Does it support cloud storage providers?

Yes, LaminDB integrates with AWS S3, Google Cloud Storage, and S3-compatible endpoints like MinIO or Cloudflare R2 for scalable data management.

How is data lineage tracked in LaminDB?

Lineage is tracked by wrapping your code with tracking functions that automatically record the inputs, outputs, and the specific version of the script or notebook used.

LaminDB is an open-source data framework specifically designed for biology that makes data queryable, traceable, and reproducible across local and cloud environments.

How does this skill handle biological ontologies?

The skill provides specialized guidance for using the Bionty module to map, standardize, and validate biological terms such as genes, cell lines, and tissues.

Can I use LaminDB for single-cell genomics?

Yes, LaminDB includes dedicated curators for AnnData and MuData formats, supporting validation and curation workflows for scRNA-seq and spatial transcriptomics.

LaminDB Biology Data Management

Name: LaminDB Biology Data Management
Author: x-cmd

byx-cmd

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数据科学与机器学习

Manages biological datasets with lineage tracking, ontology-based validation, and FAIR data principles using a unified Python API.

LaminDB is a specialized data framework designed for biological research, enabling developers and scientists to build queryable, traceable, and reproducible data lakehouses. It provides a robust platform for tracking computational workflows, annotating datasets with standardized biological ontologies—such as genes, cell types, and diseases—and ensuring data lineage from raw files to analysis results. By integrating with workflow managers like Nextflow and MLOps tools like Weights & Biases, this skill simplifies the management of complex multi-modal biological data while maintaining strict adherence to FAIR (Findable, Accessible, Interoperable, Reusable) principles.

主要功能

01Schema validation and curation for scRNA-seq, spatial, and multi-modal data

02Automatic lineage tracking for data, code, and computational environments

038 GitHub stars

04Standardized biological ontology integration for genes, cell types, and diseases

05Seamless integration with workflow managers like Nextflow and Snakemake

06Unified query interface for local and cloud-based biological data lakehouses

使用场景

01Tracking data lineage across complex bioinformatics pipelines and machine learning workflows

02Curating and validating single-cell RNA-seq datasets with canonical cell type ontologies

03Building a centralized, searchable data registry for multi-user biological research teams

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add x-cmd/skill lamindb

For use in Claude.ai and ChatGPT

Download Skill