>
-<ul>
-<li></li>
-<li></li>
-</ul></li>
+<li>Revise previous Data Analysis materials. You can find the version you took on the VLE site for 17C or 08C. However, my latest versions (in development) are here: <a href="https://3mmarand.github.io/R4BABS/">Data Analysis in R</a>. The Becoming a Bioscientist (BABS) modules replace the Laboratory and Professional Skills modules. BABS1 and BABS1 are stage one, and I’ve tried to improve them over 17C and 08C. The site is also searchable (icon top right)</li>
 </ol>
 </section>
 <section id="msc-bioinformatics-students-doing-bio00070m" class="level2">
 <h2 class="anchored" data-anchor-id="msc-bioinformatics-students-doing-bio00070m">MSc Bioinformatics students doing BIO00070M</h2>
 <ol type="1">
-<li></li>
+<li>Make sure you carry out the <a href="https://3mmarand.github.io/R4BABS/pgt52m/week-2/overview.html">preparatory work for week 2 of 52M</a></li>
 </ol>
 
 

core/week-1/workshop.html

@@ -288,6 +288,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#code-comments" id="toc-code-comments" class="nav-link" data-scroll-target="#code-comments">Code comments</a></li>
   </ul></li>
   <li><a href="#github-co-pilot-demo" id="toc-github-co-pilot-demo" class="nav-link" data-scroll-target="#github-co-pilot-demo">Github co-pilot demo</a></li>
+  <li><a href="#quarto-demo" id="toc-quarto-demo" class="nav-link" data-scroll-target="#quarto-demo">Quarto demo</a></li>
   <li><a href="#useful-exercises" id="toc-useful-exercises" class="nav-link" data-scroll-target="#useful-exercises">Useful exercises</a></li>
   <li><a href="#well-done" id="toc-well-done" class="nav-link" data-scroll-target="#well-done">🥳 Well Done! 🎉</a></li>
   <li><a href="#independent-study-following-the-workshop" id="toc-independent-study-following-the-workshop" class="nav-link" data-scroll-target="#independent-study-following-the-workshop">Independent study following the workshop</a></li>
@@ -355,9 +356,9 @@ <h2 class="anchored" data-anchor-id="why-does-it-matter">Why does it matter?</h2
 </figure>
 </div>
 <ul>
-<li><p>Five selfish reasons to work reproducibly. Alternatively, see the very entertaining <a href="https://youtu.be/yVT07Sukv9Q">talk</a></p></li>
+<li><p>Five selfish reasons to work reproducibly <span class="citation" data-cites="markowetz2015">(<a href="#ref-markowetz2015" role="doc-biblioref">Markowetz 2015</a>)</span>. Alternatively, see the very entertaining <a href="https://youtu.be/yVT07Sukv9Q">talk</a></p></li>
 <li><p>Many high profile cases of work which did not reproduce e.g.&nbsp;Anil Potti unravelled by <span class="citation" data-cites="baggerly2009">Baggerly and Coombes (<a href="#ref-baggerly2009" role="doc-biblioref">2009</a>)</span></p></li>
-<li><p><strong>Will</strong> become standard in Science and publishing e.g OECD Global Science Forum Building digital workforce capacity and skills for data-intensive science <span class="citation" data-cites="oecdglobalscienceforum2020">OECD Global Science Forum (<a href="#ref-oecdglobalscienceforum2020" role="doc-biblioref">2020</a>)</span></p></li>
+<li><p><strong>Will</strong> become standard in Science and publishing e.g OECD Global Science Forum Building digital workforce capacity and skills for data-intensive science <span class="citation" data-cites="oecdglobalscienceforum2020">(<a href="#ref-oecdglobalscienceforum2020" role="doc-biblioref">OECD Global Science Forum 2020</a>)</span></p></li>
 </ul>
 </section>
 <section id="how-to-achieve-reproducibility" class="level2">
@@ -388,14 +389,15 @@ <h2 class="anchored" data-anchor-id="project-oriented-workflow">Project-oriented
 <ul>
 <li><p>use folders to organise your work</p></li>
 <li><p>you are aiming for structured, systematic and repeatable.</p></li>
+<li><p>inputs and outputs should be clearly identifiable from structure and/or naming</p></li>
 </ul>
-<p>Example</p>
+<p>Examples</p>
 <pre><code>-- liver_transcriptome/
    |__data
       |__raw/
       |__processed/
    |__images/
-   |__R/
+   |__code/
    |__reports/
    |__figures/</code></pre>
 </section>
@@ -407,7 +409,12 @@ <h2 class="anchored" data-anchor-id="naming-things">Naming things</h2>
 <figcaption class="figure-caption">documents, CC-BY-NC, https://xkcd.com/1459/</figcaption>
 </figure>
 </div>
-<p>Guiding principle - names of files and directories should be systematic and readable by humans and machines. Have a convention!</p>
+<p>Guiding principle - Have a convention! Good file names are:</p>
+<ul>
+<li><p>machine readable</p></li>
+<li><p>human readable</p></li>
+<li><p>play nicely with sorting</p></li>
+</ul>
 <p>I suggest</p>
 <ul>
 <li><p>no spaces in names</p></li>
@@ -451,26 +458,21 @@ <h1>Documentation</h1>
 <h2 class="anchored" data-anchor-id="readme-files">Readme files</h2>
