Merge branch 'mk-julia3' into 'develop'

julia 3

See merge request R3/school/courses!163

2023/2023-03-14_ProgrammingWithJulia-3/slides/1e-exercises.md

+
+# <i class="twa twa-pencil"></i> Exercise (continued): median
+
+Let's try to shrink the approximate median function code by 90%.
+
+
+
+# <i class="twa twa-pencil"></i> Exercise: let's play the maze game (again)
+
+- Make a function that annotates the whole maze based on how many (axis-aligned) steps a person (maze inhabitant) needs to take from some point
+  - let's use the slow <i class="twa twa-water-wave"></i>wave<i class="twa twa-water-wave"></i> algorithm
+- Use `UnicodePlots` to plot interesting stuff
+  - shortest path length distribution
+  - shortest-path-length heatmap of the maze
+  - "most blocking walls" (how much time to reach the father side of the wall could be gained by removing the wall?)
+
+
+
+# Exercise: Tricky questions about the maze
+
+What is the slowest part of the "wave" solution?
+
+How can we make it faster?

2023/2023-03-14_ProgrammingWithJulia-3/slides/2a-details.md

+
+<div class=leader>
+<i class="twa twa-mechanical-arm"></i>
+<i class="twa twa-battery"></i>
+<i class="twa twa-nut-and-bolt"></i>
+<i class="twa twa-mechanical-leg"></i>
+<br>
+Compiler &amp; language internals (continued)
+</div>
+
+
+
+# What is this "compiled code"?
+
+You can inspect various stages of code representation (and reveal bugs):
+
+- `code_lowered(+)`
+- `code_typed(+)`
+- `code_typed(+, (Int, Float64))`
+- `code_llvm`
+- `code_native`
+
+What happens if we use an abstract type?
+
+
+
+<center style="font-size:200%; line-height:120%; margin-bottom: 1em">
+Performance rule #1:<br><br>
+<strong>Less instructions is typically better,</strong><br>
+<strong>less jumps is typically much better.</strong>
+</center>
+
+
+
+<center style="font-size:200%; line-height:120%; margin-bottom: 1em">
+Performance rule #2:<br><br>
+<strong>Memory allocations comprise of many instructions<br> and plenty of jumps.</strong>
+</center>
+
+
+
+# What are all these things starting with `@`?
+
+Macros allow you to generate code before compiler runs it:
+- `@info` can know what variable names to display
+- `@benchmark` can run the code several times
+- `@test` can safely wrap the failing code and print what failed
+
+## Important types for macros:
+
+- symbols: `:abc`, `:+`, ...
+- expressions: `:(1+2)`, `quote ... end`
+
+Macros are functions that get unevaluated arguments (as expressions) and return unevaluated results (as expressions).
+
+```julia
+macro clear_data(v)
+  quote
+    $(Symbol(v, :_orig)) = load_original_data()
+    $(Symbol(v, :_enriched)) = nothing
+    $(Symbol(v, :_final)) = nothing
+  end
+end
+
+@clear_data patients   # reloads patients_orig, clears patients_enriched, patients_final
+```
+
+
+
+# Macro use-cases
+
+Use macros to improve your code whenever Julia syntax is too unwieldy.
+
+```julia
+model = @reaction_network MyModel begin
+    c1, s + i --> 2i
+    c2, i --> r
+end
+```
+
+(Taken from `Catalyst.jl`)

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

+
+<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
+- 0 1 2 3 4 5 6 7 8
+S 1 0 1 2 3 4 5 6 7
+u 2 1 1 2 2 3 4 5 6
+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
+```
+
+
+
+# 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
+S  unday
+ -- *
+```
+- Make the "costs" easily parametrizable
+  - some DNA mutations are more probable than others
+  - what's a good way to parametrize the functionality?

