Notebook Gallery

This section collects runnable AnnNet notebooks with rendered outputs. To recreate them, use the linked GitHub environment file for the notebook family.

Base HowTos use the HowTo environment. Scenario notebooks each link a narrower environment for the external packages they demonstrate. Use-case notebooks are coming soon.

HowTos

Small, self-contained notebooks that show AnnNet APIs directly, including focused special-topic notebooks.

• Quickstart

  ---

  Build a directed graph, inspect it, and round-trip it through .annnet.

  Open notebook

• Attributes and views

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  Attach metadata to vertices and edges, then inspect dataframe-like views.

  Open notebook

• Tables and storage

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  Build from tables and compare CSV, Excel, native, Parquet, JSON, and NDJSON.

  Open notebook

• Slices and subgraphs

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  Manage context-specific graph state and materialize smaller graphs.

  Open notebook

• Hyperedges and traversal

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  Represent complexes/reactions and traverse local neighborhoods.

  Open notebook

• Directed hyperedges and stoichiometry

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  Work directly with directed hyperedges, incidence coefficients, and reaction-style semantics.

  Open notebook

• Multilayer

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  Work with layers, coupling edges, layer-derived slices, and supra matrices.

  Open notebook

• Multilayer math

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  Inspect supra-adjacency, Laplacians, diffusion, coupling sweeps, and tensor views.

  Open notebook

• History and reproducibility

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  Record mutations, create snapshots, diff graph states, and export history.

  Open notebook

• Backend accessors

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  Inspect optional components and dispatch to installed graph backends.

  Open notebook

• Flexible edge orientation

  ---

  Compare edge-scope and vertex-scope orientation policies on mixed graphs.

  Open notebook

Use Cases

Larger applied notebooks that combine AnnNet with external biological data, optimization, and graph learning workflows.

• Multi-condition causal signaling

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  Build patient layers from CPTAC/OmniPath data and write inferred causal subnetworks back into AnnNet.

  Coming soon.

• HEK293 heterogeneous biology graph

  ---

  Combine signaling, metabolic, complex, regulatory, organelle, and graph-learning workflows in one AnnNet object.

  Coming soon.

Scenarios

Short ecosystem bridges. They use tiny deterministic data and keep external dependencies in scenario-specific environment files.

• OmniPath table ingestion

  ---

  Load an OmniPath-style interaction table as prior knowledge without a network call.

  Open notebook · Environment

• Cytoscape CX2 export

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  Export annotated and hyperedge graphs with explicit CX2 projection modes.

  Open notebook · Environment

• PyG HeteroData export

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  Prepare typed graph data and numeric features for PyTorch Geometric.

  Open notebook · Environment

• Causal activity bridge

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  Store activity scores and causal solution edges from decoupler/CORNETO-style workflows.

  Open notebook · Environment