IntegratedOscillatorModel.jl

Author onecalfman
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1 Year Ago
Started In
November 2021

IntegratedOscillatorModel.jl

Background

This module was made during my bachelor's thesis. It implements a mathematical model developed the following publication, McKenna et. al 2016. The specific model used here is the same as in Marinelli et. al 2018 The model describes the flux of certain ions and molecules seen in the beta-cell in the human pancreas. This is done by a non linear system of first order differential equations, and it's goal is to get insights about the insulin exocytosis.

I will not explain the specific parameters of the model in this README. Please refer to the above mentioned papers and the comments in the params.jl file.

If you want to gain a broader overview of beta-Cell modeling, I can recommend this paper.

Goals

The goal of this module is to enable easy manipulation of parameters within the model, to obtain insides about its viability and inner workings. Fast calculation was also a concern, so multithreading was implemented as well as helper functions to deal with the arising problems. A novel approach is, to include the simulation of active substances in the model.

Usage

The main function to use, is the simulate function. It accepts a System struct, that has the following structure:

System

@with_kw struct System
    ode_func      :: Function = sys 
    y0            :: AbstractVecOrMat{Float64} = y0
    time          :: Integer = 60
    plot_args     :: Dict = Dict()
    params        :: Dict{String,Any} = deepcopy(params)
    plot_params   :: AbstractVector{Integer} = [1,2,3,4,5,6,7,8]
    change_params :: Dict{String,Number} = Dict()
    meds          :: Vector{Meds} = []
end

The above struct uses the Parameters.jl package.

  • ode_func
    The function, that is used as the ode function. In most cases, this parameter should stay the same.

  • y0
    The starting values. Another set of values (called y0_stat) contains the values to achieve an almost constant solution

  • time
    The simulation time in minutes

  • plot_args
    Extra arguments, that are used in the automatic plot generation

  • params
    The parameter set of the simulation. This will be modified, so copy or deepcopy should be used to mitigate unwanted side effects.

  • plot_params
    The values of the ode system that shall be contained in the generated plot.

    1. V - Membrane potential
    2. N - Potassium
    3. Ca - Calcium
    4. Ca_er - Calcium (endoplasmic reticulum)
    5. Ca_m - Calcium (mitochondria)
    6. ADP
    7. F6P
    8. FBP
  • change_params
    The key value pairs are used to modify some parameters given with the params field.

  • meds
    A list of Activa objects

Activa

Activa represent active substances, that can be added to the system as further behavior modifiers.

@with_kw mutable struct Activa
    # starting time in minutes
    time :: Real
    # duration in inutes
    duration :: Number = Inf
    # dosage
    dose :: Float64
    name :: String = ""
    # will be used in en exponential function to simulate
    # exponential dosage decrease or decline
    fade :: Float64 = 1
    # (dose, current_ode_state) -> Float64
    # This function is used to calculate the effect of a active substance
    func :: Function = id
    # The name of the param, that is modified
    param :: String
end

simulate

The interface to use, is the simulate function. It accepts a Settings object and will run a simulation accordingly. The return value is a tuple, containing an OdeSolution object, a matrix containing the solution and a plot, of the solution.

using IntegratedOscillatorModel
ode_solution, solution_matrix, solution_plot = simulate(System())

It is also possible to simulate different modifications in one command. In this scenario 3 dicts will be returned, containing the solutions, the matrices, and the plots. In addition, a plot, of all solutions, will be returned as the fourth value Because, this function uses the @threads macro to parallelize the operations, the SortedDict has a key for every value, given in the value array.

using IntegratedOscillatorModel
sol_dict, mat_dict, plot_dict, overview_plot = simulate(
    System(
        time = 120
        change_params = Dict(
            "vpdh" => 0.001
        )),
    "Jgk",
    [0.001, 0.05, 0.01]
    )

At last, two keys and two lists can be provided, like in the following example:

using IntegratedOscillatorModel
sol_dict, mat_dict, plot_dict, overview_plot = simulate(
    System(
        time = 120
        change_params = Dict(
            "vpdh" => 0.001
        )),
    "Jgk",
    [0.001, 0.05, 0.01]
    "gca",
    [200, 400, 800]
    )

simulate activa

Four types of activa are currently predefined:

Function Active Substance param
Tolb Tolbuatmid - gkatpbar
Dz Diazoxide + gkatpbar
Glucose Glucose + Jgk
KCl KalciumChloride + vk

Example

using IntegratedOscillatorModel
sol = simulate(System(
        time = 140,
        plot_params = [1,3,6],
        change_params = Dict(
            "vpdh" => 0.001,
            "Jgk" => 0.001,
            "gkca" => 800
        ),
        meds = [
            Tolb(40,  50,   duration = 20),
            Tolb(60,  100,  duration = 20),
            Tolb(80,  200,  duration = 20),
            Tolb(100, 500,  duration = 20),
            Tolb(120, 1000, duration = 20),
        ]
    ),
)

Inner Workings and Hints

Tolerance

Since the simulated ode system is quite fast oscillating, the solver will assume an initial tolerance of abstol = 1e-6 and reltol = 1e-6. If the calculation failed because of a domain error (mostly a failed sqrt(-n)) the tolerances will be decreased by 6 orders of magnitude. If the system can't by solved with a tolerance of 1e-18, the simulations fails and returns nothing.

Medication implementation

A periodic callback is called every 100 steps in the simulation, and the medications are evaluated. An evaluation at every step would be very slow and error-prone.

Reexports

The Plots and LaTeXStrings modules are reexported.

Legacy

I originally designed the module to work with a named tuple of options. This syntax is still accepted, to achieve compatibility with my bachelor's thesis simulations.