Typical analysis patterns

Most workflows in annnet fall into a small number of patterns.

Multilayer analysis

Use this when layers are part of the scientific model, for example modalities, states, or timepoints.

• Typical flow: define aspects, add layer tuples, add intra-layer and inter-layer edges, then analyze through annnet's multilayer operators or an external backend.
• Read first: Multilayer and multi-aspect graphs.
• Useful API pages: Layers, Graph.
• Notebooks: SBUC, HEK293 multilayer network.

Hyperedges and stoichiometry

Use this when binary edges are too limiting and you need directed hyperedges, weighted memberships, or SBML-style reaction structure.

• Typical flow: import SBML, inspect hyperedges, preserve stoichiometric weights, then analyze or export.
• Read first: Incidence representation.
• Useful API pages: Graph, SBML.
• Notebook: AnnNet Showcase.

Slices and scenario management

Use this when you need multiple contexts in one container, such as train/eval splits, perturbation scenarios, or condition-specific subgraphs.

• Typical flow: define slices, switch the active slice, override per-slice weights or annotations, then compare results.
• Read first: Slices and views.
• Useful API pages: Slices, Views.
• Also useful: Tracking changes.

Interoperability-first analysis

Use this when annnet is the main container and you want to move into other tools without losing structure.

• Typical flow: convert with an.to_nx or an.to_igraph, compute or edit, restore with the manifest, then save as .annnet.
• Read first: Interoperability.
• Useful API pages: NetworkX adapter, igraph adapter, Native .annnet format.
• For persistence and exchange formats: Storage and IO.

Notebook picks

• Start with AnnNet Showcase if you want the broadest introduction.
• Use Multilayer Systems Biology if multilayer biology is your main use case.
• Use SBUC without Polars if you want the same example in a lighter environment.
• Use AnnNet Demo if you want a shorter hands-on notebook.

For a broader tour of examples, open the Notebook gallery.