bio-foundation-housekeeping

Create reproducible bioinformatics project scaffolds with Pixi, LinkML, and DuckDB.

7|1|Updated Feb 2, 2026

Search Tags:#workflow #schema #scaffold #bioinformatics #environment #reproducible #data-catalog

Ready to run

npx skills add https://github.com/fmschulz/omics-skills --skill bio-foundation-housekeeping

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: bio-foundation-housekeeping
Source: https://github.com/fmschulz/omics-skills/tree/main/skills/bio-foundation-housekeeping
Command: npx skills add https://github.com/fmschulz/omics-skills --skill bio-foundation-housekeeping

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Initialize a reproducible, scalable scaffold for bioinformatics projects including standard directory layout, environment management, data schemas, and cataloging.

Core Features & Use Cases

Standardized project layout (data/, results/, schemas/, workflows/, src/, notebooks/) plus a Pixi workspace and locked environments.
Generate and integrate LinkML schemas and Pydantic models for metadata validation and data integrity.
Build a DuckDB-backed data catalog to enable fast querying of Parquet and CSV datasets in omics workflows.
Real-world usage includes starting new studies, onboarding collaborators, and ensuring reproducible analyses and reporting.

Quick Start

Create a new project path and let the scaffold initialize the directories, tooling, and documentation setup for immediate use.

Frequently Asked Questions about bio-foundation-housekeeping

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I set up a reproducible bioinformatics project scaffold with standardized directories?▼

You can initialize a reproducible bioinformatics project scaffold by generating a standard directory layout including data, results, schemas, workflows, src, and notebooks, alongside locked environment tooling and documentation.

What is the best way to initialize a Pixi workspace for genomics workflows?▼

Initializing a Pixi workspace for genomics workflows involves creating a standardized project scaffold with locked environments, LinkML schema generation, and DuckDB data cataloging to ensure reproducible analyses.

How does DuckDB data cataloging work with Parquet and CSV datasets in omics workflows?▼

DuckDB data cataloging enables fast querying of Parquet and CSV datasets in omics workflows by building a localized data catalog within the standardized project scaffold for reproducible analysis.

Can I integrate LinkML schemas and Pydantic models for metadata validation in transcriptomics projects?▼

Yes, you can generate and integrate LinkML schemas and Pydantic models within transcriptomics projects to enforce metadata validation and ensure data integrity across standardized directory layouts.

Do I need pre-existing repositories to use this bioinformatics project initialization?▼

No, this bioinformatics project initialization applies to new projects, creating a new project path and scaffolding directories, tooling, and documentation setup from scratch without requiring pre-existing repositories.