diff --git a/aio.html b/aio.html
index 73b48ec..8bc14df 100644
--- a/aio.html
+++ b/aio.html
@@ -368,7 +368,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-intro-sce"><p>Content from <a href="intro-sce.html">Introduction to Bioconductor and the SingleCellExperiment class</a></p>
 <hr>
-<p>Last updated on 2024-07-02 |
+<p>Last updated on 2024-08-06 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -569,6 +569,43 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 (e.g., numeric matrices, lists, etc.). We will here review the main
 slots of the SingleCellExperiment class as well as their getter/setter
 methods.</p>
+<div id="challenge1" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div class="callout-inner">
+<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge1"></a>
+</h3>
+<div class="callout-content">
+<p>Before SingleCellExperiments, coders working with single cell data
+would sometimes keep all of these components in separate objects e.g. a
+matrix of counts, a data.frame of sample metadata, a data.frame of gene
+annotations and so on. What are the main disadvantages of this sort of
+“from scratch” approach?</p>
+</div>
+</div>
+</div>
+<div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
+<div class="accordion-item">
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
+  <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
+</button>
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div class="accordion-body">
+<ol style="list-style-type: decimal">
+<li><p>You have to do tons of manual book-keeping! If you perform a QC
+step that removes dead cells, now you also have to remember to remove
+that same set of cells from the cell-wise metadata. Dropped un-expressed
+genes? Don’t forget to filter the gene metadata table too.</p></li>
+<li><p>All the downstream steps have to be “from scratch” as well! If
+your tables have some slight format difference from those of your
+lab-mate, suddenly the plotting code you’re trying to re-use doesn’t
+work! Agh!</p></li>
+</ol>
+</div>
+</div>
+</div>
+</div>
 <div class="section level3">
 <h3 id="the-assays">The <code>assays</code>
 <a class="anchor" aria-label="anchor" href="#the-assays"></a>
@@ -819,7 +856,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -3059,7 +3096,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3076,7 +3113,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3106,7 +3143,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -3120,7 +3157,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3151,7 +3188,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -5135,7 +5172,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -5149,7 +5186,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -5177,7 +5214,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -5190,7 +5227,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -5220,7 +5257,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -5232,7 +5269,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
diff --git a/cell_type_annotation.html b/cell_type_annotation.html
index 8b21123..9998930 100644
--- a/cell_type_annotation.html
+++ b/cell_type_annotation.html
@@ -1394,7 +1394,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1411,7 +1411,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1441,7 +1441,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -1455,7 +1455,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1486,7 +1486,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
diff --git a/index.html b/index.html
index b674be5..1725943 100644
--- a/index.html
+++ b/index.html
@@ -373,7 +373,7 @@ <h4 class="accordion-header" id="headingSolution1">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ul><li><p>Open RStudio, and click on “Help” &gt; “Check for updates”. If a
 new version is available, quit RStudio, and download the latest version
@@ -399,7 +399,7 @@ <h4 class="accordion-header" id="headingSolution2">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul><li><p>Download R from the <a href="https://cran.r-project.org/bin/windows/base/release.htm" class="external-link">CRAN
 website</a>.</p></li>
@@ -429,7 +429,7 @@ <h4 class="accordion-header" id="headingSolution3">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <ul><li><p>Open RStudio, and click on “Help” &gt; “Check for updates”. If a
 new version is available, quit RStudio, and download the latest version
@@ -453,7 +453,7 @@ <h4 class="accordion-header" id="headingSolution4">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <ul><li><p>Download R from the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a>.</p></li>
 <li><p>Select the <code>.pkg</code> file for the latest R
@@ -486,7 +486,7 @@ <h4 class="accordion-header" id="headingSolution5">
   Install R using your package manager and RStudio
   </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <ul><li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux" class="external-link">CRAN</a>, they provide
