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Teng-bio

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• 42 skills
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• 7 hours ago last updated

1. ▌
   Literature Reading And Synthesis · teng-bio bundle

   Use when the user brings scientific papers, figures, tables, reading goals, alert queues, related-literature notes, or reference piles and needs active reading strategy, claim/evidence extraction, figure unpacking, comparison across papers, literature tracking, synthesis matrices, reusable notes, or journal-club/project-decision readiness. Trigger when the user needs a reading or synthesis workflow, not for a simple one-paper summary, citation formatting, citation-manager mechanics, literature search alone, manuscript drafting, grant writing, peer review, or slide design.
   0 installs
2. ▌
   Scientific Explanatory Schematics · teng-bio bundle

   Create, critique, or redesign high-quality scientific explanatory schematics for paper notes, project technical-route notes, mechanism/principle diagrams, graphical abstracts, Obsidian/PPT reading aids, and source Figure/Table explanations. Use when users ask to make, explain, judge, improve, redraw, or replace scientific schematics; decide whether to self-draw versus use original paper figures; or mention 技术路线图, 技术机制图, 机制图, 原理图, 技术原理说明图, 流程图, 工作流图, 方法路线图, 项目路线图, 研究框架图, 模型架构图, 证据链图, 混杂控制图, 补充图, 一图流, 图解, 示意图, 配图, 论文Figure讲解, 原文图讲解, Figure/Table拆解, 关键原文图插入, 重要图表讲解, 插图太丑/不好看, 重画/美化插图, 绘图质量, graphical abstract, workflow schematic, mechanism diagram, model architecture figure, figure quality. Prioritizes high-value original Figure/Table insertion and explanation, visual hierarchy, evidence boundaries, and optional-only schematics.
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3. ▌
   Tooluniverse Literature Deep Research · teng-bio bundle

   Comprehensive literature deep research across any academic domain using 120+ ToolUniverse tools. Conducts subject disambiguation, systematic literature search with citation network expansion, evidence grading (T1-T4), and structured theme extraction. Produces detailed reports with mandatory completeness checklists, integrated models, and testable hypotheses. Use when users need thorough literature reviews, target/drug/disease profiles, topic deep-dives, claim verification, or systematic evidence synthesis. Supports biomedical (genes, proteins, drugs, diseases), computer science, social science, and general academic topics. For single factoid questions, uses a fast verification mode with inline answer.
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4. ▌
   Tooluniverse Protein Structure Retrieval · teng-bio bundle

   Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles. Creates detailed structure reports with experimental metadata, ligand information, and download links. Use when users need protein structures, 3D models, crystallography data, or mention PDB IDs (4-character codes like 1ABC) or UniProt accessions.
   0 installs
5. ▌
   Paper Context Resolver · teng-bio bundle

   Optional narrow helper skill for README-first AI repo reproduction. Use only when the README and repository files leave a narrow reproduction-critical gap and the task is to resolve a specific paper detail such as dataset split, preprocessing, evaluation protocol, checkpoint mapping, or runtime assumption from primary paper sources while recording conflicts. Do not use for general paper summary, repo scanning, environment setup, command execution, title-only paper lookup, or replacing README guidance by default.
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6. ▌
   Small Script Generator · teng-bio

   Generate a small safe helper script or automation snippet for repetitive local tasks. Use when the user asks to 写个小脚本, 生成脚本, 批量处理, 文件转换, 自动化处理, dry-run script, helper script, or needs a minimal Python/Bash/R script with safe defaults.
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7. ▌
   Skill Library Publisher · teng-bio

   Manage a GitHub-backed Codex skill library and publish newly created or updated skills using the user's standard repository workflow. Use when the user says 创建skill, 新建skill, 写skill, 更新skill, 上传skill, 同步skill库, 发布skill到GitHub, 自动上传skill, skill仓库, skill库入库, or wants future skills validated, inventoried, committed, and pushed to the skills repository.
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8. ▌
   Project Version Curator · teng-bio bundle

   Post-hoc audit, cleanup planning, and release/staging preparation for already messy project directories where many dated, v1/v2/v3, final/current, intermediate, figure, table, and script files are mixed together. Use when Codex is asked to audit existing version clutter, generate an inventory, detect duplicate/conflicting historical files, map files to accepted/candidate/legacy status using project indexes, or create a dry-run cleanup/release plan after the fact. For active development-time guardrails, new runs, promotion, baselines, or branching, use project-flow-guard instead.
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9. ▌
   Bio Research Auto Router · teng-bio bundle

