LaminDB

When to Use This Skill

Use this skill when:

• Managing biological datasets: scRNA-seq, bulk RNA-seq, spatial transcriptomics, flow cytometry, multi-modal data, EHR data
• Tracking computational workflows: Notebooks, scripts, pipeline execution (Nextflow, Snakemake, Redun)
• Curating and validating data: Schema validation, standardization, ontology-based annotation
• Working with biological ontologies: Genes, proteins, cell types, tissues, diseases, pathways (via Bionty)
• Building data lakehouses: Unified query interface across multiple datasets
• Ensuring reproducibility: Automatic versioning, lineage tracking, environment capture
• Integrating ML pipelines: Connecting with Weights & Biases, MLflow, HuggingFace, scVI-tools
• Deploying data infrastructure: Setting up local or cloud-based data management systems
• Collaborating on datasets: Sharing curated, annotated data with standardized metadata

Core Capabilities

LaminDB provides six interconnected capability areas, each documented in detail in the references folder.

1. Core Concepts and Data Lineage

Core entities:

• Artifacts: Versioned datasets (DataFrame, AnnData, Parquet, Zarr, etc.)
• Records: Experimental entities (samples, perturbations, instruments)
• Runs & Transforms: Computational lineage tracking (what code produced what data)
• Features: Typed metadata fields for annotation and querying

Key workflows:

• Create and version artifacts from files or Python objects
• Track notebook/script execution with ln.track() and ln.finish()
• Annotate artifacts with typed features
• Visualize data lineage graphs with artifact.view_lineage()
• Query by provenance (find all outputs from specific code/inputs)

Reference: references/core-concepts.md - Read this for detailed information on artifacts, records, runs, transforms, features, versioning, and lineage tracking.