 information to get the most recent version of R for common
diff --git a/instructor/aio.html b/instructor/aio.html
index f599e4f..6d3ee69 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -370,7 +370,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-intro-sce"><p>Content from <a href="intro-sce.html">Introduction to Bioconductor and the SingleCellExperiment class</a></p>
 <hr>
-<p>Last updated on 2024-07-02 |
+<p>Last updated on 2024-08-06 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 30 minutes</p>
@@ -572,6 +572,43 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 (e.g., numeric matrices, lists, etc.). We will here review the main
 slots of the SingleCellExperiment class as well as their getter/setter
 methods.</p>
+<div id="challenge1" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div class="callout-inner">
+<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge1"></a>
+</h3>
+<div class="callout-content">
+<p>Before SingleCellExperiments, coders working with single cell data
+would sometimes keep all of these components in separate objects e.g. a
+matrix of counts, a data.frame of sample metadata, a data.frame of gene
+annotations and so on. What are the main disadvantages of this sort of
+“from scratch” approach?</p>
+</div>
+</div>
+</div>
+<div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
+<div class="accordion-item">
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
+  <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
+</button>
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div class="accordion-body">
+<ol style="list-style-type: decimal">
+<li><p>You have to do tons of manual book-keeping! If you perform a QC
+step that removes dead cells, now you also have to remember to remove
+that same set of cells from the cell-wise metadata. Dropped un-expressed
+genes? Don’t forget to filter the gene metadata table too.</p></li>
+<li><p>All the downstream steps have to be “from scratch” as well! If
+your tables have some slight format difference from those of your
+lab-mate, suddenly the plotting code you’re trying to re-use doesn’t
+work! Agh!</p></li>
+</ol>
+</div>
+</div>
+</div>
+</div>
 <div class="section level3">
 <h3 id="the-assays">The <code>assays</code>
 <a class="anchor" aria-label="anchor" href="#the-assays"></a>
@@ -822,7 +859,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -3064,7 +3101,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -3081,7 +3118,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3111,7 +3148,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -3125,7 +3162,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -3156,7 +3193,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -5142,7 +5179,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -5156,7 +5193,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -5184,7 +5221,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -5197,7 +5234,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -5227,7 +5264,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -5239,7 +5276,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
diff --git a/instructor/cell_type_annotation.html b/instructor/cell_type_annotation.html
index fb1a5d2..5ea17e0 100644
--- a/instructor/cell_type_annotation.html
+++ b/instructor/cell_type_annotation.html
@@ -1396,7 +1396,7 @@ <h3 class="callout-title">Exercise 1: Clustering<a class="anchor" aria-label="an
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>NNGraphParam</code> constructor has an argument
 <code>cluster.args</code>. This allows to specify arguments passed on to
@@ -1413,7 +1413,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1443,7 +1443,7 @@ <h3 class="callout-title">Exercise 2: Cluster annotation<a class="anchor" aria-l
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the <code>goana()</code> function from the <em><a href="https://bioconductor.org/packages/3.19/limma" class="external-link">limma</a></em>
 package to identify GO BP terms that are overrepresented in the list of
@@ -1457,7 +1457,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1488,7 +1488,7 @@ <h3 class="callout-title">Exercise 3: Workflow<a class="anchor" aria-label="anch
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
diff --git a/instructor/index.html b/instructor/index.html
index ece84ac..1858eec 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -457,7 +457,7 @@ <h4 class="accordion-header" id="headingSolution1">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ul><li><p>Open RStudio, and click on “Help” &gt; “Check for updates”. If a
 new version is available, quit RStudio, and download the latest version
@@ -483,7 +483,7 @@ <h4 class="accordion-header" id="headingSolution2">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <ul><li><p>Download R from the <a href="https://cran.r-project.org/bin/windows/base/release.htm" class="external-link">CRAN
 website</a>.</p></li>
@@ -513,7 +513,7 @@ <h4 class="accordion-header" id="headingSolution3">
