리서치·학습 스킬

Summarize extracted paper text into concise Markdown memory for later Stage 2 and Stage 4 background use, with fixed section headings and no fabricated claims.

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Remove AI-generated writing patterns from rebuttal prose to make it sound natural, direct, and authentically human-authored. Use when a Stage 2 refined draft or Stage 4 follow-up response reads too formulaic, robotic, or "GPT-like". Supports academic English.

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Guides collaborative requirements discovery before implementation. Creates task directory, seeds PRD, asks high-value questions one at a time, researches technical choices, and converges on MVP scope. Use when requirements are unclear, there are multiple valid approaches, or the user describes a new feature or complex task.

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Captures executable contracts and coding conventions into .trellis/spec/ documents. Use when learning something valuable from debugging, implementing, or discussion that should be preserved for future sessions.

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Provider-independent production workflow for AI agents creating educational animated lessons, classroom explainers, STEM visualizations, history/social-science animations, training modules, microlearning clips, whiteboard-style explainers, diagram-driven videos, and generated or assembled instructional animation assets. Use when planning, scripting, storyboarding, generating, reviewing, localizing, or QAing animation whose primary purpose is learning.

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Find academic papers across up to 8 sources (OpenAlex / Semantic Scholar / CrossRef / PubMed / arXiv for English, OpenReview for AI venues, plus native-Chinese retrieval via NSSD 国家哲社文献中心 + yiigle 中华医学期刊) with adjustable depth — Quick scan (5 min) to Audit prep (3 hr). Use when the user wants to find papers, run a literature search, gather references, scope a research topic, search Chinese-language / 中文原生 literature (中文文献/中文核心/CSSCI/C刊/国内研究/国内文献/中华××期刊/心理学报/经济研究), or filter results by journal tier (中科院分区/一区/几区, Q1, JCR/SJR quartile, 影响因子/impact factor, 期刊分区, 顶刊/top journal, '按分区筛'), or export paste-ready professional search strategies / 检索式 for external databases (PubMed / WOS / Scopus / Embase / 知网 CNKI / 万方 / SinoMed — '写检索式', '导出检索式', 'WOS 检索式', '知网专业检索', 'search strategy', 'boolean search strategy'). Triggers on search verbs ('find papers', 'literature search', 'papers about X'), review types ('scoping review', 'systematic review', 'SR prep', 'literature review', 'lit review', 'help me write a lit review'), Chinese ('找文献', '找论文', '论文搜索', '学术检索', '文献检索', '文献综述', '综述前期', '求文献', '中文文献', '中文核心', 'CSSCI', 'C刊', '国内研究', '找中文的'). Outputs Shadcn HTML report + BibTeX/RIS/CSV + PRISMA-S log. Do NOT use for: concept explanations ('what is X' / 'X 是什么', e.g. '影响因子怎么算'), writing ('帮我写' / 'help me write a paragraph'), single-paper interpretation or PDF download with metadata (use paper-downloader-portable), or when the user already has a literature set (use literature-set-review).

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当系统提示需要设计引用格式、信息溯源机制、来源标注系统时调用。适用于文档问答、搜索增强生成（RAG）、代码引用、浏览器辅助等需要让用户追溯信息来源的场景。不适用于纯创作类输出（如故事、诗歌），不适用于无需溯源的常识问答，也不适用于注入防御（虽然两者都涉及内容可信度）。

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Manage the operational learnings lifecycle — load prior learnings to inform current work, harvest new patterns worth preserving, and keep the document tight over time. Provides a protocol for accumulating actionable patterns from practice that complement standards and defaults. Use when a workflow session completes and produced insights worth persisting, when starting a session that should benefit from prior patterns, or when the user says 'harvest learnings', 'what have we learned', 'capture this pattern', 'tighten learnings', 'compress learnings', or 'operational learnings'.

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Help fantasy players make start/sit, waiver, streaming, trade, draft and keeper decisions using current player news, usage, matchups and their league's scoring. Use for choosing between players, finding pickups, evaluating a deal or filling a roster need, even without an explicit research request. Excludes generic sports scores, betting and changing league rosters.

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Extract structured company lists with Firecrawl from any page or site that lists companies: accelerator batches, VC portfolios, member and sponsor lists, marketplaces and app directories, YC, Crunchbase, Product Hunt or G2. Use when the user wants those companies as a CSV, JSON, CRM-ready list or research table, even without an explicit request to scrape.