2023/2023-03-14_ProgrammingWithJulia-3/slides/img/julia.svg

+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 153.14 98.64"><defs><style>.cls-1{fill:#1a1a1a}.cls-2{fill:#4d64ae}.cls-3{fill:#ca3c32}.cls-4{fill:#9259a3}.cls-5{fill:#399746}</style></defs><title>Asset 2</title><g id="Layer_2" data-name="Layer 2"><g id="Layer_1-2" data-name="Layer 1"><g id="layer1"><g id="g3855"><g id="g945"><g id="g984"><g id="g920"><path id="path3804" d="M93.14,80.94h-13V21.13l13-3.58Z" class="cls-1"/><g id="g898"><g id="g893"><path id="path19" d="M22.17,36.33a8.9,8.9,0,1,1,8.9-8.9A8.91,8.91,0,0,1,22.17,36.33Z" class="cls-2"/></g><path id="path3819" d="M29.14,80.83A26.48,26.48,0,0,1,27.83,90a12.12,12.12,0,0,1-3.62,5.4A12.33,12.33,0,0,1,18.57,98a36.64,36.64,0,0,1-7.32.67,22.47,22.47,0,0,1-4.81-.47A13,13,0,0,1,2.9,96.93,6,6,0,0,1,.76,95.07,3.62,3.62,0,0,1,0,92.88,4.26,4.26,0,0,1,1.59,89.5a6.47,6.47,0,0,1,4.33-1.35,5,5,0,0,1,1.87.32,6,6,0,0,1,1.43.79,12,12,0,0,1,1.16,1.07c.31.4.59.77.83,1.12A7.58,7.58,0,0,0,12.72,93a2.3,2.3,0,0,0,1.15.4,1.85,1.85,0,0,0,1-.28,2,2,0,0,0,.71-1,7.18,7.18,0,0,0,.4-1.91,23.12,23.12,0,0,0,.16-3.06V40.48l13-3.58Z" class="cls-1"/></g><path id="path3802" d="M48.14,37.94V68a6.14,6.14,0,0,0,.47,2.39A6.45,6.45,0,0,0,50,72.24a7,7,0,0,0,2,1.27,6.12,6.12,0,0,0,2.4.48,4.2,4.2,0,0,0,1.61-.4,8.42,8.42,0,0,0,1.8-1.12,13.27,13.27,0,0,0,1.81-1.66,12.92,12.92,0,0,0,1.61-2.11V37.94h13v43h-13v-4a22.47,22.47,0,0,1-5.43,3.53,13.62,13.62,0,0,1-5.59,1.28,16.52,16.52,0,0,1-5.9-1,15.59,15.59,0,0,1-4.76-2.89,13.56,13.56,0,0,1-3.17-4.28,12.41,12.41,0,0,1-1.15-5.29V37.94Z" class="cls-1"/><g id="g905"><g id="g890"><path id="path13" d="M105.79,36.33a8.9,8.9,0,1,1,8.91-8.9A8.91,8.91,0,0,1,105.79,36.33Z" class="cls-3"/><path id="path25" d="M127.18,36.33a8.9,8.9,0,1,1,8.91-8.9A8.91,8.91,0,0,1,127.18,36.33Z" class="cls-4"/><path id="path31" d="M116.49,17.8a8.9,8.9,0,1,1,8.9-8.9,8.89,8.89,0,0,1-8.9,8.9Z" class="cls-5"/></g><path id="path3823" d="M100.14,40.6l13-3.58V80.94h-13Z" class="cls-1"/></g><path id="path3808" d="M140.14,58.77a37.64,37.64,0,0,0-3.77,1.87,21.89,21.89,0,0,0-3.46,2.3,12.77,12.77,0,0,0-2.55,2.67,5.12,5.12,0,0,0-1,2.94,8.53,8.53,0,0,0,.32,2.34,7,7,0,0,0,.87,1.91,5.15,5.15,0,0,0,1.23,1.27,2.67,2.67,0,0,0,1.51.48,6.3,6.3,0,0,0,3.18-1,41.31,41.31,0,0,0,3.62-2.47Zm13,22.17h-13V77.52c-.71.61-1.42,1.17-2.11,1.67a14.2,14.2,0,0,1-2.3,1.35,13.56,13.56,0,0,1-2.82.88,19.75,19.75,0,0,1-3.78.31,16,16,0,0,1-5.33-.83,12.23,12.23,0,0,1-4-2.31,10.23,10.23,0,0,1-2.51-3.53,11,11,0,0,1-.87-4.37,10.27,10.27,0,0,1,.91-4.42,13.11,13.11,0,0,1,2.55-3.57,19.36,19.36,0,0,1,3.77-2.86,40.26,40.26,0,0,1,4.65-2.31c1.67-.69,3.4-1.32,5.17-1.91l5.25-1.71,1.43-.31V49.34a11.91,11.91,0,0,0-.44-3.45,5.82,5.82,0,0,0-1.15-2.31,4,4,0,0,0-1.79-1.31,6.6,6.6,0,0,0-2.34-.4,7.38,7.38,0,0,0-2.59.4,4.37,4.37,0,0,0-1.67,1.11,3.94,3.94,0,0,0-.91,1.59,6.52,6.52,0,0,0-.28,2,9.51,9.51,0,0,1-.28,2.35,4.85,4.85,0,0,1-.91,2A4.47,4.47,0,0,1,126,52.6a6.84,6.84,0,0,1-2.9.52,7.51,7.51,0,0,1-2.51-.4,6.16,6.16,0,0,1-1.91-1.15,6,6,0,0,1-1.27-1.75,5.59,5.59,0,0,1-.44-2.18,6.42,6.42,0,0,1,1.51-4.1,13.16,13.16,0,0,1,4.06-3.3,23.45,23.45,0,0,1,5.92-2.14,31.07,31.07,0,0,1,7.12-.8,32.21,32.21,0,0,1,7.87.84,16.37,16.37,0,0,1,5.49,2.34,9.55,9.55,0,0,1,3.18,3.66,10.91,10.91,0,0,1,1,4.81Z" class="cls-1"/></g></g></g></g></g></g></g></svg>
\ No newline at end of file

2023/2023-03-14_ProgrammingWithJulia-3/slides/index.md

+
+# Programming with Julia
+
+## March 2023
+
+<div style="top: 6em; left: 0%; position: absolute;">
+    <img src="theme/img/lcsb_bg.png">
+</div>
+
+<div style="top: 1em; left: 60%; position: absolute;">
+    <img src="slides/img/julia.svg" height="200px">
+    <h1 style="margin-top:3ex; margin-bottom:3ex;">3: Numeric&scientific computing</h1>
+    <h4>
+        Miroslav Kratochvíl<br>
+        Laurent Heirendt<br>
+        LCSB, DSSE<br>
+    </h4>
+</div>
+
+<link rel="stylesheet" href="https://lcsb-biocore.github.io/icons-mirror/twemoji-amazing.css">
+<style>
+	code {border: 2pt dotted #f80; padding: .4ex; border-radius: .7ex; color:#444; }
+	.reveal pre code {border: 0; font-size: 18pt; line-height:27pt;}
+	em {color: #e02;}
+	li {margin-bottom: 1ex;}
+	div.leader {font-size:400%; line-height:120%; font-weight:bold; margin: 1em;}
+	section {padding-bottom: 10em;}
+</style>

2023/2023-03-14_ProgrammingWithJulia-3/slides/list.json

+[
+    { "filename": "index.md" },
+    { "filename": "2a-details.md" },
+    { "filename": "1e-exercises.md" },
+    { "filename": "3a-num-exercises.md" }
+]