Add more info on what virus information looks like

docs/introduction.qmd

@@ -12,6 +12,10 @@ format:
 
 The phylotree part of the virusBank platform website is developed and used as a standalone web application. This webapplication included as an [iFrame](https://www.w3schools.com/tags/tag_iframe.ASP). There are two 'sections' in the VirusBank website that point to the phylotree viz: __Viruses__ and __Toolbox__.
 
+:::{.callout-note}
+Please note that because of the app running in an iFrame, some additional configuration is required on the level of the main VirusBank website. All virus families, for instance, have to be registered there in order for the external links to function properly.
+:::
+
 In what follows, we will describe how the phylotree part is setup and how it can be updated.
 
 ## Tools

docs/scenarios.qmd

@@ -1,6 +1,7 @@
 ---
 title: Scenarios
 order: 40
+engine: knitr
 format:
   html:
     toc: true
@@ -114,7 +115,45 @@ These correspond to the tabs: Medical relevance, Symptoms and Transmission. The
 
 ![](virus-tab.png){width=80% .border}
 
-The files itself are generated with placeholder content by means of the `_js/update_family.js` script based on the family Excel file.
+The files itself are generated with placeholder content by means of the `_js/update_family.js` script based on the family Excel file. Running the `update_family.js` again will (by default) not overwrite those files once they are created.
+
+Let's quickly take a look at what kind of content can be found in the virus information files:
+
+- `_RRV-symptoms.qmd`:
+
+    ```{embed, lang="markdown"}
+    ../alphaviruses/_RRV-symptoms.qmd
+    ```
+
+- `_RRV-symptoms-fig.qmd`:
+
+  ```{embed, lang="markdown"}
+  ../alphaviruses/_RRV-symptoms-fig.qmd
+  ```
+
+- `_RRV-transmission.qmd`: We do not use text to describe transmission, only a figure.
+
+- `_RRV-transmission-fig.qmd`:
+
+    ```{embed, lang="markdown"}
+    ../alphaviruses/_RRV-transmission-fig.qmd
+    ```
+
+- `_RRV-relevance.qmd`:
+
+    ```{embed, lang="markdown"}
+    ../alphaviruses/_RRV-relevance.qmd
+    ```
+
+- `_RRV-relevance-fig.qmd`:
+
+    ```{embed, lang="markdown"}
+    ../alphaviruses/_RRV-relevance-fig.qmd
+    ```
+
+- `_RRV-toolbox.qmd`: This file should not be edited, it is dynamically populated based on the family Excel file.
+
+Some of the text files are a bit more complicated and contain additional Markdown formatting to make it readable. There are examples of viruses where figures have been integrated with the text as well. That's also possible: leave the `-fig`-file empty and add the figures to the text `.qmd` file using the proper Markdown syntax. 
 
 ## Update a tool