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3mmaRand committed Mar 28, 2024
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15 changes: 12 additions & 3 deletions core/core.html
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Expand Down Expand Up @@ -350,7 +350,7 @@ <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">21 February, 2024</p>
<p class="date">28 March, 2024</p>
</div>
</div>

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15 changes: 12 additions & 3 deletions core/week-1/overview.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

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Expand Down Expand Up @@ -346,7 +346,7 @@ <h1 class="title">Overview</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">21 February, 2024</p>
<p class="date">28 March, 2024</p>
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15 changes: 12 additions & 3 deletions core/week-1/study_after_workshop.html
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Expand Down Expand Up @@ -346,7 +346,7 @@ <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">21 February, 2024</p>
<p class="date">28 March, 2024</p>
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18 changes: 14 additions & 4 deletions core/week-1/study_before_workshop.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

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Expand Down Expand Up @@ -339,7 +339,7 @@ <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">21 February, 2024</p>
<p class="date">28 March, 2024</p>
</div>
</div>

Expand All @@ -352,7 +352,8 @@ <h1 class="title">Independent Study to prepare for workshop</h1>


<ol type="1">
<li>📖 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 filesystems. 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.</li>
<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 filesystems. 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>In previous years you have submitted and RStudio Project as part of your BABS work. In this module you will develop this by submitting a Research Compendium. A Research Compendium is a documented collection of all the digital parts of the research project including data (or access to data), code and outputs. The Compendium might be a single Quarto/RStudio Project, (like you have done previously but with better documentation) or it might be a folder including an Quarto/RStudio Project and other material/scripts including the description of unscripted processing. You might want to remind yourself of the example RStudio Project, <a href="Y12345678.zip">Y12345678.zip</a> used in BABS 2.</p></li>
</ol>


Expand Down Expand Up @@ -448,6 +449,11 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
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19 changes: 14 additions & 5 deletions core/week-1/workshop.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

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Expand Down Expand Up @@ -400,7 +400,7 @@ <h1 class="title">Workshop</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">21 February, 2024</p>
<p class="date">28 March, 2024</p>
</div>
</div>

Expand Down Expand Up @@ -440,7 +440,7 @@ <h2 class="anchored" data-anchor-id="what-is-reproducibility">What is reproducib
<h2 class="anchored" data-anchor-id="why-does-it-matter">Why does it matter?</h2>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="images/future_you.png" class="img-fluid figure-img" alt="Person working at a computer with an offstage person asking 'How is the analysis going?' The person at the computer replies 'Can't understand the date...and the data collector does not answer my emails or calls' Person offstage: 'That's terrible! So cruel! Who did collect the data? I will sack them!' Person at the computer: 'um...I did, 3 years ago.'" width="400"></p>
<p><img src="images/future_you.png" class="img-fluid figure-img" width="400"></p>
<figcaption>futureself, CC-BY-NC, by Julen Colomb</figcaption>
</figure>
</div>
Expand Down Expand Up @@ -494,7 +494,7 @@ <h2 class="anchored" data-anchor-id="project-oriented-workflow">Project-oriented
<h2 class="anchored" data-anchor-id="naming-things">Naming things</h2>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="images/xkcd-comic-file-names.png" class="img-fluid figure-img" alt="A comic figure is looking over the shoulder of another and is shocked by a list of files with names like 'Untitled 138 copy.docx' and 'Untitled 243.doc'. Caption: 'Protip: Never look in someone else's documents folder'"></p>
<p><img src="images/xkcd-comic-file-names.png" class="img-fluid figure-img"></p>
<figcaption>documents, CC-BY-NC, https://xkcd.com/1459/</figcaption>
</figure>
</div>
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15 changes: 12 additions & 3 deletions core/week-11/overview.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

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Expand Down Expand Up @@ -346,7 +346,7 @@ <h1 class="title">Overview</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">21 February, 2024</p>
<p class="date">28 March, 2024</p>
</div>
</div>

Expand Down Expand Up @@ -479,6 +479,11 @@ <h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
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Expand Down Expand Up @@ -520,7 +525,11 @@ <h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
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15 changes: 12 additions & 3 deletions core/week-11/study_after_workshop.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

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Expand Down Expand Up @@ -339,7 +339,7 @@ <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">21 February, 2024</p>
<p class="date">28 March, 2024</p>
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Expand Down Expand Up @@ -446,6 +446,11 @@ <h1 class="title">Independent Study to consolidate this week</h1>
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28 changes: 25 additions & 3 deletions core/week-11/study_before_workshop.html
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<link href="../../site_libs/quarto-html/light-border.css" rel="stylesheet">
<link href="../../site_libs/quarto-html/quarto-html.min.css" rel="stylesheet" data-mode="light">
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<meta name="author" content="Emma Rand">
<title>Data Analysis for Group Project - Independent Study to prepare for workshop</title>
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</div>
</div>

<p class="date">21 February, 2024</p>
<p class="date">28 March, 2024</p>
</section>
<section id="module-assessment" class="slide level2">
<h2>Module assessment</h2>
Expand Down Expand Up @@ -802,6 +802,24 @@ <h2>References</h2>
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Expand Down Expand Up @@ -838,7 +856,11 @@ <h2>References</h2>
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