Bio foundation housekeeping

Skill BioTender-max/awesome-bio-agent-skills/skills/omics/bio-foundation-housekeeping

A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.

Install

npx -y skills add BioTender-max/awesome-bio-agent-skills --skill bio-foundation-housekeeping

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Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.

SKILL.md

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Bio Foundation Housekeeping

Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.

Instructions

Create standard directory layout (data/, results/, schemas/, workflows/, src/, notebooks/).
Initialize Pixi workspace and lockfile; define tasks.
Define LinkML schemas and generate Pydantic models.
Create DuckDB catalog and register parquet tables.

Quick Reference

Task	Action
Run workflow	Follow the steps in this skill and capture outputs.
Validate inputs	Confirm required inputs and reference data exist.
Review outputs	Inspect reports and QC gates before proceeding.
Tool docs	See `docs/README.md`.

Input Requirements

Prerequisites:

Tools available in the active environment (Pixi/conda/system). See docs/README.md for expected tools.
Target project root is writable. Inputs:
project root (path)
metadata schema requirements
workflow engine preference (optional)

Output

pixi.toml
pixi.lock
schemas/
data/catalog.duckdb
results/bio-foundation-housekeeping/report.md
results/bio-foundation-housekeeping/logs/

Quality Gates

Schema generation succeeds and models are importable.
pixi.lock is created and consistent with pixi.toml.
DuckDB catalog is readable.
On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
Verify project root exists and is writable.
Validate generated schemas against expected fields.

Examples

Example 1: Expected input layout

project root (path)
metadata schema requirements
workflow engine preference (optional)

Troubleshooting

Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.

Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.