using ModelingToolkit
using OrdinaryDiffEq, SteadyStateDiffEq, DiffEqCallbacks
using Plots
using CSV
using DataFrames
import Dates
using Model
using Model: second, μM
Plots.default(lw=1.5)Setup model¶
@time "Build system" sys = Model.DEFAULT_SYS
tend = 205second
@time "Build problem" prob = ODEProblem(sys, [], tend)
stimstart = 30second
stimend = 120second
alg = KenCarp47()Build system: 0.000002 seconds
Build problem: 48.199849 seconds (81.23 M allocations: 5.495 GiB, 3.09% gc time, 99.58% compilation time: 17% of which was recompilation)
KenCarp47(; linsolve = nothing, nlsolve = OrdinaryDiffEqNonlinearSolve.NLNewton{Rational{Int64}, Rational{Int64}, Rational{Int64}, Nothing}(1//100, 10, 1//5, 1//5, false, true, nothing), precs = DEFAULT_PRECS, smooth_est = true, extrapolant = linear, controller = PI, autodiff = ADTypes.AutoForwardDiff(),)Without isoproterenol¶
@unpack Istim = sys
callback = build_stim_callbacks(Istim, stimend; period=1second, starttime=stimstart)
@time sol = solve(prob, alg; callback) 4.694909 seconds (7.74 M allocations: 721.069 MiB, 2.68% gc time, 77.77% compilation time)
retcode: Success
Interpolation: 3rd order Hermite
t: 4019-element Vector{Float64}:
0.0
0.019333125036189055
0.09098129266634811
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0.45611905918185036
1.0472561699065968
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3.4517764276098144
6.733791989961008
12.45011626317526
⋮
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u: 4019-element Vector{Vector{Float64}}:
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⋮
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[781.1362040727706, 780.82607582024, 0.0017645124413390822, 0.2010764584429557, 0.00033624560834254587, 0.0012115393435021679, 0.0016306585419995875, 0.0025241336143034723, 0.0016308679156621345, 0.9997189544608736 … 0.1334711229284702, 0.13347152873817553, 0.1334719423634736, 0.1334723642525209, 0.13347279488238928, 0.13345881143587593, 0.13347323476143605, 151469.09703233565, 13324.675156604142, -69.89960705042942]i = (sys.t / 1000, sys.vm)
plot(sol, idxs=i, tspan=(100second, 101second), title="Action potential", xlabel="Time (s)")
plot(sol, idxs=(sys.t / 1000, [sys.Cai_sub_SR, sys.Cai_sub_SL, sys.Cai_mean]), tspan=(100second, 101second), title="Calcium transient", xlabel="Time (s)", ylabel="Conc. (μM)", label=["Ca (SR)" "Ca (SL)" "Ca (avg)"])
plot(sol, idxs=(sys.t / 1000, sys.CaMKAct * 100), title="Active CaMKII", label=false, ylabel="Active fraction (%)", xlabel="Time (s)")
0.1uM isoproterenol¶
prob2 = remake(prob, p=[sys.ISO => 0.1μM])
@time sol2 = solve(prob2, alg; callback) 1.093273 seconds (537.67 k allocations: 228.124 MiB, 2.21% gc time)
retcode: Success
Interpolation: 3rd order Hermite
t: 4132-element Vector{Float64}:
0.0
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1.0549953577900286
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⋮
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205000.0
u: 4132-element Vector{Vector{Float64}}:
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⋮
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[923.5185756131146, 922.0781064926031, 0.0068991071489416505, 0.21141437071941388, 0.0003093027070815239, 0.0011394331792593743, 0.0015834925735772503, 0.002451163294893299, 0.0015406721799164117, 0.9997420928281263 … 0.12478483075690726, 0.1247847634675477, 0.12478468589133046, 0.12478459766643131, 0.12478449840768689, 0.12478193101892551, 0.12478438770468184, 151089.59165149767, 13693.53590156749, -70.29441667734696]
[923.7079838731553, 922.2944930180249, 0.00676850550904198, 0.2087683947926843, 0.00031592251431308675, 0.0011572826287035735, 0.0015953636932978322, 0.002469535903990686, 0.0015630830046987159, 0.9997367213644156 … 0.12411061003502882, 0.12411055278297163, 0.12411048594867893, 0.12411040919772326, 0.12411032217410492, 0.12410768698465535, 0.1241102244984837, 151142.47533252425, 13640.730190923929, -70.19392535444491]
