Summary and Setup

The best way to learn how to program is to do something useful, so this introduction to Julia is built around a common scientific task: data analysis.

Our real goal isn’t to teach you Julia, but to teach you the fundamental concepts that all programming depends on. We use Julia in our lessons because:

  1. we have to use something for examples;
  2. it’s free, open-source, and designed for high-performance computing;
  3. it is increasingly popular in scientific computing and data analysis; and
  4. it has a growing ecosystem of external packages for diverse tasks.

But the two most important things are to use whatever language your colleagues are using, so you can share your work with them easily, and to use that language well.

We are studying inflammation in patients who have been given a new treatment for arthritis, and need to analyze the first dozen data sets of their daily inflammation. The data sets are stored in CSV format (comma-separated values): each row holds information for a single patient, and the columns represent successive days. The first few rows of our first file look like this:

0,0,1,3,1,2,4,7,8,3,3,3,10,5,7,4,7,7,12,18,6,13,11,11,7,7,4,6,8,8,4,4,5,7,3,4,2,3,0,0
0,1,2,1,2,1,3,2,2,6,10,11,5,9,4,4,7,16,8,6,18,4,12,5,12,7,11,5,11,3,3,5,4,4,5,5,1,1,0,1
0,1,1,3,3,2,6,2,5,9,5,7,4,5,4,15,5,11,9,10,19,14,12,17,7,12,11,7,4,2,10,5,4,2,2,3,2,2,1,1
0,0,2,0,4,2,2,1,6,7,10,7,9,13,8,8,15,10,10,7,17,4,4,7,6,15,6,4,9,11,3,5,6,3,3,4,2,3,2,1
0,1,1,3,3,1,3,5,2,4,4,7,6,5,3,10,8,10,6,17,9,14,9,7,13,9,12,6,7,7,9,6,3,2,2,4,2,0,1,1

We want to:

  1. Calculate the average inflammation per day across all patients.
  2. Plot the result to discuss and share with colleagues.

To do all that, we’ll have to learn a little bit about programming.

Prerequisite

Prerequisites

You need to understand the concepts of files and directories and how to start a Julia interpreter before tackling this lesson. This lesson sometimes references Jupyter Notebook although you can use any Julia interpreter mentioned in the Setup.

Overview

This lesson is designed to be run on a personal computer. All of the software and data used in this lesson are freely available online, and instructions on how to obtain them are provided below.

Install Julia

To get started, download and install Julia for your operating system.

Launch Julia

To start programming in Julia, choose one of the following options:

Option A: Jupyter Notebook

  1. Open a terminal (or Command Prompt on Windows).

  2. Open Julia(Type julia and press Enter) in your terminal and type:

    JULIA 

    using Pkg
Pkg.add("IJulia") 

using IJulia
notebook()

  3. A browser window will open. Click New → Julia to start coding.

Option B: VS Code / Codium

  1. Install VS Code or VSCodium.
  2. Open VS Code and install the Julia extension (search for “Julia” in the Extensions panel).
  3. Open a new file, save it as script.jl, and start writing Julia code.

Option C: Terminal / REPL

  1. Open a terminal (or Command Prompt on Windows).

  2. Type julia and press Enter to open Julia’s interactive mode.

  3. Start typing commands, or run a script with:

    BASH 

    julia myscript.jl

Download

You also need to download some files to follow this lesson:

  1. Download juliainflammation-data.zip.
  2. Create a folder called julia-novice-inflammation on your Desktop.
  3. Move downloaded files to julia-novice-inflammation.
  4. Unzip the files.