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diff --git a/about.html b/about.html
diff --git a/core/week-2/workshop.html b/core/week-2/workshop.html
@@ -425,49 +425,49 @@ <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 136
-drwxr-xr-x 2 runner docker  4096 Oct  6 12:36 data
-drwxr-xr-x 2 runner docker  4096 Oct  6 12:36 images
--rw-r--r-- 1 runner docker  1597 Oct  6 12:36 overview.qmd
--rw-r--r-- 1 runner docker   184 Oct  6 12:36 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 69876 Oct  6 12:38 study_before_workshop.html
--rw-r--r-- 1 runner docker  4807 Oct  6 12:36 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Oct  6 12:36 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  8550 Oct  6 12:36 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Oct  6 12:38 workshop.rmarkdown</code></pre>
+drwxr-xr-x 2 runner docker  4096 Oct  6 13:48 data
+drwxr-xr-x 2 runner docker  4096 Oct  6 13:48 images
+-rw-r--r-- 1 runner docker  1597 Oct  6 13:48 overview.qmd
+-rw-r--r-- 1 runner docker   184 Oct  6 13:48 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 69876 Oct  6 13:50 study_before_workshop.html
+-rw-r--r-- 1 runner docker  4807 Oct  6 13:48 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Oct  6 13:48 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  8550 Oct  6 13:48 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Oct  6 13:50 workshop.rmarkdown</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 136K
-drwxr-xr-x 2 runner docker 4.0K Oct  6 12:36 data
-drwxr-xr-x 2 runner docker 4.0K Oct  6 12:36 images
--rw-r--r-- 1 runner docker 1.6K Oct  6 12:36 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct  6 12:36 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct  6 12:38 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct  6 12:36 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct  6 12:36 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  6 12:36 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  6 12:38 workshop.rmarkdown</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Oct  6 13:48 data
+drwxr-xr-x 2 runner docker 4.0K Oct  6 13:48 images
+-rw-r--r-- 1 runner docker 1.6K Oct  6 13:48 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct  6 13:48 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  69K Oct  6 13:50 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Oct  6 13:48 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct  6 13:48 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  6 13:48 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  6 13:50 workshop.rmarkdown</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 144K
-drwxr-xr-x 4 runner docker 4.0K Oct  6 12:38 .
-drwxr-xr-x 5 runner docker 4.0K Oct  6 12:37 ..
-drwxr-xr-x 2 runner docker 4.0K Oct  6 12:36 data
-drwxr-xr-x 2 runner docker 4.0K Oct  6 12:36 images
--rw-r--r-- 1 runner docker 1.6K Oct  6 12:36 overview.qmd
--rw-r--r-- 1 runner docker  184 Oct  6 12:36 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  69K Oct  6 12:38 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Oct  6 12:36 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Oct  6 12:36 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  6 12:36 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Oct  6 12:38 workshop.rmarkdown</code></pre>
+drwxr-xr-x 4 runner docker 4.0K Oct  6 13:50 .
+drwxr-xr-x 5 runner docker 4.0K Oct  6 13:50 ..
+drwxr-xr-x 2 runner docker 4.0K Oct  6 13:48 data
+drwxr-xr-x 2 runner docker 4.0K Oct  6 13:48 images
+-rw-r--r-- 1 runner docker 1.6K Oct  6 13:48 overview.qmd