[923.8750530326538, 922.4870927318797, 0.006645048594176623, 0.20620856578682292, 0.00032252215370975114, 0.0011749778202206054, 0.0016070371235085395, 0.002487602516362937, 0.001585268958529621, 0.9997310744691502 … 0.12347018138983448, 0.12347013324608253, 0.12347007617596374, 0.12347000987041915, 0.12346993400045339, 0.12346724633928995, 0.12346984821550039, 151193.3982674349, 13589.882627747447, -70.09582240706207]
[924.0419174188572, 922.6816275177583, 0.006511388744905307, 0.20336908687104874, 0.0003300756478920813, 0.001195109791222255, 0.00162021110242941, 0.002507991507377059, 0.0016104764469537236, 0.9997245700266495 … 0.12277339036078325, 0.12277335137594989, 0.12277330415651852, 0.12277324842007413, 0.12277318386598461, 0.12277046044665522, 0.1227731101739075, 151249.60817654952, 13533.756250676735, -69.98595955804099]
[924.088123147369, 922.735966162791, 0.00647213644950083, 0.2025209800941488, 0.00033238324594575633, 0.0012012374339692164, 0.0016241931109641332, 0.0025141543058787765, 0.0016181390558857975, 0.9997225814697647 … 0.12256800903661205, 0.12256797283812279, 0.12256792861506408, 0.12256787609306768, 0.12256781498006553, 0.12256508059326755, 0.12256774496483869, 151266.34510739014, 13517.044241552994, -69.9529221679876]plot(sol2, idxs=(sys.t / 1000, sys.vm), tspan=(100second, 101second), title="Action potential", xlabel="Time (s)")
plot(sol2, idxs=(sys.t / 1000, [sys.Cai_sub_SR, sys.Cai_sub_SL, sys.Cai_mean]), tspan=(100second, 101second), title="Calcium transcient", xlabel="Time (s)", ylabel="Conc. (μM)", label=["Ca (SR)" "Ca (SL)" "Ca (avg)"])
Comparison¶
i = (sys.t / 1000, sys.Cai_mean)
tspan = (100second, 101second)
plot(sol, idxs=i, title="Calcium transcient", lab="ISO (-)"; tspan)
plot!(sol2, idxs=i, lab="ISO (0.1uM)", xlabel="Time (s)", ylabel="Concentration (μM)"; tspan)
savefig("iso-caT.pdf")"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/iso-caT.pdf"Maximal and minimal calcium concentrations in calcium transients.
ca_ctl = sol(tspan[1]:1:tspan[2], idxs=sys.Cai_mean)
println(extrema(ca_ctl))(0.2350435455121376, 0.5781130285861966)
ca_iso = sol2(tspan[1]:1:tspan[2], idxs=sys.Cai_mean)
println(extrema(ca_iso))(0.19033626819835733, 0.7110939320137905)
i = (sys.t / 1000, sys.CaMKAct * 100)
plot(sol, idxs=i, title="Active CaMKII", lab="ISO (-)")
plot!(sol2, idxs=i, lab="ISO (0.1uM)", ylabel="Active fraction (%)", xlabel="Time (s)")
savefig("iso-camkact.pdf")"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/iso-camkact.pdf"i = (sys.t / 1000, sys.vm)
tspan = (100second, 101second)
plot(sol, idxs=i, title="Action potential", lab="ISO (-)"; tspan)
plot!(sol2, idxs=i, lab="ISO (0.1uM)", xlabel="Time (ms)", ylabel="Voltage (mV)"; tspan)
Experimental data¶
chemicaldf = CSV.read(joinpath(@__DIR__, "data/CaMKAR-chemical.csv"), DataFrame)
ts = Dates.value.(chemicaldf[!, "Time"]) ./ 10^9
ctl = chemicaldf[!, "Ctrl Mean"]
ctl_error = chemicaldf[!, "Ctrl SD"] ./ sqrt.(chemicaldf[!, "Ctrl N"])42-element Vector{Float64}:
0.02305850621757014
0.023225557529411765
0.023536003837902393
0.022995786588235295
0.023056161133316953
0.02236794743822152
0.02448575734900888
0.02631837493460871
0.029628792824062226
0.0306227531696316
⋮
0.02665056333747046
0.02525893438851731
0.024749347823716496
0.024158682609370527
0.023572491294117648
0.0240760416039372
0.023230166
0.023759599761907887
0.02369791084482974iso = chemicaldf[!, "isoproterenol 100nM Mean"]
iso_error = chemicaldf[!, "isoproterenol 100nM SD"] ./ sqrt.(chemicaldf[!, "isoproterenol 100nM N"])42-element Vector{Float64}:
0.01906411500114547
0.019397124616823788
0.019533446274478245
0.019307032321568045
0.0188119595
0.019208707594448062
0.020659484720981783
0.022823236115241556
0.02568418993766601
0.02954342161034184
⋮
0.022059148111952916
0.020698453917127702
0.020674867906488113
0.019922601239830914
0.019312468873824668
0.019367967435545023
0.018689615199686285
0.01921783399052236
0.01872515441384824plot(ts, ctl, yerr=ctl_error, lab="Control", color=:blue, markerstrokecolor=:blue)
plot!(ts, iso, yerr=iso_error, lab="ISO 100nM", color=:red, markerstrokecolor=:red)
plot!(xlabel="Time (sec.)", ylabel="CaMKII activity (A.U.)")
savefig("iso-exp.pdf")"/home/runner/work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/iso-exp.pdf"This notebook was generated using Literate.jl.