Bio Foundation Housekeeping

When to use

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

Prerequisites

• Tools installed via pixi (see pixi.toml).
• Target project root is writable.

Inputs

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

Outputs

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

Steps

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

QC 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.

Validation

• Verify project root exists and is writable.
• Validate generated schemas against expected fields.

Tools

• pixi v0.43.0
• linkml v1.9.6
• pydantic v2.12.5
• duckdb v1.4.3

Paper summaries (2023-2025)

• summaries/ (include example use cases and tool settings used)

Tool documentation

• Pixi - Package and environment management
• LinkML - Data modeling and schema generation
• Pydantic - Data validation using Python type hints
• DuckDB - In-process analytical database

References

• See ../bio-skills-references.md