68 件 ・ 関連度順
概要と使いどころ
Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences. Use when predicting MHC binding for vaccine design or neoantigen identification.
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Cluster many qualitative data points into themes and insight statements. Use when synthesising across multiple sessions or sources. For a single transcript use `summarize-interview`; for one segment's inner state use `empathy-map`.
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Turn one interview transcript into themes, supporting quotes, and action items. Use immediately after a session. For synthesising many sessions at once, use `affinity-diagram`.
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Reconcile what the numbers say with what users say, and design the study that settles it rather than restates it. Use when behavioural data and research findings point different ways. For reading the data on its own, use `behavioural-analytics`; for synthesising interviews on their own, use `affinity-diagram`.
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Build a repository that makes findings findable, reusable, and cumulative across teams. Use when the same research keeps getting redone. For synthesising one study, use `affinity-diagram`.
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Build a Says, Thinks, Does, Feels map for one user or segment. Use when sharing user understanding quickly. For a composite archetype with goals and behaviours use `user-persona`; for cross-session themes use `affinity-diagram`.
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Predict peptide-MHC class I binding and natural presentation with MHCflurry, NetMHCpan-4.1, and MixMHCpred to nominate candidate CD8 T-cell epitopes. Covers the binding-affinity (BA) vs eluted-ligand (EL/presentation) distinction, why %Rank beats raw nM for cross-allele work, the MS abundance bias that misranks low-expression neoantigens, allele-coverage inequity, and length bias. Use when scanning a protein or peptide set for class I epitopes, scoring neoantigen candidates, or choosing a binding predictor. For CD4/HLA class II see mhc-class-ii-prediction.
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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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Performs ML-based protein-ligand pose prediction and scoring using DiffDock-L (diffusion-based), Boltz-1 / Boltz-2 (foundation model with affinity), Chai-1, AlphaFold3 ligand, EquiBind, TANKBind, NeuralPLexer, and hybrid workflows (DiffDock pose + GNINA rescore + PoseBusters QC). Explicit handling of when ML beats classical docking, when classical beats ML, the PB-invalid pose problem, and rescoring as the standard production hybrid. Use when modern docking is needed: foundation-model ligand-pose prediction, AI rescoring of classical poses, or scaffold-hopping in cross-docking scenarios.
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Query BindingDB for protein-ligand binding affinity data
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A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
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Scroll-native one-page landing that overwhelms — concept, composition, asset placement, and scroll choreography derived from DESIGN.md and the measured landing-craft codex. Trigger: '랜딩 페이지', '원페이지', 'landing page', 'one-pager', 'hero to footer', '스크롤 랜딩', 'affinity.studio 같은'.
日本語の概要は準備中です。原文の説明を表示しています。
Scroll-native one-page landing that overwhelms — concept, composition, asset placement, and scroll choreography derived from DESIGN.md and the measured landing-craft codex. Trigger: '랜딩 페이지', '원페이지', 'landing page', 'one-pager', 'hero to footer', '스크롤 랜딩', 'affinity.studio 같은'.
日本語の概要は準備中です。原文の説明を表示しています。
Agent reputation scoring, performance tier system, trust calibration, and task affinity matching
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Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
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Designing scientific schematics, diagrams, and graphical abstracts. Covers tool selection (BioRender, Inkscape, Affinity, PowerPoint), design principles for pathway diagrams, mechanism schematics, experimental workflows, and journal graphical abstracts. Includes composition, icon sourcing, color for biological entities, and accessibility. Use when creating illustrative (not data-driven) scientific figures.
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smina molecular docking CLI. AutoDock Vina fork with customizable scoring functions, native SDF/MOL2/PDB ligand input, autoboxing, local energy minimization, and per-atom score breakdowns. Pipeline: receptor PDBQT prep -> ligand prep (RDKit/OpenBabel) -> dock via autobox or explicit grid -> rescore/minimize with custom scoring -> rank poses by affinity. Choose smina over Vina when you need custom scoring terms (--custom_scoring), local optimization of an existing pose (--local_only), per-atom contributions (--atom_term_data), or SDF/MOL2 ligands without manual PDBQT conversion. For unknown binding sites use diffdock; for the Python-bindings/Vinardo workflow use autodock-vina-docking.
