From 3ee744e84efaecc2e7600f892e878b5eca5ec991 Mon Sep 17 00:00:00 2001 From: Steven Shao-Ting Chiu Date: Mon, 18 Oct 2021 20:46:09 +0800 Subject: [PATCH] update --- ExpressionLevel.ipynb | 2 +- ExpressionLevelEffect.ipynb | 211 ++ .../Project.toml | 4 + .../README.md | 0 .../result/Bmh_0.001x_obs_Rtg1_n.pdf | Bin .../result/Bmh_0.001x_obs_Rtg3_n.pdf | Bin .../result/Bmh_0.01x_obs_Rtg1_n.pdf | Bin .../result/Bmh_0.01x_obs_Rtg3_n.pdf | Bin .../result/Bmh_0.1x_obs_Rtg1_n.pdf | Bin .../result/Bmh_0.1x_obs_Rtg3_n.pdf | Bin .../result/Bmh_0.2x_obs_Rtg1_n.pdf | Bin .../result/Bmh_0.2x_obs_Rtg3_n.pdf | Bin .../result/Bmh_0.3x_obs_Rtg1_n.pdf | Bin .../result/Bmh_0.3x_obs_Rtg3_n.pdf | Bin .../result/Bmh_0.4x_obs_Rtg1_n.pdf | Bin .../result/Bmh_0.4x_obs_Rtg3_n.pdf | Bin .../result/Bmh_0.5x_obs_Rtg1_n.pdf | Bin .../result/Bmh_0.5x_obs_Rtg3_n.pdf | Bin .../result/Bmh_0.6x_obs_Rtg1_n.pdf | Bin .../result/Bmh_0.6x_obs_Rtg3_n.pdf | Bin .../result/Bmh_0.7x_obs_Rtg1_n.pdf | Bin 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a/ExpressionLevel.ipynb +++ b/ExpressionLevel.ipynb @@ -147,7 +147,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Julia 1.6.1", + "display_name": "Julia 1.6.2", "language": "julia", "name": "julia-1.6" }, diff --git a/ExpressionLevelEffect.ipynb b/ExpressionLevelEffect.ipynb new file mode 100644 index 0000000..24e679f --- /dev/null +++ b/ExpressionLevelEffect.ipynb @@ -0,0 +1,211 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "0db6e64e-de69-4738-89a6-a987e3749be8", + "metadata": {}, + "outputs": [], + "source": [ + "using Pkg" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3dc2fbee-8dc0-4ffe-a17a-43d87578507a", + "metadata": {}, + "outputs": [], + "source": [ + "Pkg.activate(\"ExpressionLevelEffect\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b69ddf39-bdf0-44cb-922e-734a44f23dc8", + "metadata": {}, + "outputs": [], + "source": [ + "@time Pkg.instantiate()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "0137d189-11ce-4172-903f-4aa446c78171", + "metadata": {}, + "outputs": [], + "source": [ + "using Revise, FrequencyResponse, DifferentialEquations, LabelledArrays, Plots, ProgressMeter, Distributed\n", + "import RetroSignalModel as rs" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "fb35f107-6c3c-4913-ba68-506a66e07eea", + "metadata": {}, + "outputs": [], + "source": [ + "include(\"ExpressionLevelEffect/script/utils.jl\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2acf00dc-b69f-49b9-836b-cbf542382d1a", + "metadata": {}, + "outputs": [], + "source": [ + "# Load librarys to workers\n", + "#addprocs(length(Sys.cpu_info()) - nprocs() - 1, exeflags=\"--project=$(Base.active_project())\")\n", + "#@everywhere begin \n", + " using Revise, FrequencyResponse, DifferentialEquations, LabelledArrays, Plots, ProgressMeter\n", + " import RetroSignalModel as rs\n", + "#end\n", + "\n", + "#@everywhere begin \n", + "\n", + "\n", + " # Load Model \n", + " i_sol_PLACE_HOLDER=1\n", + " RTGm = rs.rtgM4(i_sol_PLACE_HOLDER)\n", + " param= (; u=RTGm.u, p=RTGm.p);\n", + "\n", + " # Dynamical Signal\n", + " dynmodel = DynModel(\n", + " model = RTGm.model,\n", + " u = param.u,\n", + " p = param.p,\n", + " solver= Rosenbrock23(),\n", + " signal_func = PosSine(ω=0.05,θ=(3/2)*π, amp=1),\n", + " input_i = 1,\n", + " tspan=(0.,500.),\n", + " init_ss = true # Get steady state\n", + " );\n", + "\n", + " sol = solve(dynmodel;tmax=1.);\n", + "\n", + "\n", + " function sim_square(RTGm, levels)\n", + " dynmodel = DynModel(\n", + " model = RTGm.model,\n", + " u = rs.init_u(RTGm; expLevels=levels),\n", + " p = RTGm.p,\n", + " solver= Rosenbrock23(),\n", + " signal_func= SquarePulse(\n", + " t_str = 125.,\n", + " t_end = 375,\n", + " amp_l =0.,\n", + " amp_h = 1.),\n", + " input_i = 1,\n", + " tspan=(0.,500.),\n", + " init_ss = true # Get steady state\n", + " );\n", + " sol = solve(dynmodel;tmax=1.);\n", + " return sol\n", + " end\n", + "\n", + " function mut_tuple(tup, i, mul)\n", + " vs = NamedTuple{tuple(i)}(tuple(tup[i]*mul))\n", + " return LVector(merge(tup, vs))\n", + " end\n", + "\n", + " \"\"\"\n", + " pr: protein to change\n", + " ch: change fold\n", + " obs: observe protein\n", + " \"\"\"\n", + " function ch_cmp(pr, ch, obs;i = i_sol_PLACE_HOLDER)\n", + " RTGm = rs.rtgM4(i)\n", + " levels =rs.getExpLevels(;condition=rs.DefaultCondition)\n", + "\n", + " #simulation\n", + " sol = sim_square(RTGm, levels)\n", + " sol2 = sim_square(RTGm, mut_tuple(levels, pr, ch)) \n", + "\n", + "\n", + " p = Plots.plot(sol.t,total_conc(sol, RTGm, obs), label=\"Control\")\n", + " Plots.plot!(p, sol2.t,total_conc(sol2, RTGm, obs), label=string(pr,\":\",ch,\"x\"))\n", + "\n", + " Plots.xlabel!(p, \"time\")\n", + " Plots.ylabel!(p, \"Concentration ($(obs))\")\n", + " return p\n", + " end\n", + "\n", + " function ch_cmp!(p, pr, ch, obs;i = i_sol_PLACE_HOLDER, plot_control=false)\n", + " RTGm = rs.rtgM4(i)\n", + " levels =rs.getExpLevels(;condition=rs.DefaultCondition)\n", + "\n", + " #simulation\n", + " sol2 = sim_square(RTGm, mut_tuple(levels, pr, ch)) \n", + "\n", + "\n", + " if plot_control \n", + " sol = sim_square(RTGm, levels)\n", + " Plots.plot!(p, sol.t,total_conc(sol, RTGm, obs), label=\"Control\") \n", + " end\n", + "\n", + " Plots.plot!(p, sol2.t,total_conc(sol2, RTGm, obs), label=string(pr,\":\",ch,\"x\"))\n", + "\n", + " Plots.xlabel!(p, \"time\")\n", + " Plots.ylabel!(p, \"Concentration ($(obs))\")\n", + " return p\n", + " end\n", + "\n", + " \"\"\"\n", + " ob: name of observe protein; chs: list of changes\n", + " \"\"\"\n", + " function simulation(ob, pr, chs)\n", + " plot_control = false\n", + " p_ = Plots.plot()\n", + " for c in chs \n", + " if plot_control == false \n", + " ch_cmp!(p_, pr, c, ob;plot_control=true)\n", + " plot_control = true\n", + " end\n", + " ch_cmp!(p_, pr, c, ob;plot_control=false) \n", + " end\n", + " name = string(pr,\"_\",\"foldChange\" ,\"_\",\"obs_\",ob)\n", + " @show name\n", + " Plots.savefig(p_, joinpath(dirname(@__DIR__),\"result\",\"$(name).pdf\"))\n", + " p_ = nothing\n", + " end\n", + "#end \n", + "\n", + "levels =rs.getExpLevels(;condition=rs.DefaultCondition)\n", + "prs = keys(levels)\n", + "obs = [:Rtg1_n, :Rtg3_n]\n", + "chs = [0.001,0.01,0.1,0.2,0.5,1.,2.,4. ,8., 16.,50.,100.]\n", + "\n", + "sims = [(b,pr,chs) for b in obs for pr in prs]\n", + "\n", + "#@showprogress map(x->simulation(x...), sims)\n", + "@showprogress for sim in sims \n", + " simulation(sim...)