Comprehensive drug-target intelligence — tissue expression (GTEx, HPA), pathways, protein interactions (STRING), variant landscape (ClinVar, gnomAD), druggability (DGIdb, ChEMBL approved drugs). 9 parallel research paths with citations. Use for full target profile reports, target characterization for drug discovery, and 'tell me about target X' queries.

Spatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq. Maps gene expression to tissue architecture, identifies spatially variable genes (SVGs), tissue-domain segmentation, and cell-cell interaction inference. Use for spatial gene-expression questions, tissue architecture analysis, and SVG identification.

Find and retrieve proteomics datasets from MassIVE and ProteomeXchange. Search by species, keyword, or accession; retrieve detailed metadata (instruments, publications, species, PTMs studied). Use for locating public proteomics datasets to reanalyze, comparing instrument/protocol coverage across studies, and pre-download dataset evaluation.

Cancer treatment recommendations from molecular profile (mutations + cancer type + biomarkers) — FDA-approved + investigational therapies, resistance mechanisms, matching clinical trials, prognosis. Uses CIViC, ClinVar, OpenTargets, ClinicalTrials.gov. Use for tumor-board treatment recommendations, evidence-tiered actionability assessment, and FDA-precedent-driven therapy selection.

Microscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count statistics, dose-response curves, and ANOVA/Dunnett on image-derived measurements. Uses pandas/numpy/scipy/scikit-image. Use for analyzing tabular outputs from CellProfiler/ImageJ, image-derived measurement statistics, and image-based assay quantification.

GPCR receptor pharmacology — agonist/antagonist/inverse-agonist/biased-agonist classification, GPCRdb structural data, receptor-ligand binding analysis, antibody-target interface (SAbDab). Use for GPCR drug discovery, biased-agonism analysis, receptor subtype selectivity questions, and orthosteric vs allosteric pocket characterization.

Drug regulatory and approval research — FDA substance registry, ATC/EPC classification, EMA decisions, generic-drug status, FDA Orange Book exclusivity, NDA/BLA pathways. Use for jurisdiction-aware approval status (FDA vs EMA), generic vs brand availability, exclusivity expiry tracking, and regulatory pathway selection. Always specifies the market when reporting status.

Generate comprehensive disease research reports covering genetics (causal genes, GWAS, OMIM), pathways (Reactome, KEGG), drugs (existing therapies, repurposing candidates), clinical trials, epidemiology (prevalence, incidence), and phenotypes (HPO). Use for full disease overviews, comprehensive disease characterization, and orphan/rare-disease profiling.

Cross-species gene comparison and ortholog analysis. Integrates Ensembl Compara orthologs, NCBI Gene, UniProt, OLS, Monarch, and OpenTargets to identify orthologs, paralogs, sequence conservation, functional conservation across species, and lineage-specific gene gains/losses. Use for phylogenetic gene tracing, model-organism mapping, and evolutionary-genomics queries.

AI-driven patient-to-trial matching for precision oncology and rare-disease care. Transforms a patient's molecular profile (mutations, biomarkers, expression) and clinical state into ranked clinical-trial recommendations with evidence tiers. Searches ClinicalTrials.gov, the EU CTIS register (European/EEA trials), AND the ISRCTN registry (UK/international) plus cross-references CIViC, OpenTargets, ChEMBL, and FDA labels. Use for matching patients to trials by genotype, biomarker-driven trial selection, trial-eligibility scoring, and finding trials across the US, Europe, and the UK.

Translate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies. Use for standardizing cancer-type nomenclature in EHR free-text, building cohorts in OncoKB or GDC, mapping tumor-board notes to ontology codes, and ensuring consistent terminology across cancer-genomics pipelines.

Discover novel small-molecule binders for protein targets using structure-based and ligand-based screening. Covers druggability assessment, known-ligand mining (ChEMBL, BindingDB), similarity expansion, ADMET filtering, and synthesis feasibility. Use for hit identification, virtual screening, target-to-compounds workflows, and lead-finding before commit-to-medchem.

Use when writing or debugging MPS quotations and anti-quotations — "node literals" that create SNode trees inline in behavior, typesystem, intentions, generator, and other model code. Covers heavy quotations (`Quotation`, `<...>`), light quotations (`NodeBuilder`, constructor-style for bootstrapping), and the four anti-quotation varieties: child (`%(...)%`), list (`*(...)*`), reference (`^(...)^`), property (`$(...)$`). Reach for this skill whenever the task involves splicing runtime values into quoted node trees or choosing between heavy and light quotations.

Analyze an MPS language by name — discover concepts, properties, references, children, aspects (editor/constraints/behavior), and metadata. Use when investigating an unfamiliar language, exploring concept structure, or finding sample nodes to use as templates for JSON blueprints.

Define concepts, interface concepts, enumerations, and constrained data types in an MPS language's `structure` aspect. Covers smart-reference detection, alias rules, cardinality, INamedConcept usage, bulk creation, and the full `mps_mcp_alter_structure` / `mps_mcp_query_structure` reference. Use when authoring or modifying a language's structure model.

Code style rules for IntelliJ codebase. Use when writing or reviewing code for style compliance.

Use when adding a compiler or tool output parser for the Problems panel. Touches src/diagnostics/<name>.ts, src/diagnostics/build.ts, package.json (cmake.enabledOutputParsers), and package.nls.json. Triggers: "add parser", "new diagnostic parser", "parse compiler output".

Implements new RobustMQ MQTT connector integrations end-to-end using project conventions. Use when the user asks to add, implement, or support a new connector type such as webhook, opentsdb, clickhouse, influxdb, cassandra, mqtt bridge, or protocol-compatible targets.

7×24 chaos testing for RobustMQ. Injects broker-kill and network-delay faults, validates SDK client resilience across Python/Go/Rust/Java, and publishes a Markdown + JSON report to GitHub after each run.

Guided journey from a large aged codebase everyone fears to touch to one that is safe to change, legible, bounded, and resilient - paid down in place without a rewrite. Orchestrates eight skills phase by phase - working-with-legacy-code, refactoring-patterns, clean-code, software-design-philosophy, clean-architecture, pragmatic-programmer, release-it, domain-driven-design - asking the user questions at every decision point and recording results in the project docs/ folder (TESTING.md, TECH-DEBT.md, REMOVE-TECHNICAL-DEBT-PLAN.md) so the journey resumes across sessions. Use when the user wants to tame a legacy codebase, pay down technical debt safely, avoid a big-bang rewrite, or says 'we are afraid to touch this code'. For a fresh vibe-coded prototype, improve-code-quality; for greenfield structure, design-code-architecture; for a product-and-UX pass, improve-app; to optimize a working codebase for speed, architecture-optimization. For one framework in isolation, invoke that skill directly.