Tutorials

The tutorials below are Jupyter notebooks that walk you through every major NeKo feature, from building your first network to comparing two signalling models.

#	Notebook	Topics covered
1	Network Building	Create a Network, load resources, connect_nodes
2	Add Resources	Extend the interaction universe with custom databases
3	Stepwise Connection	Fine-grained connection strategies
4	Connect Upstream	Link upstream regulators to a seed node set
5	Phosphosite Network	Build a kinase–substrate network from PhosphoSitePlus
6	Ontology	Map nodes to Gene Ontology terms and phenotypes
7	Tissue Mapping	Filter interactions by tissue expression
8	Compare Networks	Diff two networks and highlight differences
9	Recreating Famous Pathways	Reproduce well-known signalling diagrams
10	Import & Complete a Network	Import from SIF / GraphML and fill gaps
11	Network History	Snapshot, branch, and diff network states

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Running the notebooks locally

git clone https://github.com/sysbio-curie/Neko.git
cd Neko
pip install nekomata
jupyter lab notebooks/

Note

Notebooks that download data (e.g., from OmniPath) require internet access and might take a minute on first run while the database is cached locally.