「deep sea」の検索結果

Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not have specific observations yet. For formulating testable hypotheses from data use hypothesis-generation.

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Open-source embedding database for AI applications. Store embeddings and metadata, perform vector and full-text search, filter by metadata. Simple 4-function API. Scales from notebooks to production clusters. Use for semantic search, RAG applications, or document retrieval. Best for local development and open-source projects.

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Build AI scientist systems with the ToolUniverse Python SDK for scientific research. Covers the 3 calling patterns (`tu.run` portable dict API, `tu.tools.X` function API, direct class instantiation), tool loading, batch execution, MCP server integration, and embedding-based tool search. Use for SDK programming, custom tool composition, benchmarking pipelines, and integrating ToolUniverse into research workflows.

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Orchestrates the full path from differential expression results to redundancy-collapsed functional enrichment: choose ORA vs GSEA, convert gene IDs per method, run enrichGO/enrichKEGG/enrichPathway/enrichWP or gseGO/gseKEGG (clusterProfiler, ReactomePA, rWikiPathways), and visualize. Use when a DESeq2/edgeR/limma result must become enriched GO terms, KEGG/Reactome/WikiPathways pathways, or a GSEA leading edge; when the input is a full ranking for all genes (GSEA, named decreasing vector) or only a pre-selected list (ORA plus a defensible background universe); or when assembling DE-to-pathway end to end. The DE list and ranking statistic come from differential-expression/de-results; per-method nuance lives in the pathway-analysis skills.

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Identify drug repurposing candidates via target-based, compound-based, and disease-based strategies. Combines drug-target-disease network reasoning with mechanism rationale, clinical-trial precedent, and patent/regulatory feasibility. Use for hypothesis-generating repurposing for orphan diseases, finding existing drugs for new indications, and prioritizing candidates by evidence and feasibility.

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Performs 3D shape-based similarity searching using ROCS (OpenEye), USRCAT (ultra-fast), Open3DAlign (RDKit), ESPSim (electrostatic), and ShaEP with explicit handling of Tanimoto-Combo (shape + color), shape vs ECFP4 complementarity, conformer-ensemble searching, alignment optimization, and scaffold hopping. Use when searching for shape-mimicking compounds with different scaffolds, identifying bioisosteric replacements, prospective scaffold hopping, or expanding hit series beyond 2D similarity.

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コードを書く時の実装原則（deep module 設計・seam・テスタビリティ・シーム限定 TDD・コメント規約・リーダブルコード）。新しい module・関数・エンドポイント・画面の追加、DB への書き込み、認可・入力検証の追加、既存構造を変えるリファクタを含む実装の開始時に使用。CSS・HTML・テンプレート等のフロントエンド資産も対象。既存関数内の数行修正と lint/CI 等の設定ファイルでは使わない。TypeScript/Python/Go の言語別ガイドを同梱。境界: バグ・エラーの原因調査は systematic-debugging が先、提出前の diff 確認は self-review。

Shared vocabulary for designing deep modules. Use when the user wants to design or improve a module's interface, find deepening opportunities, decide where a seam goes, make code more testable or AI-navigable, or when another skill needs the deep-module vocabulary.

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Conduct multi-round deep research on any GitHub Repo. Use when users request comprehensive analysis, timeline reconstruction, competitive analysis, or in-depth investigation of GitHub. Produces structured markdown reports with executive summaries, chronological timelines, metrics analysis, and Mermaid diagrams. Triggers on Github repository URL or open source projects.

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Interact with DeerFlow AI agent platform via its HTTP API. Use this skill when the user wants to send messages or questions to DeerFlow for research/analysis, start a DeerFlow conversation thread, check DeerFlow status or health, list available models/skills/agents in DeerFlow, manage DeerFlow memory, upload files to DeerFlow threads, or delegate complex research tasks to DeerFlow. Also use when the user mentions deerflow, deer flow, or wants to run a deep research task that DeerFlow can handle.

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Create comprehensive academic research notes with deep literature coverage. Auto-detects language (EN prompt→EN output, TR prompt→TR output). Supports Obsidian markdown and PDF. Performs 8-15 iterative search cycles with 25-50+ sources for comprehensive coverage. Uses footnote citations and visual overviews.

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[21] UNDERSTAND. Deep research workflow for this project using 150% scope (100% core + 50% boundary), evidence-based reasoning, and structured investigation notes. Use when the task requires investigation, root-cause analysis, or mapping unknown areas. Always maintain a research log file that captures findings, hypotheses, and next branches; use web.run when external verification is needed.

