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概要と使いどころ
Build accessible, composable UI with @base-ui/react primitives and project styling tokens. Use when creating or refining unstyled primitive components and behavior-heavy UI such as overlays, menus, popovers, dialogs, and form controls, or defining custom component APIs. Prefer the moai-library-shadcn skill when copied-in shadcn components are the primary implementation path.
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Master effective code review practices to provide constructive feedback, catch bugs early, and foster knowledge sharing while maintaining team morale. Use when reviewing pull requests, establishing review standards, or mentoring developers.
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Create a source-faithful single-product FF&E cut sheet or spec book entry from a supplied PDF or product URL. Preserve selected identity and source limits; use ffe-spec-book for a complete FF&E book and spec-writer for Project Manual requirements.
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Extract structured FF&E specs from a list of product URLs into a schedule. Use to pull or bulk-import product-page data; not for PDF catalogs.
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Reviews code for security vulnerabilities and guides secure implementation using OWASP Top 10:2025, ASVS 5.0, the OWASP Top 10 for LLM Applications (2026), and the OWASP Top 10 for Agentic Applications (2026). Use when reviewing code or a diff for security issues, implementing authentication, authorization, sessions, or cryptography, handling untrusted input, files, or URLs, hardening config, dependencies, or CI, or building LLM and AI agent features.
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Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features. Core for ChIP-seq peak annotation, region filtering, genome arithmetic. Use tabix for indexed single-region queries; use deeptools for normalized bigWig coverage.
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Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs, eQTLs, chromatin state). Scores range 1a (strongest) to 7 (none). Use for GWAS hit prioritization, regulatory variant annotation, cis-regulatory discovery. Use clinvar-database for pathogenicity; gwas-database for trait associations.
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Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. Retrieve TF peaks overlapping a region (chr:start-end), peaks near a gene, TFs by species, peaks filtered by biotype (promoter, enhancer), and BED files for a TF-cell type pair. Use for TF co-occupancy, regulatory annotation, and TF binding atlases. Use jaspar-database for PWM motifs; encode-database for ENCODE tracks.
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All-in-one FASTQ QC and adapter trimming. Auto-detects Illumina adapters, filters low-quality reads, corrects paired-end overlaps, emits HTML+JSON QC in one pass. 3-10x faster than Trim Galore/Trimmomatic. First step before STAR, BWA-MEM2, or Salmon.
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ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs, taxonomy, cross-refs. For multi-DB Python use bioservices; for NCBI-only use pubmed-database or Biopython Entrez.
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Counts RNA-seq reads overlapping GTF gene features. Takes sorted STAR BAMs plus GTF; outputs a per-gene tab-delimited matrix across samples. Handles strandedness (0/1/2), paired-end, multi-sample batch counting in one command, and outputs assignment statistics. Use Salmon for alignment-free quantification; use featureCounts when STAR BAMs already exist.
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Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinvar-database; for somatic cancer PGx use cosmic-database or opentargets-database; for drug bioactivity use chembl-database-bioactivity.
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Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metadata (resolution, method, organism, sample), map download URLs, fitted PDB IDs, and citations. Keyword search via EBI Search. No auth. For atomic coordinates use pdb-database; for AlphaFold predictions use alphafold-database-access.
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AiZynthFinder retrosynthetic route planning (CASP) from AstraZeneca Molecular AI. Monte Carlo tree search guided by a template-based neural expansion policy recursively disconnects a target SMILES until precursors are found in a purchasable stock. Covers config.yml (v4 format), aizynthcli batch screening, the AiZynthFinder/AiZynthExpander Python API, one-step disconnections, custom stocks via smiles2stock, scorers, Retro*/breadth-first/DFPN search alternatives, and reading output.json.gz / trees.json. Use for synthesis route planning, synthesizability screening, and building-block/precursor search. For reaction barriers use neb-irc-activation-energy; for 2D reaction scheme drawing use rdkit-chemdraw-cdxml.
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Core Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms (ICRS/Galactic/AltAz/FK5), FITS I/O, tables (FITS/HDF5/VOTable/CSV), cosmology (Planck18, distance/age), precise time (UTC/TAI/TT/TDB, Julian, barycentric), WCS pixel-world mapping, model fitting. For general tables use pandas/polars; for radio interferometry use CASA.
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Universal QA checklist for generated scientific plots: overlapping labels, clipped text, missing axes/legends, overcrowded data, and cross-journal resolution/format guidance.
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Query bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title, abstract, authors, category, DOI, version history) and PDFs. No auth. For peer-reviewed biomedical use pubmed-database; broader scholarly search use openalex-database.
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Query OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts. Search by keyword, author, DOI, ORCID, or ID; filter by year, OA, citations, field; retrieve citations, references, author disambiguation. Free, no auth. For PubMed use pubmed-database; preprints use biorxiv-database.
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Query and download NCI Imaging Data Commons (IDC) cancer radiology and pathology datasets via the idc-index Python client. No authentication required: the parquet index ships inside the pip wheel, SQL runs locally via DuckDB, and DICOM downloads stream from public S3/GCS buckets through s5cmd. Use sql_query() for DuckDB cohort selection, get_collections/get_patients/get_dicom_studies/get_dicom_series for hierarchical browsing, download_from_selection() for downloads, and get_viewer_URL() for OHIF/Slim links. Use pydicom-medical-imaging for local DICOM reading; histolab for whole-slide pathology preprocessing.
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Search the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism, instrument, disease, software), fetch project metadata, list and download RAW/PEAK/RESULT/FASTA files (with FTP/Aspera URLs), look up which projects mention a UniProt accession, and find similar projects. PRIDE v3 no longer exposes peptide/PSM-level identification endpoints — for spectrum-level data download the project's RESULT files. Use uniprot-protein-database for protein sequences; interpro-database for domain architecture.
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Create and train AI learning plugins with AgentDB's 9 reinforcement learning algorithms. Includes Decision Transformer, Q-Learning, SARSA, Actor-Critic, and more. Use when building self-learning agents, implementing RL, or optimizing agent behavior through experience.
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Consolidate IBRK trade CSV files from a directory into a summary report. Groups trades by symbol, underlying, date, strike, buy/sell, and open/close. Outputs both markdown and CSV.
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Report delta-adjusted notional exposure across all IBKR accounts. Calculates option deltas using Black-Scholes and reports long/short exposure by account and underlying. Use when user asks about delta exposure, portfolio risk, or directional exposure.
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Detect institutional whale activity in options for a given underlying. Use when the user asks about unusual options activity, large block trades, whale trades, or institutional options flow for a specific symbol.
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