   Broad auto-router for vague Chinese or English bioinformatics, life-science research, omics, manuscript, paper-writing, reviewer-response, data-availability, PPT, literature-method, accession, GEO/SRA, RNA-seq, enrichment, workflow, or evidence-pack tasks when the user does not name a specific skill. Use for prompts like 帮我看看这些结果, 这个能不能写文章, 下一步怎么做, 整理一下生信结果, 写论文, 改文章, 审稿意见怎么回, 做组会PPT. Routes to bioinfo-evidence-orchestrator, bio-paper-writing, bio-results-writing, bio-methods-writing, bio-polishing, bio-reviewer-response, bio-data-code-availability, bio-paper2ppt, literature-method-data-miner, and existing tooluniverse/pubmed/reproduction skills.
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10. ▌
    Project Literature Bridge · teng-bio bundle

    Connects a local research/project directory with an external literature library and generates an independent Obsidian project-literature bridge knowledge base pairing project summaries, short topic-focused paper notes, evidence records, method reuse, risks, and next actions. Use when 用户要项目总结和论文说明搭配、项目-文献桥接、项目报告与文献库、Obsidian项目文献库、外置文献库索引、根据项目报告整理参考文献、把论文映射到项目模块、文献证据矩阵、论文标题要简短概括主题、逐篇精读论文、每篇文章总结、论文深度笔记、deep paper note、deeppapernote、paper-reading-workflow、literature-reading-and-synthesis.
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11. ▌
    Bio Data Code Availability · teng-bio bundle

    Prepare or audit Data Availability and Code Availability statements for bioinformatics manuscripts. Use for 生信数据可用性, 代码可用性, GEO/SRA/ENA/BioProject/BioSample/PRIDE/Zenodo/GitHub accession, FAIR清单, source data. Do not invent repository records, accessions, DOIs, licences, embargo dates, or access restrictions.
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12. ▌
    Tooluniverse Rnaseq Deseq2 · teng-bio bundle

    Production-ready RNA-seq differential expression analysis using PyDESeq2. Performs DESeq2 normalization, dispersion estimation, Wald testing, LFC shrinkage, and result filtering. Handles multi-factor designs, multiple contrasts, batch effects, and integrates with gene enrichment (gseapy) and ToolUniverse annotation tools (UniProt, Ensembl, OpenTargets). Supports CSV/TSV/H5AD input formats and any organism. Use when analyzing RNA-seq count matrices, identifying DEGs, performing differential expression with statistical rigor, or answering questions about gene expression changes.
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13. ▌
    Literature Method Data Miner · teng-bio bundle

    Interpret short Chinese literature-method prompts as a request to mine research methods and data from papers. Use when the user says 文献是怎么做的、这篇文献怎么做的、这些文献怎么做的、参考文献是怎么做的、文献里的方法、文献方法、参考文献的做法、从文献找科研方法、从文献收集数据、正文和附录数据、补充材料数据、根据文献找实验设计, even when papers were not provided and should be found through deep research first. In `.project_os` projects, route through research-project-os before recording literature findings.
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14. ▌
    Systematic Literature Review · teng-bio bundle

    当用户明确要求"做系统综述/文献综述/related work/相关工作/文献调研"时使用。AI 自定检索词，多源检索→去重→AI 逐篇阅读并评分（1–10分语义相关性与子主题分组）→按高分优先比例选文→自动生成"综/述"字数预算→资深领域专家自由写作（固定摘要/引言/子主题/讨论/展望/结论），保留正文字数与参考文献数硬校验，强制导出 PDF 与 Word。支持多语言翻译与智能编译（en/zh/ja/de/fr/es）。
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15. ▌
    Tooluniverse Gene Enrichment · teng-bio bundle

    Perform comprehensive gene enrichment and pathway analysis using gseapy (ORA and GSEA), PANTHER, STRING, Reactome, and 40+ ToolUniverse tools. Supports GO enrichment (BP, MF, CC), KEGG, Reactome, WikiPathways, MSigDB Hallmark, and 220+ Enrichr libraries. Handles multiple ID types (gene symbols, Ensembl, Entrez, UniProt), multiple organisms (human, mouse, rat, fly, worm, yeast), customizable backgrounds, and multiple testing correction (BH, Bonferroni). Use when users ask about gene enrichment, pathway analysis, GO term enrichment, KEGG pathway analysis, GSEA, over-representation analysis, functional annotation, or gene set analysis.
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16. ▌
    Bioinfo Evidence Orchestrator · teng-bio bundle