+-rw-r--r-- 1 runner docker  184 Oct  6 13:48 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  69K Oct  6 13:50 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Oct  6 13:48 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Oct  6 13:48 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  6 13:48 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Oct  6 13:50 workshop.rmarkdown</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/omics/omics.html b/omics/omics.html
@@ -283,21 +283,47 @@ <h1 class="title">Omics Data Analysis for Group Project</h1>
 <h1>Content</h1>
 <section id="omics-1-hello-data" class="level2">
 <h2 class="anchored" data-anchor-id="omics-1-hello-data">Omics 1: Hello data!</h2>
-<p>before - sequence data fundamentals - where have the data come from - processing so far - why log2 - overarching aims</p>
-<p>workshop - set up a project and create the organisation - meta data - open in understanding the data numbers of variables, organisation - importing - exploring, what kind of values are they, how many missing - qc plots - removing the useless, writing to files</p>
-<p>after - document what you have done - format your figures</p>
+<p>This week you will meet your data. The independent study will concisely cover how these data were generated and how they have been processed before being given to you. There will also be an overview of the analysis we will carry out over three workshops. In the workshop, you will learn what steps to take to get a good understanding of ’omics data before you consider any statistical analysis. This is an often overlooked, but very valuable and informative, part of any data pipeline. It gives you the deep understanding of the data structures and values that you will need to code and trouble-shoot code, allows you to spot failed or problematic samples and informs your decisions on quality control.</p>
 </section>
 <section id="omics-2-statisitcal-analysis" class="level2">
 <h2 class="anchored" data-anchor-id="omics-2-statisitcal-analysis">Omics 2: Statisitcal Analysis</h2>
-<p>before - which genes matter: expression, DE - goal of DE - how does DE work - multiple testing: FDR - say what comparisons we will do</p>
+<p>before</p>
+<ul>
+<li>which genes matter: expression, DE</li>
+<li>goal of DE</li>
+<li>how does DE work</li>
+<li>multiple testing: FDR</li>
+<li>say what comparisons we will do</li>
+</ul>
 <p>workshop - open project import the data - revise! - prep for DE - lists of genes - writing to files</p>
-<p>after - document what you have done - repeat on another comparison</p>
+<p>after</p>
+<ul>
+<li>document what you have done</li>
+<li>repeat on another comparison</li>
+</ul>
 </section>
 <section id="omics-3-visualising-and-interpreting" class="level2">
 <h2 class="anchored" data-anchor-id="omics-3-visualising-and-interpreting">Omics 3: Visualising and Interpreting</h2>
-<p>before - recap what we have - volcano plot described - GO terms -</p>
-<p>workshop - open project import the data - revise! - volcano plot - kable table? knitr::kable(df) |&gt; kableExtra::kable_styling() - annotating with go terms</p>
-<p>after - document what you have done - repeat on another comparison</p>
+<p>before</p>
+<ul>
+<li>recap what we have</li>
+<li>volcano plot described</li>
+<li>GO terms</li>
+<li></li>
+</ul>
+<p>workshop</p>
+<ul>
+<li>open project import the data</li>
+<li>revise!</li>
+<li>volcano plot</li>
+<li>kable table? knitr::kable(df) |&gt; kableExtra::kable_styling()</li>
+<li>annotating with go terms</li>
+</ul>
+<p>after</p>
+<ul>
+<li>document what you have done</li>
+<li>repeat on another comparison</li>
+</ul>
 
