Add more introduction.

presentation.qmd

@@ -17,12 +17,29 @@ title-slide-attributes:
     data-background-size: cover
     data-background-image: inclusions/blurred-asper.jpg
     data-background-opacity: "0.5"
+    data-background-color: "black"
 date: "2024-01-15"
 bibliography: "BibDataBase.bib"
 ---
 
 # Relivance of fungi {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
+::: incremental
+
+* Fungi are a diverse taxa.
+
+* A lot good things
+    - Fermentation.
+    - Plant health.
+    - Nutrient cycling.
+* A lot of chaos too
+    - Food insecurity.
+    - Toxicity of food.
+    - Diseases in animals.
+:::
+
+## The WHO priority pathogens {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
+
 ![The priority fungal pathogens identified by
 the WHO [@worldhealthorganizationwhoWHOFungalPriority2022]](
 inclusions/who-priorities.png)
@@ -68,7 +85,7 @@ work with it -->
 
 phylogeography.
 
-## Nextstrain {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
+## Phylogeography using nextstrain {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
 Using `nextstrain` for fungal pathogens [@hadfieldNextstrainRealtimeTracking2018]. An example:
 
@@ -81,28 +98,62 @@ Using `nextstrain` for fungal pathogens [@hadfieldNextstrainRealtimeTracking2018
 
 > This has not yet been done because $\dots$
 
-* Whole genome sequences of fungi are upcoming: [@fanComparativeGenomeSequence2020; @lofgrenPangenomeAspergillusFumigatus2022; @rhodesPopulationGenomicsConfirms2022]
+::: incremental
+
+* Whole genome sequences (WGS) of fungi are [upcoming]{.alert}: [@fanComparativeGenomeSequence2020; @lofgrenPangenomeAspergillusFumigatus2022; @rhodesPopulationGenomicsConfirms2022]
+
+* Existing solutions [don't consider]{.alert} WGS data.
 
-* Standardisation is not a focus in the _A. fumigatus_ domain.
+* Standardisation is [not a focus]{.alert} in the _A. fumigatus_ domain.
 
+:::
 
 # Method {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
-1. Harmonise _existent_ metadata.
+::: incremental
+
+1. Harmonise [existent]{.alert} metadata.
+
+2. Develop a system for harmonising [new]{.alert} metadata.
+
+3. Analyse [phylogeography]{.alert} of *A. fumigatus*.
 
-2. Develop a system for harmonising _new_ metadata.
+4. Generalise the workflow to [other fungi]{.alert}.
 
-3. Analyse phylogeography of *A. fumigatus*.
+:::
+
+::: notes
+
+Why me? I have the domain knowledge and network, and the technical ability
+and will power to pull it off.
+
+:::
 
-4. Generalise the workflow to other fungi.
 
 # Outlook {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
-* This would represent an innovation in the fungal database field.
+::: incremental
+
+* A new method of data collection.
 
 * Existing solutions, like [globalfungi](https://globalfungi.com/) only focus
 on the _ITS_ sequence.
 
-* The solution could be generalised to plant epidemiology also.
+* The solution [could be generalised]{.alert} to plant epidemiology also.
+
+:::
+
+# References {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
 
-# References {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
\ No newline at end of file
+## More information {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
+
+* [`sibbe.bakker@wur.nl`](mailto:sibbe.bakker@wur.nl)
+
+* Read my [pre-proposal](https://bookdown.org/sibbe_l_bakker/pre-proposal/)
+
+* I thank Eveline Snelders and Christopher Wandabwa for reviewing my work.
+
+## Cited works {background-color="black" background-image="inclusions/blurred-asper.jpg" background-size="cover" background-opacity="0.5"}
+
+::: {#refs}
+:::