julia3 moreless done

2023/2023-03-14_ProgrammingWithJulia-3/slides/3a-num-exercises.md

-# Exercise: Let's align some DNA!
 
-Let's do bioinformatics; simple short 2-sequence alignment can be done with
-Levenshtein algorithm.
+<div class=leader>
+<i class="twa twa-volcano"></i>
+<i class="twa twa-mount-fuji"></i>
+<i class="twa twa-snow-capped-mountain"></i>
+<i class="twa twa-mountain"></i>
+<i class="twa twa-sunrise-over-mountains"></i>
+<br>
+Julia for scientific computing 
+</div>
+
+
+
+# What you mostly do in scientific/numeric computing?
+
+- `LinearAlgebra.jl`, `SparseArrays.jl`
+  - easily utilizes `CUDA.jl`, `AMDGPU.jl`, `Metal.jl`
+- statistics
+- simulations (typically custom made)
+- neural networks, ODEs, constrained problems (next time)
+- plotting!
+
+
+
+# Statistics in Julia
+
+- `StatsBase.jl` for all "base" runctions (correlations, medians, quantiles, ranks, ...)
+- `Distances.jl` for measuring distances/similarities
+- `Distributions.jl` for generating numbers
+- `HypothesisTests.jl` for getting p-values
+- `Clustering.jl`
+
+See more at [juliastats.org](https://juliastats.org)
+
+
+
+# Mini-exercise
+
+- Plot the correlations between the columns of our maze in a heatmap
+- Order the heatmap by similarity (from hclust) to visualize clusters
+
+
+
+# Simulation exercise: Let's layout some graphs!
+
+<img src="img/graph.jpeg" width="70%">
+
+
+
+# Simulation exercise: Let's layout some graphs!
+
+- Read a set of edges (integer pairs)
+- Simulate that the vertices are pushed around by 2 forces:
+  - quadratic attractive force ("gravity")
+  - inverse quadratic attractive force
+  - no momentum or any other kind of physics!
+- Draw what happens after a few rounds of simulation
+
+
+
+# Exercise: Let's align some <i class="twa twa-dna"></i>DNA<i class="twa twa-dna"></i>!
 
 ```
   - S a t u r d a y
@@ -12,9 +69,18 @@ n 3 2 2 2 3 3 4 5 6
 d 4 3 3 3 3 4 3 4 5
 a 5 4 3 4 4 4 4 3 4
 y 6 5 4 4 5 5 5 4 3
+
+* not actual DNA
 ```
 
-- Print out the alignment nicely
+
+
+# Exercise: Let's align some <i class="twa twa-dna"></i>DNA<i class="twa twa-dna"></i>!
+
+Let's do bioinformatics; simple short 2-sequence alignment can be done with
+Levenshtein algorithm.
+
+- Print out the alignment nicely (is it unique?)
 ```
  ++ *
 Saturday