设计技能

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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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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Designs covalent inhibitors and warheads targeting cysteine, 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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Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).

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End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.

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Master REST and GraphQL API design principles to build intuitive, scalable, and maintainable APIs that delight developers. Use when designing new APIs, reviewing API specifications, or establishing API design standards.

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How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`.

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Suite of tools for creating elaborate, multi-component claude.ai HTML artifacts using modern frontend web technologies (React, Tailwind CSS, shadcn/ui). Use for complex artifacts requiring state management, routing, or shadcn/ui components - not for simple single-file HTML/JSX artifacts.

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Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-aware task design, and building systems that actually work for neurodivergent minds.

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Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

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Write Ruby gems following Andrew Kane's proven patterns and philosophy. Use when creating new Ruby gems, refactoring existing gems, designing gem APIs, or when the user wants clean, minimal, production-ready Ruby library code. Triggers on requests like "create a gem", "write a Ruby library", "design a gem API", or mentions of Andrew Kane's style.

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Implement proven backend architecture patterns including Clean Architecture, Hexagonal Architecture, and Domain-Driven Design. Use when architecting complex backend systems or refactoring existing applications for better maintainability.

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Propose a new change with all artifacts generated in one step. Use when the user wants to quickly describe what they want to build and get a complete proposal with design, specs, and tasks ready for implementation.

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Implement Google's Material Design 3 (Material You) UI system. Primary: Jetpack Compose Material3 (MaterialTheme, components, adaptive layout). Also Flutter and limited web (@material/web, maintenance mode). Covers tokens, 30+ components, layout, theming, M3 Expressive (platform matrix), and accessibility. Use when: "material design", "MD3", "material you", "Jetpack Compose", "MaterialTheme", "material component", "md3 button".

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Shape reusable library APIs for Compose modules. Design public composables, split sample-app code from reusable library code, review naming and extensibility.

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Interactive logo & brand design strategist. Runs a strategy workshop, narrows a creative direction, lands a single centralized concept, then outputs a condensed branding table plus 10+ logo ideas with rationale. Use when the user wants to design a logo, develop a brand identity, write a logo brief, brainstorm logo concepts, or run brand strategy before sketching. Triggers include "design a logo", "logo ideas", "brand identity", "help me with my logo", "logo brief", "what should my logo be".

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Prepare, execute and verify authorized Fusion CAD changes using resolved entities, explicit units and state-bound plans. Use for reviewed parameter, sketch, feature, assembly or configuration operations.

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Configure and diagnose Fusion interoperability, transport selection, scoped profiles and qualification. Use for setup or connection problems, not design edits.

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Inspect an explicit Fusion design, parameters, geometry, references, configuration and health without editing it. Use for model understanding or engineering audits.

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Develop, challenge, and document Chisel processor microarchitecture designs before implementation. Use when discussing or writing design documents for processor pipelines, queues, issue logic, rename, ROB, LSU, caches, MSHRs, forwarding, wakeup, replay, flush, privilege, exceptions, or other cycle-accurate hardware mechanisms; when converting design conversations into stable Markdown specifications; or when reviewing a proposed Chisel CPU design for correctness, timing, area, verification cost, and cross-document consistency.

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Document-driven workflow for implementing, reviewing, and verifying Chisel processor and memory-subsystem RTL. Use when Codex must work from maintained Architecture and Design, trace a complete integration surface, reason in synthesized-hardware terms, keep source-adjacent _codex.md summaries current, avoid redundant or overprotective logic, or run focused functional verification.

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Design randomized controlled trials for causal inference. Use when user mentions: randomized evaluation, RCT, field experiment, randomized experiment, treatment assignment, causal impact, experimental design, control group, intervention evaluation.

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Auto-activate for litestar_saq, SAQPlugin, SAQConfig, QueueConfig, TaskQueues, CronJob, litestar workers run, background jobs, schedules, or SAQ UI. Not for litestar-queues, Celery, RQ, or Dramatiq.

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PRD 到高保真 UI 交付对齐 / 桌面工作台 UI mockup：当用户已有 PRD、UI 规范、真实前端项目路径、截图或页面状态清单， 需要先从 PRD 提炼 UI 结构、状态模型和 ASCII 布局，再进入高保真 mockup、项目原生 preview 或开发交付 handoff 时使用。 优先输出项目原生 preview route/component；只有早期概念确认或无法接入真实项目时才输出 standalone HTML。 必须包含结构阶段产物、screen contract、component map、implementation notes、截图/验证结果和 HTML/preview 的迁移边界。

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