\n", + "end" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1164fbba-b9a8-4f92-a5fa-b481962f885f", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Julia 1.6.2", + "language": "julia", + "name": "julia-1.6" + }, + "language_info": { + "name": "" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/PlottingMakie/Project.toml b/ExpressionLevelEffect/Project.toml similarity index 75% rename from PlottingMakie/Project.toml rename to ExpressionLevelEffect/Project.toml index fc61ea5..440a340 100755 --- a/PlottingMakie/Project.toml +++ b/ExpressionLevelEffect/Project.toml @@ -4,9 +4,13 @@ authors = ["stevengogogo "] version = "0.1.0" [deps] +Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83" +Dierckx = "39dd38d3-220a-591b-8e3c-4c3a8c710a94" DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" FrequencyResponse = "23be90ff-b906-42a4-9508-8c19908ecbef" +Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" +Optim = "429524aa-4258-5aef-a3af-852621145aeb" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca" PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee" diff --git a/PlottingMakie/README.md b/ExpressionLevelEffect/README.md similarity index 100% rename from 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z3;}n2fQwK+;{n?OzytFu46TlSg&}^UkCzt$>@$AB [similar(collect(i)) for i in paramSpace]) +concs = (;A0, B0, P0) +for k in [:A0,:B0,:P0] + for i in eachindex(paramSpace[k]) + conT = merge(concs, NamedTuple{(k,)}((paramSpace[k][i],))) + IC50[k][i] = findIC50(conT...) + end +end + +for k in [:n_s] + for i in eachindex(paramSpace[k]) + conT = merge(psR, NamedTuple{(k,)}((paramSpace[k][i],))) + IC50[k][i] = findIC50(A0,B0,P0;psR=conT) + end +end + + +# Plot +figT, axs = plt.subplots(2,2, figsize=(11,11)) +for (i,k) in enumerate(keys(IC50)) + axs[i].plot(paramSpace[k], IC50[k]) + k ∈ keys(alias) ? k = alias[k] : nothing + axs[i].set_xlabel(string("Expression level of ",k)) + axs[i].set_ylabel("IC\$_{50}\$ of s on BmhMks inhibition") +end +axs[end].set_xlabel("n\$_s\$") +plt.display_figs() +figT.savefig(joinpath(dirname(@__DIR__),"result", "Thrshold_Bmh.pdf")) + + + +# Simulation +s_ic50 = findIC50(A0, B0, P0; IC50_Bmh = ps.k13ID, psR=psR) +S = 0.1:0.01:1 +fig, ax = plt.subplots(2,2, figsize=(11,11)) +ax[1].plot(S, P.(S), label="Mks") +ax[2].plot(S, PA.(S), label="Rtg2Mks") +ax[3].plot(S, PB.(S), label="BmhMks") +ax[4].plot(S, A.(S), label="Rtg2_act") +#ax[5].plot(S, A_.(S), label="Rtg2_ina") +#ax[6].plot(S, A_.(S) .+ PA.(S) .+ A.(S), label="Rtg2_total") +#ax[7].plot(S, P.(S) .+ PA.(S) .+ PB.(S), label="Mks_total") +ax[3].axhline(ps.k13ID, xmin=0,xmax=s_ic50-0.01,color="black", linestyle="--") +ax[3].axvline(s_ic50, ymin=0,ymax=PB(s_ic50)/200,color="black", linestyle="--") +ax[3].text(0-0.1, PB(s_ic50)-5, "K\$^{13}_{DI}\$") +ax[3].text(s_ic50-0.05, -30, "IC\$_{50}\$") + +[a.legend(loc="upper right") for a in ax] +[a.xaxis.set_ticks([0,1]) for a in ax] +[a.set_xlabel("Mitochondrial Damage (\$s\$, AU)") for a in ax] +[a.set_ylabel("Concentration (AU)") for a in ax] +plt.display_figs() +fig.savefig(joinpath(dirname(@__DIR__),"result", "analytical_Rtg2.pdf")) \ No newline at end of file diff --git a/PlottingMakie/script/conc_adjust_stationary.jl b/ExpressionLevelEffect/script/conc_adjust_stationary.jl similarity index 100% rename from PlottingMakie/script/conc_adjust_stationary.jl rename to ExpressionLevelEffect/script/conc_adjust_stationary.jl diff --git a/PlottingMakie/script/concentration_adjust_square_response.jl b/ExpressionLevelEffect/script/concentration_adjust_square_response.jl similarity index 100% rename from PlottingMakie/script/concentration_adjust_square_response.jl rename to ExpressionLevelEffect/script/concentration_adjust_square_response.jl diff --git a/PlottingMakie/script/utils.jl b/ExpressionLevelEffect/script/utils.jl similarity index 100% rename from PlottingMakie/script/utils.jl rename to ExpressionLevelEffect/script/utils.jl diff --git a/PlottingMakie/src/PlottingMakie.jl b/ExpressionLevelEffect/src/PlottingMakie.jl similarity index 100% rename from PlottingMakie/src/PlottingMakie.jl rename to ExpressionLevelEffect/src/PlottingMakie.jl diff --git a/PlottingMakie/test/output/heatmap.svg b/ExpressionLevelEffect/test/output/heatmap.svg similarity index 100% rename from PlottingMakie/test/output/heatmap.svg rename to ExpressionLevelEffect/test/output/heatmap.svg diff --git a/PlottingMakie/test/plot_heatmap.jl b/ExpressionLevelEffect/test/plot_heatmap.jl similarity index 100% rename from PlottingMakie/test/plot_heatmap.jl rename to ExpressionLevelEffect/test/plot_heatmap.jl diff --git a/PlottingMakie/test/runtests.jl b/ExpressionLevelEffect/test/runtests.jl similarity index 100% rename from PlottingMakie/test/runtests.jl rename to ExpressionLevelEffect/test/runtests.jl diff --git a/PlottingMakie/test/test_MakieTeX.jl b/ExpressionLevelEffect/test/test_MakieTeX.jl similarity index 100% rename from PlottingMakie/test/test_MakieTeX.jl rename to ExpressionLevelEffect/test/test_MakieTeX.jl diff --git a/FrequencyResponse.ipynb b/FrequencyResponse.ipynb index 2e7bb40..7109ef2 100755 --- a/FrequencyResponse.ipynb +++ b/FrequencyResponse.ipynb @@ -24,8 +24,7 @@ ], "source": [ "using Pkg\n", - "Pkg.activate(\"FrequencyResponse\")\n", - "Pkg.instantiate()" + "Pkg.activate(\"FrequencyResponse\")" ] }, { @@ -1410,7 +1409,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Julia 1.6.1", + "display_name": "Julia 1.6.2", "language": "julia", "name": "julia-1.6" }, @@ -1418,7 +1417,7 @@ "file_extension": ".jl", "mimetype": "application/julia", "name": "julia", - "version": "1.6.1" + "version": "1.6.2" } }, "nbformat": 4, diff --git a/PlottingMakie/Manifest.toml b/PlottingMakie/Manifest.toml deleted file mode 100755 index f426856..0000000 --- a/PlottingMakie/Manifest.toml +++ /dev/null @@ -1,1862 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -[[AbstractAlgebra]] -deps = ["InteractiveUtils", "LinearAlgebra", "Markdown", "Random", "RandomExtensions", "SparseArrays", "Test"] -git-tree-sha1 = "7df2949bfd757e426897a4b579fbd5dc776ff8c9" -uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d" -version = "0.12.0" - -[[AbstractFFTs]] -deps = 