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[22] UNDERSTAND. Deep research from all sources — internal (code, git, logs) AND external (web, docs, best practices). Use when choosing libraries, investigating solutions, understanding legal/technical questions, comparing approaches, or anytime you need comprehensive knowledge from both project context and world knowledge. Triggers on "research", "investigate", "find best approach", "what do others do", "compare options", or complex questions requiring multiple sources.

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Conduct multi-round deep research on any GitHub Repo. Use when users request comprehensive analysis, timeline reconstruction, competitive analysis, or in-depth investigation of GitHub. Produces structured markdown reports with executive summaries, chronological timelines, metrics analysis, and Mermaid diagrams. Triggers on Github repository URL or open source projects.

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Interact with DeerFlow AI agent platform via its HTTP API. Use this skill when the user wants to send messages or questions to DeerFlow for research/analysis, start a DeerFlow conversation thread, check DeerFlow status or health, list available models/skills/agents in DeerFlow, manage DeerFlow memory, upload files to DeerFlow threads, or delegate complex research tasks to DeerFlow. Also use when the user mentions deerflow, deer flow, or wants to run a deep research task that DeerFlow can handle.

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Use when user requests research requiring multiple sources, comprehensive analysis, or synthesis across topics - technical research, domain knowledge gathering, market analysis, or learning about complex subjects

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Automate Deepgram tasks via Rube MCP (Composio). Always search tools first for current schemas.

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Uses Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and recurring web monitoring. Best for requests that explicitly need current web evidence, academic-source discovery, repeated entity lookups, exhaustive reports, or ongoing change tracking.

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Looks up precomputed AlphaGenome Atlas effects for any GRCh38 single-nucleotide variant (AVI score with Phred and 18 SHAP feature attributions, plus raw and quantile scores for RNA-seq, DNase, ATAC, ChIP-TF, ChIP-histone, CAGE, PRO-cap, splicing, polyadenylation and contact-map tracks), scores variants or scans windows on demand with the AlphaGenome model for human and mouse (variant scoring, in silico mutagenesis, REF-versus-ALT track prediction), and builds Atlas website deep links. Use when the user mentions AlphaGenome, AlphaGenome Atlas, AVI or AlphaGenome Variant Impact, DeepMind variant effect prediction, or wants to prioritise or mechanistically interpret non-coding, regulatory, splicing, enhancer, promoter, or chromatin-accessibility effects of SNVs from a VCF, credible set, or region. Research use only; not a clinical tool.

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Courses whose content rests on current, external or real-world facts that must be verified against live sources before being taught — recent events, market or policy data, product and version specifics, scientific developments, named cases. Researches the topic first, keeps a claim-to-source ledger, and grounds the outline and every page in what was actually fetched. Use when the request depends on up-to-date or externally checkable facts; not for timeless textbook topics that stand on established knowledge alone.

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Two related workflows for a locally-cloned codebase, in one skill. Documentation mode produces a single, comprehensive, verifiable architecture document primarily by reading files on disk (local-first) — use it whenever the user wants to understand, map, document, research, or onboard onto a codebase ("research this repo", "write up the architecture", "do an architecture deep dive", "document how this codebase works", "map the system design", "create an onboarding doc"). Modernization mode generates a phased plan to modernize, migrate, upgrade, or rewrite a legacy system ("modernize this", "plan the migration", "how would we rewrite this", "how do we get off this legacy stack"); if no architecture document exists yet it first runs Documentation mode, then continues straight through to the plan. It assumes the legacy stack may be dead, runs a time-boxed feasibility spike, and picks the highest achievable rung on a safety ladder instead of demanding a fully-green legacy CI gate up front.

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Periodic architecture survey — walks the module graph and reports ranked deepening candidates (shallow modules, hypothetical seams, logic behind the wrong seam). Survey, not rescue: it finds candidates and hands them to the captain; it never refactors on its own.

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Create comprehensive industry and sector landscape reports covering market dynamics, competitive positioning, key players, and thematic trends. Use for client requests, sector initiations, thematic research pieces, or internal knowledge building. Triggers on "sector overview", "industry report", "market landscape", "sector analysis", "industry deep dive", or "thematic research".

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Deep research framework for pre-IPO / private companies (Ant Group, SpaceX, Stripe, ByteDance...). Six analyst lenses — business model, financial forensics, competitive landscape, risk & governance, tech & IP, alternative-data signals — run in parallel via run_swarm, then cross-validated for signal consistency before any verdict. Built around the core challenge of private-company work: information is scarce, so every data point carries a confidence label (high / medium / low), inference is shown separately from fact, and 'I don't know' is a valid output. Outputs a fair-value range, exit-path analysis, and an information-gap map. Use for any unlisted company where you need to judge what the business is actually worth.

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