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
- Jupyter lab
- Julia (version 1.7+)
- IJulia
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.
Julia programming language runtime can be installed in the official website (https://julialang.org/downloads/)
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")
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.
Open the project folder with terminal, and then in the Julia REPL prompt
using Pkg
Pkg.activate(".")
Pkg.instantiate()
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.