dr-cook

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.

Guide users through computational omics analysis pipelines across three tracks: differential expression analysis (DEG), enrichment analysis (GO/KEGG/GSEA), and network pharmacology (target prediction, PPI networks, hub genes). Use when performing bioinformatics analysis, DEG analysis, differential expression, enrichment analysis, GSEA, GO enrichment, KEGG pathway analysis, network pharmacology, protein-protein interaction, PPI network construction, hub gene identification, scRNA-seq, single-cell analysis, bulk RNA-seq, 生信分析, 差异基因, 富集分析, 网络药理学, 靶点预测. Do NOT trigger for: data-visualizer (plotting and figure generation only), method-designer (experimental design and study planning only).

Generate publication-quality scientific figures and visualizations for academic manuscripts. Use when creating data visualization, plot, figure, chart, graph, heatmap, volcano plot, boxplot, violin plot, PCA plot, UMAP, survival curve, Kaplan-Meier, forest plot, scientific figure, publication figure, ggplot, matplotlib, R plot, Python plot, enrichment bubble chart, PPI network visualization, network figure, 数据可视化, 画图, 图表, 可视化. Do NOT trigger for: bioinformatics-assistant (analysis pipelines and computational methods), method-designer (experimental design and study planning).

Guide researchers through experimental design decisions. Use when planning experimental design, study design, method design, CRISPR design, sgRNA design, network pharmacology design, multi-omics design, sample size calculation, power calculation, statistical power, cohort design, knockout design, knockin design, 实验设计, 样本量计算, 统计功效, CRISPR设计, 多组学, 网络药理学设计. Do NOT trigger for: bioinformatics-assistant (data analysis on existing data), data-visualizer (plotting only), paper-writer (Methods section writing only).

Polish and refine academic Chinese writing for publication in Chinese-language journals. Use when improving Chinese grammar, vocabulary, sentence fluency, or domain-specific terminology in Chinese manuscripts, abstracts, or grant sections. Triggers on: Chinese polish, Chinese academic writing, 中文润色, 学术中文, 中文写作, 中文修改, 学术写作润色, polish Chinese, improve Chinese writing, academic Chinese, Chinese manuscript. Does NOT trigger on translation tasks: en-to-zh (English to Chinese translation) or zh-to-en (Chinese to English translation).

Translate English academic text to Chinese. Use when converting English manuscripts, abstracts, or scientific content to Chinese academic writing. Handles TCM terminology mapping, bioinformatics term standardization, and academic Chinese register. Triggers on: translate to Chinese, English to Chinese, 翻译成中文, 英译中, translate to simplified Chinese.

Polish and refine academic English writing. Use when improving grammar, word choice, sentence structure, or discipline-specific terminology in English manuscripts, abstracts, or grant sections. Triggers on: polish English, improve writing, refine language, proofread, academic English, 英文润色, 语言修改, 英文修改, 改善英文, 润色.

Translate Chinese academic text to English. Use when converting Chinese manuscripts, abstracts, grant sections, or TCM terminology to academic English. Maintains technical precision, academic register, and correct domain-specific terminology. Triggers on: translate to English, Chinese to English, 翻译成英文, 中译英, translate abstract, translate methods.

Validate and correct citation formatting in academic manuscripts. Use when checking references, fixing citation style errors, validating in-text citation matching, auditing self-citation rates, or formatting to Vancouver, APA, or GB/T 7714-2015. Triggers on: check citations, fix references, validate reference list, citation errors, self-citation audit, Vancouver/APA/GB/T 7714, 检查参考文献, 格式化引用, 自引检查. Do NOT trigger on: literature review, paper download, manuscript writing, English polishing, or peer review comments.

Retrieve full-text academic articles and literature metadata. Use when downloading papers, getting full text from PubMed Central, fetching article metadata by PMID or DOI, or building structured download lists for papers behind paywalls. Triggers on: download paper, get full text, fetch article, retrieve literature, PubMed download, PMC, PMID, DOI lookup, 下载文献, 获取全文, 文献下载, 下载论文, 获取PDF.

Synthesize and review academic literature. Use when summarizing multiple papers, extracting themes, creating literature review tables, or preparing systematic/narrative reviews. Triggers on: review literature, summarize papers, literature synthesis, systematic review, narrative review, 文献综述, 文献整理, 综述, 系统综述, 整理文献, 文献分析, 文献总结.

Identify research gaps and generate research questions from literature. Use when finding unexplored areas, understudied populations, methodological limitations, or conflicting findings in a field. Triggers on: research gap, find gaps, what's missing, unexplored, understudied, research question, hypothesis generation, 研究空白, 未探索, 找差距, 研究问题, 科学假说, 选题建议.

Review academic manuscripts in two modes: self-review (author pre-submission checklist) or peer-review (formal referee report). Use when checking your own paper before submission, or when writing a referee report for a journal. Triggers on: review paper, self-review, self-check, peer review, referee report, manuscript evaluation, 审稿, 自查, 审稿意见, 自我审查, 同行评审, 论文评审, 修改意见.

Draft professional journal submission cover letters for manuscript submission. Use when users need a cover letter, submission letter, journal cover letter, or want to submit a manuscript to a journal. Triggers on: cover letter, submission letter, journal cover letter, manuscript submission, write cover letter, draft cover letter, cover letter for journal, 投稿信, 期刊投稿, 投稿函. Do NOT trigger for: rebuttal-writer (revision response letters to reviewers), grant-writer (grant proposal writing).

Draft competitive grant proposals and research funding applications. Use when writing or drafting NSFC grant sections, research proposals, project proposals, or reviewing existing grant drafts. Triggers on: grant proposal, grant application, grant writing, NSFC, National Natural Science Foundation, research proposal, project proposal, 基金申请, 国家自然科学基金, 基金标书, 科研项目申请, 立项依据, 研究方案. Does NOT trigger on manuscript writing (use paper-writer) or journal submission cover letters (use cover-letter-writer).

Draft academic manuscript sections (IMRaD format). Use when writing or drafting introduction, methods, results, discussion, or abstract sections of a research paper. Adapts to target journal style and research domain. Triggers on: write paper, draft manuscript, write introduction, write methods, write results, write discussion, write abstract, IMRaD, 写论文, 写introduction, 写方法, 写结果, 写讨论, 稿件起草, 论文写作.

Draft professional peer review response letters and revision rebuttals. Use when writing a response to reviewers, rebuttal letter, point-by-point response, revision letter, or appeal of a rejection decision. Triggers on: rebuttal, response to reviewers, point-by-point response, reviewer comments, revision letter, appeal rejection, 回复审稿意见, 逐条回复, 修改说明, 审稿回复. Does NOT trigger on paper-reviewer (reviewing a paper for others) or citation-checker.