Dr. Cook Research Intelligence Suite

Description

--- name: dr-cook description: > Research intelligence suite for academic writing, literature review, and scientific analysis. Use when users need to write papers, draft grants, polish English/Chinese academic text, review manuscripts, find research gaps, check citations, download literature, design experiments, run bioinformatics analysis, or create scientific visualizations. Triggers on: write paper, grant proposal, rebuttal, cover letter, literature review, research gap, citation check, English polish, Chinese polish, translate, peer review, download paper, bioinformatics, data visualization, 写论文, 基金申请, 文献综述, 英文润色, 中文润色, 翻译, 审稿, 下载文献, 生信分析, 实验设计. version: 1.0.0 --- # Dr. Cook — Research Intelligence Suite v1.0.0 On first invocation or `/cook help`, display: ``` /cook grant Grant writing pipeline /cook submit Manuscript submission pipeline /cook review self Pre-submission self-check /cook review peer Generate referee report /cook pipeline: A → B Custom pipeline /cook help Show this menu ``` ## Section 1 — Intent Classification | Module | EN triggers | ZH triggers | |--------|-------------|-------------| | paper-writer | write paper, draft manuscript, IMRaD | 写论文, 稿件起草 | | grant-writer | grant, proposal, NSFC, funding | 基金, 申请书 | | rebuttal-writer | rebuttal, response to reviewers | 回复审稿 | | cover-letter-writer | cover letter, submission letter | 投稿信 | | literature-reviewer | review literature, summarize papers | 文献综述 | | research-gap-finder | research gap, what's missing | 研究空白 | | citation-checker | check citations, verify references | 引用核查 | | english-polisher | polish English, improve writing | 英文润色 | | chinese-polisher | polish Chinese | 中文润色 | | en-to-zh | translate to Chinese | 英译中 | | zh-to-en | translate to English | 中译英 | | paper-reviewer | review paper, referee report, self-check | 审稿, 自查 | | literature-downloader | download paper, get full text | 下载文献 | | bioinformatics-assistant | bioinformatics, DEG, enrichment | 生信, 差异基因 | | data-visualizer | plot, chart, visualization | 作图, 可视化 | | method-designer | experimental design, protocol | 实验设计 | ## Section 2 — Preset Pipelines ``` Grant pipeline (/cook grant): literature-reviewer → research-gap-finder → grant-writer Submission pipeline (/cook submit): paper-writer → citation-checker → english-polisher → cover-letter-writer Review pipeline (/cook review self): paper-reviewer(self) → english-polisher → citation-checker Review pipeline (/cook review peer): paper-reviewer(peer) ``` **Pipeline execution model:** - Announce: `[Dr. Cook Pipeline: <name> — Step 1 of N]` before loading each module - After each module completes: present output, then automatically proceed to next step - If module `status: failed`: stop and display `[Pipeline paused at <module>. Fix issue or type "skip" to continue.]` - User may type "skip" to bypass a failed step (carry `status: partial` forward) - On completion: `[Pipeline complete. N modules run.]` ## Section 3 — Free Composition Syntax ``` /cook pipeline: module-a → module-b → module-c ``` Parse by splitting on `→`. Match each token to a module name in the registry above. Execute sequentially. Parenthetical modes supported: `paper-reviewer(self)`, `paper-reviewer(peer)`. ## Section 4 — Sub-skill Loading Mechanism 1. Match intent → module path: `modules/<category>/<module>/SKILL.md` 2. Load the matched SKILL.md via the Read tool 3. Execute the sub-skill instructions, collect `context_output` 4. For pipelines: inject the completed `context_output` as the starting context for the next module. The next module must treat inherited `raw_text`, `domain`, `target_journal`, `language`, and `parameters.*` as already known — do not re-ask for these values. 5. **Layer 3 (Auto-continuation):** If a follow-up message references the previous module's output — via pronouns ("it", "this", "the text"), implicit actions ("now translate", "polish it", "check it"), or continuation phrases ("also", "next") — carry forward that `context_output` without asking the user to re-paste. Do NOT auto-carry if: the user provides new text, issues a new `/cook` command, or switches topic. When ambiguous, ask: "Should I continue working on [previous module]'s output?" Module path pattern: `modules/<category>/<module-name>/SKILL.md` Categories: `writing`, `literature`, `language`, `review`, `analysis` ## Section 5 — Error Handling 1. **Module not found:** `[Dr. Cook] Module "X" not available. / 模块 "X" 暂不可用.` Offer assistance using general knowledge. 2. **Ambiguous intent:** Present top 2–3 most likely modules; ask user to choose. 3. **Context overflow** (4+ modules, approaching token limit): Summarize intermediate `context_output` before passing forward; alert user.

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