    Bioinformatics evidence orchestration skill. Use when the user asks to analyze, validate, reproduce, inspect, organize, or prepare evidence from bioinformatics datasets, omics results, gene lists, workflows, database records, accessions, papers, or figures before writing. Routes to existing skills such as tooluniverse, pubmed-database, literature-method-data-miner, tooluniverse-rnaseq-deseq2, tooluniverse-gene-enrichment, sequence/protein/phylogenetics skills, scientific-critical-thinking, and reproduction skills. Produces EVIDENCE_PACK.md, risk tables, figure inventories, and missing-information lists. Do not use for manuscript prose drafting, polishing, reviewer responses, or PPT writing. 中文触发词：生信分析、组学分析、数据库查证、GEO、SRA、accession、QC、富集分析、RNA-seq、DESeq2、整理证据、写论文前整理结果、复现生信流程。
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17. ▌
    Tooluniverse Sequence Retrieval · teng-bio bundle

    Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles. Creates detailed reports with sequence metadata, cross-database references, and download options. Use when users need nucleotide sequences, protein sequences, genome data, or mention GenBank, RefSeq, EMBL accessions.
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18. ▌
    Bug Repro Plan · teng-bio

    Create a minimal repeatable bug reproduction plan with environment, steps, expected vs actual behavior, and evidence checklist. Use when the user asks 复现 bug, 最小复现, reproduce issue, bug repro, 问题复现步骤, or before debugging an unclear failure.
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19. ▌
    Log Summarizer · teng-bio

    Summarize noisy logs, errors, command output, or run logs into likely causes and next steps. Use when the user provides 日志, 报错, error output, traceback, CI logs, run logs, 长任务失败日志, or asks 分析日志 / 看报错 / 找失败原因.
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20. ▌
    Ppt Image First · teng-bio bundle

    Build presentation plans for PPT / slides / decks through a conversation-first workflow, then propose multiple visual directions with preview images before writing deck specs. Use when the user asks to create a PPT, presentation, deck, 答辩稿, 路演 deck, 产品介绍 PPT, 汇报 PPT, or when the user has only a topic or rough materials and needs help clarifying structure, style, and page planning before generation.
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21. ▌
    Project Skeleton · teng-bio

    Thin Chinese trigger/alias for bootstrapping or resuming a `.project_os/` research project harness. Use when the user says 项目骨架, 新项目骨架, 搭项目骨架, 初始化项目骨架, 项目工作流骨架, 研究项目骨架, 科研项目骨架, 开工, 继续项目, 继续下一步, 大项目, 逐步推进, 制定计划, 拆解任务, 当前进展, 恢复上下文, task_plan.md, findings.md, progress.md, 项目状态, 写一个项目状态文档, 开始分析, 先跑, 先画, 绘图, or 画图 in a durable project; then defer to research-project-os.
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22. ▌
    Ticket Breakdown · teng-bio

    Break a standalone non-.project_os task, ticket, issue, or frontier problem into small ordered steps with acceptance checks. Use when the user asks to 拆任务, 拆步骤, 分解任务, 制定小计划, 把当前问题拆小, 把当前任务拆成更小的验收步骤, 验收步骤, 验收条件, ticket breakdown, or issue breakdown. In `.project_os` projects, research-project-os routes first.
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23. ▌
    Bio Paper Writing · teng-bio bundle

    Draft or restructure bioinformatics manuscripts from EVIDENCE_PACK.md, figures, tables, analysis summaries, or Chinese notes. Use for 生信论文, 写abstract, 写introduction, 写Results, 写Discussion, 根据结果写论文, 中文实验记录写英文论文. Do not run analyses, validate accessions, or fabricate datasets, statistics, software versions, mechanisms, or citations.
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24. ▌
    CI Failure Triage · teng-bio

    Diagnose CI/build/test pipeline failures and separate deterministic failures from flakes. Use when the user mentions CI 失败, pipeline failed, GitHub Actions, build failed, test failed in CI, flaky CI, 构建失败, or wants CI failure triage.
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25. ▌
    Auto Deep Research · teng-bio bundle

    Automatically orchestrates web search, raw web context, and deep research for requests to search, 查资料, 搜资料, 深度搜索, 调研, 文献综述, 找论文/资料/来源, look up, research, gather sources, compare current tools, or verify online claims. Use when the user asks for search/research without naming a specific search skill; it routes only through Brave spellcheck, autosuggest, web search, LLM context, and local report orchestration. 中文追加触发词：寻找参考文献、搜索文献、查参考文献、找相关论文、找几篇论文、文献搜索、论文搜索、参考文献怎么找、根据文献找来源。
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26. ▌
    Project Flow Guard · teng-bio bundle