 
 </section>

diff --git a/omics/week-3/images/fastaq_file_format.png b/omics/week-3/images/fastaq_file_format.png
diff --git a/omics/week-3/overview.html b/omics/week-3/overview.html
@@ -65,7 +65,7 @@
 <link rel="stylesheet" href="../../styles.css">
 </head>
 
-<body class="nav-sidebar floating nav-fixed fullcontent">
+<body class="nav-sidebar floating nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
@@ -239,7 +239,16 @@
 </nav>
 <div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
 <!-- margin-sidebar -->
-
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+        <nav id="TOC" role="doc-toc" class="toc-active">
+    <h2 id="toc-title">On this page</h2>
+
+  <ul>
+  <li><a href="#learning-objectives" id="toc-learning-objectives" class="nav-link active" data-scroll-target="#learning-objectives">Learning objectives</a></li>
+  <li><a href="#instructions" id="toc-instructions" class="nav-link" data-scroll-target="#instructions">Instructions</a></li>
+  </ul>
+</nav>
+    </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
@@ -267,22 +276,24 @@ <h1 class="title">Overview</h1>
 
 </header>
 
-<p>xxxxx</p>
+<p>This week you will meet your data. The independent study will concisely cover how these data were generated and how they have been processed before being given to you. There will also be an overview of the analysis we will carry out over three workshops. In the workshop, you will learn what steps to take to get a good understanding of ’omics data before you consider any statistical analysis. This is an often overlooked, but very valuable and informative, part of any data pipeline. It gives you the deep understanding of the data structures and values that you will need to code and trouble-shoot code, allows you to spot failed or problematic samples and informs your decisions on quality control.</p>
 <section id="learning-objectives" class="level3">
 <h3 class="anchored" data-anchor-id="learning-objectives">Learning objectives</h3>
+<p>The successful student will be able to:</p>
 <ul>
-<li>dd</li>
-<li>dd.</li>
-<li>dd</li>
-<li>d</li>
+<li>explore ’omics data to find the number of rows and columns and know how these correspond to samples and variables</li>
+<li>explore the distribution of expression measures across whole data sets, across variables and across samples by summarising and plotting</li>
+<li>explain what distributions are expected and interpret the distributions they have</li>
+<li>explain on what basis we might filter out variables or samples</li>
+<li>import, explore and filter ’omics data reproducibly so they can understand and reuse their code in the future</li>
 </ul>
 </section>
 <section id="instructions" class="level3">
 <h3 class="anchored" data-anchor-id="instructions">Instructions</h3>
 <ol type="1">
 <li><p><a href="../../omics/week-3/study_before_workshop.html">Prepare</a></p>
 <ol type="i">
-<li>📖 Read how the data were generated and how they have been processed so far.</li>
+<li>📖 Read how the data were generated and how they have been processed so far, insstall</li>
 </ol></li>
 <li><p><a href="../../omics/week-3/workshop.html">Workshop</a></p>
 <ol type="i">

diff --git a/omics/week-3/study_after_workshop.html b/omics/week-3/study_after_workshop.html
@@ -65,7 +65,7 @@
 <link rel="stylesheet" href="../../styles.css">
 </head>
 
-<body class="nav-sidebar floating nav-fixed fullcontent">
+<body class="nav-sidebar floating nav-fixed">
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
@@ -239,7 +239,9 @@
 </nav>
 <div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
 <!-- margin-sidebar -->
-
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+
+    </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 

