Rerun-sims

Manifest.toml

@@ -797,9 +797,9 @@ version = "1.11.0"
 
 [[deps.GLFW_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"]
-git-tree-sha1 = "fcb0584ff34e25155876418979d4c8971243bb89"
+git-tree-sha1 = "b7bfd56fa66616138dfe5237da4dc13bbd83c67f"
 uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89"
-version = "3.4.0+2"
+version = "3.4.1+0"
 
 [[deps.GPUArraysCore]]
 deps = ["Adapt"]
@@ -2819,9 +2819,9 @@ version = "1.28.1+0"
 
 [[deps.libpng_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
-git-tree-sha1 = "5cb3c5d039f880c0b3075803c8bf45cb95ae1e91"
+git-tree-sha1 = "de8ab4f01cb2d8b41702bab9eaad9e8b7d352f73"
 uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f"
-version = "1.6.51+0"
+version = "1.6.53+0"
 
 [[deps.libvorbis_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll"]

docs/bcl-data-fit.ipynb

@@ -0,0 +1,287 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "e39c5573",
+   "metadata": {},
+   "source": [
+    "# Pacing data\n",
+    "\n",
+    "Experiments vs simulations."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "83bfe6d9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "using ModelingToolkit\n",
+    "using OrdinaryDiffEq, SteadyStateDiffEq, DiffEqCallbacks\n",
+    "using Plots\n",
+    "using CSV\n",
+    "using DataFrames\n",
+    "using CaMKIIModel\n",
+    "using CaMKIIModel: second\n",
+    "Plots.default(lw=1.5)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a2f8930a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sys = build_neonatal_ecc_sys(simplify=true, reduce_iso=true, reduce_camk=true)\n",
+    "tend = 500second\n",
+    "prob = ODEProblem(sys, [], tend)\n",
+    "stimstart = 100second\n",
+    "stimend = 300second\n",
+    "@unpack Istim = sys\n",
+    "alg = KenCarp47()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4913c735",
+   "metadata": {},
+   "source": [
+    "## Pacing duration and CaMKII activity\n",
+    "\n",
+    "### Experiments"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "24c3f0e3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "durationdf = CSV.read(joinpath(@__DIR__, \"data/CaMKAR-duration.csv\"), DataFrame)\n",
+    "ts = durationdf[!, \"Time(sec)\"]\n",
+    "fifteen = durationdf[!, \"1Hz 15sec (Mean)\"]\n",
+    "fifteen_error = durationdf[!, \"1Hz 15sec (SD)\"] ./ sqrt.(durationdf[!, \"1Hz 15sec (N)\"])\n",
+    "thirty = durationdf[!, \"1Hz 30sec (Mean)\"] .+ 0.25\n",
+    "thirty_error = durationdf[!, \"1Hz 30sec (SD)\"] ./ sqrt.(durationdf[!, \"1Hz 30sec (N)\"])\n",
+    "sixty = durationdf[!, \"1Hz 60sec (Mean)\"]\n",
+    "sixty_error = durationdf[!, \"1Hz 60sec (SD)\"] ./ sqrt.(durationdf[!, \"1Hz 60sec (N)\"])\n",
+    "ninety = durationdf[!, \"1Hz 90sec (Mean)\"] .- 0.25\n",
+    "ninety_error = durationdf[!, \"1Hz 90sec (SD)\"] ./ sqrt.(durationdf[!, \"1Hz 90sec (N)\"])\n",
+    "\n",
+    "## 30 sec timeseries +0.25 and 90 sec timeseries -0.25 for a consistent baseline before pacing.\n",
+    "plot(ts, fifteen, yerr=fifteen_error, lab=\"15 sec\", color=:blue, markerstrokecolor=:blue)\n",
+    "plot!(ts, thirty, yerr=thirty_error, lab=\"30 sec\", color=:red, markerstrokecolor=:red)\n",
+    "plot!(ts, sixty, yerr=sixty_error, lab=\"60 sec\", color=:orange, markerstrokecolor=:orange)\n",
+    "plot!(ts, ninety, yerr=ninety_error, lab=\"90 sec\", color=:green, markerstrokecolor=:green)\n",
+    "plot!(title=\"Experiment\", xlabel=\"Time (s)\", ylabel=\"CaMKII activity (AU)\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5a5465b5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "savefig(\"pacing-duration-exp.pdf\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6179dde0",
+   "metadata": {},
+   "source": [
+    "### Simulation"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1135d95a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "stimstart = 30second\n",
+    "callback15 = build_stim_callbacks(Istim, stimstart + 15second; period=1second, starttime=stimstart)\n",
+    "sol15 = solve(prob, alg; callback=callback15)\n",
+    "callback30 = build_stim_callbacks(Istim, stimstart + 30second; period=1second, starttime=stimstart)\n",
+    "sol30 = solve(prob, alg; callback=callback30)\n",
+    "callback60 = build_stim_callbacks(Istim, stimstart + 60second; period=1second, starttime=stimstart)\n",
+    "sol60 = solve(prob, alg; callback=callback60)\n",
+    "callback90 = build_stim_callbacks(Istim, stimstart + 90second; period=1second, starttime=stimstart)\n",
+    "sol90 = solve(prob, alg; callback=callback90)\n",
+    "idxs = (sys.t / 1000, sys.CaMKAct * 100)\n",
