Notebook Gallery
This is the single index for runnable annnet notebooks. The sections follow the work being demonstrated; the Explanations section covers concepts and choices separately.
Base HowTos use the HowTo environment. Scenario and use-case notebooks link their dedicated environments.
Core graph workflows
These notebooks cover construction, graph structure, context, values, and reproducibility.
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Quickstart
Build a directed graph, inspect it, and round-trip it through
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Attributes and views
Attach metadata to nodes and edges, then inspect dataframe-like views.
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Tables and storage
Build from tables and compare CSV, Excel, native, Parquet, JSON, and NDJSON.
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Slices and subgraphs
Manage context-specific graph state and materialize smaller graphs.
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Hyperedges and traversal
Represent complexes or reactions and traverse local neighborhoods.
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Directed hyperedges and stoichiometry
Work directly with directed hyperedges, incidence coefficients, and reaction-style semantics.
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Multilayer
Work with layers, coupling edges, layer-derived slices, and supra matrices.
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Multilayer math
Inspect supra-adjacency, Laplacians, diffusion, coupling sweeps, and tensor views.
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History and reproducibility
Record mutations, create snapshots, diff graph states, and export history.
Interoperability and storage
These notebooks show the boundaries where annnet connects to another backend, format, or workflow.
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Backend accessors
Inspect optional components and dispatch to installed graph backends.
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Flexible edge orientation
Compare edge-scope and node-scope orientation policies on mixed graphs.
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Backend lazy proxies
Inspect deferred backend conversion and the optional dependency boundary.
Applied workflows
These larger notebooks combine graph structure with external biological data, optimization, or graph-learning tools.
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Multi-condition causal signaling
Fit a signed signaling network to perturbation experiments with CORNETO, then keep the selected network and predicted activities in AnnNet.
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TGF-beta fibrosis response
Combine signaling, regulation, protein complexes, and metabolism across mechanism and time layers in one AnnNet object.
Scenarios
Short ecosystem bridges use small deterministic data and scenario-specific environments.
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OmniPath table ingestion
Load an OmniPath-style interaction table as prior knowledge without a network call.
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Cytoscape CX2 export
Export annotated and hyperedge graphs with explicit CX2 projection modes.
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PyG HeteroData export
Prepare typed graph data and numeric features for PyTorch Geometric.
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Causal activity bridge
Store activity scores and causal solution edges from decoupler/CORNETO-style workflows.