diff --git a/omics/week-3/study_before_workshop.html b/omics/week-3/study_before_workshop.html
@@ -361,22 +361,12 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
 </section>
 <section id="omics-workshops" class="slide level2">
 <h2>Omics workshops</h2>
+<p>What the data are and something about what has been done to the raw data to get get.</p>
 <ul>
 <li>🐸 the difference between the control and the FGF treated sibling at S30</li>
 <li>🐭 the difference between HSPC and Prog cells</li>
 <li>🍂 ???????</li>
 </ul>
-<p>See later workshops.</p>
-</section>
-<section id="sequence-data" class="slide level2">
-<h2>Sequence Data</h2>
-<ul>
-<li>reads</li>
-<li>quality control</li>
-<li>align/pseudoalign</li>
-<li>quantify</li>
-<li>normalise</li>
-</ul>
 </section>
 <section id="aims" class="slide level2">
 <h2>Aims</h2>
@@ -389,6 +379,18 @@ <h2>Aims</h2>
 </ul></li>
 </ul>
 </section>
+<section id="sequence-data" class="slide level2">
+<h2>Sequence Data</h2>
+<ul>
+<li><p>The raw data are “reads” from a sequencing machine. Reads are short sequences of DNA or RNA.</p></li>
+<li><p>The reads are aligned to a reference genome or transcriptome. The reads are then counted to quantify the expression of each gene. The counts are normalised to allow comparison between samples.</p></li>
+<li><p>reads</p></li>
+<li><p>quality control</p></li>
+<li><p>align/pseudoalign</p></li>
+<li><p>quantify</p></li>
+<li><p>normalise</p></li>
+</ul>
+</section>
 <section id="what-is-a-read" class="slide level2">
 <h2>What is a read</h2>
 <ul>
@@ -397,8 +399,7 @@ <h2>What is a read</h2>
 <li>sequences and information about each sequence’s read accuracy</li>
 </ul></li>
 </ul>
-
-<img data-src="images/fastaq_file_format.png" class="r-stretch"></section>
+</section>
 <section id="differential-expression" class="slide level2">
 <h2>Differential expression</h2>
 <ul>
@@ -411,9 +412,9 @@ <h2>Differential expression</h2>
 <h2>Stem cells: background</h2>
 <p>Cells were sorted using flow cytometry on the basis of cell surface markers. There are three cell types:</p>
 <ul>
-<li><p>long-term haematopoetic stem cells (LT-HSCs) defined as : Lineage<sup>-</sup> ckit<sup>+</sup> Sca1<sup>+</sup> CD34<sup>-</sup> Flk2<sup>-</sup></p></li>
-<li><p>haematopoetic stem and progenitor cells (HSPCs) defined as : Lineage<sup>-</sup> Sca1<sup>+</sup> ckit<sup>+</sup></p></li>
-<li><p>progenitor cells (Progs) defined as : Lineage<sup>-</sup> Sca1<sup>-</sup> ckit<sup>+</sup></p></li>
+<li><p>long-term haematopoetic stem cells (LT-HSCs)</p></li>
+<li><p>haematopoetic stem and progenitor cells (HSPCs)</p></li>
+<li><p>progenitor cells (Progs)</p></li>
 </ul>
 <p>Each cell is then sequenced to quantify all the transcripts in each cell. different transcripts (genes) were identified.</p>
 </section>
@@ -423,7 +424,7 @@ <h2>Stem cells: background</h2>
 <li>Raw data: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682">GEO Series GSE81682</a></li>
 <li>Illumina HiSeq</li>
 <li>short reads 150-300bp</li>
-<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5305050/">A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation</a> <span class="citation" data-cites="nestorowa2016">(<a href="#/deliverables" role="doc-biblioref" onclick="">Nestorowa et al. 2016</a>)</span></li>
+<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5305050/">A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation</a> <span class="citation" data-cites="nestorowa2016">(<a href="#/revise-pivot-longer-1" role="doc-biblioref" onclick="">Nestorowa et al. 2016</a>)</span></li>
 <li>3,840 samples</li>
 <li>Reads were aligned using G-SNAP and the mapped reads were assigned to Ensembl genes HTSeq</li>
 <li>GSE81682_HTSeq_counts.txt.gz (bottom of the page). And <a href="../data/jillian/GSE81682_HTSeq_counts.zip">GSE81682_HTSeq_counts.txt.zip</a></li>
@@ -459,7 +460,7 @@ <h2>Frog development: background</h2>
 <li>Raw data: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81682">GEO Series GSE81682</a></li>
 <li>Illumina HiSeq</li>
 <li>short reads 150-300bp</li>
-<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5305050/">A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation</a> <span class="citation" data-cites="nestorowa2016">(<a href="#/deliverables" role="doc-biblioref" onclick="">Nestorowa et al. 2016</a>)</span></li>
+<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5305050/">A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation</a> <span class="citation" data-cites="nestorowa2016">(<a href="#/revise-pivot-longer-1" role="doc-biblioref" onclick="">Nestorowa et al. 2016</a>)</span></li>
 <li>3,840 samples</li>
 <li>Reads were aligned using G-SNAP and the mapped reads were assigned to Ensembl genes HTSeq</li>
 <li>GSE81682_HTSeq_counts.txt.gz (bottom of the page). And <a href="../data/jillian/GSE81682_HTSeq_counts.zip">GSE81682_HTSeq_counts.txt.zip</a></li>
@@ -482,7 +483,7 @@ <h2>Frog development: Aims</h2>
 <section id="section" class="slide level2">
 <h2></h2>
 </section>
-<section id="deliverables" class="slide level2 smaller scrollable">
+<section id="deliverables" class="slide level2">
 <h2>Deliverables</h2>
 <ol type="1">
 <li><p>Describe the data</p>
@@ -505,6 +506,12 @@ <h2>Deliverables</h2>
 <li><p>Interpret the biology by reporting on a few group of genes and the processes in which they are involved.</p></li>
 <li><p>Report on your chosen genes and explain why you think they are good candidates for follow up work</p></li>
 </ol>
+</section>
+<section id="revise-pivot-longer" class="slide level2">
+<h2>revise pivot longer</h2>
+</section>
+<section id="revise-pivot-longer-1" class="slide level2 smaller scrollable">
+<h2>revise pivot longer</h2>
 
 <div class="footer footer-default">
 <p>🔗 <a href="https://3mmarand.github.io/BIO00088H-data/omics/week-3/overview.html">About Omics 1: Hello data!</a></p>