dr-cook

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.