build based on 89c7d52

jchitpin · Nov 12, 2024 · 9c1dc49 · 9c1dc49
1 parent 7141c31
commit 9c1dc49
Show file tree

Hide file tree

Showing 69 changed files with 6,043 additions and 4 deletions.
diff --git a/stable b/stable
@@ -1 +1 @@
-v2.0.1
+v2.0.2
diff --git a/v2 b/v2
@@ -1 +1 @@
-v2.0.1
+v2.0.2
diff --git a/v2.0 b/v2.0
@@ -1 +1 @@
-v2.0.1
+v2.0.2
diff --git a/v2.0.2/.documenter-siteinfo.json b/v2.0.2/.documenter-siteinfo.json
@@ -0,0 +1 @@
+{"documenter":{"julia_version":"1.10.6","generation_timestamp":"2024-11-12T20:50:11","documenter_version":"1.7.0"}}
diff --git a/v2.0.2/assets-compile/custom-tikz.sty b/v2.0.2/assets-compile/custom-tikz.sty
@@ -0,0 +1,160 @@
+% Tikz libraries
+\usepackage{tikz}
+\usetikzlibrary{%
+    patterns, plotmarks, backgrounds, shapes, arrows, calc, trees, positioning,
+    chains, shapes.geometric, decorations.pathreplacing,
+    decorations.pathmorphing, shapes.arrows, decorations.markings, quotes, 
+    shapes.geometric, arrows.meta, spy, fit, matrix, math, bending, graphs,
+    graphs.standard, through
+}
+
+%% Define main node types
+% Vertical split circle with either sides filled with different colours
+\makeatletter
+\tikzset{circle split part fill/.style  args={#1,#2}{%
+    alias=tmp@name,%
+        postaction={%
+            insert path={%
+                \pgfextra{%
+                    \pgfpointdiff{\pgfpointanchor{\pgf@node@name}{center}}
+                    {\pgfpointanchor{\pgf@node@name}{east}}
+                    \pgfmathsetmacro\insiderad{\pgf@x}
+                    \fill[#1] (\pgf@node@name.base)
+                        ([xshift=-\pgflinewidth]\pgf@node@name.east)
+                        arc
+                        (0:180:\insiderad-\pgflinewidth)--cycle;
+                    \fill[#2] (\pgf@node@name.base)
+                    ([xshift=\pgflinewidth]\pgf@node@name.west)
+                    arc
+                    (180:360:\insiderad-\pgflinewidth)--cycle;
+                }
+            }
+        }
+    }
+}
+\makeatother
+
+\tikzstyle{gem_node} = [% black gem node for the input metabolic network
+    circle,
+    draw=black,
+    fill=black,
+    minimum height=0.15cm
+]
+\tikzstyle{gem_node_ph} = [% placeholder gem node for input metabolic network
+    circle,
+    draw=none,
+    fill=none,
+    minimum height=0.15cm
+]
+\tikzstyle{gem_edge} = [% edge style linking gem nodes
+    -,
+    line width=2pt
+]
+\tikzstyle{carbonDraw} = [% edge style linking molecules
+    -,
+    draw,
+    line width=1.75pt
+]
+\tikzstyle{ball} = [%
+    circle,
+    draw=black,
+    minimum height=0.70cm,
+    line width=1.0pt,
+    align=center,
+    fill=cgrey,
+    fill opacity=1.0,
+    text opacity=1.0,
+    text centered,
+    text=black,
+    inner sep=0.5pt,
+    font=\LARGE
+]
+\tikzstyle{carbon} = [% individual carbon atom node
+    circle,
+    draw=black,
+    fill=white,
+    inner sep=3.0pt,
+    line width=0.75pt
+]
+\tikzstyle{carbonBlank} = [% carbon atom node for white background
+    circle,
+    draw=white,
