디자인 스킬

Quantify homologous recombination deficiency (HRD) from tumor copy number using the three genomic-scar metrics — loss of heterozygosity (LOH), large-scale state transitions (LST), and telomeric allelic imbalance (TAI) — with scarHRD, and via the whole-genome HRDetect and CHORD models. Covers the genomic instability score, the PARP-inhibitor clinical context, whole-genome-doubling correction, and the scar-versus-state distinction. Use when computing an HRD score for PARP-inhibitor eligibility, deriving LOH/LST/TAI scars from allele-specific copy number, deciding between scar-based and mutational-signature HRD methods, or interpreting an HRD result in a BRCA-reverted or low-purity tumor.

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Discover RBP binding motifs from CLIP-seq peaks or single-nucleotide crosslink sites using HOMER, MEME/STREME, kpLogo, mCross (CL-position-registered motifs), PEKA (positional k-mer enrichment), RBPamp (affinity), and RNA Bind-n-Seq (RBNS) cross-validation. Use when characterizing RBP sequence specificity, registering motifs to crosslink positions, validating in vivo CLIP motifs against in vitro RBNS Kd, reconciling motif disagreements across tools, or correcting for the uracil crosslinking bias that contaminates raw CLIP motif logos.

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Infer orthologous genes and gene families across species using OrthoFinder3 (HOG-based phylogenetic orthology), SonicParanoid2, Broccoli, ProteinOrtho, OMA / FastOMA hierarchical orthologous groups, eggNOG-mapper, JustOrthologs, and TOGA whole-genome-alignment orthology. Use when building single-copy ortholog sets for phylogenomics, classifying co-orthologs and in/out-paralogs after gene duplication, propagating functional annotation via orthology with awareness of the ortholog conjecture, distinguishing speciation from duplication via gene-tree species-tree reconciliation, computing Quest-for-Orthologs benchmark performance, or running synteny-aware ortholog detection in WGD-affected lineages.

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Designs PROTACs, molecular glues, and bivalent degraders with explicit handling of E3 ligase choice (VHL, CRBN, IAP, MDM2, KEAP1), linker design (length, composition, rigidity), ternary complex prediction (PRosettaC, DeepTernary, AlphaFold3 with constraints), cooperativity (alpha), DC50 / Dmax characterization, hook effect, and prediction-experiment reconciliation. Use when designing targeted protein degraders, planning linker SAR, predicting ternary complex stability, or building generative degrader workflows.

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Designs covalent inhibitors and warheads targeting cysteine (most common, 98% of covalent drugs), lysine, serine, threonine, tyrosine, and aspartate residues, with explicit handling of warhead reactivity (acrylamide, chloroacetamide, vinyl sulfone, sulfonyl fluoride, fluorosulfate, aldehyde, boronate, nitrile), reversibility (kinact/Ki, t_residence), glutathione (GSH) stability, intrinsic reactivity assays, and covalent docking (DOCKovalent, GOLD, HCovDock). Use when designing covalent inhibitors for targeted covalent inhibition (TCI), KRAS G12C-style approaches, or rationalizing covalent SAR.

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Designs novel molecules using REINVENT 4 (de novo, scaffold decoration, linker design, R-group, molecular optimization), MolMIM, Diffusion-based generators (DiGress, DiffSMol), and JT-VAE with explicit handling of multi-parameter optimization (MPO), goal-directed scoring functions, transfer/reinforcement/curriculum learning, synthetic accessibility scoring, and chemical space exploration vs exploitation. Use when designing new chemical matter against a target, decorating a scaffold, linking fragments, or optimizing a hit for multiple ADMET / activity properties simultaneously.

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Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, building-block availability (eMolecules, Enamine, Mcule), forward prediction validation (Molecular Transformer), and disconnection-aware multi-objective search (MO-MCTS). Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.

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Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue), MMSplice (modular per-region CNN with calibrated ΔPSI), SpliceTransformer/TrASPr (tissue-aware transformers), SpliceVault (empirical 300K-RNA lookup of likely mis-splicing outcomes), CADD-Splice (composite score). Applies the ClinGen SVI 2023 framework for ACMG/AMP variant interpretation (PVS1, PP3, BP4 evidence codes), HGVS splicing nomenclature (c.123+1G>A, c.123-3T>G, r.spl?), extended-window scoring for deep-intronic pseudoexons, tissue-specific predictions, branchpoint variant detection (BPHunter, LaBranchoR), and splice-switching ASO design. Use when interpreting splice impact of clinical variants, prioritizing VUS, identifying deep-intronic pathogenic variants, or designing ASOs.

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Add MAUI DevFlow to a .NET MAUI project with agent package references, MauiProgram.cs registration, Blazor WebView support, GTK variants, Central Package Management guidance, and verification commands. USE FOR: first-time DevFlow setup, reviewing what files to edit, choosing DevFlow packages, or continuing after `maui devflow init` installs skills. DO NOT USE FOR: troubleshooting an already-integrated app that cannot connect, iterative app debugging, UI inspection, or generic MAUI build failures (use maui-devflow-debug). INVOKES: maui devflow CLI and dotnet CLI.