+    "\n",
+    "plot(sol15, idxs=idxs, tspan=(0second, 205second), lab=\"15 sec\", color=:blue)\n",
+    "plot!(sol30, idxs=idxs, tspan=(0second, 205second), lab=\"30 sec\", color=:red)\n",
+    "plot!(sol60, idxs=idxs, tspan=(0second, 205second), lab=\"60 sec\", color=:orange)\n",
+    "plot!(sol90, idxs=idxs, tspan=(0second, 205second), lab=\"90 sec\", color=:green)\n",
+    "plot!(title=\"Simulation\", xlabel=\"Time (s)\", ylabel=\"CaMKII activity (%)\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5d5599f7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "savefig(\"pacing-duration-sim.pdf\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6209d573",
+   "metadata": {},
+   "source": [
+    "### Phosphorylated fraction"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2fbd5b3b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "idxs = (sys.t / 1000, (sys.CaMKP + sys.CaMKA + sys.CaMKA2) * 100)\n",
+    "plot(sol15, idxs=idxs, tspan=(0second, 205second), lab=\"15 sec\", color=:blue)\n",
+    "plot!(sol30, idxs=idxs, tspan=(0second, 205second), lab=\"30 sec\", color=:red)\n",
+    "plot!(sol60, idxs=idxs, tspan=(0second, 205second), lab=\"60 sec\", color=:orange)\n",
+    "plot!(sol90, idxs=idxs, tspan=(0second, 205second), lab=\"90 sec\", color=:green)\n",
+    "plot!(title=\"Simulation\", xlabel=\"Time (s)\", ylabel=\"Phosphorylated CaMKII (%)\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "70df2b76",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "savefig(\"pacing-duration-phos.pdf\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6df99024",
+   "metadata": {},
+   "source": [
+    "## Pacing frequency and CaMKII activity\n",
+    "\n",
+    "### Experiments"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ba30e1bc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "freqdf = CSV.read(joinpath(@__DIR__, \"data/CaMKAR-freq.csv\"), DataFrame)\n",
+    "ts = 0:5:205\n",
+    "onehz = freqdf[!, \"1Hz (Mean)\"]\n",
+    "onehz_error = freqdf[!, \"1Hz (SD)\"] ./ sqrt.(freqdf[!, \"1Hz (N)\"])\n",
+    "twohz = freqdf[!, \"2Hz (Mean)\"]\n",
+    "twohz_error = freqdf[!, \"2Hz (SD)\"] ./ sqrt.(freqdf[!, \"2Hz (N)\"])\n",
+    "\n",
+    "plot(ts, onehz, yerr=onehz_error, lab=\"1 Hz\", color=:blue, markerstrokecolor=:blue)\n",
+    "plot!(ts, twohz, yerr=twohz_error, lab=\"2 Hz\", color=:red, markerstrokecolor=:red)\n",
+    "plot!(title=\"Experiment\", xlabel=\"Time (s)\", ylabel=\"CaMKII activity (AU)\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b5f1b294",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "savefig(\"pacing-frequency-exp.pdf\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "588d3456",
+   "metadata": {},
+   "source": [
+    "### Simulations"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "18df9887",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tend = 205.0second\n",
+    "prob = ODEProblem(sys, [], tend)\n",
+    "stimstart = 30.0second\n",
+    "stimend = 120.0second\n",
+    "callback = build_stim_callbacks(Istim, stimend; period=1second, starttime=stimstart)\n",
+    "sol1 = solve(prob, alg; callback)\n",
+    "\n",
+    "callback2 = build_stim_callbacks(Istim, stimend; period=0.5second, starttime=stimstart)\n",
+    "sol2 = solve(prob, alg; callback=callback2)\n",
+    "idxs = (sys.t / 1000, sys.CaMKAct * 100)\n",
+    "\n",
+    "plot(sol1, idxs=idxs, lab=\"1 Hz\", color=:blue)\n",
+    "plot!(sol2, idxs=idxs, lab=\"2 Hz\", color=:red)\n",
+    "plot!(title=\"Pacing frequency\", xlabel=\"Time (s)\", ylabel=\"CaMKII activity (%)\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "326ddd77",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "savefig(\"pacing-frequency-sim.pdf\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "81231962",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "idxs = (sys.t / 1000, (sys.CaMKP + sys.CaMKA + sys.CaMKA2) * 100)\n",
+    "plot(sol1, idxs=idxs, lab=\"1 Hz\", color=:blue)\n",
+    "plot!(sol2, idxs=idxs, lab=\"2 Hz\", color=:red)\n",
+    "plot!(title=\"Pacing frequency\", xlabel=\"Time (s)\", ylabel=\"Phosphorylated CaMKII (%)\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "eae708c7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "savefig(\"pacing-frequency-phos.pdf\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Julia 1.12.2",
+   "language": "julia",
+   "name": "julia-1.12"
+  },
+  "language_info": {
+   "file_extension": ".jl",
+   "mimetype": "application/julia",
+   "name": "julia",
+   "version": "1.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}