+    fill=white,
+    inner sep=3.0pt,
+    line width=0.75pt
+]
+\tikzstyle{carbonGrey} = [% greyed out carbon atom node
+    circle,
+    draw,
+    draw opacity=0.25,
+    fill opacity=0.25,
+    inner sep=3.0pt,
+    line width=0.75pt
+]
+\tikzstyle{ring6} = [%
+    regular polygon,
+    regular polygon sides=6,
+    draw,
+    inner sep=0.5cm,
+    line width=1.75pt
+]
+\tikzstyle{ring5} = [%
+    regular polygon,
+    regular polygon sides=5,
+    draw,
+    inner sep=0.5cm,
+    line width=1.75pt
+]
+\tikzstyle{reactionArrow} = [% reaction arrow style
+    -stealth,
+    line width=3.0pt,
+    draw=black
+]
+\tikzstyle{chmcArrow} = [% reaction arrow style
+    -stealth,
+    line width=6.0pt,
+    draw=black
+]
+\tikzstyle{chmcArrow2} = [% reaction arrow style
+    -stealth,
+    line width=12.0pt,
+    draw=black
+]
+\tikzstyle{subpanelArrow} = [% reaction arrow style
+    -stealth,
+    line width=9.0pt,
+    draw=black
+]
+\tikzstyle{labelFont} = [% standard label font size
+    font=\LARGE
+]
+\tikzset{%
+    labelSankey/.style={%
+        fill=white,
+        fill opacity=0.0,
+        text opacity=1,
+        inner sep=3pt,
+        text=black!50!black!50!black,
+        inner xsep=3pt,
+        font=\Large,
+        align=center,
+    },
+}
+
+\tikzmath{%
+    \sep=0.5pt;
+    \innerspace=0.25pt;
+    \outerspace=1.0pt;
+    \rxnspace=5pt;
+    \fluxspace=0.5pt;
+    \multispace = 0.5pt;
+}
+
+\tikzset{
+    double arrow/.style args={#1 colored by #2 and #3}{
+        -stealth,line width=#1,#2, % first arrow
+        postaction={draw,-stealth,#3,line width=(#1)/2.5,
+            shorten <=(#1)/3,shorten >=2*(#1)/3}, % second arrow
+    }
+}
+%\draw[double arrow=1pt colored by blue and white]
diff --git a/v2.0.2/assets-compile/generate-plots.sh b/v2.0.2/assets-compile/generate-plots.sh
@@ -0,0 +1,81 @@
+#!/usr/bin/env bash
+
+## Tutorial: CHMC (metabolic networks)
+# Plot toy network and CHMC as PDF and PNG
+pdflatex -shell-escape toy-network-1.tex
+pdflatex -shell-escape toy-network-1-chmc.tex
+
+# Plot toy network CHMC via MarkovWeightedEFMs
+julia toy-network-1-chmc-analysis.jl # generates toy-network-1-chmc-makie.png
+
+# Crop PNGs and set background solid white
+magick toy-network-1.png -gravity East -chop 672x0 toy-network-1.png
+magick toy-network-1.png -gravity West -chop 632x0 -background white -alpha remove -alpha off toy-network-1.png
+magick toy-network-1-chmc.png -background white -alpha remove -alpha off toy-network-1-chmc.png
+magick toy-network-1-chmc-makie.png -gravity East -chop 250x0 toy-network-1-chmc-makie.png
+magick toy-network-1-chmc-makie.png -gravity West -chop 250x0 -background white -alpha remove -alpha off toy-network-1-chmc-makie.png
+
+# Remove logs
+rm toy-network-1.aux toy-network-1.log
+rm toy-network-1-chmc.aux toy-network-1-chmc.log
+
+# Move PNGs to assets
+mv toy-network-1.png ../assets/
+mv toy-network-1-chmc.png ../assets/
+mv toy-network-1-chmc-makie.png ../assets/
+
+## Tutorial: CHMC (ion channels)
