lamindb-data-management

npx skills add BioTender-max/awesome-bio-agent-skills --skill lamindb-data-management --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# LaminDB — Biological Data Management ## Overview LaminDB is an open-source data framework for biology that makes data queryable, traceable, and FAIR (Findable, Accessible, Interoperable, Reusable). It combines data lakehouse architecture, lineage tracking, biological ontology validation, and a unified Python API for managing biological datasets from raw files to annotated, curated artifacts. ## When to Use - Managing and versioning biological datasets (scRNA-seq, spatial, flow cytometry, multi-modal) - Tracking computational lineage (which code produced which data) - Validating and curating data against biological ontologies (cell types, genes, tissues, diseases) - Building queryable data lakehouses across multiple experiments - Ensuring reproducibility with automatic environment and provenance capture - Integrating with workflow managers (Nextflow, Snakemake) or MLOps (W&B, MLflow) - Standardizing metadata with ontology-based annotation (Bionty) - For **single-cell analysis pipelines** (clustering, DE), use scanpy instead - For **ontology lookups only** without data management, use bionty directly ## Prerequisites ```bash pip install lamindb # With extras for specific data types

pip install lamindb
With extras for specific data types
pip install 'lamindb[bionty,zarr,fcs]'
lamin login
lamin init --storage ./my-data --name my-project
Or with cloud storage:
lamin init --storage s3://my-bucket --name my-project --db postgresql://...