Alterlab Lamindb
Skill Verified ActiveThis skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating data with biological ontologies, building data lakehouses, or ensuring data lineage and reproducibility in biological research. Covers data management, annotation, ontologies (genes, cell types, diseases, tissues), schema validation, integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms (W&B, MLflow), and deployment strategies. Part of the AlterLab Academic Skills suite.
To provide researchers with a unified platform for managing, annotating, and tracking biological data throughout its lifecycle, ensuring queryability, reproducibility, and FAIR compliance.
Features
- Data management for biological datasets
- Automatic data lineage tracking
- Support for biological ontologies (genes, cell types, etc.)
- Schema validation and annotation
- Integrations with workflow managers (Nextflow, Snakemake) and MLOps platforms
- Support for multiple storage backends (S3, GCS, local)
Use Cases
- Managing scRNA-seq, spatial, and flow cytometry datasets
- Tracking computational workflows and ensuring reproducibility
- Curating and validating data with biological ontologies
- Building queryable data lakehouses for biological research
- Integrating ML pipelines with experiment tracking
Non-Goals
- Replacing raw data files entirely (artifacts point to original data)
- Performing primary data analysis (focus is on management and lineage)
- Acting as a standalone application without a Python environment
Installation
npx skills add AlterLab-IEU/AlterLab-Academic-SkillsRuns the Vercel skills CLI (skills.sh) via npx — needs Node.js locally and at least one installed skills-compatible agent (Claude Code, Cursor, Codex, …). Assumes the repo follows the agentskills.io format.
Quality Score
VerifiedTrust Signals
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