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API + Python SDK for ordering cell-free protein expression and binding assays. Submit sequences for expression (10–100 µg), measure binding affinity (KD) against targets, track status, and retrieve results programmatically — no wet-lab setup. Built for ML-guided directed evolution and antibody/nanobody optimization. Requires Adaptyv account and API key.
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Use DGL-LifeSci and dgllife for molecular graph learning, molecule featurization, datasets, property prediction, reaction prediction, binding affinity, model-zoo/pretrained models, and molecular generation workflows.
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Route Boltz package tasks for biomolecular structure and affinity prediction, data preparation, training, and evaluation workflows.
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Think and work like an expert Molecular Biologist. Use when a task calls for Molecular Biologist judgment. Reasons from central-dogma sequence flow, binding affinity (Kd/Km/kcat), gene regulation, and biological-versus-technical replicate structure through MIQE-compliant RT-qPCR, ddPCR, Western/flow/microscopy, CRISPR editing with rescue, and IWGAV antibody validation while treating off-target reagent effects, batch effects, mycoplasma and cell-line misidentification, and toxicity-driven artifacts as first-class failure modes.
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Think and work like an expert Fluid Mechanics Engineer. Use when a task calls for Fluid Mechanics Engineer judgment. Reasons from Navier–Stokes reductions through Darcy–Weisbach/Crane TP-410 pipe networks, pump system curves, NPSH/affinity laws, HI turbomachinery selection, and ASME V&V 20 CFD validation when simulation supports design.
日本語の概要は準備中です。原文の説明を表示しています。
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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产品设计 / UX 设计 (产品设计 / UX 设计 (Product Design / UX Design) — 数字产品的用户体验设计：从用户研究 → 信息架构 → 交互设计 → 视觉/UI → 可用性测试 → 设计系统的认知操作系统，面向 UX designer / product designer / interaction designer / UX researcher / design systems engineer / design lead，以及想入行、转岗、服务这行(设计外包、设计工具厂商、研究平台)的视角。覆盖: (a) 第一性张力 — **用户中心/研究驱动 (user-centered, 'you are not the user', research before pixels, observe behavior not opinions) ⇄ 商业目标/约束/交付 (business goals, north-star metrics, ship it, designer 服务于产品成功不是个人作品集)**; **设计直觉/品味/craft (taste, aesthetics, 'attractive things work better' — Norman 情感化设计) ⇄ 数据/实验/A-B 测试 (data-driven, metrics, experimentation, 'opinions are not data')**; **用户说的 (stated preference, 访谈里说喜欢) ⇄ 用户做的 (revealed behavior, 行为观察 > 自陈, usability test 看人真实卡在哪)**; **一致性/设计系统/规范 (consistency, design system, Jakob's law 用户带着别处的习惯来, 复用组件) ⇄ 创新/打破模式 (innovation, 该不该破规范)**; **减法/简化 (simplicity, Krug 'Don't Make Me Think', less but better — Dieter Rams) ⇄ 功能丰富/利益相关者塞需求 (feature creep, stakeholder pressure)**; **UX(体验/流程/研究) ⇄ UI(视觉/像素/组件)** 