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+[![CI](https://github.com/stevengogogo/MitoChannelAnalysis/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/stevengogogo/MitoChannelAnalysis/actions/workflows/ci.yml) [![docs](https://github.com/stevengogogo/MitoChannelAnalysis/actions/workflows/docs.yml/badge.svg?branch=main)](https://github.com/stevengogogo/MitoChannelAnalysis/actions/workflows/docs.yml) + Graphical Abstract -> Codes, data and notebooks for the manuscript titled "Mathematical Modeling and Analysis of Mitochondrial Retrograde Signaling Dynamics" +Codes, data and notebooks for the manuscript titled "Mathematical Modeling and Analysis of Mitochondrial Retrograde Signaling Dynamics" ---- ## Notebooks @@ -15,21 +16,12 @@ |[SteadyStates.ipynb](SteadyStates.ipynb)|[SteadyStates/](SteadyStates/)|Steady state solutions under multiple knockout conditions and visualization| -## Simulations - -|Folder|Description| -|---|---| -|[Analysis on multiple solutions](FrequencyResponse/notebooks)|These notebooks are generated by other solutions. The primary solution is used in [FrequencyResponse.ipynb](FrequencyResponse.ipynb). Noted that the save error shown in each notebook is expected because these notebooks are directly converted by [run_sol.jl](run_sol.jl)| -|[Effects of RTG concentrations](PlottingMakie/result/)|Concentrations of RTG proteins are manipulated to investigate the effect of expression level on signaling| - ---- - ## Toolbox Developed for this Research - Ultrasensitivity Analysis: https://github.com/stevengogogo/EstimHill.jl - Steady State Explorer: https://github.com/stevengogogo/FindSteadyStates.jl -- API of Mathematical model of mitochondiral retrograde signaling: https://github.com/stevengogogo/RetroSignalModel.jl + ## Environment @@ -172,8 +164,4 @@ Select the kernel with the name `Julia 8 Threads` to initiate Julia with multipl ## Analysis of multiple solutions -10 out of 270+ solutions are plotted under the jupyter notebooks at [result/](FrequencyResponse/notebooks). Noted that these notebooks are modified from [FrequencyResponse.ipynb](FrequencyResponse.ipynb) by [run_sol.jl](run_sol.jl). Some minor errors including save path errors can be ignored when viewing these files. - -## Analysis on levels of concentrations - -Effect of RTG concentrations are simulated and displayed at [result/](PlottingMakie/result/). +10 out of 270+ solutions are plotted under the jupyter notebooks at [result/](PlottingMakie/result/). Noted that these notebooks are modified from [FrequencyResponse.ipynb](FrequencyResponse.ipynb) by [run_sol.jl](run_sol.jl). Some minor errors including save path errors can be ignored when viewing these files. \ No newline at end of file diff --git a/RobustAnalysis.ipynb b/RobustAnalysis.ipynb index b2bd51b..2d0fbfa 100755 --- a/RobustAnalysis.ipynb +++ b/RobustAnalysis.ipynb @@ -973,7 +973,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Julia 1.6.1", + "display_name": "Julia 1.6.2", "language": "julia", "name": "julia-1.6" }, diff --git a/SteadyStates.ipynb b/SteadyStates.ipynb index c0cee78..4adec5f 100755 --- a/SteadyStates.ipynb +++ b/SteadyStates.ipynb @@ -1629,7 +1629,7 @@ ], "metadata": { "kernelspec": { - "display_name": "Julia 1.6.1", + "display_name": "Julia 1.6.2", "language": "julia", "name": "julia-1.6" },