 <p>READMEs are a form of documentation which have been widely used for a long time. They contain all the information about the other files in a directory. They can be extensive but need not be. Concise is good. Bullet points are good</p>
 <ul>
-<li><p>Give a project description, brief</p></li>
+<li><p>Give a project title and description, brief</p></li>
+<li><p>start date, last updated date and contact information</p></li>
 <li><p>Outline the folder structure</p></li>
 <li><p>Give software requirements: programs and versions used or required. There are packages that give session information in R <span class="citation" data-cites="sessioninfo">Wickham et al. (<a href="#ref-sessioninfo" role="doc-biblioref">2021</a>)</span> and Python <span class="citation" data-cites="ostblomjoel2019">Ostblom, Joel (<a href="#ref-ostblomjoel2019" role="doc-biblioref">2019</a>)</span></p></li>
 </ul>
 <p>R:</p>
-<pre><code>```
-#| eval: false
-sessioninfo::session_info()
-```</code></pre>
+<p><code>sessioninfo::session_info()</code></p>
 <p>Python:</p>
-<pre><code>```
-#| eval: false
-import session_info
-session_info.show()
-
-```</code></pre>
+<p><code>import session_info</code></p>
+<p><code>session_info.show()</code></p>
 <ul>
 <li><p>Instructions run the code, build reports, and reproduce the figures etc</p></li>
 <li><p>Where to find the data, outputs</p></li>
 <li><p>Any other information that needed to understand and recreate the work</p></li>
+<li><p>Ideally, a summary of changes with the date</p></li>
 </ul>
 <pre><code>-- liver_transcriptome/
    |__data
@@ -510,6 +512,9 @@ <h2 class="anchored" data-anchor-id="code-comments">Code comments</h2>
 <section id="github-co-pilot-demo" class="level1">
 <h1>Github co-pilot demo</h1>
 </section>
+<section id="quarto-demo" class="level1">
+<h1>Quarto demo</h1>
+</section>
 <section id="useful-exercises" class="level1">
 <h1>Useful exercises</h1>
 <ul>
@@ -520,11 +525,15 @@ <h1>Useful exercises</h1>
 <p>🎬 <a href="">Update R</a></p>
 <p>🎬 <a href="https://posit.co/download/rstudio-desktop/">Update RStudio</a>. You will need the prelease <a href="https://dailies.rstudio.com/rstudio/desert-sunflower/">Dessert Sunflower</a> for github Copilot integration</p></li>
 <li><p>Install package building tools</p>
-<p>🎬 Install Rtools (windows) or Xcode (mac)</p></li>
+<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>Install Quarto</p>
 <p>🎬 <a href="https://quarto.org">Install Quarto</a></p></li>
+<li><p>Install Zotero</p>
+<p>🎬 Install <a href="https://www.zotero.org/">Zotero</a></p>
+<p>🎬 <a href="https://www.zotero.org/user/register">Sign up for an account</a></p></li>
 </ul>
 <p>You’re finished!</p>
 </section>
@@ -550,6 +559,9 @@ <h1>Independent study following the workshop</h1>
 <div id="ref-baggerly2009" class="csl-entry" role="listitem">
 Baggerly, Keith A, and Kevin R Coombes. 2009. <span>“DERIVING CHEMOSENSITIVITY FROM CELL LINES: FORENSIC BIOINFORMATICS AND REPRODUCIBLE RESEARCH IN HIGH-THROUGHPUT BIOLOGY.”</span> <em>Ann. Appl. Stat.</em> 3 (4): 1309–34. <a href="https://doi.org/10.2307/27801549">https://doi.org/10.2307/27801549</a>.
 </div>
+<div id="ref-markowetz2015" class="csl-entry" role="listitem">
+Markowetz, Florian. 2015. <span>“Five Selfish Reasons to Work Reproducibly.”</span> <em>Genome Biol.</em> 16 (December): 274. <a href="https://doi.org/10.1186/s13059-015-0850-7">https://doi.org/10.1186/s13059-015-0850-7</a>.
+</div>
 <div id="ref-nationalacademiesofsciences2019" class="csl-entry" role="listitem">
 National Academies of Sciences, Engineering, Medicine, Policy, Global Affairs, Engineering, Medicine Committee on Science, Public Policy, Board on Research Data, et al. 2019. <em>Understanding Reproducibility and Replicability</em>. National Academies Press (US). <a href="https://www.ncbi.nlm.nih.gov/books/NBK547546/">https://www.ncbi.nlm.nih.gov/books/NBK547546/</a>.
 </div>

core/week-2/workshop.html

@@ -283,9 +283,16 @@ <h1 class="title">Workshop</h1>
 <section id="session-overview" class="level2"><h2 class="anchored" data-anchor-id="session-overview">Session overview</h2>
 <p>In this workshop you will</p>
 </section><section id="file-formats" class="level2"><h2 class="anchored" data-anchor-id="file-formats">File formats</h2>
-<p>Data files. - Sequences data - Image data - Structure data</p>
+<p>Data files. - Sequences data - Image data - Structure data PDB/mmCIF www.pdb.org</p>
 <p>Similarities and differences</p>
 <p>🎬</p>
+<p>what is markdown</p>
+<p>Google Colab</p>
+<p>snippets</p>
+<p>python</p>
+<p>differences between r and python</p>
+<p>rstudio terminal</p>
+<p>basic bash</p>
 <p>You’re finished!</p>
 </section></section><section id="well-done" class="level1"><h1>🥳 Well Done! 🎉</h1>
 </section><section id="independent-study-following-the-workshop" class="level1"><h1>Independent study following the workshop</h1>