Systems Biology & Julia - Workshop

This is the repository for the Julia for Systems Biology workshop on September 11th 2023.

About the Workshop

The workshop offers an introduction on how the Julia programming language can be used in Systems Biology and provides instructions on how to implement both machine learning and bottom up models in Julia.

Organizers

Shauna O'Donovan	Max de Rooij	Natal van Riel	Balázs Erdős

Workshop Schedule

The current workshop schedule is as follows. It may, however, still be subject to changes.

Time	Description	Contents
10:00 - 10:15	Welcome and Introductions	-
10:15 - 11:15	Getting started with Julia	Julia syntax, types, programming basics
11:15 - 11:30	Coffee break	-
11:30 - 12:30	Machine learning in Julia	Implementing basic ML workflows
12:30 - 13:30	lunch break + networking	-
13:30 - 14:45	Dynamic Models in Julia I	Simulating ODE models in Julia
14:45 - 15:00	Coffee break	-
15:00 - 16:15	Dynamic Models in Julia II	More on ODE models, parameter estimtation, package interoperability
16:15	Closing

Julia Installation and Environment Setup

Here you will find some instructions on how to make sure the code from this repository can run on your computer. The workshop is built to fully work with Julia version 1.9. In this instruction, we will assume you are installing Julia 1.9, but any other version is installed in a similar way.

Installing Julia using the Julia version manager (juliaup) (recommended)

The first step is to install the Julia version manager (juliaup), which enables you to have multiple Julia versions installed on your machine. This step is not mandatory for a properly working version of Julia, but it is useful if you are planning to use Julia for your own projects in the future.

Windows:

Note The winget command may not be available on your machine! In that case, you can download Julia from the Microsoft Store. If your organization prevents use of the Microsoft Store, you can follow the download instructions from https://julialang.org when clicking Download

Open your favorite terminal, or press Win+R, type cmd in the text bar and press 'run'.

winget install julia -s msstore

Linux & MacOS:

From the command line execute

curl -fsSL https://install.julialang.org | sh

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Afterwards, you can restart the terminal environment. You can install a specific version of Julia using

juliaup add <version>

You can list the versions available to you using

juliaup list

We recommend to start with installing the latest stable version, dubbed release by running

juliaup add release

If this is your only Julia version, juliaup will automatically label this as the default version.

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Setting up VSCode

Julia was found to work the best using the VSCode IDE, which you can download here. After downloading and installing VSCode, navigate to the VSCode marketplace, which has the following icon:

Type Julia in the search bar and install the Julia Language Support extension.

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Setting up the workshop environment

After installing Julia, you can either fork this repository to your own Github account and download the code from there, or download the code directly from this repository into a Zip-file by selecting Code -> Download ZIP.

Put the workshop code in a nice folder and open this folder from VSCode.

Now there are two ways to initialize the environment.

1. Use the first code block in the 01-Getting-Started file

Uncomment the first code block in the 01-Getting-Started.ipynb file to automatically set up the environment.

2. Use the VSCode terminal

In case a terminal is not open yet, click Terminal->New Terminal from the top bar and execute

julia

To start the Julia REPL.

Then, press ] to change from Julia to the package manager, which is indicated by >julia changing to >pkg. Then, execute:

activate .

Warning Make sure to remember the dot . at the end of this command.

To activate the workshop environment. Then execute (also from the Pkg terminal)

instantiate

To install all the required packages. You should now be able to run all the notebooks in this workshop environment.

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Troubleshooting

Error opening notebooks in Windows VS Code

In Windows, we noticed that notebooks may sometimes error when trying to open them in Visual Studio Code. This has to do with the path length limit in the Windows filesystem. The easiest fix is to place the repository folder in a directory that is higher up, so the paths will not be too long.

Notes

• The file src/Julia-sysbio-workshop.jl is included only to make sure automated testing is possible. This is necessary, due to the (current) implementation of this functionality in Julia, supporting only automated testing for packages. Therefore, we cleverly disguised this project as a package to get the full automated testing experience. This file has no functional contents otherwise.