BrainSimulation-Workshop

Materials for the Track 4 workshop "Towards translational and mechanistic whole-brain simulations with The Virtual Brain" (FAIR Brain Data Science Bootcamp, 12–13 May 2026).

Repository layout

• slides.qmd — RevealJS workshop slides (root).
• agenda/agenda.qmd — printable workshop agenda (renders to PDF / DOCX).
• notebooks/*.qmd — hands-on session sources (rendered to .ipynb for participants).
• bibliography.bib — shared references for both documents.
• _quarto.yml — project-level Quarto config (bibliography, link defaults).
• pyproject.toml / uv.lock / .python-version — pinned Python environment.
• img/ — logos and figures.

Python environment (uv)

The Python environment is managed with uv. The lockfile and Python pin are committed, so the environment is reproducible across machines.

# one-time, after cloning
uv sync

This reads pyproject.toml + uv.lock and creates a .venv/ with the exact package versions.

To add a new dependency:

uv add <package>          # updates pyproject.toml and uv.lock

Rendering

Quarto (>= 1.8) must be installed separately. Run Quarto through uv run so it picks up the project's .venv Python:

# slides — RevealJS HTML
uv run quarto render slides.qmd
uv run quarto preview slides.qmd      # live reload during editing

# agenda — PDF + DOCX
uv run quarto render agenda/agenda.qmd

# hands-on notebooks — convert qmd → ipynb (no execution)
uv run quarto convert notebooks/1_introduction.qmd
# …or convert all of them at once:
for f in notebooks/*.qmd; do uv run quarto convert "$f"; done

The .qmd files under notebooks/ are the source of truth; the generated .ipynb files are gitignored and produced on demand for the hands-on sessions.

Authoring code on slides

Quarto chunk fences control whether a code block is executed:

• ```{python} — runs and shows code + output
• ```python (plain markdown, no braces) — shows code only, never runs
• ```{python} with #| eval: false — styled like an executable chunk but skipped
• #| echo: false — runs but hides the source
• #| output: false — runs but hides the output