llm-patterns
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AI-first application patterns, LLM testing, prompt management
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uniprot-database
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Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For Python workflows with multiple databases, prefer bioservices (unified interface to 40+...
pathml
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Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model...
datacommons-client
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Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health...
generate-image
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Generate or edit images using AI models (FLUX, Gemini). Use for general-purpose image generation including photos, illustrations, artwork, visual assets, concept art, and any image that is not a...
new-feature
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Plan new features/integrations following SOLID principles. Analyzes codebase architecture, researches official documentation and best practices, designs extensible solution, and creates...
scvi-tools
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Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration...
geopandas
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Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations,...
ena-database
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Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
gtars
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High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML...
pennylane
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Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or needing device portability...
pylabrobot
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Vendor-agnostic lab automation framework. Use when controlling multiple equipment types (Hamilton, Tecan, Opentrons, plate readers, pumps) or needing unified programming across different vendors....
hmdb-database
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Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.
implement
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Implement code from a GitHub issue specification. Explores codebase, researches docs, creates temporary implementation plan, then implements incrementally (small piece β test β commit β next)....
ensembl-database
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Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
reactome-database
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Query Reactome REST API for pathway analysis, enrichment, gene-pathway mapping, disease pathways, molecular interactions, expression analysis, for systems biology studies.
omero-integration
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Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
plotly
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Interactive visualization library. Use when you need hover info, zoom, pan, or web-embeddable charts. Best for dashboards, exploratory analysis, and presentations. For static publication figures...
android-kotlin
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Android Kotlin development with Coroutines, Jetpack Compose, Hilt, and MockK testing
qiskit
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IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution,...