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Found 4 Skills
This 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.
OpenBio API for biological data access and computational biology tools. Use when: (1) Querying biological databases (PDB, UniProt, ChEMBL, etc.), (2) Searching scientific literature (PubMed, bioRxiv, arXiv), (3) Running structure prediction (Boltz, Chai, ProteinMPNN), (4) Performing pathway/enrichment analysis, (5) Designing molecular biology experiments (primers, cloning), (6) Analyzing variants and clinical data.
Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more.
Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels). Performs pathway enrichment, protein-pathway mapping, keyword searches, and systems-level analysis. Use when analyzing gene sets, exploring biological pathways, or investigating systems-level biology.