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Produce an intensive, cited analytical report: executive summary, multi-angle findings, contrarian views, open questions, and full sources. Use only when the user needs rigorous synthesis of a complex topic (scientific, technical, policy, or market-analytical) that cannot be answered with a short search, and wants a formal written report, not a recommendation list. Do not use for product picks, top-N lists, quick lookups, or routine "find out about X" tasks. If the request does not clearly need this kind of report, do not use this skill. Do not use for a literature review over published papers. This skill collects evidence from the open web. A request for the literature on a biomedical, clinical, life-science, or other scientific topic — papers, studies, trials, preprints — belongs to firecrawl-research-papers, which queries Firecrawl's paper index (PubMed, bioRxiv, medRxiv, arXiv) instead of searching websites.

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Research markets and companies with Firecrawl using current, cited figures: market size, growth, trends, financials and earnings. Use when the user asks for market research, an industry overview or a comparison of companies by the numbers, since these figures change faster than training data.

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Enrich and research the people and companies the user names or supplies with Firecrawl Alexandria data: background on a person, a professional profile URL to look up, whether someone still holds a role, missing columns in a table or CSV of people or companies, firmographics for company domains (industry, headcount, funding, location), and pre-call or meeting briefs. Use whenever the request is about specific named people or companies, even without the word enrich, since roles, headcount and funding change faster than training data. Not for finding new prospects (use firecrawl-lead-gen) or a company's published press, sales or support contacts (use firecrawl-business-contacts).

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Find and synthesize research papers, whitepapers, PDFs, technical reports, and academic sources with Firecrawl Research, using semantic paper search, related-paper expansion, and in-body verification over Firecrawl's paper index — largely biomedical and life-science literature from PubMed, bioRxiv, and medRxiv, plus arXiv preprints in CS, physics, and math. Use when the user wants a literature review, systematic review, survey of studies, paper summary, research landscape, or sourced synthesis from scholarly and industry publications, including clinical, drug, gene, disease, epidemiology, and public-health topics. Prefer this over a general web-research workflow whenever the evidence base is published papers rather than web pages.

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The Auto 档 scenario — a soft-plan orchestrator for a complete fundamental equity research thesis: understand → financials → valuation → synthesize. The body is a soft plan (stages), not a rigid DAG; correctness is enforced by each referenced skill's own requires: preconditions, never by this plan's rigidity (Q2).

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Adversarial verification of research theses — cross-run/cross-thesis contradiction via the entity index, pre-mortem (Klarman/Kahneman: assume the loss already happened, reverse the path), inversion (Munger: invert, always invert), and wrong_if falsifiability review. ≈50-finding cap sorted by severity; content-derived finding IDs; incremental scoping with three backstops; lifecycle hooks at pillar-complete / thesis-complete / pre-reduction.

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Create a research thesis — theses/{nnn}-{slug}/ via mkdir-as-CAS, pillar-prioritized spec.md, initialized thesis.md, and the thesis-quality checklist. Refuses creation while the workspace constitution is unratified (spec 046 Q83 A+).

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Author the research plan — fundamentals first, trade ideas last; Constitution Check evaluated twice; Deviation Register with mandatory Expiry; emits the four side artifacts (brief/entities/reproduce/contracts). Technical (market_data_stage: early) theses MUST emit the entities.md bars schema before implement (Q42).

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Execute research tasks — checklist soft gate, phase dispatch with explicit thesis_dir, budget enforcement (halt + approval card on overrun), skill_pin recording (version_hash content-hashed per skill directory), [x] written on completion.

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The research-domain clarification skill — find underspecified items in a thesis spec.md (prose wrong_if, universe rows without rationale, missing budget/expiry/pins, ambiguous pillars), ask the human structured questions WITH options (max 5 per round), encode the answers back into spec.md's Clarifications section, and re-evaluate checklists/thesis-quality.md after every write (Q32 bidirectional maintenance).

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Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or EnFormer. Use when correcting Tn5 bias with neural networks beyond k-mer models, predicting per-base accessibility profiles, scoring in silico variant effects at GWAS or rare-variant SNPs, discovering motifs via DeepLIFT/TF-MoDISco from a trained model, or generating cell-type-specific accessibility predictions for unobserved cell states.

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Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinical or research applications.

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Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2025 Nat Genet; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

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Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications. Use when interpreting clinical significance of variants.

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