Tutorials

• Context-specific metabolic networks from omics
• Single sample intracellular signalling network inference
• Multi-receptor integration with CARNIVAL
• Implementing an alternative network sampler
• Exploring alternative solutions with \(\epsilon\)-perturbation sampling
• Knowledge-primed Neural Networks (KPNNs) for single cell data

Additional Tutorials

• Multi-condition signalling network inference

Running tutorials locally

Each tutorial is self-contained and includes its own pixi.toml. To execute all notebooks via Pixi:

# Run all tutorials (outputs go to build/)
poetry run python docs/tutorials/run_notebooks.py

# Run a single tutorial by folder name
poetry run python docs/tutorials/run_notebooks.py ml

# Rewrite notebooks in place (overwrites original .ipynb files)
poetry run python docs/tutorials/run_notebooks.py ml --rewrite

# Use local CORNETO source instead of the pinned PyPI version
poetry run python docs/tutorials/run_notebooks.py ml --editable-corneto

# Point to a specific CORNETO checkout
poetry run python docs/tutorials/run_notebooks.py ml --editable-corneto --corneto-root /path/to/corneto