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Zeyuyang-0420
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lamindb

Manage and analyze biological datasets with lineage tracking and schema validation.

Updated May 8, 2026
Search Tags:#MLOps#data management#data lineage#biological datasets#FAIR compliance#workflow managers
One-click install
npx skills add https://github.com/Zeyuyang-0420/bio-ai-research-skills --skill lamindb-zeyuyang-0420
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: lamindb
Source: https://github.com/Zeyuyang-0420/bio-ai-research-skills/tree/main/categories/compute-data-infrastructure/lamindb
Command: npx skills add https://github.com/Zeyuyang-0420/bio-ai-research-skills --skill lamindb-zeyuyang-0420

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires lamindb, bionty, wetlab, lamindb-clinical, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

This Skill helps manage and analyze biological datasets by providing a unified platform for data management, annotation, ontologies, schema validation, and integration with workflow managers and MLOps platforms.

Core Features & Use Cases

  • Data Management: Manage biological datasets, track computational workflows, curate and validate data with biological ontologies.
  • Schema Validation: Validate datasets against predefined schemas.
  • Integration: Integrates with workflow managers (Nextflow, Snakemake, Redun) and MLOps platforms (W&B, MLflow, HuggingFace, scVI-tools).
  • Use Case: For a single-cell RNA-seq analysis, LaminDB can be used to track data lineage, manage annotations, and integrate with ML pipelines for model training and validation.

Quick Start

To start using LaminDB, first install it and initialize an instance:

pip install lamindb
lamin init --storage ./mydata

Then, import your datasets and start tracking your workflows:

ln track
ln Artifact.get(key="path/to/your/data.h5ad").load()
# ... your analysis code ...
ln finish

Frequently Asked Questions about lamindb

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I track data lineage for single-cell RNA-seq analysis?▼

Track single-cell RNA-seq data lineage by running the track command before analysis and finish after. This logs transformations and ensures computational workflow reproducibility for biological datasets.

What is FAIR compliance for biological dataset management?▼

FAIR compliance in biological dataset management means data is findable, accessible, interoperable, and reusable. It is achieved through schema validation, ontology-based annotation, and tracking data lineage across workflows.

Can I integrate LaminDB with existing MLOps platforms and workflow managers?▼

Yes, LaminDB integrates with workflow managers like Nextflow and Snakemake, plus MLOps platforms including W&B, MLflow, and HuggingFace. This connects data management directly to model training pipelines.

Does LaminDB support schema validation for spatial and flow cytometry data?▼

Yes, LaminDB supports schema validation for spatial and flow cytometry data. It validates datasets against predefined schemas and curates data using biological ontologies to ensure consistency.

Do I need Python to manage biological datasets with LaminDB?▼

Yes, Python is required to manage biological datasets with LaminDB. You need to install the lamindb package via pip and initialize a local storage instance before tracking workflows and loading artifacts.

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