Skills

Builds and executes bioinformatics analysis pipelines for genomics, transcriptomics, and proteomics data. Supports single-cell RNA-seq analysis with Scanpy, differential expression with PyDESeq2, sequence alignment, variant calling, gene ontology enrichment, and pathway analysis using KEGG and Reactome databases.

Performs cheminformatics and molecular property analysis using RDKit, PubChem, and ChEMBL. Supports SMILES/InChI parsing, molecular descriptor calculation, drug-likeness filtering (Lipinski, Veber), ADMET prediction, substructure search, and structure-activity relationship (SAR) analysis for drug discovery workflows.

Builds and queries typed knowledge graphs for structured agent memory and composable skills. Creates entities (people, projects, tasks, events, documents), links related objects, enforces constraints, and plans multi-step actions as graph transformations. Enables persistent, queryable memory across agent sessions.

Analyzes SQL queries and database schemas to identify performance bottlenecks and suggest optimizations. Recommends index strategies, query rewrites, denormalization opportunities, and partitioning schemes. Explains EXPLAIN plans and provides before/after comparisons with expected performance improvements.

Designs normalized database schemas from business requirements. Covers entity relationships, indexing strategies, migration planning, and performance considerations. Supports PostgreSQL, MySQL, MongoDB, and other databases with dialect-specific optimizations.