Practical introduction to Julia for modelling and data analysis in biodiversity and earth sciences

This repository contains materials for the WSL Julia Workshop 2023 Practical introduction to Julia for modelling and data analysis in biodiversity and earth sciences, held on the 24th and 27th of March 2023 at WSL Birmensdorf. It should contain useful resources and guidelines to curious ecologists and glaciologists who want to get an overview or get started with the Julia language. It also contains ideas of research projects related to biodiversity and earth sciences, to be conducted with Julia.

Content

The repository is organized by days and sessions. Please refer to the Program section to navigate within the repo.

Requirements

To follow the workshop materials, you need to have the following software installed on your computer:

• Julia
• Jupyter

Additionally, we recommend to use

• VSCode

as an IDE, together with the Julia extension.

Please refer to the installation instructions for further information on how to proceed.

Usage

To use the workshop materials, clone this repository to your local machine:

git clone https://github.com/vboussange/WSLJuliaWorkshop2023.git

Program

How you should read this program

• 🎤 : Talk
• 💻: Hands-on exercises
• 🎤💻: Interactive session

Day 1: Introduction to the Language, hands on exercises

8:50 Arrival at Englersaal, WSL (ask at the reception if you don't
know where that is)

Morning session 1

9:00 - 10:30

• 🎤 Greetings to the Workshop (@Mauro and @Victor) 9:00-9:10
• 🎤 Overview of the Julia programming language (@Mauro) 9:10-9:30
• 🎤💻 Practical: your first lines of Julia code (@Mauro) 9:30-10:30
  • Basic syntax and data types
  • Control flow and conditional statements

Coffee break

10:30 - 11:00

Morning session 2

11-12:30

• 🎤 Why I like Julia (@Victor) 11:00-11:15

• Package and project management (@Victor) 11:15-11:45

  • 💻🎤 Introduction to Pkg.jl
  • 💻Exercise: activate an environment and run the associated script
  • 💻Exercise: Develop your first Julia project - Part 1

• 💻🎤 VS code workflow and remote development (@Victor) 11:45-12:30

  • VSCode editor
  • Remote development

Lunch

12:30 - 13:30

Afternoon session 3

13:30 - 15:00

• 🎤 Overview of the ecosystem (@Mauro) 13:30-13:45

• 🎤 💻 DataFrames, broadcasting, loading CSV (@Victor) 13:45-14:05

• 💻 Hands-on exercises 14:05-14:30

• 🎤 💻 Plotting and visualisation (@Mauro) 14:30-14:45

• 💻 Hands-on exercises continued 14:45-15:00

Coffee break

15:00 - 15:30

Afternoon session 4

• 🎤 Why I like Julia (@Ludovic) 15:30-15:40
• 🎤 💻 Saving and loading data in Julia (@Mauro) -15:40-15:55
• 💻 Coding the game of life 15:55-17:00

🍻 Apéro

17:00-🌙

Day 2: Project-oriented day

The goal of this second-day workshop is to provide participants with an opportunity to deepen their knowledge of the Julia programming language through biodiversity and glaciology-related projects.

Morning session 1

• 🎤 💻 Geospatial data handling (@Mauro) 9:00-9:30

  • Hands-on exercises

• 🎤 💻 Performant Julia code and profiling (@Mauro) 9:30-10:00

  • Introduction
  • Hands-on exercises

• 🎤 💻 Parallel computing (@Victor) 10:00-10:30

  • Multithreading
  • Multiprocessing
  • Exercise: Parallelizing the Game of Life

Coffee break

10:30-11:00

Morning session 2

• 💻🎤Julia projects managements 11:00-11:30

  • 💻Exercise: Develop your first Julia project - Part 2

• 🎤 Interface with Python, R, MATLAB (@Victor) 11:30-12:00

• 🎤 Track Introductions (@Victor and @Mauro) 12:00-12:30

  • Biodiversity track
  • Glaciology track

Lunch

Afternoon session 3

• 💻 Project session 13:30-15:00

Coffee break

15:00-15:30

Afternoon session 4

• 🎤 Why I like Julia (@Ivan) 15:30-15:40

• 💻 Project session 15:40-16:30

• 🎤 Wrap-up and feedback 16:30 - 17:00

Projects

Biodiversity track

• Deep learning-based Species Distribution Model
• Constructing a benchmark of PiecewiseInference.jl against ApproxBayes.jl and Turing.jl
• Time series modelling

Glaciology track

• Subglacial water routing

• Ice thickness estimation

Additional resources

• Julia official list of tutorials
• Introduction to Julia, JuliaCon 2022, and the YouTube video (3 hours)
• Introductory Julia tutorial by Martin D. Maas
• Julia Workshop for Data Science

Acknowledgments

The workshop materials are based on numerous resources, which have been indicated in the different sections.

We thank WSL Biodiversity center, the Ecosystem and Landscape Evolution and The Laboratory of Hydraulics, Hydrology and Glaciology for supporting and funding this workshop.

Contact

If you have any questions or feedback, feel free to contact the main authors of this workshop, @vboussange and @mauro3. You can also create a pull request.