   If you already have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <ul><li><p>Open RStudio, and click on “Help” &gt; “Check for updates”. If a
 new version is available, quit RStudio, and download the latest version
@@ -537,7 +537,7 @@ <h4 class="accordion-header" id="headingSolution4">
   If you don’t have R and RStudio installed
   </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <ul><li><p>Download R from the <a href="https://cran.r-project.org/bin/macosx/" class="external-link">CRAN website</a>.</p></li>
 <li><p>Select the <code>.pkg</code> file for the latest R
@@ -570,7 +570,7 @@ <h4 class="accordion-header" id="headingSolution5">
   Install R using your package manager and RStudio
   </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <ul><li>Follow the instructions for your distribution from <a href="https://cloud.r-project.org/bin/linux" class="external-link">CRAN</a>, they provide
 information to get the most recent version of R for common
diff --git a/instructor/intro-sce.html b/instructor/intro-sce.html
index 2153856..321396b 100644
--- a/instructor/intro-sce.html
+++ b/instructor/intro-sce.html
@@ -328,7 +328,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction to Bioconductor and the SingleCellExperiment class</h1>
-        <p>Last updated on 2024-07-02 |
+        <p>Last updated on 2024-08-06 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -523,6 +523,41 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 (e.g., numeric matrices, lists, etc.). We will here review the main
 slots of the SingleCellExperiment class as well as their getter/setter
 methods.</p>
+<div id="challenge1" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div class="callout-inner">
+<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge1"></a>
+</h3>
+<div class="callout-content">
+<p>Before SingleCellExperiments, coders working with single cell data
+would sometimes keep all of these components in separate objects e.g. a
+matrix of counts, a data.frame of sample metadata, a data.frame of gene
+annotations and so on. What are the main disadvantages of this sort of
+“from scratch” approach?</p>
+</div>
+</div>
+</div>
+<div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
+<div class="accordion-item">
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
+  <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
+</button>
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div class="accordion-body">
+<ol style="list-style-type: decimal"><li><p>You have to do tons of manual book-keeping! If you perform a QC
+step that removes dead cells, now you also have to remember to remove
+that same set of cells from the cell-wise metadata. Dropped un-expressed
+genes? Don’t forget to filter the gene metadata table too.</p></li>
+<li><p>All the downstream steps have to be “from scratch” as well! If
+your tables have some slight format difference from those of your
+lab-mate, suddenly the plotting code you’re trying to re-use doesn’t
+work! Agh!</p></li>
+</ol></div>
+</div>
+</div>
+</div>
 <div class="section level3">
 <h3 id="the-assays">The <code>assays</code>
 <a class="anchor" aria-label="anchor" href="#the-assays"></a></h3>
@@ -770,7 +805,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -889,7 +924,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/instructor/intro-sce.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/instructor/intro-sce.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-07-02",
+  "dateModified": "2024-08-06",
   "datePublished": "2024-08-06"
 }
 
diff --git a/instructor/large_data.html b/instructor/large_data.html
index f6723ac..4f005a0 100644
--- a/instructor/large_data.html
+++ b/instructor/large_data.html
@@ -1198,7 +1198,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1212,7 +1212,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1240,7 +1240,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1253,7 +1253,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1283,7 +1283,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -1295,7 +1295,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
diff --git a/intro-sce.html b/intro-sce.html
index 0be1095..d577789 100644
--- a/intro-sce.html
+++ b/intro-sce.html
@@ -328,7 +328,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction to Bioconductor and the SingleCellExperiment class</h1>
-        <p>Last updated on 2024-07-02 |
+        <p>Last updated on 2024-08-06 |
 
         <a href="https://github.com/ccb-hms/osca-carpentries/edit/main/episodes/intro-sce.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -521,6 +521,41 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 (e.g., numeric matrices, lists, etc.). We will here review the main
 slots of the SingleCellExperiment class as well as their getter/setter
 methods.</p>
+<div id="challenge1" class="callout challenge">
+<div class="callout-square">
+<i class="callout-icon" data-feather="zap"></i>
