Modelling and Simulation (ModSim)

Course material for Modelling and Simulation of Biosystems (I002445), Bachelor of Bioscience Engineering, Ghent University: course notes, exercise notebooks, examples and the course website.

Launching Pluto

To launch Pluto, either:

• open a terminal in the top level folder, and run julia launch_pluto.jl
• open a Julia terminal in the top level folder, and run include("launch_pluto.jl")

Repository layout

• src/: source of the course website (see website_maintenance.md). Every file in here becomes a page.
• exercises/: the exercise notebooks.
  • exercises/student_notebooks/ is the single source of truth for the exercises handed out to students.
  • exercises/solved_notebooks/ contains the solved versions.
  • src/exercises/*.jl are generated copies for the website; never edit them by hand (see below).
• notebook-checks/: tooling around the notebooks.
  • check_notebooks.jl runs all solved notebooks; executed by CI (.github/workflows/CheckNotebooks.yml).
  • sync_exercises.jl regenerates src/exercises/ from exercises/student_notebooks/; CI runs it with --check and fails when the website copies are out of sync.
• project/: the course project.
• examples/: worked examples used in the lectures.
• The course notes themselves (Typst sources, figures and the notebooks that generate them) live in the private repository ModSim-course-notes; they are not part of this repo.
• pluto-deployment-environment/: the Julia environment used to build the website (Julia 1.12). Keep its Project.toml and Manifest.toml up to date when you add packages to notebooks that are rendered on the website.

Website

All website content lives in src/; the details are in website_maintenance.md.

• A push to main triggers .github/workflows/ExportNotebooks.yml, which builds the site and deploys it to the gh-pages branch (GitHub Pages). Pull requests get a preview under previews/PR<n>.
• To preview locally, run julia develop.jl in the top level folder (or use the VS Code task PlutoPages: run development server).
• Use Julia 1.12, the version the site environment was resolved with. With juliaup: juliaup override set 1.12 inside this folder.

If you need a more in-depth example of the different pages, usage of tags, etc., check out release v2425.1 and run the server on that code. Alternatively, have a look at the original github source of the template or the current website accompanying that repo.