using Model
using Model: second, μM
using CSV
using DataFrames
using DiffEqCallbacks
using DifferentialEquations
using ModelingToolkit
using OrdinaryDiffEqSDIRK
using Plots
using SteadyStateDiffEq
import Dates
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 = KenCarp4()Build system: 0.000023 seconds (38 allocations: 1.766 KiB)
Build problem: 35.632040 seconds (56.51 M allocations: 2.769 GiB, 4.92% gc time, 99.41% compilation time: 11% of which was recompilation)
KenCarp4(; linsolve = nothing, nlsolve = OrdinaryDiffEqNonlinearSolve.NLNewton{Rational{Int64}, Rational{Int64}, Rational{Int64}, Nothing}(1//100, 10, 1//5, 1//5, false, true, nothing), smooth_est = true, extrapolant = linear, step_limiter! = trivial_limiter!, autodiff = ADTypes.AutoForwardDiff(), concrete_jac = nothing,)Without isoproterenol¶
@unpack Istim = sys
callback = build_stim_callbacks(Istim, stimend; period=1second, starttime=stimstart)
@time sol = solve(prob, alg; callback) 7.808646 seconds (15.47 M allocations: 710.800 MiB, 9.53% gc time, 80.08% compilation time)
retcode: Success
Interpolation: 3rd order Hermite
t: 5071-element Vector{Float64}:
0.0
0.01933312407287676
0.0714686572016017
0.15042606626184363
0.29780952882673073
0.6163053593874049
1.4062585982334244
3.0222276331880495
5.675944491235782
9.164284961703544
⋮
164742.3367775606
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178622.59509658653
183574.34039534253
189355.59670978156
195136.8530242206
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205000.0
u: 5071-element Vector{Vector{Float64}}:
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⋮
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[790.9941271049524, 790.6176783481759, 0.0021170124866557124, 0.20947486655550257, 0.0003140198433466279, 0.001152246333713192, 0.0015918209660109772, 0.0024640269420278665, 0.0015566322988858803, 0.9997374292442891 … 0.13572847131653346, 0.1357290342767823, 0.13572960882333873, 0.13573019560144042, 0.13573079529795593, 0.13571180271929217, 0.13573140864479719, 151293.43169010038, 13499.262478973647, -70.22397787237131]
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[788.5778078111124, 788.2283490227638, 0.0019699994733617422, 0.2039271817569036, 0.00032844856167276923, 0.0011908713425627273, 0.001617235274869156, 0.0025033584978238453, 0.0016050306341047682, 0.9997256719290667 … 0.13424535688608208, 0.1342458304068511, 0.13424631344138124, 0.13424680652500998, 0.13424731022761513, 0.13423120896823562, 0.13424782515644587, 151408.69441764394, 13384.371923666613, -70.01085102197581]
[787.9712261432263, 787.6283572542015, 0.001934079202048638, 0.2024572777939682, 0.0003324313834955821, 0.0012014532148224867, 0.0016241216514637185, 0.0025140158274476613, 0.001618263948960182, 0.9997222356376478 … 0.13386446660473975, 0.13386492101007397, 0.13386538451818478, 0.13386585764195855, 0.13386634092737337, 0.13385087489629968, 0.13386683495621152, 151439.0132648695, 13354.147738794918, -69.95367155962873]
[787.5860108871439, 787.2472784243223, 0.0019115310549257815, 0.2015108526302152, 0.0003350326785965431, 0.0012083464123315256, 0.0016285902951905585, 0.0025209314496608985, 0.001626878333047969, 0.9997199891845507 … 0.13362181027691844, 0.13362225330701835, 0.1336227052024094, 0.13362316646284353, 0.1336236376203171, 0.13360855345773046, 0.13362411924171383, 151458.4883330062, 13334.73292957433, -69.91669512629275]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), title="Active CaMKII", label=false, ylabel="Active CaMKII fraction", xlabel="Time (s)")
0.1uM isoproterenol¶
prob2 = remake(prob, p=[sys.ISO => 0.1μM])
@time sol2 = solve(prob2, alg; callback) 1.252889 seconds (53.28 k allocations: 11.678 MiB, 4.17% gc time)
retcode: Success
Interpolation: 3rd order Hermite
t: 5547-element Vector{Float64}:
0.0
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0.07146682621423228
0.15042564972415
0.29782293916361985
0.6165636739497988
1.408588299017812
