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Networkx network propagation starter

Skill ma-compbio-lab/SkillFoundry/skills/systems-biology/networkx-network-propagation-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill networkx-network-propagation-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.2 KB, 266 tokens by cl100k_base, as published. Nobody here has run it

NetworkX Network Propagation Starter

Use this skill to propagate signal from one or more seed nodes over a small weighted interaction graph with personalized PageRank.

What it does

  • Loads a deterministic weighted edge list and a small seed-node set.
  • Runs NetworkX personalized PageRank as a lightweight propagation surrogate.
  • Emits ranked node scores, top non-seed hits, and basic graph statistics in JSON.

When to use it

  • You need a verified local starter for network propagation.
  • You want a deterministic way to score neighbors around seed genes before using larger pathway or interaction resources.

Example

python3 skills/systems-biology/networkx-network-propagation-starter/scripts/run_networkx_network_propagation.py \
  --input skills/systems-biology/networkx-network-propagation-starter/examples/toy_network.tsv \
  --seeds skills/systems-biology/networkx-network-propagation-starter/examples/toy_seeds.txt \
  --top-k 5 \
  --out scratch/networkx-propagation/summary.json

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/systems-biology/networkx-network-propagation-starter/tests -p 'test_*.py'
  • Repository smoke target: make smoke-network-propagation

Keep looking

Skills are one crate of 328,083. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.