What is bio-foundation-housekeeping?

A data-management setup for a bioinformatics project, with rules for metadata, normalized Parquet tables, and a searchable DuckDB catalog. Metadata describes samples, runs, files, results, and their origins.

Defining project metadata schemas, generating Pydantic validation models, checking relationships such as sample-to-run and result-to-file, and creating a queryable catalog.

It catches malformed records, unexpected fields, duplicate identifiers, and broken links between related records before analysis outputs are written.

bio-foundation-housekeeping — Skill for Claude Code by fmschulz

Install

Getting it into your agent

It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.

Clone the repo

git clone --depth 1 https://github.com/fmschulz/omics-skills

agentmods

npx agentmods add skills/fmschulz/omics-skills/bio-foundation-housekeeping

Made for: Claude Code.

Or install omics-skills, the plugin that ships this one along with the rest of its 34 skills, 4 agents.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-foundation-housekeeping/github.svg)](https://agentmods.dev/skills/fmschulz/omics-skills/bio-foundation-housekeeping)

Your own site

<a href="https://agentmods.dev/skills/fmschulz/omics-skills/bio-foundation-housekeeping"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-foundation-housekeeping/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/fmschulz/omics-skills/bio-foundation-housekeeping"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-foundation-housekeeping.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 46 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,629 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector pass 7 Sept 2026

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00046	$0.01629
Opus 5	$0.00023	$0.00814
Sonnet 5	$0.00009	$0.00326
Haiku 4.5	$0.00005	$0.00163

Measured 10d ago against content hash 15fb1ad0b637, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

bio-foundation-housekeeping scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 10d ago.

The scan reads SKILL.md. This mod also ships 4 executable files (scripts/build_metadata_catalog.py, scripts/build_sample_catalog.py, scripts/check_schema_compatibility.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/bio-foundation-housekeeping/SKILL.md · 125 lines

How it starts

The opening of the file, as written. The whole thing — 125 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Bio Foundation Housekeeping

Add validated metadata models and a queryable catalog to an existing bioinformatics project. This is an independent entry point when the layout already exists; if it does not, complete bioinformatics-project as a separate setup task.

Instructions

Confirm bioinformatics-project has established input/output boundaries, project records, and a pinned environment. Do not create a competing project layout.
Adapt schemas/project-metadata.yaml for the sample, run, file, result, and provenance records the project needs. Keep identifiers stable and declare types, required fields, enumerations, and patterns in the schema.
Generate Pydantic models with scripts/generate_models.py. The command pins LinkML and Pydantic, rejects changed outputs, imports the generated module, and can assert that expected classes exist.
Validate the complete metadata bundle with the generated MetadataBundle model. Reject unexpected fields and malformed types before checking relationships.
Check unique identifiers and foreign keys across record collections before writing outputs. At minimum, verify run-to-sample, file-to-run, result-to-input/output-file, and provenance-to-result links.
Normalize validated records into one Parquet table per record class plus bridge tables for multivalued relationships. Register the tables and their relative paths, row counts, and SHA-256 values in DuckDB.
Exercise the full boundary with scripts/build_metadata_catalog.py and the bundled valid, model-invalid, and foreign-key-invalid fixtures. Use scripts/build_sample_catalog.py only for the smaller sample-only smoke path.
Before adopting a project-specific extension or migrating stored records, run scripts/check_schema_compatibility.py. Optional slots and new classes are compatible; required additions and constraint changes are reported as breaking. Keep a versioned input/expected migration fixture like fixtures/schema-migration-v1-to-v1.1.json for every supported transition.

Read the full file on GitHub · 125 lines

Files

What ships with it

20 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

10d ago First seen · 125 lines · 46 tokens per session scan A 15fb1ad0b637

Subscribe to this mod's changes

bio-foundation-housekeeping is a skill published in the GitHub repository fmschulz/omics-skills (7 stars, last pushed 5d ago), licensed MIT. It adds 46 tokens to every session and 1,629 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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