+</div>
+<div class="callout-inner">
+<h3 class="callout-title">Challenge<a class="anchor" aria-label="anchor" href="#challenge1"></a>
+</h3>
+<div class="callout-content">
+<p>Before SingleCellExperiments, coders working with single cell data
+would sometimes keep all of these components in separate objects e.g. a
+matrix of counts, a data.frame of sample metadata, a data.frame of gene
+annotations and so on. What are the main disadvantages of this sort of
+“from scratch” approach?</p>
+</div>
+</div>
+</div>
+<div id="accordionSolution1" class="accordion challenge-accordion accordion-flush">
+<div class="accordion-item">
+<button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
+  <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
+</button>
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div class="accordion-body">
+<ol style="list-style-type: decimal"><li><p>You have to do tons of manual book-keeping! If you perform a QC
+step that removes dead cells, now you also have to remember to remove
+that same set of cells from the cell-wise metadata. Dropped un-expressed
+genes? Don’t forget to filter the gene metadata table too.</p></li>
+<li><p>All the downstream steps have to be “from scratch” as well! If
+your tables have some slight format difference from those of your
+lab-mate, suddenly the plotting code you’re trying to re-use doesn’t
+work! Agh!</p></li>
+</ol></div>
+</div>
+</div>
+</div>
 <div class="section level3">
 <h3 id="the-assays">The <code>assays</code>
 <a class="anchor" aria-label="anchor" href="#the-assays"></a></h3>
@@ -768,7 +803,7 @@ <h3 class="callout-title">Exercise 1<a class="anchor" aria-label="anchor" href="
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>The <code>SingleCellExperiment</code> constructor function can be
 used to create a new <code>SingleCellExperiment</code> object.</p>
@@ -887,7 +922,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "identifier": "https://ccb-hms.github.io/osca-carpentries/intro-sce.html",
   "dateCreated": "2024-01-10",
-  "dateModified": "2024-07-02",
+  "dateModified": "2024-08-06",
   "datePublished": "2024-08-06"
 }
 
diff --git a/large_data.html b/large_data.html
index f87207e..d0e86be 100644
--- a/large_data.html
+++ b/large_data.html
@@ -1196,7 +1196,7 @@ <h3 class="callout-title">Exercise 1: Out of memory representation<a class="anch
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>See the <code>HDF5Array</code> function for reading from HDF5 and the
 <code>writeHDF5Array</code> function for writing to HDF5 from the <em><a href="https://bioconductor.org/packages/3.19/HDF5Array" class="external-link">HDF5Array</a></em>
@@ -1210,7 +1210,7 @@ <h4 class="accordion-header" id="headingHint1"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1238,7 +1238,7 @@ <h3 class="callout-title">Exercise 2: Parallelization<a class="anchor" aria-labe
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use the function <code>system.time</code> to obtain the runtime of
 each job.</p>
@@ -1251,7 +1251,7 @@ <h4 class="accordion-header" id="headingHint2"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>TODO</p>
 </div>
@@ -1281,7 +1281,7 @@ <h3 class="callout-title">Exercise 3: Conversion to Seurat<a class="anchor" aria
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint3" aria-expanded="false" aria-controls="collapseHint3">
   <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 </button>
-<div id="collapseHint3" class="accordion-collapse collapse" aria-labelledby="headingHint3" data-bs-parent="#accordionHint3">
+<div id="collapseHint3" class="accordion-collapse collapse" data-bs-parent="#accordionHint3" aria-labelledby="headingHint3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
@@ -1293,7 +1293,7 @@ <h4 class="accordion-header" id="headingHint3"> Give me a hint </h4>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>Use Seurat’s <code>DimPlot</code> function.</p>
 </div>
diff --git a/md5sum.txt b/md5sum.txt
index cc68a15..cfb3af3 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -4,7 +4,7 @@
 "config.yaml" "b0d664d3d6abdd0e98b16282e1c03107" "site/built/config.yaml" "2024-07-02"
 "index.md" "495939ddd3f110be3bbcd49b60f4a7ce" "site/built/index.md" "2024-07-02"
 "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-07-02"
-"episodes/intro-sce.Rmd" "fffab405c45c9b0e52a5c34070958b65" "site/built/intro-sce.md" "2024-07-02"
+"episodes/intro-sce.Rmd" "5d23a77886d651cb1aa1b97a93d2e085" "site/built/intro-sce.md" "2024-08-06"
 "episodes/eda_qc.Rmd" "fac7397fb4caf04a9dc411b5e316ed60" "site/built/eda_qc.md" "2024-07-02"
 "episodes/cell_type_annotation.Rmd" "0aee6fee81ace65c93a9e39b0916a2cb" "site/built/cell_type_annotation.md" "2024-07-02"
 "episodes/multi-sample.Rmd" "75798a2bb3500220ff7b3c1d88cadf41" "site/built/multi-sample.md" "2024-07-02"
diff --git a/pkgdown.yml b/pkgdown.yml
index 1e4424c..903f8f5 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-08-06T01:10Z
+last_built: 2024-08-06T21:28Z