Mitochodria Retrograde signalling ODE model

Codes, data and notebooks for the manuscript titled "Mathematical Modeling and Analysis of Mitochondrial Retrograde Signaling Dynamics"

Forked from Steven's results: https://github.com/ntumitolab/MitoRetroDynamics

Requirements

1. Jupyter lab
2. Julia (version 1.7+)
3. IJulia

JupyterLab installation

The simulations are executed and displayed via JupyterLab. It is an IDE for literal programming. In this project, Julia kernel is used in Jupyterlab, and extra installation is needed to use Julia with Jupyterlab.

pip3 install jupyterlab

See https://jupyterlab.readthedocs.io/en/stable/getting_started/installation.html for further instruction.

Installing Julia

Julia programming language runtime can be installed in the official website (https://julialang.org/downloads/)

IJulia

IJulia (https://julialang.github.io/IJulia.jl/stable/manual/installation/) is a Julia package for kernel installation for Jupyter.

The installation requires Julia Package manager (Pkg, https://docs.julialang.org/en/v1/stdlib/Pkg/), which is a built-in package in Julia. To install IJulia, one needs to open Julia REPL (Read–eval–print loop) using the following command line.

julia

The Julia REPL begins in the terminal after submitting julia command. The next step is to install IJulia with package manager (Pkg). Copy-paste the following code block to Julia REPL

using Pkg
Pkg.add("IJulia")
Pkg.build("IJulia")

Enabling a multi-threaded kernel

Some notebooks use multithread algorithms to speed up. The multithread process can be set by IJulia in Julia REPL.

using IJulia
IJulia.installkernel("Julia 8 Threads", env=Dict(
    "JULIA_NUM_THREADS" => "8",
))

where JULIA_NUM_THREADS represents number of threads that can be used in the Julia process, and this can not be changed after a Julia process is initiated. Though the number of threads is set as 8, it can be changed and usually depends on the hardware setup.

Set up of simulation environments

Open the project folder with terminal, and then in the Julia REPL prompt

using Pkg
Pkg.activate(".")
Pkg.instantiate()

Run notebooks

IN the Julia REPL prompt

using IJulia
IJulia.jupyterlab(dir=pwd())

Select the kernel with the name Julia 8 Threads to initiate Julia with multiple threads. After successfully initiation, one can see Julia 8 Threads 1.6 located at the top right corner.