agentsclimarketplace

Networkx graph construction starter

Skill ma-compbio-lab/SkillFoundry/skills/systems-biology/networkx-graph-construction-starter

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

Install
npx -y skills add ma-compbio-lab/SkillFoundry --skill networkx-graph-construction-starter

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

SKILL.md

1.3 KB, 280 tokens by cl100k_base, as published. Nobody here has run it

NetworkX Graph Construction Starter

Use this skill to build a deterministic toy biological interaction graph and summarize basic network properties with NetworkX.

What it does

  • Loads a small TSV edge list representing a pathway-like interaction graph.
  • Builds a NetworkX graph with edge attributes.
  • Summarizes node and edge counts, connected components, degree centrality, and a shortest path example.
  • Writes compact JSON that can feed downstream reporting or agent-planning steps.

When to use it

  • You need a local starter for graph-construction workflows in systems biology.
  • You want a deterministic network summary before moving on to propagation, enrichment, or causal-network tasks.

Example

python3 skills/systems-biology/networkx-graph-construction-starter/scripts/run_networkx_graph_construction.py \
  --input skills/systems-biology/networkx-graph-construction-starter/examples/toy_pathway_edges.tsv \
  --source-node EGFR \
  --target-node STAT3 \
  --out scratch/networkx/graph_summary.json

Verification

  • Skill-local tests: python3 -m unittest discover -s skills/systems-biology/networkx-graph-construction-starter/tests -p 'test_*.py'
  • Repository smoke: python3 -m unittest tests.smoke.test_phase25_agent_clinical_proteomics_graph_skills -v

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.