的职责之争, **designer 该不该写代码 (design engineer / 'should designers code')**; (b) 核心工作流 / pipeline (最标准、最易蒸高质量+CLI 化) — Double Diamond (发现 discover → 定义 define → 开发 develop → 交付 deliver) / Design Thinking (共情 empathize → 定义 → 构思 ideate → 原型 prototype → 测试 test) / Design Sprint (Jake Knapp 5 天冲刺); 完整链: 用户研究 (访谈/问卷/可用性测试/卡片分类) → persona / journey map / JTBD → 信息架构 IA + 用户流 user flow → 线框 wireframe (低保真) → 交互/原型 prototype (高保真) → 视觉 UI / 设计系统落地 → 可用性测试 usability testing → handoff 给开发 → 度量迭代 (北极星 / HEART 框架); (c) 工具栈 — 设计/原型 (Figma 绝对主导 / Sketch 衰退 / Adobe XD 已停更 / Framer 高保真+建站 / Penpot 开源 / Principle / ProtoPie 微交互); 协作白板 (FigJam / Miro / Mural); 用户研究 (Maze / UserTesting / Lookback / Dovetail 研究库 / Optimal Workshop 卡片分类树测试 / Hotjar / Microsoft Clarity 热图); 设计系统/交付 (Storybook / 蓝湖(中) / Zeplin / design tokens / Tokens Studio); 度量 (Amplitude / Mixpanel / 北极星指标); AI 新兴 (Figma AI / v0 by Vercel / Galileo AI / Uizard / Cursor 给 design engineer); (d) 知识正典 — Don Norman《The Design of Everyday Things》(affordance/signifier/mapping 圣经)、Steve Krug《Don't Make Me Think》(可用性入门)、Alan Cooper《About Face》《The Inmates Are Running the Asylum》(交互设计/persona 起源)、Jakob Nielsen 10 Usability Heuristics + NN/g 文章库、Jake Knapp《Sprint》、Jeff Gothelf《Lean UX》、Teresa Torres《Continuous Discovery Habits》、Erika Hall《Just Enough Research》、Julie Zhuo《The Making of a Manager》、《Refactoring UI》(Adam Wathan/Steve Schoger)、《Universal Principles of Design》、Laws of UX (Jon Yablonski)、《100 Things Every Designer Needs to Know About People》(Susan Weinschenk)、IDEO/Stanford d.school 设计思维材料; (e) figures/流派 — 认知心理/人因派 (Don Norman 认知科学奠基、Susan Weinschenk 行为心理、Kathryn Whitenton); 可用性工程派 (Jakob Nielsen 启发式/折扣可用性、Steve Krug、Jared Spool UIE); 交互设计/目标导向派 (Alan Cooper goal-directed/persona、Kim Goodwin); 设计思维派 (IDEO Tim Brown、David Kelley d.school); 精益/持续探索派 (Jeff Gothelf Lean UX、Teresa Torres continuous discovery、Marty Cagan《Inspired》产品发现); 设计系统/系统化派 (Brad Frost Atomic Design、Nathan Curtis design tokens、Alla Kholmatova); 视觉/UI craft 派 (Adam Wathan & Steve Schoger Refactoring UI、Dieter Rams 'less but better' 工业设计遗产); 设计领导/职业派 (Julie Zhuo、Aarron Walter 情感化设计、John Maeda); 移动优先 (Luke Wroblewski 'Mobile First'); (f) 行业话术/黑话 — affordance 可供性 / signifier 意符 / mental model 心智模型 / IA 信息架构 / heuristic evaluation 启发式评估 / usability 可用性 / a11y accessibility 无障碍 / WCAG / persona 用户画像 / journey map 用户旅程 / JTBD jobs-to-be-done / north-star metric 北极星 / HEART 框架 / wireframe 线框 / mockup / prototype 原型 / fidelity 保真度 (lo-fi/hi-fi) / design system 设计系统 / design token 设计令牌 / atomic design 原子设计 / component library 组件库 / handoff 交付 / red routes 关键路径 / dark pattern 暗黑模式 / Fitts's law / Hick's law / Jakob's law / Miller 7±2 / progressive disclosure 渐进披露 / above the fold / hamburger menu / skeuomorphism vs flat / micro-interaction / empty state / edge case / happy path / design debt 设计债 / dogfooding / dot voting / affinity mapping 亲和图 / card sorting 卡片分类 / tree testing / A/B test / NPS / SUS (System Usability Scale); (
日本語の概要は準備中です。原文の説明を表示しています。