Warning

This tutorial is currently out-of-date. I am planning to update the tutorial in the near future.

ODE Modelling and Parameter Estimation with Julia

This repository contains sample files explaining the basics of Julia, required to get started with ODE modelling, as well as some more advanced tutorials on simulating systems of ordinary differential equations, performing sensitivity analysis, parameter estimation and parameter identifiability analysis. In short, this repository contains all basic components needed to get started with using Julia.

Getting Started with Julia

To start using Julia, you can download the latest version from julialang.org to be able to start using it. To be able to use it in VS Code, you also require the Julia VS Code extension.

The REPL

The command line in Julia is called the REPL (Read-Eval-Print-Loop). When opening Julia, this is what launches. From here, we can execute julia code, install packages, manage projects or run code files. The output of julia code will be printed, unless ended with a semi-colon (;). For example, the following code will print the value '3'

julia> 1 + 2

The Julia package manager (Pkg)

Installing packages happens through Pkg, the julia package manager. This also includes functionality for environments. When opening Julia, we can instantiate the package manager by pressing "]". We can press backspace to return to the regular Julia REPL. After activating Pkg, you can install a package by typing add <package name>. The convenient plotting package Plots.jl can be installed using

pkg> add Plots

This will install the Plots library in the global environment. To create a new environment, use

pkg> activate <.path/to/working/directory>

Once this has been activated, you can add packages in a similar way. When you start adding packages, notice that a Project.toml file and sometimes a Manifest.toml file will be created. These files contain the project dependencies and allow others to easily set up an environment with the same project dependencies as yours using

pkg> activate <.path/to/working/directory>
pkg> instantiate

In a similar way, you can use the Project.toml and Manifest.toml files in this project to set up the right environment for running all code. When starting Julia from the project directory, you can use pkg> activate . to activate the current working directory as a new environment. After activating the right environment for this tutorial, you can get started with the first notebook.