lamindb

lamindb is a skill for Claude Code, Codex from foryourhealth111-pixel/Vibe-Skills. It costs 135 tokens per session (3,252 once invoked), scanned A, a copy of lamindb, Apache-2.0.

A Python-based data framework for managing biological datasets and the workflows that produce results from them. It makes data searchable, tracks links between inputs and outputs, supports versioning, and uses biological standards for annotation.

In plain words
What is it for?
Use it with datasets such as single-cell RNA sequencing, spatial transcriptomics, flow cytometry, and clinical data, while tracking notebooks, scripts, pipelines, validation, and biological metadata.
Why use it?
It helps researchers find the right dataset and understand where a result came from. It also supports repeatable analysis and more consistent descriptions of biological data.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

Good fit Use it with datasets such as single-cell RNA sequencing, spatial transcriptomics, flow cytometry, and clinical data, while tracking notebooks, scripts, pipelines, validation, and biological metadata.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/foryourhealth111-pixel/vibe-skills/lamindb
About the project

Vibe-Skills is a collection and routing system that helps AI agents discover, select, and coordinate specialized skills for completing tasks. It is intended for agents that need to organize workflows across many installed capabilities. The catalogue entries are skills and an agent belonging to this system.

foryourhealth111-pixel/Vibe-Skills · 3,252 stars · on GitHub

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add foryourhealth111-pixel/Vibe-Skills --skill lamindb
Clone the repo
git clone --depth 1 https://github.com/foryourhealth111-pixel/Vibe-Skills

Made for: Claude Code, Codex.

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.

agentmods badge for lamindb

README.md
[![agentmods](https://agentmods.dev/badge/skills/foryourhealth111-pixel/vibe-skills/lamindb/github.svg)](https://agentmods.dev/skills/foryourhealth111-pixel/vibe-skills/lamindb)
Your own site
<a href="https://agentmods.dev/skills/foryourhealth111-pixel/vibe-skills/lamindb"><img src="https://agentmods.dev/badge/skills/foryourhealth111-pixel/vibe-skills/lamindb/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.

agentmods 80×15 button for lamindb

Your own site · 80×15
<a href="https://agentmods.dev/skills/foryourhealth111-pixel/vibe-skills/lamindb"><img src="https://agentmods.dev/badge/skills/foryourhealth111-pixel/vibe-skills/lamindb.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 135 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,252 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.
Origin 91% copy Near-identical to another mod 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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00135 $0.03252
Opus 5 $0.00068 $0.01626
Sonnet 5 $0.00027 $0.00650
Haiku 4.5 $0.00014 $0.00325

Measured 9d ago against content hash 885173892efd, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

lamindb 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 9d ago.

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.

Origin

This is a copy

91% identical to lamindb — 98 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

bundled/skills/lamindb/SKILL.md · 385 lines

How it starts

The opening of the file, as written. The whole thing — 385 lines — stays where its author put it; the contents beside it link to each section on GitHub.

LaminDB

Overview

LaminDB is an open-source data framework for biology designed to make data queryable, traceable, reproducible, and FAIR (Findable, Accessible, Interoperable, Reusable). It provides a unified platform that combines lakehouse architecture, lineage tracking, feature stores, biological ontologies, LIMS (Laboratory Information Management System), and ELN (Electronic Lab Notebook) capabilities through a single Python API.

Core Value Proposition:

  • Queryability: Search and filter datasets by metadata, features, and ontology terms
  • Traceability: Automatic lineage tracking from raw data through analysis to results
  • Reproducibility: Version control for data, code, and environment
  • FAIR Compliance: Standardized annotations using biological ontologies

When to Use This Skill

Use this skill when:

  • Managing biological datasets: scRNA-seq, bulk RNA-seq, spatial transcriptomics, flow cytometry, multi-modal data, EHR data
  • Tracking computational workflows: Notebooks, scripts, pipeline execution (Nextflow, Snakemake, Redun)
  • Curating and validating data: Schema validation, standardization, ontology-based annotation
  • Working with biological ontologies: Genes, proteins, cell types, tissues, diseases, pathways (via Bionty)
  • Building data lakehouses: Unified query interface across multiple datasets
  • Ensuring reproducibility: Automatic versioning, lineage tracking, environment capture
  • Integrating ML pipelines: Connecting with Weights & Biases, MLflow, HuggingFace, scVI-tools
  • Deploying data infrastructure: Setting up local or cloud-based data management systems
  • Collaborating on datasets: Sharing curated, annotated data with standardized metadata

Core Capabilities

LaminDB provides six interconnected capability areas, each documented in detail in the references folder.

1. Core Concepts and Data Lineage

Core entities:

  • Artifacts: Versioned datasets (DataFrame, AnnData, Parquet, Zarr, etc.)
  • Records: Experimental entities (samples, perturbations, instruments)
  • Runs & Transforms: Computational lineage tracking (what code produced what data)
  • Features: Typed metadata fields for annotation and querying

Read the full file on GitHub · 385 lines

Files

What ships with it

6 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.

  1. 9d ago First seen · 385 lines · 135 tokens per session scan A 885173892efd

Subscribe to this mod's changes

lamindb is a skill published in the GitHub repository foryourhealth111-pixel/Vibe-Skills (3,252 stars, last pushed 12d ago), licensed Apache-2.0. It adds 135 tokens to every session and 3,252 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 0 findings. It is 91% identical to lamindb, differing in 98 lines, and is treated as a copy.