    Development-time project flow/version guard for Codex across any project. Use to prevent version confusion when work creates or regenerates nontrivial artifacts, promotes accepted outputs, branches long-lived directions, packages releases, or reorganizes files. It treats runs as provenance, not the human result entry point, and prefers md/tsv/json ledgers such as `RESULTS_INDEX.md`, `RUNS_INDEX.tsv`/`.project_flow/RUNS.tsv`, and `RUN_MANIFEST.json`. Trigger on 重跑, 重新生成, 重新绘图, 再生成一版, 改一版, 调整一下, 换参数, 换参考, 基于这版, 保留这个版本, 就用这个, 设为当前版本, make current, accept, promote, 冻结当前版本, 保存当前状态, snapshot, baseline, seal, 开分支, 新分析方向, 基于这个版本继续, branch, same data new analysis, release, 投稿, 打包, 清理旧版本, 整理目录, delete old versions, or similar.
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27. ▌
    Bio Methods Writing · teng-bio bundle

    Draft reproducible bioinformatics Methods from workflow provenance, commands, configs, EVIDENCE_PACK.md, software lists, and author notes. Use for 生信Methods, 材料与方法, workflow写法, 可复现方法, RNA-seq/富集/单细胞/系统发育方法写作. Do not run or debug analyses, infer missing parameters, or fabricate versions, genome builds, accessions, or thresholds.
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28. ▌
    Bio Results Writing · teng-bio bundle

    Write bioinformatics Results sections from figures, tables, EVIDENCE_PACK.md, analysis summaries, and Chinese result notes. Use for 生信Results, 根据图表写结果, RNA-seq结果写作, 富集结果写作, 单细胞/多组学结果段落. Do not run analyses, change statistics, or fabricate p values, FDR, sample sizes, figure panels, or mechanisms.
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29. ▌
    Research Project Os · teng-bio bundle

    General repository-local research/project harness under `.project_os/` and first router for long-running, multi-step projects across domains. Use for research-project-os, project harness, 项目骨架, 通用项目工作台, 开工, 继续项目, 继续当前任务, 继续下一步, 大项目, 长期项目, 逐步推进, 当前进展, 恢复上下文, 制定计划, 拆解任务, plan out, break down, organize multi-step work, task_plan.md, findings.md, progress.md, 开始分析, 先跑, 先画, 绘图, 画图, 生成结果, 开始运行, 记录结果, 当前结果, run provenance, RESULTS_INDEX, DATA_ASSETS, current_task, result promotion, release workflow, 外置数据, 恢复检查. In any `.project_os/` project, also use before domain commands such as 系统发育, 发育树, 进化树, Newick, FASTA比对, PHYLIP, Nexus, alignment/tree/parsimony/treeness/RCV, ortholog, 同源基因, 分子进化, bootstrap, model training, 深度学习, R绘图, Python分析, and before 项目状态/写一个项目状态文档/更新项目状态文档/总结项目状态/记录当前项目进度/项目文档太大/拆分项目文档; establishes branch/task/run/result/assets first.
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30. ▌
    Repo Intake And Plan · teng-bio bundle

    Narrow helper skill for README-first AI repo reproduction. Use when the task is specifically to scan a repository, read the README and common project files, extract documented commands, classify inference, evaluation, and training candidates, and return the smallest trustworthy reproduction plan to the main orchestrator. Do not use for environment setup, asset download, command execution, final reporting, paper lookup, or end-to-end orchestration. 中文触发词：论文代码仓库、复现仓库、README扫描、复现计划、仓库结构、推理/评估/训练命令提取、最小可信复现计划。
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31. ▌
    Bio Reviewer Response · teng-bio bundle

    Draft, audit, or revise point-by-point reviewer responses for bioinformatics manuscripts. Use for 生信审稿回复, 逐点回复, 大修回复, reviewer质疑batch effect/FDR/外部验证/数据泄露/样本量/方法可复现. Do not claim analyses, revisions, citations, line numbers, figures, or validations were completed unless supplied by the author.
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32. ▌
    Config File Explainer · teng-bio

    Explain a configuration file and its key options, risks, and safe changes. Use when the user asks 解释配置, 看一下 config, config.toml, yaml/json/toml 配置, 配置项什么意思, 哪些配置可以改, configuration file explainer.
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33. ▌
    Minimal Run And Audit · teng-bio bundle