3.0488198638071347
5.761261029809148
9.352615992565255
⋮
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176658.48311073577
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u: 5547-element Vector{Vector{Float64}}:
[830.0, 830.0, 0.0026, 0.07192, 0.07831, 0.26081, 0.00977, 0.00188, 0.09243, 0.22156 … 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 0.12113, 150952.75035000002, 13838.37602, -68.79268]
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⋮
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[925.5608015584186, 924.0991098442189, 0.006984592969803034, 0.20998370562656749, 0.0003128171265859714, 0.0011489820799900103, 0.0015898751568157923, 0.002461038908187206, 0.0015527087515645709, 0.9997393340452287 … 0.12447263010060713, 0.12447251792780512, 0.12447239420740959, 0.12447225851549153, 0.12447211040077674, 0.1244708734593299, 0.12447194938240429, 151116.02435907428, 13666.9995680837, -70.24031660650789]
[925.7498484275657, 924.3054928506815, 0.006900431956213579, 0.20822732643522748, 0.0003172879238582698, 0.0011609793893685078, 0.0015978051310838758, 0.0024733120865345383, 0.0015677153591447364, 0.9997355594538301 … 0.12402184654872145, 0.12402174576308671, 0.12402163405251154, 0.12402151101850217, 0.12402137623686019, 0.12401996633285939, 0.12402122925557554, 151151.29417403205, 13631.777078587154, -70.17336915691263]
[925.9261846296321, 924.4989655513078, 0.006817336151410563, 0.20647106422713263, 0.0003218213123726305, 0.0011731219957364825, 0.0016058230219464411, 0.002485722002086028, 0.0015829575536285868, 0.9997316692333209 … 0.12357740428651101, 0.12357731402494856, 0.12357721343039028, 0.12357710212838978, 0.12357697972034751, 0.12357541884962454, 0.12357684578153069, 151186.4220021359, 13596.696846749532, -70.1060120689347]
[926.1155863280125, 924.7079581547636, 0.006722457670835329, 0.20443722934489025, 0.0003271987657664071, 0.0011874703269760104, 0.0016152210566082196, 0.002500266893579212, 0.0016009094234706676, 0.9997270422823145 … 0.12307037305437081, 0.12307029385400599, 0.12307020496863484, 0.1230701060499356, 0.12306999672711859, 0.12306829108490717, 0.12306987660508434, 151226.9338340303, 13556.240411303173, -70.02748874358929]
[926.2352591152539, 924.8407294016781, 0.006659069100116455, 0.20306036016812115, 0.0003308599799486048, 0.0011972653727253305, 0.001621655008863868, 0.0025102244732195496, 0.0016132530045805307, 0.9997238617260228 … 0.12273177024270683, 0.12273169796506293, 0.12273161642166922, 0.1227315252810409, 0.1227314241903118, 0.12272963512736192, 0.12273131277348168, 151254.2598687407, 13528.952010783207, -69.97399851918148]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")
savefig("iso-caT.png")"/home/github/actions-runner-2/_work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/iso-caT.png"Maximal and minimal calcium concentrations in calcium transients.
ca_ctl = sol(tspan[1]:1:tspan[2], idxs=sys.Cai_mean)
println(extrema(ca_ctl))(0.23518492665182758, 0.5899267472743499)
ca_iso = sol2(tspan[1]:1:tspan[2], idxs=sys.Cai_mean)
println(extrema(ca_iso))(0.1913450036716734, 0.7276881462895101)
i = (sys.t / 1000, sys.CaMKAct)
plot(sol, idxs=i, title="", lab="ISO (-)")
plot!(sol2, idxs=i, lab="ISO (0.1uM)", ylabel="Active CaMKII fraction", xlabel="Time (s)")
savefig("iso-camkact.pdf")
savefig("iso-camkact.png")"/home/github/actions-runner-2/_work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/iso-camkact.png"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 (s)", ylabel="Voltage (mV)"; tspan)
savefig("iso-ap.pdf")
savefig("iso-ap.png")"/home/github/actions-runner-2/_work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/iso-ap.png"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 (s)", ylabel="CaMKII activity (A.U.)")
savefig("iso-exp.pdf")
savefig("iso-exp.png")"/home/github/actions-runner-2/_work/camkii-cardiomyocyte-model/camkii-cardiomyocyte-model/docs/iso-exp.png"This notebook was generated using Literate.jl.