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Use this skill when the user asks how to design or improve a Preventive Maintenance (PM) program for a fleet — mileage vs time intervals, A/B/C/D inspection levels, ATA standards, common PM tasks, scheduling software, cost tracking, and how PM affects roadside inspections + CSA scores. Reference ATA Equipment Maintenance Council standards.

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Use this skill to design a vehicle preventive maintenance schedule. Covers manufacturer recommendations, industry-standard intervals, and how to set carrier-specific triggers.

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Use this skill to design an annual driver refresher training program. Covers what to cover, frequency, documentation, and ROI.

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Use when a dispatcher, operations manager, or owner asks how to plan loads to minimize empty (deadhead) miles, sequence freight efficiently, balance regional capacity, design dedicated loops, or build a load-pairing strategy across customers. Covers loaded-ratio math, lane balance, region-pair pricing, and software-supported optimization.

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Use this skill when the user asks about trucking dispatch software — McLeod, TMW (Trimble), Tailwind, Truckbase, AscendTMS — vs load boards — DAT, Truckstop, 123Loadboard, Convoy, Uber Freight. Covers the workflow (find load, book, dispatch, run, settle), how dispatch software integrates with ELDs + accounting + customer EDI, and what small fleets vs larger fleets typically use.

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Use this skill when the user asks how to design or improve a fleet safety scorecard — what KPIs to track, how to weight them, telematics signals vs document compliance vs roadside outcomes, monthly cadence, driver-facing vs admin-facing dashboards, gamification considerations, peer-comparison metrics, and how a scorecard ties to insurance premiums + retention. Reference SMS Methodology v3.20 for industry-standard weights.

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Expert landscape designer transforming yards through photo mapping, 3D visualization, seasonal planning, and deep plant knowledge. Specializes in fast-growing privacy screens (knows arborvitae pitfalls), architecture-appropriate design, outdoor living spaces, and realistic maintenance expectations. Activate on "landscape design", "yard design", "garden planning", "plant selection", "privacy screen", "outdoor living", "backyard makeover", "arborvitae", "hedge", "fast growing tree", "landscaping ideas". NOT for interior design (use interior-design-expert), hardscape construction (consult contractors), or lawn care chemicals (consult local experts).

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Design resilient React error handling with Error Boundaries, Sentry integration, recovery UI, retry patterns, and graceful degradation. Activate on: error boundary, crash recovery, Sentry, error fallback UI, retry logic, unhandled exceptions. NOT for: form validation errors (use form-validation-architect), API error codes (use api-architect).

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Operationalizing an expungement website — user intake flows, document generation pipelines, court filing integrations, payment processing, state-by-state workflow variations, customer support for sensitive populations, and the handoff between automated systems and human legal review. Activate on 'expungement operations', 'legal tech SaaS', 'court filing integration', 'document automation pipeline', 'expungement business', 'legal service workflow', 'multi-state legal operations'. NOT for expungement law itself (use national-expungement-expert), web design (use legal-tech-web-design), or legal document drafting (use recovery-app-legal-terms).

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Build low-fidelity wireframes, screen mockups, and user-flow diagrams in Frame0 (the hand-drawn Balsamiq-style wireframing tool) through its connected MCP server. Use when asked to wireframe a screen, sketch a UI, make a low-fi mockup, lay out an app's screens, or diagram a user flow with clickable links. Triggers: "wireframe", "frame0", "low-fi mockup", "sketch a screen", "user flow", "lo-fi", "rough out the UI". NOT for high-fidelity visual design, brand systems, or color/typography polish (use web-design-expert / Figma); NOT for production UI code (use frontend skills).

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Interpret and design bounded FIPA communicative-act exchanges using XC00037H semantics while keeping delivery, authority, and external effects separate. NOT for proving delivery, task authorization, or external effect completion.

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Schema design, normalization decisions, indexing strategies, and migration safety for relational databases. Use when designing tables, choosing between normalize vs denormalize, selecting index types, planning zero-downtime migrations, or setting up connection pooling. Activate on "schema design", "normalization", "denormalization", "foreign key", "index strategy", "migration", "connection pooling", "composite key", "surrogate key", "soft delete", "polymorphic association". NOT for PostgreSQL-specific query tuning or EXPLAIN analysis (use postgresql-optimization), NoSQL or document database design, or cloud database provisioning.

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Creates comprehensive documentation for design systems - token tables, usage guidelines, component examples, and accessibility notes. Use after generating tokens to create developer-friendly docs.

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Master of text-based visual communication using ASCII art, Unicode box-drawing, and structured diagram notation. Creates clear, maintainable diagrams for systems, processes, hierarchies, relationships, and psychological structures. Proactively generates diagrams to enhance understanding. Activate on visualization needs, system architecture, process flows, psychological mapping, or when complex concepts would benefit from visual representation. NOT for photo editing, vector graphics, or GUI-based design tools.

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Domain-Driven Design methodology using bounded contexts, ubiquitous language, and strategic/tactical patterns

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