add summary page

_quarto.yml

@@ -29,9 +29,9 @@ book:
     - itol-visualisation-1.qmd
     - make-a-tree.qmd
     - tree-refinement.qmd
-#    - summary.qmd
+    - summary.qmd
 #    - glossary.qmd
-#    - resources.qmd
+    - resources.qmd
     - references.qmd
 
 bibliography: references.bib

index.qmd

@@ -30,8 +30,8 @@ The workshop is not formally assessed although, as noted above, all the material
 There are four formative exercises in this workshop, and they can be found on the workshop [MyPlace page]({{< var myplace.bm211 >}}). You should complete these as part of the workshop.
 
 - [Formative quiz 1]({{< var myplace.quiz1 >}})
-- [Formative quiz 1]({{< var myplace.quiz2 >}})
-- [Formative quiz 1]({{< var myplace.quiz3 >}})
-- [Formative quiz 1]({{< var myplace.quiz4 >}})
+- [Formative quiz 2]({{< var myplace.quiz2 >}})
+- [Formative quiz 3]({{< var myplace.quiz3 >}})
+- [Formative quiz 4]({{< var myplace.quiz4 >}})
 :::
 

intro.qmd

@@ -36,7 +36,7 @@ The `R` software ecosystem is a very powerful tool for computational biology and
 ::: { .callout-note }
 You can produce equivalent trees to those you will produce in these exercises using standalone tools like `figtree` and `dendroscope`. Some tree visualisations can only be achieved in specialised packages, or with tools like `ggtree`.
 
-`ggtree` is an `R` packages that extends the `ggplot2` data visualisation package to visualise and annotate phylogenetic trees (or any other tree-like structure!).
+`ggtree` is an `R` package that extends the `ggplot2` data visualisation package to visualise and annotate phylogenetic trees (or any other tree-like structure!).
 
 - [`ggtree` homepage](https://guangchuangyu.github.io/ggtree/)
 - [The `ggtree` book](https://yulab-smu.top/treedata-book/)

summary.qmd

@@ -1,7 +1,43 @@
 # Summary
 
-In summary, this book has no content whatsoever.
+In this workshop you have learned how to build, visualise, and interpret phylogenetic trees. By using UniProt, `MUSCLE`, and `iToL`, you have been gaining experience with the same research-level tools that biologists and bioinformaticians use in their day-to-day work.
+
+::: { .callout-tip title="What you have learned" }
+After working through the material, you should now be able to:
+
+- upload a phylogenetic tree into `iToL`
+- explain the meaning of branching events and branch lengths in a phylogenetic tree
+- explain how a phylogenetic tree represents history and ancestry
+- explain the concept of a _clade_ in phylogenetics
+- explain the difference between a phylogram and cladogram
+- generate a variety of phylogenetic tree types using `iToL`
+- describe and interpret the _topology_ of a tree
+- describe and interpret _branch lengths_ of a tree
+- explain how rotation of a tree, and clades within the tree, affects what the tree represents
+- use UniProt to obtain annotation and functional information about a protein sequence
+- use UniProt to identify and download homologues of a protein sequence
+- generate a protein multiple sequence alignment using `MUSCLE`
+- produce a Neighbour-Joining phylogenetic tree using `Simple Phylogeny`
+- visualise a phylogenetic tree using `iToL`
+- midpoint root a tree in `iToL`
+- colour highlight clades of a tree in `iToL`
+- explain the difference between a _gene tree_ and a _species tree_
+- compare a gene tree with a species tree to interpret evolutionary history
+:::
+
+::: { .callout-important }
+If you have not done so already, please don't forget to complete the four formative exercises in this workshop, and they can be found on the workshop [MyPlace page]({{< var myplace.bm211 >}}). You should complete these as part of the workshop.
+
+- [Formative quiz 1]({{< var myplace.quiz1 >}})
+- [Formative quiz 2]({{< var myplace.quiz2 >}})
+- [Formative quiz 3]({{< var myplace.quiz3 >}})
+- [Formative quiz 3]({{< var myplace.quiz4 >}})
+:::
+
+## That's All, Folks!
+
+Thank you for taking part in this workshop. We hope you enjoyed it, and found it interesting.
+
+::: { .callout-caution title="Tell us about problems with the workshop, what you liked, or how you think it can be improved!"}
+We would be very grateful to head feedback [by email](mailto:{{< var admin.email >}}) or through the [GitHub repository issues page]({{< var github.issues >}}).
 
-```{r}
-1 + 1
-```