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LaminDB Bio Data Lakehouse Assistant

Guides Claude through LaminDB artifact registration, querying, validation, ontology annotation, and lineage tracking.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

Gives Claude accurate, up-to-date patterns for working with LaminDB, the open-source lineage-native lakehouse for biology.

  • Artifacts: register DataFrame/AnnData/Zarr/Parquet objects, version them, group into collections
  • Lineage: ln.track()/ln.finish(), @ln.flow()/@ln.step(), view_lineage()
  • Validation: schema-driven curation via DataFrameCurator, AnnDataCurator, SpatialDataCurator, TileDB-SOMA curator
  • Ontologies: standardize genes, cell types, tissues, diseases with Bionty
  • Integrations & deployment: Nextflow, Snakemake, Redun, W&B, MLflow, S3/GCS/Postgres setup
  • Security defaults: check only for named env vars, never echo credentials

Who it's for

  • Bioinformaticians handling scRNA-seq, spatial transcriptomics, flow cytometry, or EHR data
  • Biotech/pharma data engineers who need reproducibility and FAIR metadata
  • Teams moving a LaminDB instance from local SQLite to cloud PostgreSQL

Examples

  1. "Standardize the cell_type column of this h5ad against the CL ontology and save a validated artifact."
  2. "Query artifacts whose key starts with scrna/ where tissue=PBMC and condition=treated."
  3. "Write a Nextflow step that pulls the input fastq from LaminDB and registers counts.csv as an output artifact."

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/lamindb/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/lamindb folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/lamindb/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/lamindb ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills directory: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r scientific-agent-skills/skills/lamindb ~/.claude/skills/
  4. Confirm the bundled references/ folder came along: ls ~/.claude/skills/lamindb
  5. Install LaminDB: uv pip install 'lamindb==2.5.1' (verify the current release first)
  6. Run lamin login, then lamin init --storage ./mydata to create an instance
  7. Restart Claude Code and try a prompt like "register this AnnData file in LaminDB" to trigger the skill.
View source on GitHub ↗License: MIT