    Trusted-lane execution and reporting skill for README-first AI repo reproduction. Use when the task is specifically to capture or normalize evidence from the selected smoke test or documented inference or evaluation command and write standardized `repro_outputs/` files, including patch notes when repository files changed. Do not use for training execution, initial repo intake, generic environment setup, paper lookup, target selection, or end-to-end orchestration by itself.
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34. ▌
    Research Orchestrator · teng-bio bundle

    Orchestrate, compare, verify, and merge multiple deep research reports into a single authoritative document. Use this skill whenever the user uploads 2+ research reports/documents and wants them compared, verified, merged, deduplicated, fact-checked, or synthesized into one. Also trigger when the user says 'compare research', 'merge reports', 'verify links in my research', 'combine deep research', 'check sources', 'fact-check these documents', 'create unified report', 'best of all research', or mentions having multiple deep research outputs. Trigger even if the user just uploads several long documents and asks to 'make one good version'. Do NOT use for single-document editing, simple summaries, or non-research content. 中文触发词：根据这几篇文献有什么想法、整合这几篇文献、比较这几篇论文、合并多篇文献、核验这些文献来源、从多篇文献提炼结论、综合多个研究报告。
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35. ▌
    Paper Reading Workflow · teng-bio

    Use when the user asks to read, 精读, 总结, 拆解, 批判性审读, or make an Obsidian note for a research paper, PDF, arXiv paper, DOI, paper URL, or local literature file, especially when they care about 论文怎么做, 方法/数据/实验, 证据强度, 局限, 复现, or 项目借鉴.
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36. ▌
    Grill Me · teng-bio

    Interview the user one question at a time to clarify a plan, requirement, research design, workflow, or implementation approach before execution. Use when the user wants to discuss/完善方案/商量方案/先别写代码/先不要写代码/先定流程/先完善流程/先问清楚/先规划/需求澄清/方案评审/风险梳理/把思路问透, or when they ask to stress-test a plan without immediately doing the task.
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37. ▌
    Find Skills · teng-bio

    Helps users discover, compare, and install agent skills. Use when the user asks how to do X with a skill, says find a skill / is there a skill, wants tools/templates/workflows, or in Chinese asks 搜索skill, 找skill, 找一下有没有, 有没有skill, 安装skill, 管理skill, 管理 skill 库, skill库, skill 库, 补全skill生态, 自动触发skill, or wants to extend agent capabilities. In a research-project-os ecosystem, use this as the discovery layer; when `.project_os/` exists, record decisions through the harness instead of parallel planning files.
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38. ▌
    LLM Context · teng-bio

    USE FOR RAG/LLM grounding. Returns pre-extracted web content (text, tables, code) optimized for LLMs. GET + POST. Adjust max_tokens/count based on complexity. Supports Goggles, local/POI. For AI answers use answers. Recommended for anyone building AI/agentic applications.
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39. ▌
    Tooluniverse · teng-bio bundle

    Router for ToolUniverse tasks. Routes to 105+ specialized skills (disease/drug/target research, genomics, proteomics, clinical decision support, etc.) or uses 2300+ scientific tools. Covers tool discovery, multi-hop queries, workflows, and report generation. Use for scientific research, biological data, drug/target/disease relationships, or any biology/medicine/chemistry question. Verifies facts against databases (UniProt, PubMed, ChEMBL, ClinVar, GWAS Catalog).
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40. ▌
    Bio Paper2ppt · teng-bio bundle

    Create Chinese presentation plans or PPTX decks from bioinformatics papers, EVIDENCE_PACK.md, figures, tables, abstracts, or reading notes. Use for 生信论文转PPT, 组会汇报, journal club, 多组学/单细胞/算法论文汇报. Focus on story, workflow, evidence figures, limitations, and discussion questions; do not run analyses or fabricate results.
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41. ▌
    Bio Polishing · teng-bio bundle

    Polish, restructure, or translate bioinformatics manuscript prose while preserving evidence boundaries. Use for 生信论文润色, 中译英, SCI润色, Results润色, Discussion润色, 摘要润色, 术语统一, overclaim检查. Do not add new analyses, citations, statistics, accessions, software versions, or biological mechanisms not supplied by the user.
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42. ▌
    Deeppapernote · teng-bio bundle

    Generate a high-quality deep-reading note for a single paper and write it into an Obsidian-style vault. Use when the user gives a paper title, DOI, URL, arXiv ID, Zotero item, or local PDF and wants a polished Markdown note with strong structure, evidence-based analysis, and figure placeholders.
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