+# Plot Markov state model as PDF and PNG
+pdflatex -shell-escape ion-channel-mc.tex
+
+# Plot toy network CHMC via MarkovWeightedEFMs
+julia ion-channel-chmc-analysis.jl # generates ion-channel-chmc-makie.png
+
+# Set background solid white
+magick ion-channel-mc.png -background white -alpha remove -alpha off ion-channel-mc.png
+
+# Remove logs
+rm ion-channel-mc.aux ion-channel-mc.log
+
+# Move PNGs to assets
+mv ion-channel-mc.png ../assets/
+mv ion-channel-chmc-makie.png ../assets/
+
+## Tutorial ACHMC (one-carbon)
+# Plot toy network as PDF and PNG
+pdflatex -shell-escape toy-network-2-achmc.tex
+
+# Set background solid white
+magick toy-network-2-achmc.png -background white -alpha remove -alpha off toy-network-2-achmc.png
+
+# Remove logs
+rm toy-network-2-achmc.aux toy-network-2-achmc.log
+
+# Move PNGs to assets
+mv toy-network-2-achmc.png ../assets/
+
+## Tutorial: ACHMC (glucose)
+# Plot network as PDF and PNG
+pdflatex -shell-escape toy-network-1-achmc.tex
+
+# Set background solid white
+magick toy-network-1-achmc.png -background white -alpha remove -alpha off toy-network-1-achmc.png
+
+# Remove logs
+rm toy-network-1-achmc.aux toy-network-1-achmc.log
+
+# Move PNGs to assets
+mv toy-network-1-achmc.png ../assets/
+
+## Logo
+pdflatex -shell-escape logo.tex
+
+# Remove logs
+rm logo.aux logo.log
+
+# Convert to SVG
+inkscape --export-type=svg logo.pdf
+
+# Move logo to assets
+mv logo.svg ../assets/
+
diff --git a/v2.0.2/assets-compile/ion-channel-chmc-analysis.jl b/v2.0.2/assets-compile/ion-channel-chmc-analysis.jl
@@ -0,0 +1,62 @@
+using MarkovWeightedEFMs
+using CairoMakie
+
+# Parameters
+c = 0.1 # Ca2+ (uM)
+I = 0.1 # IP3 (uM)
+a1 = 50
+a2 = 0.035
+a4 = 3.5
+a5 = 65
+a6 = 25
+a7 = 10
+a8 = 0.035
+a9 = 0.15
+a10 = 1.25
+a11 = 110
+b1 = 2.5
+b2 = 1.25
+b3 = 0.25
+b4 = 12.5
+b5 = 10
+b7 = 0.25
+b9 = 0.2
+b10 = 2.5
+b11 = 20
+K1 = b1 / a1
+K2 = b2 / a2
+K4 = b4 / a4
+K5 = b5 / a5
+K7 = b7 / a7
+K9 = b9 / a9
+K10 = b10 / a10
+a3 = (b3 * K4) / (K1 * K2)
+b6 = (a6 * K5 * K7) / K1
+b8 = (a8 * K2 * K10) / K9
+
+# Markov transition rate matrix
+Q = [
+  0  c*a6 0    I*a7 0    0    0  0    0    0
+  b6 0    c*a4 0    I*a1 0    0  0    0    0
+  0  b4   0    0    0    I*a3 0  0    0    0
+  b7 0    0    0    c*a5 0    a9 0    0    0
+  0  b1   0    b5   0    c*a2 0  a9   0    a11
+  0  0    b3   0    b2   0    0  0    a10  0
+  0  0    0    b9   0    0    0  c*a5 0    0
+  0  0    0    0    b9   0    b5 0    c*a8 0
+  0  0    0    0    0    b10  0  b8   0    0
+  0  0    0    0    b11  0    0  0    0    0
+];
+
+# Markov transition probability matrix
+T = Q ./ sum(Q, dims=2)
+
+res = steady_state_efm_distribution(T);
+
+# Static backend for plotting
+CairoMakie.activate!(type = "png")
+
+# Plot and save
+fig = plot_chmc(T, 1)
+save("ion-channel-chmc-makie.png", fig)
+
diff --git a/v2.0.2/assets-compile/ion-channel-chmc-tikz.tex b/v2.0.2/assets-compile/ion-channel-chmc-tikz.tex
diff --git a/v2.0.2/assets-compile/ion-channel-chmc.tex b/v2.0.2/assets-compile/ion-channel-chmc.tex